write a hypothesis that describes how genetic dominance occurs

What Is Genetic Dominance and How Does It Work?

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• Cell Biology
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• B.A., Biology, Emory University
• A.S., Nursing, Chattahoochee Technical College

Have you ever wondered why you have that particular eye color or hair type? It's all due to gene transmission. As discovered by  Gregor Mendel , traits are inherited by the transmission of  genes  from parents to their offspring. Genes are segments of  DNA  located on our  chromosomes . They are passed on from one generation to the next through  sexual reproduction . The gene for a specific trait can exist in more than one form or  allele . For each characteristic or trait,  animal cells  typically inherit two alleles. Paired alleles can be  homozygous  (having identical alleles) or  heterozygous  (having different alleles) for a given trait.

When the allele pairs are the same, the  genotype  for that trait is identical and the  phenotype  or characteristic that is observed is determined by the homozygous alleles. When the paired alleles for a trait are different or heterozygous, several possibilities may occur. Heterozygous dominance relationships that are typically seen in animal cells include complete dominance, incomplete dominance, and co-dominance.

Key Takeaways

• Gene transmission explains why we have particular traits like eye or hair color. Traits are inherited by children based on gene transmission from their parents.
• A specific trait's gene can exist in more than one form, called an allele. For a specific trait, animal cells usually have two alleles.
• One allele can mask the other allele in a complete dominance relationship. The allele that is dominant completely masks the allele that is recessive.
• Similarly, in an incomplete dominance relationship, one allele does not completely mask the other. The result is a third phenotype that is a mixture.
• Co-dominance relationships occur when neither of the alleles is dominant and both alleles are expressed completely. The result is a third phenotype with more than one phenotype observed.

Complete Dominance

 Ion-Bogdan DUMITRESCU/Moment/Getty Images

In complete dominance relationships, one allele is dominant and the other is recessive. The dominant allele for a trait completely masks the recessive allele for that trait. The phenotype is determined by the dominant allele. For example, the genes for seed shape in pea plants exists in two forms, one form or allele for round seed shape (R) and the other for wrinkled seed shape (r) . In pea plants that are heterozygous for seed shape, the round seed shape is dominant over the wrinkled seed shape and the genotype is (Rr).

Incomplete Dominance

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In incomplete dominance relationships, one allele for a specific trait is not completely dominant over the other allele. This results in a third phenotype in which the observed characteristics are a mixture of the dominant and recessive phenotypes. An example of incomplete dominance is seen in hair type inheritance. Curly hair type (CC) is dominant to straight hair type (cc) . An individual who is heterozygous for this trait will have wavy hair (Cc) . The dominant curly characteristic is not fully expressed over the straight characteristic, producing the intermediate characteristic of wavy hair. In incomplete dominance, one characteristic may be slightly more observable than another for a given trait. For example, an individual with wavy hair may have more or fewer waves than another with wavy hair. This indicates that the allele for one phenotype is expressed slightly more than the allele for the other phenotype.

Co-dominance

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In co-dominance relationships, neither allele is dominant, but both alleles for a specific trait are completely expressed. This results in a third phenotype in which more than one phenotype is observed. An example of co-dominance is seen in individuals with the sickle cell trait. Sickle cell disorder results from the development of abnormally shaped red blood cells . Normal red blood cells have a biconcave, disc-like shape and contain enormous amounts of a protein called hemoglobin. Hemoglobin helps red blood cells bind to and transport oxygen to cells and tissues of the body. Sickle cell is a result of a mutation in the hemoglobin gene . This hemoglobin is abnormal and causes blood cells to take on a sickle shape. Sickle-shaped cells often become stuck in blood vessels blocking normal blood flow. Those that carry the sickle cell trait are heterozygous for the sickle hemoglobin gene, inheriting one normal hemoglobin gene and one sickle hemoglobin gene. They do not have the disease because the sickle hemoglobin allele and normal hemoglobin allele are co-dominant with regard to cell shape. This means that both normal red blood cells and sickle-shaped cells are produced in carriers of the sickle cell trait. Individuals with sickle cell anemia are homozygous recessive for the sickle hemoglobin gene and have the disease.

Differences Between Incomplete Dominance and Co-dominance

Pink / Peter Chadwick LRPS/Moment/Getty Images - Red and white / Sven Robbe/EyeEm/Getty Images

Incomplete Dominance vs. Co-dominance

People tend to confuse incomplete dominance and co-dominance relationships. While they are both patterns of inheritance, they differ in gene expression. Some differences between the two are listed below:

1. Allele Expression

• Incomplete Dominance: One allele for a specific trait is not completely expressed over its paired allele. Using flower color in tulips as an example, the allele for red color (R) does not totally mask the allele for white color (r) .
• Co-dominance: Both alleles for a specific trait are completely expressed. The allele for red color (R) and the allele for white color (r) are both expressed and seen in the hybrid.

2. Allele Dependence

• Incomplete Dominance: The effect of one allele is dependent upon its paired allele for a given trait.
• Co-dominance: The effect of one allele is independent of its paired allele for a given trait.

3. Phenotype

• Incomplete Dominance: The hybrid phenotype is a mixture of the expression of both alleles, resulting in a third intermediate phenotype. Example: Red flower (RR) X White flower (rr) = Pink flower (Rr)
• Co-dominance: The hybrid phenotype is a combination of the expressed alleles, resulting in a third phenotype that includes both phenotypes. (Example: Red flower (RR) X White flower (rr) = Red and white flower (Rr)

4. Observable Characteristics

• Incomplete Dominance: The phenotype may be expressed to varying degrees in the hybrid. (Example: A pink flower may have lighter or darker coloration depending on the quantitative expression of one allele versus the other.)
• Co-dominance: Both phenotypes are fully expressed in the hybrid genotype .

In incomplete dominance relationships, one allele for a specific trait is not completely dominant over the other allele. This results in a third phenotype in which the observed characteristics are a mixture of the dominant and recessive phenotypes. In co-dominance relationships, neither allele is dominant but both alleles for a specific trait are completely expressed. This results in a third phenotype in which more than one phenotype is observed.

• Reece, Jane B., and Neil A. Campbell. Campbell Biology . Benjamin Cummings, 2011.
• Incomplete Dominance in Genetics
• A Genetics Definition of Heterozygous
• What Does Homozygous Mean in Genetics?
• Phenotype: How a Gene Is Expressed As a Physical Trait
• How Do Alleles Determine Traits in Genetics?
• Introduction to Mendel's Law of Independent Assortment
• Mendel's Law of Independent Assortment
• Genes and Genetic Inheritance
• Co-Dominance in Evolution
• What Is Mendel's Law of Segregation?
• What Are Traits?
• Types of Non-Mendelian Genetics
• Heterozygous Traits
• Monohybrid Cross: A Genetics Definition
• Law of Multiple Alleles
• Dihybrid Cross in Genetics

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Gregor Mendel and the Principles of Inheritance

Traits are passed down in families in different patterns. Pedigrees can illustrate these patterns by following the history of specific characteristics, or phenotypes, as they appear in a family. For example, the pedigree in Figure 1 shows a family in which a grandmother (generation I) has passed down a characteristic (shown in solid red) through the family tree. The inheritance pattern of this characteristic is considered dominant , because it is observable in every generation. Thus, every individual who carries the genetic code for this characteristic will show evidence of the characteristic. In contrast, Figure 2 shows a different pattern of inheritance, in which a characteristic disappears in one generation, only to reappear in a subsequent one. This pattern of inheritance, in which the parents do not show the phenotype but some of the children do, is considered recessive . But where did our knowledge of dominance and recessivity first come from?

Gregor Mendel’s Courage and Persistence

Mendel was curious about how traits were transferred from one generation to the next, so he set out to understand the principles of heredity in the mid-1860s. Peas were a good model system, because he could easily control their fertilization by transferring pollen with a small paintbrush. This pollen could come from the same flower (self-fertilization), or it could come from another plant's flowers (cross-fertilization). First, Mendel observed plant forms and their offspring for two years as they self-fertilized, or "selfed," and ensured that their outward, measurable characteristics remained constant in each generation. During this time, Mendel observed seven different characteristics in the pea plants, and each of these characteristics had two forms (Figure 3). The characteristics included height (tall or short), pod shape (inflated or constricted), seed shape (smooth or winkled), pea color (green or yellow), and so on. In the years Mendel spent letting the plants self, he verified the purity of his plants by confirming, for example, that tall plants had only tall children and grandchildren and so forth. Because the seven pea plant characteristics tracked by Mendel were consistent in generation after generation of self-fertilization, these parental lines of peas could be considered pure-breeders (or, in modern terminology, homozygous for the traits of interest). Mendel and his assistants eventually developed 22 varieties of pea plants with combinations of these consistent characteristics.

Mendel not only crossed pure-breeding parents, but he also crossed hybrid generations and crossed the hybrid progeny back to both parental lines. These crosses (which, in modern terminology, are referred to as F 1 , F 1 reciprocal, F 2 , B 1 , and B 2 ) are the classic crosses to generate genetically hybrid generations.

Understanding Dominant Traits

Understanding recessive traits.

When conducting his experiments, Mendel designated the two pure-breeding parental generations involved in a particular cross as P 1 and P 2 , and he then denoted the progeny resulting from the crossing as the filial, or F 1 , generation. Although the plants of the F 1 generation looked like one parent of the P generation, they were actually hybrids of two different parent plants. Upon observing the uniformity of the F 1 generation, Mendel wondered whether the F 1 generation could still possess the nondominant traits of the other parent in some hidden way.

To understand whether traits were hidden in the F 1 generation, Mendel returned to the method of self-fertilization. Here, he created an F 2 generation by letting an F 1 pea plant self-fertilize (F 1 x F 1 ). This way, he knew he was crossing two plants of the exact same genotype . This technique, which involves looking at a single trait, is today called a monohybrid cross . The resulting F 2 generation had seeds that were either round or wrinkled. Figure 4 shows an example of Mendel's data.

When looking at the figure, notice that for each F 1 plant, the self-fertilization resulted in more round than wrinkled seeds among the F 2 progeny. These results illustrate several important aspects of scientific data:

• Multiple trials are necessary to see patterns in experimental data.
• There is a lot of variation in the measurements of one experiment.
• A large sample size, or "N," is required to make any quantitative comparisons or conclusions.

In Figure 4, the result of Experiment 1 shows that the single characteristic of seed shape was expressed in two different forms in the F 2 generation: either round or wrinkled. Also, when Mendel averaged the relative proportion of round and wrinkled seeds across all F 2 progeny sets, he found that round was consistently three times more frequent than wrinkled. This 3:1 proportion resulting from F 1 x F 1 crosses suggested there was a hidden recessive form of the trait. Mendel recognized that this recessive trait was carried down to the F 2 generation from the earlier P generation .

Mendel and Alleles

As mentioned, Mendel's data did not support the ideas about trait blending that were popular among the biologists of his time. As there were never any semi-wrinkled seeds or greenish-yellow seeds, for example, in the F 2 generation, Mendel concluded that blending should not be the expected outcome of parental trait combinations. Mendel instead hypothesized that each parent contributes some particulate matter to the offspring. He called this heritable substance "elementen." (Remember, in 1865, Mendel did not know about DNA or genes.) Indeed, for each of the traits he examined, Mendel focused on how the elementen that determined that trait was distributed among progeny. We now know that a single gene controls seed form, while another controls color, and so on, and that elementen is actually the assembly of physical genes located on chromosomes. Multiple forms of those genes, known as alleles , represent the different traits. For example, one allele results in round seeds, and another allele specifies wrinkled seeds.

One of the most impressive things about Mendel's thinking lies in the notation that he used to represent his data. Mendel's notation of a capital and a lowercase letter ( Aa ) for the hybrid genotype actually represented what we now know as the two alleles of one gene : A and a . Moreover, as previously mentioned, in all cases, Mendel saw approximately a 3:1 ratio of one phenotype to another. When one parent carried all the dominant traits ( AA ), the F 1 hybrids were "indistinguishable" from that parent. However, even though these F 1 plants had the same phenotype as the dominant P 1 parents, they possessed a hybrid genotype ( Aa ) that carried the potential to look like the recessive P 1 parent ( aa ). After observing this potential to express a trait without showing the phenotype, Mendel put forth his second principle of inheritance: the principle of segregation . According to this principle, the "particles" (or alleles as we now know them) that determine traits are separated into gametes during meiosis , and meiosis produces equal numbers of egg or sperm cells that contain each allele (Figure 5).

Dihybrid Crosses

Mendel had thus determined what happens when two plants that are hybrid for one trait are crossed with each other, but he also wanted to determine what happens when two plants that are each hybrid for two traits are crossed. Mendel therefore decided to examine the inheritance of two characteristics at once. Based on the concept of segregation , he predicted that traits must sort into gametes separately. By extrapolating from his earlier data, Mendel also predicted that the inheritance of one characteristic did not affect the inheritance of a different characteristic.

Mendel tested this idea of trait independence with more complex crosses. First, he generated plants that were purebred for two characteristics, such as seed color (yellow and green) and seed shape (round and wrinkled). These plants would serve as the P 1 generation for the experiment. In this case, Mendel crossed the plants with wrinkled and yellow seeds ( rrYY ) with plants with round, green seeds ( RRyy ). From his earlier monohybrid crosses, Mendel knew which traits were dominant: round and yellow. So, in the F 1 generation, he expected all round, yellow seeds from crossing these purebred varieties, and that is exactly what he observed. Mendel knew that each of the F 1 progeny were dihybrids; in other words, they contained both alleles for each characteristic ( RrYy ). He then crossed individual F 1 plants (with genotypes RrYy ) with one another. This is called a dihybrid cross . Mendel's results from this cross were as follows:

• 315 plants with round, yellow seeds
• 108 plants with round, green seeds
• 101 plants with wrinkled, yellow seeds
• 32 plants with wrinkled, green seeds

Thus, the various phenotypes were present in a 9:3:3:1 ratio (Figure 6).

Next, Mendel went through his data and examined each characteristic separately. He compared the total numbers of round versus wrinkled and yellow versus green peas, as shown in Tables 1 and 2.

Table 1: Data Regarding Seed Shape

Table 2: Data Regarding Pea Color

The proportion of each trait was still approximately 3:1 for both seed shape and seed color. In other words, the resulting seed shape and seed color looked as if they had come from two parallel monohybrid crosses; even though two characteristics were involved in one cross, these traits behaved as though they had segregated independently. From these data, Mendel developed the third principle of inheritance: the principle of independent assortment . According to this principle, alleles at one locus segregate into gametes independently of alleles at other loci. Such gametes are formed in equal frequencies.

Mendel’s Legacy

More lasting than the pea data Mendel presented in 1862 has been his methodical hypothesis testing and careful application of mathematical models to the study of biological inheritance. From his first experiments with monohybrid crosses, Mendel formed statistical predictions about trait inheritance that he could test with more complex experiments of dihybrid and even trihybrid crosses. This method of developing statistical expectations about inheritance data is one of the most significant contributions Mendel made to biology.

But do all organisms pass their on genes in the same way as the garden pea plant? The answer to that question is no, but many organisms do indeed show inheritance patterns similar to the seminal ones described by Mendel in the pea. In fact, the three principles of inheritance that Mendel laid out have had far greater impact than his original data from pea plant manipulations. To this day, scientists use Mendel's principles to explain the most basic phenomena of inheritance.

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• v.180(3); 2008 Nov

Dominance, Overdominance and Epistasis Condition the Heterosis in Two Heterotic Rice Hybrids

* Key Lab of the Ministry of Education for Plant Developmental Biology, College of Life Science, Wuhan University, Wuhan 430072, China, † National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China and ‡ Department of Breeding, China National Hybrid Rice Research and Development Center, Changsha 410125, China

Zhaoming Chen

Two recombinant inbred (RI) populations having 194 and 222 lines each, derived, respectively, from a highly heterotic inter- ( IJ ) and intrasubspecific ( II ) hybrid, were backcrossed to their respective parents. The RI and two backcross populations along with F 1 and its two parents of each hybrid were evaluated for nine important traits, including grain yield and eight other yield-related traits. A total of 76 quantitative trait loci (QTL) for the IJ hybrid and 41 QTL for the II hybrid were detected in the RI population, midparent heterosis of two backcross populations, and two independent sets of data by summation ( L 1 + L 2 ) and by subtraction ( L 1 − L 2 ) of two backcross populations ( L 1 and L 2 ). The variance explained by each QTL ranged from 2.6 to 58.3%. In the IJ hybrid, 42% (32) of the QTL showed an additive effect, 32% (24) a partial-to-complete dominant effect, and 26% (20) an overdominant effect. In the II hybrid, 32% (13) of the QTL demonstrated an additive effect, 29% (12) a partial-to-complete dominant effect, and 39% (16) an overdominant effect. There were 195 digenic interactions detected in the IJ hybrid and 328 in the II hybrid. The variance explained by each digenic interaction ranged from 2.0 to 14.9%. These results suggest that the heterosis in these two hybrids is attributable to the orchestrated outcome of partial-to-complete dominance, overdominance, and epistasis.

HETEROSIS, a term to describe the superiority of heterozygous genotypes over their corresponding parental genotypes ( S hull 1908 ), has been under investigation for ∼100 years, but no consensus exists about the genetic basis underlying this very important phenomenon. Two contending hypotheses, the dominance hypothesis and the overdominance hypothesis, were proposed to explain this phenomenon about one century ago. The dominance hypothesis attributes heterosis to canceling of deleterious or inferior recessive alleles contributed by one parent, by beneficial or superior dominant alleles contributed by the other parent in the heterozygous genotypes at different loci ( D avenport 1908 ; B ruce 1910 ; J ones 1917 ). The overdominance hypothesis attributes heterosis to the superior fitness of heterozygous genotypes over homozygous genotypes at a single locus ( E ast 1908 ; S hull 1908 ).

Molecular markers and their linkage maps have greatly facilitated the identification of individual loci conditioning heterosis and the estimation of gene action of underlying loci. Quantitative trait locus (QTL) mapping studies aiming at understanding the genetic basis of heterosis have been conducted in rice and other crops ( X iao et al . 1995 ; L i et al . 1997 , 2001 ; Y u et al . 1997 ; L uo et al . 2001 ; H ua et al . 2002 , 2003 ; S emel et al . 2006 ; F rascaroli et al . 2007 ; M elchinger et al . 2007a , b ). Evidence from such studies suggests that heterosis may be attributable to dominance ( X iao et al . 1995 ; C ockerham and Z eng 1996 ), overdominance ( S tuber et al . 1992 ; L i et al . 2001 ; L uo et al . 2001 ), pseudo-overdominance due to tightly linked loci with beneficial or superior dominant alleles in repulsion phase ( C row 2000 ; L ippman and Z amir 2007 ), or epistasis ( S chnell and C ockerham 1992 ; L i et al . 2001 ; L uo et al . 2001 ).

Heterosis is the base of the great success in hybrid rice. Currently, hybrid rice accounts for ∼55% of the total planting acreage of paddy rice in China and the annual increased rice production resulting from planting hybrid rice amounts to ∼20 million metric tones, which can provide a main staple food for >70 million people ( L u et al . 2002 ). Hybrid rice varieties have a yield advantage of ∼10–20% over the best conventional inbred varieties using similar cultivation conditions ( L u e t al . 2002 ). Besides the large planting in China, hybrid rice varieties are also widely planted in >20 countries around the world.

Previous studies indicated the genetic basis of heterosis in rice is very complicated and various, depending on study materials and analysis approaches ( X iao et al . 1995 ; Y u et al . 1997 ; L i et al . 2001 ; H ua et al . 2002 , 2003 ). The objective of this study was to identify the main-effect QTL and digenic epistatic loci underlying heterosis of nine important agronomic and economic traits of rice and estimate the gene action of each QTL and interaction using a triple-testcross cross (TTC) design to shed light on the understanding of the genetic basis of heterosis in two diverse and highly heterotic rice hybrids.

MATERIALS AND METHODS

Populations:.

Two highly heterotic rice hybrids, one intersubspecific between 9024 ( indica ) and LH422 ( japonica ) and one intrasubspecific between Zhenshan97 ( indica ) and Minghui63 ( indica ), were employed in this study. From the F 1 of the intersubspecific hybrid (designated as IJ hybrid hereafter), 194 F 7 lines were developed by single-seed descent. From the F 1 of the intrasubspecific hybrid (designated as II hybrid hereafter), 222 F 12 lines were developed through 11 consecutive selfing generations. Each of these F 7 and F 12 lines was derived from a different F 2 plant. No positive or negative selection was performed during each of the selfing generations. A single plant from each of these 194 F 7 lines and 222 F 12 lines was chosen randomly and backcrossed to each of its two respective parents to produce backcross progeny and selfed to generate F 8 or F 13 lines.

Phenotypic variation:

For the IJ hybrid, two backcross populations having 194 lines each, 194 F 8 recombinant inbred lines (RILs), along with the two parental lines and their F 1 , were arranged in a field in a randomized complete block design with two replications for phenotypic evaluation in the summer season of 1992 at the China National Hybrid Rice Research and Development Center, Changsha, Hunan, China. Twenty-seven plants (three rows × 9 plants per row) were planted at a density of 300,000 plants per hectare in each of 1170 plots. The middle 5 plants in the central row of each plot were used for phenotypic trait evaluation and data collection.

For the II hybrid, the two backcross populations with 222 lines each, the corresponding 222 F 13 RILs, along with two parental lines and their F 1 , were laid out in a field in a randomized complete block design with two replications for phenotypic evaluation in the summer season of 2006 at the experimental farm of the Huazhong Agricultural University, Wuhan, Hubei, China. Twenty-one-day-old seedlings were transplanted into three-row plots with each plot consisting of a single row of a RIL and two rows of backcross (BC) hybrids. There were seven plants in each row, with 16.7 cm between plants within each row and 26.7 cm between rows. The middle five plants in each row were used for phenotypic trait evaluation and data collection.

Nine quantitative traits of agronomic and economic importance evaluated were heading date (HD) (in days), plant height (PH) (in centimeters), tillers per plant (TP), panicle length (PL) (in centimeters), filled grains per panicle (FGPP), percentage of seed set (SS), grain density (GD) (in grain numbers per centimeter of panicle length), 1000-grain weight (KGW) (in grams), and grain yield (YD) (in tons/hectare). Means over replications, for each trait, for the RIL and each of two backcross populations, were used for QTL and other analyses.

Analysis of field data and of heterosis:

For each hybrid, data of recombinant inbred (RI) and BC populations were analyzed separately. SAS PROC GLM (SAS I nstitute 1996 ) was used to test the differences among RILs and the corresponding BC hybrids. Heterosis was evaluated in BC populations by midparental heterosis (Hmp). Hmp = F 1 − (RIL + recurrent parent)/2. F 1 's are mean trait values of individual BC hybrids while RIL is the corresponding RIL parent for each of the BC hybrids, and recurrent parent is 9024 or LH422 in the IJ hybrid and Zhenshan 97 or Minghui 63 in the II hybrid. To distinguish one from another, the RIL is designated as RILij in the IJ hybrid and as RILii in the II hybrid.

Following K earsey et al . (2003) and F rascaroli et al . (2007) , the crosses of the n RILs to the two recurrent parents are referred as “ L 1 i ” and “ L 2 i ” ( i = 1 ∼ n ), respectively. The two independent sets of data by summation ( L 1 i + L 2 i ) and by subtraction ( L 2 i − L 1 i ) of the two BC populations' values hereafter are referred to as the “SUM” data set and the “DIFF” data set, respectively. Variation within the SUM data set is due to additive effects and variation within the DIFF data set is due to dominance effects when combined over two BC populations.

In this study, for the IJ hybrid, L 1 i and L 2 i represent the n = 194 RILs to 9024 and LH422, respectively; while for the II hybrid, L 1 i and L 2 i represent the n = 222 RILs to Zhenshan97 and Minghui63, respectively. To distinguish one from another, the two data sets SUM and DIFF in the IJ hybrid are referred as SUMij and DIFFij and those in the II hybrid as SUMii and DIFFii.

NCIII and TTC analysis:

ANOVA was used to test for additive ( L 1 i + L 2 i ) and dominance ( L 2 i − L 1 i ) variation by following the standard North Carolina design III (NCIII) and for epistatic variation ( L 1 i + L 2 i − P ) by following the extended TTC design as described by K earsey and J inks (1968) , with P indicated as the RI population in this study. Additive ( V A ) and dominance ( V D ) components of genetic variance were estimated and used to calculate the average degree of dominance [as √(2 V D / V A )], which is a weighted mean of the level of dominance over all segregating loci ( K earsey and P ooni 1996 ).

Genetic linkage maps:

For the IJ hybrid, a subset of 141 polymorphic RFLP markers was selected from the rice high-density molecular map ( C ausse et al . 1994 ) to construct the linkage map of the RI population by X iao et al . (1995) . For the II hybrid, a linkage map was constructed by X ing et al . (2002) , which consisted of 221 marker loci and covered a total of 1796 cM.

QTL mapping and detection of dominance degree of main-effect QTL and epistatic-effect QTL:

Qtl mapping:.

QTL analysis was performed separately for the RI, the midparental heterosis (Hmp) of two backcross populations, and two independent data sets SUM and DIFF in the IJ hybrid and the II hybrid. In the absence of epistasis, the analysis of RIL and SUM data sets identifies QTL with an additive effect ( a ), whereas the analysis of Hmp and DIFF data sets detects QTL with a dominance effect ( d ) ( F rascaroli et al . 2007 ).

Analysis of main-effect QTL (M-QTL) was conducted in each mapping population by composite-interval mapping, using WinQTLcart ( Z eng 1994 ). A LOD score of 2.0 was selected as the threshold for the presence of a main-effect QTL based on the total map distance and the average distance between markers. QTL detected in different populations or for different traits were considered as common if their estimated map position was within a 20-cM distance ( G roh et al . 1998 ), which is a common approach in comparative mapping. Following F rascaroli et al . (2007) , in the absence of epistasis, the expectation of genetic effects in RIL, SUM, Hmp, and DIFF data was a , a , d / 2 , and d .

Analysis of digenic interaction was conducted in each mapping population by the mixed linear approach and by the use of the computer software QTLMAPPER ver. 1.0 ( W ang et al . 1999 ). The analysis was first conducted without considering epistasis to confirm the QTL detected with the method previously described and then with epistasis considered in the model. A threshold of LOD ≥ 3.0 ( P < 0.001) was used for declaring the presence of a putative pair of epistatic QTL.

Genetic analysis methods for estimating QTL dominance degree:

North Carolina design III (NCIII) was put forward by C omstock and R obinson (1952) . In a NCIII design, male progeny from generation 2 (F 2 , which were treated as a base population) of two inbred strains are backcrossed to their grandmothers (marked as L 1 and L 2 ), and their progeny are arranged in a completely randomized block design ( C omstock and R obinson 1952 ). In 1968, an NCIII design was developed by Kearsey and Jinks. In their theory, the F 3 , F 4 , … , F n , double haploid (DH), and RIL also can be treated as base populations. Following Kearsey, the base population was crossed to the two parents (P 1 and P 2 ) indicated as L 1 and L 2 . With the data of L 1 + L 2 and L 1 − L 2 , the genetic parameters of QTL such as additive effect, dominant effect, and the degree of dominance could be estimated.

On the basis of the correlation analysis of detected M-QTL and digenic interaction proposed by H u et al . (1995 , 2002 ), regression and variance analysis of two data L 1 + L 2 and L 1 − L 2 when the base population was the DH population could be deduced as follows ( Tables 1 and ​ and2 2 ).

Genetic expectation of regression coefficients of L 1 + L 2 and L 1 − L 2 when the base population was the DH population

b ′ i ( i = 1 ∼ K , where K is the total number of markers in linkage map) is indicated as a regression coefficient. a i ( i = 1 ∼ K ) and d i ( i = 1 ∼ K ) are denoted as the additive effect and the dominant effect, respectively; i a 1 a 2 is the additive × additive epistatic effect, i a 1 a 2 a 3 is the additive × additive × additive epistatic effect, etc. l d 1 d 2 is the dominance × dominance epistatic effect, l d 1 d 2 d 3 is the dominance × dominance × dominance epistatic effect, etc. r m denotes the recombinant value. For the RI population, the expectations were similar to those in the DH population except for r m , which was replaced by 2 r ′ m /(1 + 2 r ′ m ) and 4 r ″ m /(1 + 6 r ″ m ), respectively. The r ′ m and r ″ m were recombinant values for two RI populations (selfing population and sib-mating population), respectively ( H u et al . 2002 ). d 1 / a 1 is indicated as the dominant degree of main-effect QTL, l d 1 d 2 / i a 1 a 2 as the epistasis dominance degree (EDD), and l d 1 d 2 d 3 / i a 1 a 2 a 3 as the epistasis dominance degree among three markers, etc.

Genetic expectation of variance components of L 1 + L 2 and L 1 − L 2 when the base population was the DH population

On the basis of the methodology proposed, we developed a software QTLIII (not published yet), which is suitable for analyzing the additive effect, dominant effect, and dominance degree of QTL (including one-factor, two-factor, and three-factor ANOVA, see Tables 1 and ​ and2). 2 ). In this study, it was used to estimate dominance degree of main-effect and epistatic-effect QTL.

The degree of dominance of a M-QTL was estimated as | d/a |. For this purpose, for all QTL declared as significant within any data set, dominant and additive effects were estimated in SUM and DIFF data sets by QTLIII with ANOVA analysis. These estimates were used to calculate | d/a | and classify the QTL as additive (A) (| d/a | < 0.2), partial dominance (PD) (0.2 ≤ | d/a | < 0.8), dominance (D) (0.8 ≤ | d/a | < 1.2), and overdominance (OD) (| d/a | ≥ 1.2) according to S tuber et al . (1987) .

Genetic expectations of the parameters estimated in the epistatic models differ on the basis of genetic composition of data sets analyzed. For the SUM data set, the estimated interaction is expected to be predominantly additive × additive ( aa ), whereas for the DIFF data set it is expected to be predominantly dominance × dominance ( dd ). In this study, | dd/aa |, defined as epistasis dominance degree (EDD), was estimated by the software QTLIII with ANOVA analysis. These estimates were used to calculate | dd/aa | to classify the epistatic QTL as A (| dd/aa | < 0.2), PD (0.2 ≤ | dd/aa | < 0.8), D (0.8 ≤ | dd/aa | < 1.2), and OD (| dd/aa | ≥ 1.2).

Relationship between genomewide or chromosomewide molecular marker heterozygosity and phenotypic trait performance and heterosis:

GGT ( V an 1999 ) was used to calculate genome ratios (percentage of total genome originated from one parental genome) for each line in the RI population, initially for the whole genome and then for each chromosome. Relationship between molecular marker heterozygosity and phenotypic performance was tested by regressing phenotypic performance on whole-genome heterozygosity in two backcross populations in both IJ and II hybrids. Meanwhile, to elucidate the relationship between observed heterosis and heterozygosity, (i) the Hmp and DIFF values were respectively regressed against heterozygosity across the whole genome using linear regression (when the DIFF data set was used as a dependent variable, genome heterozygosity of each backcross population was the independent variable), and (ii) the Hmp values were regressed against heterozygosity on individual chromosomes by multiple regression.

F 1 heterosis:

In the IJ hybrid, LH422 showed significant higher mean trait values than 9024 ( Table 3 ). All nine traits except heading date in F 1 had a higher value than both parents. For midparental heterosis, yield showed the strongest significant heterosis (25.58%), followed by 1000-grain weight (15.82%), plant height (15.34%), panicle length (9.42%), tillers per plant (8.00%), seed set (4.06%), and heading date (1.74%). However, the F 1 hybrid had a lower trait value for filled grains per panicle and grain density than the parental lines, with negative heterosis of 2.08 and 10.17%, respectively.

Mean values of nine important agronomic traits of P 1 , P 2 , F 1 , RIL, and their two backcross populations in two rice elite hybrids

For a description of agronomic traits see materials and methods .

In the II hybrid, the parent Minghui63 had a significantly higher phenotypic value than Zhenshan97 for all nine traits investigated ( Table 3 ). The F 1 hybrid had 91 days to heading, similar to Minghui63, which took more days to heading than Zhenshan97. The values of the other traits were significantly higher in F 1 than in both parents. The midparental heterosis of the F 1 plants was strongest for yield (83.09%), followed by filled grains per panicle (29.13%), plant height (21.94%), heading date (17.46%), seed set (16.68%), grain density (13.86%), panicle length (13.42%), tillers per plant (11.09%), and 1000-grain weight (8.21%).

Heterosis in RI and BC populations:

RIL and parental inbred mean values ( Table 3 ) were not significantly different for any trait in both IJ and II hybrids.

Significant heterosis for yield was observed in II hybrid BC populations, but not in IJ hybrid BC populations. Most of the other traits did not show significant heterosis in BC populations of both IJ and II hybrids.

For the IJ hybrid, the mean values of the 9024BC and LH422BC populations were 80.96 and 81.21 for heading date, 107.28 and 110.83 for plant height, 10.38 and 9.55 for tillers per plant, 24.60 and 25.27 for panicle length, 83.20 and 98.28 for filled grains per panicle, 60.66 and 62.75 for seed set, 5.60 and 6.25 for grain density, 26.31 and 24.45 for 1000-grain weight, and 6.14 and 6.18 for yield. The heterosis was 24.45 (29.5%) and 3.12 (7.0%) for heading date, 6.45 (6.4%) and 5.10 (4.6%) for plant height, −0.30 (−2.8%) and 0.28 (3.0%) for tillers per plant, 1.65 (7.2%) and 1.36 (5.5%) for panicle length, −5.90 (−6.6%) and −1.56 (−1.8%) for filled grains per panicle, −7.39 (−10.9%) and 4.62 (6.9%) for seed set, 0.62 (12.5%) and 0.97 (20.8%) for grain density, 2.19 (9.1%) and 1.58 (5.9%) for 1000-grain weight, and −0.16 (−2.5%) and 0.14 (2.3%) for yield, in the 9024BC and LH422BC populations, respectively.

For the II hybrid, the mean values of the Zhenshan97BC and Minghui63BC populations were 75.44 and 85.44 for heading date, 113.11 and 113.50 for plant height, 11.99 and 12.00 for tillers per plant, 23.32 and 24.81 for panicle length, 121.81 and 126.15 for filled grains per panicle, 79.42 and 81.29 for seed set, 5.22 and 5.09 for grain density, 26.26 and 26.74 for 1000-grain weight, and 6.73 and 7.56 for yield. The heterosis values were −11.53 (−15.9%) and −1.53 (−1.8%) for heading date, 1.72 (1.7%) and 2.11 (1.9%) for plant height, 0.59 (1.1%) and 0.59 (0.9%) for tillers per plant, −0.75 (−3.5%) and 0.74 (3.1%) for panicle length, 4.7 (4.5%) and 9.04 (7.7%) for filled grains per panicle, 4.89 (10.7%) and 8.75 (13.6%) for seed set, 0.34 (7.1%) and 0.21 (4.3%) for grain density, −1.64 (−0.64%) and −0.16 (−0.6%) for 1000-grain weight, and 1.82 (36.9%) and 1.04 (15.9%) for yield in the Zhenshan97BC and Minghui63BC populations, respectively.

TTC analysis allows us to test nonallelic interactions. Significant additive × additive ([ aa ]) epistasis was detected for all traits in both IJ and II hybrids ( Table 4 ). The epistasis due to additive × dominance or dominance × dominance ([ ad ] and [ dd ]) was significant for all traits in the IJ hybrid and all the traits except tillers per plant in the II hybrid.

NCIII and TTC analyses of the two rice hybrids

* P ≤ 0.05, ** P ≤ 0.01, *** P ≤ 0.005.

In this study, NCIII analysis led to the estimates of V A (additive variance) and V D (dominance variance), which were always highly significant ( P < 0.005) in both hybrids, except for the V D of tillers per plant in the II hybrid, which was significant at P < 0.05 ( Table 4 ).

QTL detected in RIL, SUM, two Hmp, and DIFF data sets in IJ and II hybrids are shown in Tables 5 and ​ and6, 6 , respectively. In total, 76 and 41 QTL were revealed in five data sets of IJ and II hybrids, respectively. Most of these QTL explained <10% of variation individually. Five QTL (6.76%) in the IJ hybrid and 4 (9.76%) in the II hybrid accounted for >20% of phenotypic variation individually.

Main-effect QTL resolved in the IJ hybrid

Effects estimated in 9024Hmp and LH422Hmp were multiplied by 2, and the values estimated in LH422Hmp and the DIFF were multiplied by (−1).

Main-effect QTL resolved in the II hybrid

Effects obtained in Zhenshan97Hmp and Minghui63Hmp were multiplied by 2, and the values obtained in LH422Hmp and the DIFF were also multiplied by (−1).

In the IJ hybrid, 10 QTL were detected. Three showed an additive effect, 4 a partial-to-complete dominant effect, and 3 an overdominant effect. Six of the 9 QTL showing a dominant effect identified in Hmp and DIFFij were negative, with alleles from 9024 increasing the trait value. In the II hybrid, 8 QTL were found. Three exhibited an additive effect and 5 a partial-to-complete dominant effect. Four of the 5 QTL displaying a dominant effect revealed in Hmp and DIFFii were positive, with alleles from Minghui63 increasing the trait value.

In the IJ hybrid, 12 QTL were found. Six were classified as additive, 3 as partial-to-complete dominance, and 4 as overdominance. In the II hybrid, 4 QTL were detected. Three were found to be additive and 1 in Zhenshan97Hmp to be overdominant. No QTL was identified in SUMii.

In the IJ hybrid, four QTL were identified with two showing an additive effect, one an overdominant effect, and one a partial dominant effect. No QTL was found in the LH422Hmp and DIFFij data sets. In the II hybrid, five QTL were detected with two exhibiting an additive effect, one a dominant effect, and two an overdominant effect.

In the IJ hybrid, 11 QTL were found with 5 classified as an additive effect, 4 as an overdominant effect, and 2 as a partial-to-complete dominant effect. In the II hybrid, 2 QTL in RIL and 1 QTL in SUMii were detected, displaying an additive effect and with alleles from Minghui63 increasing the trait value.

In the IJ hybrid, six QTL were found with three behaving like an additive effect, two like a partial-dominant effect, and one like an overdominant effect. In the II hybrid, two QTL were detected with one appearing to be an overdominant effect and one a partial-dominant effect. No QTL was revealed in Hmp and DIFFii.

In the IJ hybrid, 10 QTL were found with 4 displaying an additive effect, 4 a partial-dominant effect, and 2 an overdominant effect. In the II hybrid, only 1 QTL was detected in DIFFii data, showing overdominant effect, and the alleles from Zhenshan97 increased the trait value.

In the IJ hybrid, seven QTL were identified with two exhibiting an additive effect, two a partial-to-complete dominant effect, and three an overdominant effect. No QTL was detected in 9024Hmp. In the II hybrid, four QTL were revealed with two showing an additive effect, one a partial-dominant effect, and one an overdominant effect. No QTL was found in Minghui63Hmp and DIFFii data sets.

In the IJ hybrid, 10 QTL were revealed with 5 displaying an additive effect, 3 a partial-dominant effect, and 2 an overdominant effect. No QTL was found in 9024Hmp. In the II hybrid, 8 QTL were detected with 2 showing an additive effect, 3 a partial-to-complete dominant effect, and 3 an overdominant effect.

In the IJ hybrid, six QTL were identified with two exhibiting an additive effect, three a dominant effect, and one an overdominant effect. No QTL was found in SUMij and LH422Hmp. In the II hybrid, six QTL were detected with one showing an additive effect and five an overdominant effect. No QTL was found in Zhenshan97Hmp and SUMii data sets.

Digenic interaction:

Table 7 shows the digenic interactions detected in DIFFij data in the IJ hybrid. A total of 46 digenic interactions were found in DIFFij data. No significant interaction was found for yield. The variation explained by individual interaction ranges from 2.0 to 10.1%. The proportion of total variation explained by all digenic interaction was ∼30% in most traits. The highest value of total variation was observed for panicle length in the DIFFij data set (45.1%), which mainly reflected the dominance × dominance digenic interactions.

Digenic interactions in the DIFFij data set in the IJ hybrid

* P ≤ 0.05, ** P ≤ 0.01, *** P ≤ 0.001.

Table 8 shows the digenic interaction identified in DIFFii data in the II hybrid. In total, 81 digenic interactions were revealed. Each interaction generally showed modest R 2 < 10% for all significant interactions except one interaction with 18.1%. However, in the IJ hybrid, the total variation explained by all digenic interactions was >40% for most of the traits. The highest value of total R 2 was observed for SS in the DIFFii data set (52.7%).

Digenic interactions in the DIFFii data set in the II hybrid

Table 9 summarizes the digenic interaction detected in RIL, SUM, Hmp, and DIFF data sets of IJ and II hybrids. Most of the detected interactions involved QTL without a significant main effect and each interaction showed a modest R 2 < 10% for all traits. However, it should be noted that an interaction occurred between two significant M-QTL in Minghui63Hmp for 1000-grain weight, which explained 43.4% of phenotypic variation (data not shown here).

Summaries of digenic interaction in five data sets of the two hybrids

In the IJ hybrid, the number of digenic interactions detected for each trait varies from none to 10 in the RILij population with an average of 3.22, and the variance explained ( R 2 ) by each pair was up to 39.1% with an average of 16.4%. The number of digenic interactions detected in the SUMij data set varies from two to 7 with an average 3.44, and the R 2 of each pair varies from 10.9 to 44.7% with an average of 21.8%. For digenic interaction of dominance × dominance, on average, 1.11, 1.11, and 2.00 QTL pairs with an additive effect were detected in 9024Hmp, LH422Hmp, and DIFFij and had a contribution rate of 6.0, 6.4, and 12.2%, respectively; 2.11, 2.44, and 2.22 QTL pairs with partial-to-complete dominance were detected in 9024Hmp, LH422Hmp, and DIFFij and had a contribution rate of 14.7, 15.2, and 13.3%, respectively; and 1.67, 1.33, and 0.89 QTL pairs with overdominance were detected in 9024Hmp, LH422Hmp, and DIFFij and had a contribution rate of 10.6, 8.4, and 4.5%, respectively.

For the II hybrid, the number of digenic interactions identified for each trait varies from none to 12 in the RILii population with an average of 8.11 and had a contribution rate ( R 2 ) up to 87.0%, with an average of 47.9%. The number of digenic interactions detected in the SUMii data set varies from none to 14 with an average of 7.44, and each pair had an R 2 up to 59.4% with an average of 40.4%. For digenic interaction of dominance × dominance, on average, 1.44, 0.11, and 1.22 QTL pairs with additive effect were detected in Zhenshan97Hmp, Minghui63Hmp, and DIFFii and had a contribution rate of 7.0, 0.7, and 7.4%, respectively; 5.44, 1.56, and 2.44 QTL pairs with partial-to-complete dominance were detected in Zhensha97Hmp, Minghui63Hmp, and DIFFii and had a contribution rate of 27.7, 13.8, and 11.8%, respectively; and 2.44, 0.89, and 5.33 QTL pairs with overdominance were detected in Zhenshan97Hmp, Minghui63Hmp, and DIFFii and had a contribution rate of 12.2, 5.3, and 25.3%, respectively.

Relationship between trait performance and genomewide or chromosomewide marker heterozygosity:

The correlation coefficients ( Table 10 ) between level of genomewide heterozygosity and performance per se of the two backcross populations were not significant for most of the traits in both IJ and II hybrids (except plant height in 9024BC and 1000-grain weight in Minghui63BC). The analysis of the relationship between level of heterozygosity and level of heterosis (as evaluated in Hmp and DIFF) showed that correlation coefficients, for several traits, were slightly higher than those previously shown, but still not significant for most traits. The significant correlation coefficients were found for plant height, heading date, and 1000-grain weight in the IJ hybrid and for tillers per plant in the II hybrid.

Correlation coefficients between genomewide molecular marker heterozygosity and phenotypic values

* P ≤ 0.05, ** P ≤ 0.01.

In this study, the Hmp value was regressed against heterozygosity on individual chromosomes using multiple linear regression ( Table 11 ). The hybrid performance was also poorly associated with marker heterozygosity in most chromosomes. There were 8, 6, 8, and 5 significant regressions between trait value and marker heterozygosity in individual chromosomes resolved in 9024Hmp, LH422Hmp, Zhenshan97Hmp, and Minghui63Hmp, respectively. Nineteen of these 27 (70.3%) significant regressions were associated with one or two M-QTL and/or digenic interaction. In the IJ hybrid, the F -test value was significant for panicle length and grain density in 9024Hmp and for plant height and heading date in LH422Hmp. While in the II hybrid, the F -test value was significant for plant height in Zhenshan97Hmp and for yield in Minghui63Hmp. The coefficients ( r 2 ) for most traits were <0.10 in both IJ and II hybrids.

Significant regression coefficients of midparent values of backcross populations on individual chromosome marker heterozygosity for the indicated traits

* P ≤ 0.05, ** P ≤ 0.01, *** P ≤ 0.001. Italics indicate the presence of a QTL on a particular chromosome.

Choice of the experimental design and statistical methods:

NCIII and TTC designs are most suitable for studies of heterosis in the presence of epistasis because they provide estimates of augmented dominance effects ( K usterer et al . 2007a , b ). Meanwhile, compared with the F 2 or the F 3 population, RILs as parents for producing testcross progenies offer few advantages. First, the effects of linkage are reduced because linkage disequilibrium between tightly linked loci is almost half of that in the F 2 population. Second, use of homozygous parents (RIL) maximizes the genetic variance among testcross progenies and leads to an increased power in F -tests and reduced standard errors of variance component and dominance effect estimates since RILs are homozygous at almost all of the genetic loci while F 2 plants have 50% heterozygous loci. Third, RILs are immoral and testcross progeny can be repeatedly generated and tested as needed.

Up to now, several studies have been conducted to try to understand the genetic basis of heterosis in rice ( X iao et al . 1995 ; L i et al . 2001 ; L uo et al . 2001 ; H ua et al . 2002 , 2003 ). However, the causes underlying this important phenomenon have remained unclear and none of these studies quantified the gene action of QTL. In this study, with two derived data sets (SUM and DIFF) and the software developed by us, we resolved the dominance degree for all of the M-QTL and digenic interactions. The statistical method employed in this study is much more precise and informative to understand the causes of heterosis in rice since it classifies underlying QTL into A, PD, D, and OD on the basis of degree of dominance.

It should be noted that the A, PD, D, and OD referred to in this study are different from the additive effect, dominant effect, and overdominant effect in a traditional dominant–additive model. In fact, as well as in hybrid F 1 , since each locus is in heterozygosis, only gene action of dominance, dominance × dominance, dominance × dominance × dominance, etc., existed in Hmp and DIFF. Therefore, in this study, A, PD, D, and OD were treated only as a scale for quantifying the degree of dominance ( d ) or dominance × dominance ( dd ) effect.

Heterosis for the traits studied:

In the two hybrids investigated here, grain yield showed the strongest heterosis among the nine traits studied (25.58% in the IJ hybrid and 83.09% in the II hybrid), consistent with the findings of previous studies conducted on rice ( L i et al . 2001 ; L uo et al . 2001 ) as well as other cereal crops ( T ollenaar et al . 2004 ; H oecker et al . 2006 ). Heterosis for the other traits was <20% in the IJ hybrid and <30% in the II hybrid. Negative heterosis for filled grains per panicle and grain density was observed in the IJ hybrid. These results confirm that heterosis of yield components was much less than grain yield itself ( L i et al . 2001 ).

For the IJ hybrid, the Hmp of some backcross lines was stronger than that of F 1 , while some other backcross lines expressed an Hmp in the opposite direction. This result is in harmony with the study conducted by M ei et al . (2005) in which an indica/japonica hybrid was also used. It can be concluded that heterosis was generally related to the average level of heterozygosity in a hybrid population but poorly correlated with heterozygosity at the individual level ( Z hang et al . 1995 ; Y u et al . 1997 ). This conclusion also can be confirmed by the fact that the correlation between marker heterozygosity and trait expression is negligible.

For the II hybrid, the heterosis in BC populations was much lower than that in F 1 . This may be due to the fact that the two intraspecific parents are more genetically similar than the two interspecific parents of IJ hybrids. The reduction in the proportion of heterozygous loci in the BCF 1 population probably caused the reduced average level of heterosis in the BCF 1 compared to the hybrid between two parents.

For the traits showing highly significant epistasis, V A and V D estimates are to some extent biased ( K earsey and P ooni 1996 ) and so are the average degree of dominance estimates. In the IJ hybrid, highly significant [ aa ], [ ad ], and [ dd ] epistasis was observed for all the traits studied. In the II hybrid, the average degree of dominance for most traits was <1.00, except for plant height (1.18) and grain yield (1.20), suggesting an important contribution of overdominance to the heterosis of these two traits. For epistasis conducted by TTC analysis, [ aa ] was highly significant ( P ≤ 0.005) for all traits, and [ ad ] and [ dd ] for most of traits, except for yield and grain density (significant at P ≤ 0.01), panicle length (significant at P ≤ 0.05), and tillers per plant (not significant). Therefore, epistasis appeared to be of more importance than intralocus interaction in affecting heterosis in these two elite hybrids. A similar conclusion was drawn in Arabidopsis by K usterer et al . (2007a) in which a TTC family derived from the Arabidopsis C24 × Col-0 was analyzed, and it was found that epistasis across environments was more important for most traits. However, in the TTC design with recombinant inbred lines of the maize B73 × H99 ( F rascaroli et al . 2007 ), the epistasis was found not significant for most traits.

Genetic basis of heterosis in two highly heterotic hybrids of rice:

Our analyses allowed the identification of several QTL for each of the traits investigated. Most individual QTL explained modest variation (<10%), and only four QTL in the IJ hybrid and five QTL in the II hybrid contributed >20% variation individually ( Tables 5 and ​ and6), 6 ), confirming that the heterosis is a polygenic phenomenon ( H allauer and M iranda 1981 ; K usterer et al . 2007a ).

The proportion of QTL with an additive or a dominant effect is different between the two hybrids. Among the 74 main-effect QTL detected in the IJ hybrid, 24 (32%) showed a gene action of partial-to-complete dominance, 20 (26%) showed overdominance, and 32 (42%) showed an additive effect; while among the 41 main-effect QTL identified in the II hybrid, 12 (29%) exhibited partial-to-complete dominance, 16 (39%) showed overdominance, and 13 (32%) showed an additive effect. These results indicate that dominance and overdominance played an important role in conditioning the heterosis in these two hybrids. Also, the results from the dominance degree (| d/a |) of main-effect QTL estimated by QTLIII with regression analysis and by WinQTLcart ( Z eng 1994 ) show that, although the dominance degrees were not exactly consistent with each other by the three approaches (ANOVA, regression analysis, WinQTLcart), the proportions of QTL detected with dominance and with overdominance were >25% each.

The importance of dominance and overdominance conditioning the heterosis of these two hybrids seems different. In the IJ hybrid, the proportion of QTL showing a gene action of overdominance is less than that with partial-to-complete dominance. This result was also found in the study conducted by X iao et al . (1995) using the same materials, but a different analysis method. However, in the II hybrid, the proportion of QTL exhibiting a gene action of overdominance is more than the proportion of those having a gene action of partial-to-complete dominance. This result is in harmony with other studies, especially the work conducted on the F 2:3 families derived from the cross between Zhenshan97 and Minghui63 by Y u et al . (1997) . However, although a relatively higher portion of QTL demonstrated overdominance in the II hybrid, QTL exhibiting high levels of overdominant effects are not necessarily indicative of true overdominance, but rather can be the result of dominant alleles linked in repulsion (pseudo-overdominance).

Compared to M-QTL detected in these two hybrids, only two QTL for heading date were found in a similar genomic region bordered by the same molecular markers. This may be due to the fact that very few markers were common across these two linkage maps. On chromosome 1, one QTL was detected between RG811 and RG173 in the IJ hybrid, showing an additive effect. One QTL between RM243 and RG173 was detected in the II hybrid, displaying a partial-dominant effect. On chromosome 8, one QTL between RG333 and RZ562 in the IJ hybrid and one between C1121 and RG333 in the II hybrid exhibited an additive effect, thus suggesting that, even in the same or a similar genomic region bordered by the same molecular markers in different hybrids, the gene action of QTL could be different due to interaction of different alleles at the QTL. It should be noted that, for the two hybrids that were planted in different environments, the type of gene action may be influenced by environmental effect.

Various levels of negative dominance were observed at some QTL for each trait, indicating that heterozygosity was not necessarily always favorable for the expression of the trait even in highly heterotic hybrids. For both hybrids studied here, dominant effects of the detected QTL were always bidirectional, resulting in the cancellation of positive and negative dominant effects contributed by different QTL controlling the trait, which explains the poor relationship observed between marker heterozygosity and trait expression. A good consistency was also found in other studies of rice ( Y u et al . 1997 ; M ei et al . 2005 ), but in contrast with the study ( F rascaroli et al . 2007 ) in maize.

There were a large number of digenic interactions found to have effects on the traits of the two hybrids studied here. Two pronounced features were notably found for the epistasis in this study. First, although individual interaction had a modest R 2 (phenotypic variation), <10% in most cases (data not shown) for each trait of the two hybrids, the total variation explained by all the significant digenic interactions for the trait was much greater than that by all the M-QTL affecting the same trait for most traits.

Similar to a large number of empirical studies in other selfing and outcrossing plant species ( A llard 1988 ; L i et al . 2001 ; M ei et al . 2005 ), most epistasis occurred between complementary loci with no detectable main effects. In many fewer cases, epistasis occurred between a M-QTL and a complementary locus and in only seven cases in the IJ hybrid and two in the II hybrid between M-QTL. By using the same population of IJ hybrids reported here, X iao et al . (1995) was unable to detect epistasis due to the unavailability of appropriate mapping methodology ( L i et al . 2001 ).

It should be noted that the two digenic interactions in the II hybrid occurred between M-QTL accounting for a large variation for 1000-grain weight detected in Minghui63Hmp and for panicle length detected in Zhenshan97BC, explaining 43.4 and 23.8% of the variation, respectively (data not shown). When a M-QTL is involved in the epistatic interaction, the effect of the single-locus QTL is mostly dependent on the genotypes of the other locus and can sometimes be negated by the genotypes of a second locus. Thus an attempt to utilize the QTL in the breeding programs needs to consider such epistatic effects, especially the interaction occurring between two significant M-QTL and having a high phenotypic variation.

Another feature of digenic interaction in this study is that both partial-to-complete dominance and overdominance played an important role in conditioning heterosis. Shown in Table 9 is the relative importance of additive and nonadditive gene action of digenic interaction summarized by comparing the genetic effects detected in the SUM and DIFF data sets by QTL with ANOVA analysis.

For the additive × additive digenic interactions, there were an average of 3.22 and 3.44 pairs detected in the RILij and SUMij data sets for each trait in the IJ hybrid, contributing 16.4 and 21.8% phenotypic variation, respectively; while in the II hybrid, an average of 8.11 and 7.44 pairs were detected in the RILii and SUMii data sets for each trait, explaining 47.9 and 40.4% of the phenotypic variation, respectively.

There were a total of 135 and 188 dominance × dominance digenic interactions detected in Hmp and DIFF in the IJ and II hybrids, respectively. The proportion of digenic interactions displaying partial-to-complete dominance was a little more than that showing overdominance in both hybrids. There were 62 (45.2%) and 85 (45.2%) digenic interactions that behaved like partial-to-complete dominance, 36 (26.7%) and 78 (41.5%) digenic interactions that exhibited overdominance, and 37 (28.1%) and 25 (13.3%) digenic interactions that displayed an additive effect, in IJ and II hybrids, respectively.

The poor relationship between total genomewide molecular marker heterozygosity and phenotypic trait performance was observed for almost all the traits in this study ( Table 10 ). This result is different from the study of maize performed by F rascaroli et al . (2007) in which they found that there was a high relationship between marker heterozygosity level and performance per se and heterosis (as evaluated in Hmp and DIFF) for most traits. To further investigate the relationship between observed heterosis and heterozygosity, Hmp value was regressed against heterozygosity on individual chromosomes, using multiple linear regression. As shown in Table 11 , the hybrid performance was also poorly associated with marker heterozygosity in most chromosomes, although it was relatively more significant than that with whole-genome heterozygosity. Nineteen of the 27 (70.4%) significant regressions by individual chromosomes were associated with one or two M-QTL and/or digenic interaction, indicating that marker heterozygosity in individual chromosomes in QTL regions was important for phenotypic variation. This finding is consistent with S yed and C hen 's (2005) result of the relationship between heterozygosity and heterosis in Arabidopsis. Therefore, the hybrid vigor is poorly related to heterozygosity of the whole genome and on individual chromosomes in rice, which further confirms that the genetic basis or mechanism of heterosis of rice is different from that of maize.

Our results indicate that heterosis in rice is very complex, reflected by the large number of loci involved, their wide genomic distribution, and complex epistatic relationships, and that the nonallelic interactions (epistasis) play a relatively more important role than allelic interactions (M-QTL) in conditioning the heterosis of these two highly heterotic hybrids, implicating that marker-assisted selection in heterosis breeding to significantly enhance the heterosis of desirable traits may be very challenging.

So far almost all of the documented studies on revealing the genetic basis of heterosis are limited to classical quantitative genetics and QTL mapping using molecular markers. The advancements in functional genomics have created a novel avenue to study the genetic basis of heterosis at the gene-expression level. DNA microarrays can quantify expression of tens of thousands of genes on a single DNA chip ( S chena et al . 1998 ). The timing, level, and relationship of the transcription of two different alleles of the same gene in the hybrids can be compared with that of their corresponding parental lines by using microarrays ( S tupar and S pringer 2006 ; S wanson -W agner et al . 2006 ). Functional genomics approaches to elucidating the genetic basis of heterosis would turn the study of this very important and still controversial issue into a new chapter in its history. Evidence from functional expression studies of genes underlying heterosis would elevate our understanding of the genetic basis of heterosis to a new level.

Acknowledgments

We gratefully acknowledge the expert technical assistance of Qifa Zhang on trial design and analysis and the skillful assistance of Yingguo Zhu in field trials. We thank Jinhua Xiao and Yunchun Song for valuable suggestions for improving the manuscript. This work was financially supported by the 973 Program (no. 2006CB101707), the 863 Program (no. 2003AA207160), the National Natural Science Foundation of China (no. 30270760), and the Key Grant Project of the Chinese Ministry of Education (no. 307018).

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6.5 Types of Dominance

As we discussed in the previous section on polygenic traits, in humans most characteristics do not fit into two different phenotypes — complex traits, e.g., height, hair texture, skin colour etc., seemingly do not follow Mendelian analysis. As more scientists began analyzing genetic crosses using different types of plants and animals, it was found that while some traits obeyed Mendel’s laws (they were determined by a single gene with 1 dominant and 1 recessive allele), many other traits did not. In such cases, there were no definite recessive or dominant traits observed, or more than two alleles identified in a particular cross. In some instances, traits seem to be determined by more than one gene (multifactorial), and the environment also seemed to play a role through interaction with genes, to produce varying phenotypes.

These examples of the behaviour of certain traits implies a more complex array of interactions are at play, as these do not generate the typical Mendelian phenotypic ratios. We are extending Mendel’s Laws in order to provide explanations for the behaviour of such traits, and not necessarily challenging them.

One of the first concepts we need to understand, is that dominance is not always complete. Thus far, we have looked at the concept of dominance and recessiveness, whereby these conditions arise upon crossing two pure-breeding lines to create hybrids, and the hybrids are identical in phenotype to one parent for the particular trait in question. In this simplistic case, the allele passed down by that parent is said to be completely dominant when compared with the allele passed down by the parent whose trait is not manifested in the hybrid offspring. This type of arrangement is termed complete dominance .

As we will now see, there are two other types of Dominance — namely, incomplete dominance and co-dominance .

Complete Dominance

An example of a simple phenotype, is flower color in Mendel’s peas. We have already said that one allele as a homozygote produces purple flowers, while the other allele as a homozygote produces white flowers. But what about a heterozygous individual that has one purple allele and one white allele? What is the phenotype of a heterozygote?

This can only be determined by experimental observation. We know from observation that individuals heterozygous for the purple and white alleles of the flower colour gene have purple flowers. Thus, the allele associated with purple colour is, therefore, said to be dominant to the allele that produces the white colour. The white allele, whose phenotype is masked by the purple allele in a heterozygote, is recessive to the purple allele. The dominant/recessive character is a relationship between two alleles and must be determined by observation of the heterozygote phenotype.

Sometimes, to represent this relationship, a dominant allele will be written as a capital letter (e.g., A ) while a recessive allele will be written in lower case (e.g., a ). However, this is not the only system. Many different systems of genetic symbols are in use. The most common are shown in Table 6.5.1  Also note, genotypes (alleles) are usually written in italics and chromosomes and proteins are not. For example, the white gene in Drosophila melanogaster on the X chromosome encodes a protein called WHITE, which is a pigment precursor transmembrane transporter enzyme.

Take a look at the video below. Incomplete Dominance, Codominance, Polygenic Traits, Epistasis, by Amoeba Sisters (2015) on YouTube, which discusses the various types of dominance and polygenic traits.

Incomplete Dominance

Other than the complete dominant and recessive relationship, other relationships can exist between alleles. In incomplete dominance (also called semi-dominance ), both alleles affect the trait additively, and the phenotype of the heterozygote shows a typically intermediate between the homozygotes, which is often referred to as blended phenotype. For example, alleles for colour in carnation flowers (and many other species) exhibit incomplete dominance. Plants with alleles for red petals (RR) when crossed with a plant with alleles for white petals (rr) have offspring which have pink petals (Rr). We say that the R and the r alleles show incomplete dominance because neither allele is completely dominant over the other ( Figure 6.5.3 ). Even though in Figure 6.5.3, there is the use of capital and common letters to indicate the two incompletely dominant alleles, a better way to represent such alleles would be the use of superscripts on the same letter e.g., R 1 and R 2 .

Co-Dominance

Co-dominance is another type of allelic relationship in which a heterozygous individual expresses the phenotype of both alleles simultaneously. An example of co-dominance is found within the ABO blood group of humans. The ABO gene has three common alleles that were named (for historical reasons) I A , I B , and i . People homozygous for I A or I B display only A or B type antigens, respectively, on the surface of their blood cells, and therefore, have either type A or type B blood ( Figure 6.5.4 ). Heterozygous I A I B individuals have both A and B antigens on their cells, and so have type AB blood. Note that the heterozygote expresses both alleles simultaneously, and is not some kind of novel intermediate between A and B. Co-dominance is, therefore, distinct from incomplete dominance, although they are sometimes confused.

It is also important to note that the third allele, i , does not make either antigen and thus is recessive to the other alleles.  I A /i  or I B /i   individuals display only A or B antigens, respectively. People homozygous for the i allele have type O blood.

This is a useful reminder that different types of dominance relationships can exist, even for alleles of the same gene.

Media Attributions

• Figure 6.5.1 2013 09 10 Tomate by Friedrich Haag, CC-BY-SA-4.0 , via Wikimedia Commons
• Figure 6.5.2 14 05LawOfSegregation 2 L by Ashinkaaa ,  CC BY-SA 4.0 , via Wikimedia Commons
• Figure 6.5.3 0 9 11aIncompleteDominance-L by RudLus02 ,  CC BY-SA 4.0 , via Wikimedia Commons
• Figure 6.5.4 Blood Type Codominance by DylanAudette, CC0 1.0 Universal Public Domain , via Wikimedia Commons

Amoeba Sisters. (2015, May 25). Incomplete dominance, codominance, polygenic traits, and epistasis! (video file). YouTube. https://www.youtube.com/watch?v=YJHGfbW55l0

Long Descriptions

• Figure 6.5.1 Two tomatoes: one is large and red in colour, and the other is small and orange in colour. The image seeks to demonstrate the variety of phenotypes that are possible with multifactorial traits, which are determined by more than one gene. [Back to Figure 6.5.1 ]
• Figure 6.5.2 Cross to demonstrate complete dominance. P generation is pure bred purple flowers crossed with pure breeding white flowers, resulting in all purple flowers (heterozygous) in the F1 generation. The F2 generation produces flowers in a ratio of 3 purple to 1 white, which is typical of complete dominance in a monohybrid cross. [Back to Figure 6.5.2 ]
• Figure 6.5.3 Cross to demonstrate incomplete dominance. P generation is pure-bred red flowers crossed with pure breeding white flowers. The F1 generation produced is comprised of pink flowers only, which is indicative of incomplete dominance between these two alleles controlling flower colour. [Back to Figure 6.5.3 ]
• Figure 6.5.4 The variety of blood types in humans. Four phenotypes are shown which are A, B, O and AB. These phenotypes are the result of combinations of alleles which exemplify co-dominance (A and B) as well as alleles which exemplify complete dominance (A and B over O). The combinations of alleles result on specific antigens being expressed on red blood cells of that organism, resulting in the four typical blood group phenotypes seen in humans. [Back to Figure 6.5.4 ]

Introduction to Genetics Copyright © 2023 by Natasha Ramroop Singh, Thompson Rivers University is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License , except where otherwise noted.

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AP®︎/College Biology

Course: ap®︎/college biology   >   unit 5.

• Introduction to heredity
• Fertilization terminology: gametes, zygotes, haploid, diploid
• Alleles and genes
• Worked example: Punnett squares
• Mendel and his peas
• The law of segregation

The law of independent assortment

• Probabilities in genetics
• Mendelian genetics

Introduction

What is the law of independent assortment, example: pea color and pea shape genes, independent assortment vs. linkage, the reason for independent assortment, check your understanding.

• (Choice A)   1 / 4 ‍   A 1 / 4 ‍  
• (Choice B)   3 / 4 ‍   B 3 / 4 ‍  
• (Choice C)   3 / 16 ‍   C 3 / 16 ‍  
• (Choice D)   1 / 16 ‍   D 1 / 16 ‍  

Attribution:

• “ Laws of inheritance ,” by OpenStax College, Biology ( CC BY 3.0 ). Download the original article for free at http://cnx.org/contents/[email protected] .
• " Laws of inheritance ," in Principles of Biology , by Robert Bear, David Rintoul, Bruce Snyder, Martha Smith-Caldas, Christopher Herren, and Eva Horne, OpenStax, ( CC BY 4.0 ). Download the original article for free at http://cnx.org/contents/[email protected] .

Works cited:

• Reid, J. B., and Ross, J. J. (2011). Mendel's genes: Towards a full molecular characterization. Genetics 189 (1), 3-10. http://dx.doi.org/10.1534/genetics.111.132118 . Retrieved from www.ncbi.nlm.nih.gov/pmc/articles/PMC3176118/.

References:

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8 Chapter 8: Mendel’s Experiments and Heredity

Chapter outline.

• 8.1 Mendelian Genetics

8.2 Characteristics and Traits

8.3 laws of inheritance.

• 8.4 Chromosomal Theory and Genetic Linkage
• 8.5 Chromosomal Basics of Inherited Disorders

Figure 8.1 The species of pea plant the Gregor Mendel used in his experiments to discover patterns of inheritance.

Learning Objectives

 You will be able to describe how traits are passed to offspring:

•  Identify the relationship between chromosomes, genes and alleles.
• Understand the principles of simple inheritance
• Identify the terms homozygous, heterozygous, dominant and recessive
• Use a Punnett square to predict the inheritance of a simple trait
• Recognize that most human traits have complex inheritance patterns.
• Understand the genetics of sex determination
• Describe some examples of genetic disorders
• Understand how chromosomes contribute to disorders

8.1 | Mendelian Genetics

Figure 8.2 Johann Gregor Mendel is considered the father of genetics. 1.Johann Gregor Mendel, Versuche über Pflanzenhybriden Verhandlungen des naturforschenden Vereines in Brünn, Bd. IV für das Jahr, 1865 Abhandlungen,3–47. [for English translation see http://www.mendelweb.org/Mendel.plain.html]

Mendel’s Model System

Mendel’s seminal work was accomplished using the garden pea, Pisum sativum , to study inheritance. This species naturally self-fertilizes, such that pollen encounters ova within individual flowers. The flower petals remain sealed tightly until after pollination, preventing pollination from other plants. The result is highly inbred, or “true-breeding,” pea plants. These are plants that always produce offspring that look like the parent. By experimenting with true-breeding pea plants, Mendel avoided the appearance of unexpected traits in offspring that might occur if the plants were not true breeding. The garden pea also grows to maturity within one season, meaning that several generations could be evaluated over a relatively short time. Finally, large quantities of garden peas could be cultivated simultaneously, allowing Mendel to conclude that his results did not come about simply by chance.

Mendelian Crosses

Mendel performed hybridizations, which involve mating two true-breeding individuals that have different traits. In the pea,which is naturally self-pollinating, this is done by manually transferring pollen from the anther of a mature pea plant ofone variety to the stigma of a separate mature pea plant of the second variety. In plants, pollen carries the male gametes(sperm) to the stigma, a sticky organ that traps pollen and allows the sperm to move down the pistil to the female gametes(ova) below. To prevent the pea plant that was receiving pollen from self-fertilizing and confounding his results, Mendelpainstakingly removed all of the anthers from the plant’s flowers before they had a chance to mature.Plants used in first-generation crosses were called P0, or parental generation one, plants (Figure 12.3). Mendel collectedthe seeds belonging to the P0 plants that resulted from each cross and grew them the following season. These offspring werecalled the F1, or the first filial (filial = offspring, daughter or son), generation. Once Mendel examined the characteristicsin the F1 generation of plants, he allowed them to self-fertilize naturally. He then collected and grew the seeds from the F1plants to produce the F2, or second filial, generation. Mendel’s experiments extended beyond the F2 generation to the F3 andF4 generations, and so on, but it was the ratio of characteristics in the P0−F1−F2 generations that were the most intriguingand became the basis for Mendel’s postulates.

Chapter 12 | Mendel’s Experiments and Heredity 315

Figure 8.3 In one of his experiments on inheritance patterns, Mendel crossed plants that were true-breeding for violet flower color with plants true-breeding for white flower color (the P generation). The resulting hybrids in the F1generation all had violet flowers. In the F2 generation, approximately three quarters of the plants had violet flowers, and one quarter had white flowers.

Garden Pea Characteristics Revealed the Basics of Heredity

In his 1865 publication, Mendel reported the results of his crosses involving seven different characteristics, each with two contrasting traits. A trait is defined as a variation in the physical appearance of a heritable characteristic. The characteristics included plant height, seed texture, seed color, flower color, pea pod size, pea pod color, and flower position. For the characteristic of flower color, for example, the two contrasting traits were white versus violet. To fully examine each characteristic, Mendel generated large numbers of F1 and F2 plants, reporting results from 19,959 F2 plants alone. His findings were consistent.What results did Mendel find in his crosses for flower color? First, Mendel confirmed that he had plants that bred true for white or violet flower color. Regardless of how many generations Mendel examined, all self-crossed offspring of parents with white flowers had white flowers, and all self-crossed offspring of parents with violet flowers had violet flowers. In addition, Mendel confirmed that, other than flower color, the pea plants were physically identical.

Once these validations were complete, Mendel applied the pollen from a plant with violet flowers to the stigma of a plant with white flowers. After gathering and sowing the seeds that resulted from this cross, Mendel found that 100 percent of theF1 hybrid generation had violet flowers. Conventional wisdom at that time would have predicted the hybrid flowers to be pale violet or for hybrid plants to have equal numbers of white and violet flowers. In other words, the contrasting parental traits were expected to blend in the offspring. Instead, Mendel’s results demonstrated that the white flower trait in the F1 generation had completely disappeared.

Importantly, Mendel did not stop his experimentation there. He allowed the F1 plants to self-fertilize and found that, of F2-generation plants, 705 had violet flowers and 224 had white flowers. This was a ratio of 3.15 violet flowers per one white flower, or approximately 3:1. When Mendel transferred pollen from a plant with violet flowers to the stigma of a plant with white flowers and vice versa, he obtained about the same ratio regardless of which parent, male or female, contributed which trait. This is called a reciprocal cross—a paired cross in which the respective traits of the male and female in one cross become the respective traits of the female and male in the other cross. For the other six characteristics Mendel examined, the F1 and F2 generations behaved in the same way as they had for flower color. One of the two traits would disappear completely from the F1 generation only to reappear in the F2 generation at a ratio of approximately 3:1 (Table 12.1).

Upon compiling his results for many thousands of plants, Mendel concluded that the characteristics could be divided into expressed and latent traits. He called these, respectively, dominant and recessive traits. Dominant traits are those that are inherited unchanged in a hybridization. Recessive traits become latent, or disappear, in the offspring of a hybridization.The recessive trait does, however, reappear in the progeny of the hybrid offspring. An example of a dominant trait is the violet-flower trait. For this same characteristic (flower color), white-colored flowers are a recessive trait. The fact that the recessive trait reappeared in the F2 generation meant that the traits remained separate (not blended) in the plants of the F1 generation.

Mendel also proposed that plants possessed two copies of the trait for the flower-color characteristic, and that each parent transmitted one of its two copies to its offspring, where they came together. Moreover, the physical observation of a dominant trait could mean that the genetic composition of the organism included two dominant versions of the characteristic or that it included one dominant and one recessive version. Conversely, the observation of a recessive trait meant that the organism lacked any dominant versions of this characteristic.

So why did Mendel repeatedly obtain 3:1 ratios in his crosses? To understand how Mendel deduced the basic mechanisms of inheritance that lead to such ratios, we must first review the laws of probability.

Probability Basics

Probabilities are mathematical measures of likelihood. The empirical probability of an event is calculated by dividing the number of times the event occurs by the total number of opportunities for the event to occur. It is also possible to calculate theoretical probabilities by dividing the number of times that an event is expected to occur by the number of times that it could occur. Empirical probabilities come from observations, like those of Mendel. Theoretical probabilities come from knowing how the events are produced and assuming that the probabilities of individual outcomes are equal. A probability of one for some event indicates that it is guaranteed to occur, whereas a probability of zero indicates that it is guaranteed not to occur.

8.2 | Characteristics and Traits

By the end of this section, you will be able to:• Explain the relationship between genotypes and phenotypes in dominant and recessive gene systems• Develop a Punnett square to calculate the expected proportions of genotypes and phenotypes in a monohybrid cross• Explain the purpose and methods of a test cross• Identify non-Mendelian inheritance patterns such as incomplete dominance, co-dominance, recessive lethals, multiple alleles, and sex linkage.

For cases in which a single gene controls a single characteristic, a diploid organism has two genetic copies that may or may not encode the same version of that characteristic. Gene variants that arise by mutation and exist at the same relative locations on homologous chromosomes are called alleles. Mendel examined the inheritance of genes with just two allele forms, but it is common to encounter more than two alleles for any given gene in a natural population.

Phenotypes and Genotypes

Two alleles for a given gene in a diploid organism are expressed and interact to produce physical characteristics. The observable traits expressed by an organism are referred to as its phenotype. An organism’s underlying genetic makeup, consisting of both physically visible and non-expressed alleles, is called its genotype. Mendel’s hybridization experiments demonstrate the difference between phenotype and genotype. When true-breeding plants in which one parent had yellow pods and one had green pods were cross-fertilized, all of the F1 hybrid offspring had yellow pods. That is, the hybrid offspring were phenotypically identical to the true-breeding parent with yellow pods. However, we know that the allele donated by the parent with green pods was not simply lost because it reappeared in some of the F2 offspring. Therefore, theF1 plants must have been genotypically different from the parent with yellow pods.The P1 plants that Mendel used in his experiments were each homozygous for the trait he was studying. Diploid organisms that are homozygous at a given gene, or locus, have two identical alleles for that gene on their homologous chromosomes.Mendel’s parental pea plants always bred true because both of the gametes produced carried the same trait. When P1 plants with contrasting traits were cross-fertilized, all of the offspring were heterozygous for the contrasting trait, meaning that their genotype reflected that they had different alleles for the gene being examined.

Dominant and Recessive Alleles

Our discussion of homozygous and heterozygous organisms brings us to why the F1 heterozygous offspring were identical to one of the parents, rather than expressing both alleles. In all seven pea-plant characteristics, one of the two contrasting alleles was dominant, and the other was recessive. Mendel called the dominant allele the expressed unit factor; the recessive allele was referred to as the latent unit factor. We now know that these so-called unit factors are actually genes on homologous chromosome pairs. For a gene that is expressed in a dominant and recessive pattern, homozygous dominant and heterozygous organisms will look identical (that is, they will have different genotypes but the same phenotype). The recessive allele will only be observed in homozygous recessive individuals (Table 8.4).

Several conventions exist for referring to genes and alleles. For the purposes of this chapter, we will abbreviate genes using the first letter of the gene’s corresponding dominant trait. For example, violet is the dominant trait for a pea plant’s flower color, so the flower-color gene would be abbreviated as V (note that it is customary to italicize gene designations). Furthermore, we will use uppercase and lowercase letters to represent dominant and recessive alleles, respectively. Therefore, we would refer to the genotype of a homozygous dominant pea plant with violet flowers as VV, a homozygous recessive pea plant with white flowers as vv, and a heterozygous pea plant with violet flowers as Vv.

The Punnett Square Approach for a Monohybrid Cross

When fertilization occurs between two true-breeding parents that differ in only one characteristic, the process is called a monohybrid cross, and the resulting offspring are monohybrids. Mendel performed seven monohybrid crosses involving contrasting traits for each characteristic. On the basis of his results in F1 and F2 generations, Mendel postulated that each parent in the monohybrid cross contributed one of two paired unit factors to each offspring, and every possible combination of unit factors was equally likely. To demonstrate a monohybrid cross, consider the case of true-breeding pea plants with yellow versus green pea seeds. The dominant seed color is yellow; therefore, the parental genotypes were YY for the plants with yellow seeds and yy for the plants with green seeds, respectively.

A Punnett square, devised by the British geneticist Reginald Punnett, can be drawn that applies the rules of probability to predict the possible outcomes of a genetic cross or mating and their expected frequencies. To prepare a Punnett square, all possible combinations of the parental alleles are listed along the top (for one parent) and side (for the other parent) of a grid, representing their meiotic segregation into haploid gametes. Then the combinations of egg and sperm are made in the boxes in the table to show which alleles are combining. Each box then represents the diploid genotype of a zygote, or fertilized egg, that could result from this mating. Because each possibility is equally likely, genotypic ratios can be determined from a Punnett square. If the pattern of inheritance (dominant or recessive) is known, the phenotypic ratios can be inferred as well. For a monohybrid cross of two true-breeding parents, each parent contributes one type of allele. In this case, only one genotype is possible. All offspring are Yy and have yellow

seeds ( Figure 8.4 ).

Figure 8.4 In the P generation, pea plants that are true-breeding for the dominant yellow phenotype are crossed with plants with the recessive green phenotype. This cross produces F1 heterozygotes with a yellow phenotype.

Punnett square analysis can be used to predict the genotypes of the F2 generation.A self-cross of one of the Yy heterozygous offspring can be represented in a  Punnett square because each parent can donate one of two different alleles. Therefore, the offspring can potentially have one of four allele combinations: YY,Yy, yY, or yy ( Figure 8.4 ). Notice that there are two ways to obtain the Yy genotype: a Y from the egg and a y from the sperm, or a y from the egg and a Y from the sperm. Both of these possibilities must be counted. Recall that Mendel’s pea plant characteristics behaved in the same way in reciprocal crosses. Therefore, the two possible heterozygous combinations produce offspring that are genotypically and phenotypically identical despite their dominant and recessive alleles deriving from different parents. They are grouped together. Because fertilization is a random event, we expect each combination to be equally likely and for the offspring to exhibit a ratio of YY:Yy:yy genotypes of 1:2:1 ( Figure 8.4 ). Furthermore, because the YY and Yy offspring have yellow seeds and are phenotypically identical, applying the sum rule of probability, we expect the offspring to exhibit a phenotypic ratio of 3 yellow:1 green. Indeed, working with large sample sizes, Mendel observed approximately this ratio in every F2 generation resulting from crosses for individual traits.Mendel validated these results by performing an F3 cross in which he self-crossed the dominant- and recessive-expressingF2 plants. When he self-crossed the plants expressing green seeds, all of the offspring had green seeds, confirming that all green seeds had homozygous genotypes of yy. When he self-crossed the F2 plants expressing yellow seeds, he found that one-third of the plants bred true, and two-thirds of the plants segregated at a 3:1 ratio of yellow:green seeds. In this case, the true-breeding plants had homozygous (YY) genotypes, whereas the segregating plants corresponded to the heterozygous(Yy) genotype. When these plants self-fertilized, the outcome was just like the F1 self-fertilizing cross.

The Test Cross Distinguishes the Dominant Phenotype

Figure 8.6 Alkaptonuria is a recessive genetic disorder in which two amino acids, phenylalanine and tyrosine, are not properly metabolized. Affected individuals may have darkened skin and brown urine, and may suffer joint damage and other complications. In this pedigree, individuals with the disorder are indicated in blue and have the genotype aa. Unaffected individuals are indicated in yellow and have the genotype AA or Aa. Note that it is often possible to determine a person’s genotype from the genotype of their offspring. For example, if neither parent has the disorder but their child does, they must be heterozygous. Two individuals on the pedigree have an unaffected phenotype but unknown genotype. Because they do not have the disorder, they must have at least one normal allele, so their genotype gets the “A?” designation.What are the genotypes of the individuals labeled 1, 2 and 3?

Alternatives to Dominance and Recessiveness

Mendel’s experiments with pea plants suggested that: (1) two “units” or alleles exist for every gene; (2) alleles maintain their integrity in each generation (no blending); and (3) in the presence of the dominant allele, the recessive allele is hidden and makes no contribution to the phenotype. Therefore, recessive alleles can be “carried” and not expressed by individuals.Such heterozygous individuals are sometimes referred to as “carriers.” Further genetic studies in other plants and animals have shown that much more complexity exists, but that the fundamental principles of Mendelian genetics still hold true. In the sections to follow, we consider some of the extensions of Mendelism. If Mendel had chosen an experimental system that exhibited these genetic complexities, it’s possible that he would not have understood what his results meant.

Incomplete Dominance

Mendel’s results, that traits are inherited as dominant and recessive pairs, contradicted the view at that time that offspring exhibited a blend of their parents’ traits. However, the heterozygote phenotype occasionally does appear to be intermediate between the two parents. For example, in the snapdragon, Antirrhinum majus ( Figure 8.7 ), a cross between a homozygous parent with white flowers (CWCW) and a homozygous parent with red flowers (CRCR) will produce offspring with pink flowers (CRCW). (Note that different genotypic abbreviations are used for Mendelian extensions to distinguish these patterns from simple dominance and recessiveness.) This pattern of inheritance is described as incomplete dominance, denoting the expression of two contrasting alleles such that the individual displays an intermediate phenotype. The allele for redCRCW:1 CWCW, and the phenotypic ratio would be 1:2:1 for red:pink:white.

Figure 8.7 These pink flowers of a heterozygote snapdragon result from incomplete dominance. (credit:“storebukkebruse”/Flickr)

Codominance

A variation on incomplete dominance is codominance, in which both alleles for the same characteristic are simultaneously expressed in the heterozygote. An example of codominance is the MN blood groups of humans. The M and N alleles are expressed in the form of an M or N antigen present on the surface of red blood cells. Homozygotes (LMLM andLNLN) express either the M or the N allele, and heterozygotes (LMLN) express both alleles equally. In a self-cross between heterozygotes expressing a codominant trait, the three possible offspring genotypes are phenotypically distinct. However, the 1:2:1 genotypic ratio characteristic of a Mendelian monohybrid cross still applies.

Multiple Alleles

Mendel implied that only two alleles, one dominant and one recessive, could exist for a given gene. We now know that this is an oversimplification. Although individual humans (and all diploid organisms) can only have two alleles for a given gene, multiple alleles may exist at the population level such that many combinations of two alleles are observed. Note that when many alleles exist for the same gene, the convention is to denote the most common phenotype or genotype among wild animals as the wild type (often abbreviated “+”); this is considered the standard or norm. All other phenotypes or genotypes are considered variants of this standard, meaning that they deviate from the wild type. The variant may be recessive or dominant to the wild-type allele.An example of multiple alleles is coat color in rabbits ( Figure 8.8 ). Here, four alleles exist for the c gene. The wild-type version, C+C+, is expressed as brown fur. The chinchilla phenotype, cchcch, is expressed as black-tipped white fur. TheHimalayan phenotype, chch, has black fur on the extremities and white fur elsewhere. Finally, the albino, or “colorless”phenotype, cc, is expressed as white fur. In cases of multiple alleles, dominance hierarchies can exist. In this case, the wild type allele is dominant over all the others, chinchilla is incompletely dominant over Himalayan and albino, and Himalayan is dominant over albino. This hierarchy, or allelic series, was revealed by observing the phenotypes of each possible heterozygote offspring.

Figure 8.8 Four different alleles exist for the rabbit coat color (C) gene.The complete dominance of a wild-type phenotype over all other mutants often occurs as an effect of “dosage” of a specific gene product, such that the wild-type allele supplies the correct amount of gene product whereas the mutant alleles cannot.For the allelic series in rabbits, the wild-type allele may supply a given dosage of fur pigment, whereas the mutants supply a lesser dosage or none at all. Interestingly, the Himalayan phenotype is the result of an allele that produces a temperature sensitive gene product that only produces pigment in the cooler extremities of the rabbit’s body.Alternatively, one mutant allele can be dominant over all other phenotypes, including the wild type. This may occur when the mutant allele somehow interferes with the genetic message so that even a heterozygote with one wild-type allele copy expresses the mutant phenotype. One way in which the mutant allele can interfere is by enhancing the function of the wild type gene product or changing its distribution in the body. One example of this is the Antennapedia mutation in Drosophila(Figure 12.9). In this case, the mutant allele expands the distribution of the gene product, and as a result, the Antennapedia heterozygote develops legs on its head where its antennae should be.

Figure 8.9 As seen in comparing the wild-type Drosophila (left) and the Antennapedia mutant (right), the Antennapedia mutant has legs on its head in place of antennae.

Multiple Alleles Confer Drug Resistance in the Malaria Parasite

Malaria is a parasitic disease in humans that is transmitted by infected female mosquitoes, including Anopheles gambiae (Figure 12.10a), and is characterized by cyclic high fevers, chills, flu-like symptoms, and severe anemia. Plasmodium falciparum and P. vivax are the most common causative agents of malaria, and P. falciparum is the most deadly (Figure 12.10b). When promptly and correctly treated, P. falciparum malaria has a mortality rate of 0.1 percent. However, in some parts of the world, the parasite has evolved resistance to commonly used malaria treatments, so the most effective malarial treatments can vary by geographic region.

Figure 8.10

2. Sumiti Vinayak, et al., “Origin and Evolution of Sulfadoxine Resistant Plasmodium falciparum,” Public Library of Science Pathogens 6, no. 3 (2010):e1000830, doi:10.1371/journal.ppat.1000830.

X-Linked Traits

In humans, as well as in many other animals and some plants, the sex of the individual is determined by sex chromosomes.The sex chromosomes are one pair of non-homologous chromosomes. Until now, we have only considered inheritance patterns among non-sex chromosomes, or autosomes. In addition to 22 homologous pairs of autosomes, human females have a homologous pair of X chromosomes, whereas human males have an XY chromosome pair.

Although the Y chromosome contains a small region of similarity to the X chromosome so that they can pair during meiosis, the Y chromosome is much shorter and contains many fewer genes. When a gene being examined is present on the X chromosome, but not on the Y chromosome, it is said to be X-linked. Eye color in Drosophila was one of the first X-linked traits to be identified. Thomas Hunt Morgan mapped this trait to the X chromosome in 1910. Like humans, Drosophila males have an XY chromosome pair, and females are XX. In flies, the wild-type eye color is red (XW) and it is dominant to white eye color (Xw) (Figure 12.11). Because of the location of the eye-color gene, reciprocal crosses do not produce the same offspring ratios. Males are said to be hemizygous, because they have only one allele for any X-linked characteristic. Hemizygosity makes the descriptions of dominance and recessiveness irrelevant for XY males. Drosophila males lack a second allele copy on the Y chromosome; that is, their genotype can only be XWY or XwY. In contrast, females have two allele copies of this gene and can be XWXW, XWXw, or XwXw.

Figure 8.11 In Drosophila, several genes determine eye color.

The genes for white and vermilion eye colors are located on the X chromosome. Others are located on the autosomes. Clockwise from top left are brown, cinnabar, sepia, vermilion, white, and red. Red eye color is wild-type and is dominant to white eye color.In an X-linked cross, the genotypes of F1 and F2 offspring depend on whether the recessive trait was expressed by the male or the female in the P1 generation. With regard to Drosophila eye color, when the P1 male expresses the white-eye phenotype and the female is homozygous red-eyed, all members of the F1 generation exhibit red eyes (Figure 12.12).The F1 females are heterozygous (XWXw), and the males are all XWY, having received their X chromosome from the homozygous dominant P1 female and their Y chromosome from the P1 male. A subsequent cross between the XWXw female and the XWY male would produce only red-eyed females (with XWXW or XWXw genotypes) and both red- and white-eyed males (with XWY or XwY genotypes). Now, consider a cross between a homozygous white-eyed female and a male with red eyes. The F1 generation would exhibit only heterozygous red-eyed females (XWXw) and only white-eyed males (XwY).Half of the F2 females would be red-eyed (XWXw) and half would be white-eyed (XwXw). Similarly, half of the F2 males would be red-eyed (XWY) and half would be white-eyed (XwY).

Figure 8.12

Discoveries in fruit fly genetics can be applied to human genetics. When a female parent is homozygous for a recessive X linked trait, she will pass the trait on to 100 percent of her offspring. Her male offspring are, therefore, destined to express the trait, as they will inherit their father’s Y chromosome. In humans, the alleles for certain conditions (some forms of colorblindness, hemophilia, and muscular dystrophy) are X-linked. Females who are heterozygous for these diseases are said to be carriers and may not exhibit any phenotypic effects. These females will pass the disease to half of their sons and will pass carrier status to half of their daughters; therefore, recessive X-linked traits appear more frequently in males than females.In some groups of organisms with sex chromosomes, the gender with the non-homologous sex chromosomes is the female rather than the male. This is the case for all birds. In this case, sex-linked traits will be more likely to appear in the female, in which they are hemizygous. Human Sex-linked DisordersSex-linkage studies in Morgan’s laboratory provided the fundamentals for understanding X-linked recessive disorders in humans, which include red-green color blindness, and Types A and B hemophilia. Because human males need to inherit only one recessive mutant X allele to be affected, X-linked disorders are disproportionately observed in males. Females must inherit recessive X-linked alleles from both of their parents in order to express the trait. When they inherit one recessiveX-linked mutant allele and one dominant X-linked wild-type allele, they are carriers of the trait and are typically unaffected. Carrier females can manifest mild forms of the trait due to the inactivation of the dominant allele located on one of the X chromosomes. However, female carriers can contribute the trait to their sons, resulting in the son exhibiting the trait, or they can contribute the recessive allele to their daughters, resulting in the daughters being carriers of the trait (Figure 12.13).Although some Y-linked recessive disorders exist, typically they are associated with infertility in males and are therefore not transmitted to subsequent generations.

Figure 8.13 The son of a woman who is a carrier of a recessive X-linked disorder will have a 50 percent chance of being affected. A daughter will not be affected, but she will have a 50 percent chance of being a carrier like her mother.

Watch this video ( http://openstaxcollege.org/l/sex-linked_trts ) to learn more about sex-linked traits.

A large proportion of genes in an individual’s genome are essential for survival. Occasionally, a nonfunctional allele for an essential gene can arise by mutation and be transmitted in a population as long as individuals with this allele also have a wild-type, functional copy. The wild-type allele functions at a capacity sufficient to sustain life and is therefore considered to be dominant over the nonfunctional allele. However, consider two heterozygous parents that have a genotype of wild type/nonfunctional mutant for a hypothetical essential gene. In one quarter of their offspring, we would expect to observe individuals that are homozygous recessive for the nonfunctional allele. Because the gene is essential, these individuals might fail to develop past fertilization, die in utero, or die later in life, depending on what life stage requires this gene.

Dominant lethal alleles are very rare because, as you might expect, the allele only lasts one generation and is not transmitted. However, just as the recessive lethal allele might not immediately manifest the phenotype of death, dominant lethal alleles also might not be expressed until adulthood. Once the individual reaches reproductive age, the allele may be unknowingly passed on, resulting in a delayed death in both generations. An example of this in humans is Huntington’s disease, in which the nervous system gradually wastes away (Figure 12.14). People who are heterozygous for the dominant Huntington allele (Hh) will inevitably develop the fatal disease. However, the onset of Huntington’s disease may not occur until age 40, at which point the afflicted persons may have already passed the allele to 50 percent of their offspring.

Figure 8.14 The neuron in the center of this micrograph (yellow) has nuclear inclusions characteristic of Huntington’sdisease (orange area in the center of the neuron). Huntington’s disease occurs when an abnormal dominant allele forthe Huntington gene is present. (credit: Dr. Steven Finkbeiner, Gladstone Institute of Neurological Disease, The Taube-Koret Center for Huntington’s Disease Research, and the University of California San Francisco/Wikimedia)

8.3 | Laws of Inheritance

By the end of this section, you will be able to:

• Explain Mendel’s law of segregation and independent assortment in terms of genetics and the events of meiosis
• Use the forked-line method and the probability rules to calculate the probability of genotypes and phenotypes from multiple gene crosses
• Explain the effect of linkage and recombination on gamete genotypes
• Explain the phenotypic outcomes of epistatic effects between genes

Mendel generalized the results of his pea-plant experiments into four postulates, some of which are sometimes called“laws,” that describe the basis of dominant and recessive inheritance in diploid organisms. As you have learned, more complex extensions of Mendelism exist that do not exhibit the same F2 phenotypic ratios (3:1). Nevertheless, these laws summarize the basics of classical genetics.

Pairs of Unit Factors, or Genes

Mendel proposed first that paired unit factors of heredity were transmitted faithfully from generation to generation by the dissociation and reassociation of paired factors during gametogenesis and fertilization, respectively. After he crossed peas with contrasting traits and found that the recessive trait resurfaced in the F2 generation, Mendel deduced that hereditary factors must be inherited as discrete units. This finding contradicted the belief at that time that parental traits were blended in the offspring.

Alleles Can Be Dominant or Recessive

Mendel’s law of dominance states that in a heterozygote, one trait will conceal the presence of another trait for the same characteristic. Rather than both alleles contributing to a phenotype, the dominant allele will be expressed exclusively. The recessive allele will remain “latent” but will be transmitted to offspring by the same manner in which the dominant allele is transmitted. The recessive trait will only be expressed by offspring that have two copies of this allele (Figure 12.15), and these offspring will breed true when self-crossed.

Since Mendel’s experiments with pea plants, other researchers have found that the law of dominance does not always hold true. Instead, several different patterns of inheritance have been found to exist.

Figure 8.15 The child in the photo expresses albinism, a recessive trait.

Equal Segregation of Alleles

Observing that true-breeding pea plants with contrasting traits gave rise to F1 generations that all expressed the dominant trait and F2 generations that expressed the dominant and recessive traits in a 3:1 ratio, Mendel proposed the law of segregation. This law states that paired unit factors (genes) must segregate equally into gametes such that offspring have an equal likelihood of inheriting either factor. For the F2 generation of a monohybrid cross, the following three possible combinations of genotypes could result: homozygous dominant, heterozygous, or homozygous recessive. Because heterozygotes could arise from two different pathways (receiving one dominant and one recessive allele from either parent), and because heterozygotes and homozygous dominant individuals are phenotypically identical, the law supports Mendel’s observed 3:1 phenotypic ratio. The equal segregation of alleles is the reason we can apply the Punnett square to accurately predict the offspring of parents with known genotypes. The physical basis of Mendel’s law of segregation is the first division of meiosis, in which the homologous chromosomes with their different versions of each gene are segregated into daughter nuclei. The role of the meiotic segregation of chromosomes in sexual reproduction was not understood by the scientific community during Mendel’s lifetime.

Independent Assortment

Mendel’s law of independent assortment states that genes do not influence each other with regard to the sorting of alleles into gametes, and every possible combination of alleles for every gene is equally likely to occur. The independent assortment of genes can be illustrated by the dihybrid cross, a cross between two true-breeding parents that express different traits for two characteristics. Consider the characteristics of seed color and seed texture for two pea plants, one that has green, wrinkled seeds (yyrr) and another that has yellow, round seeds (YYRR). Because each parent is homozygous, the law of segregation indicates that the gametes for the green/wrinkled plant all are yr, and the gametes for the yellow/round plant are all YR. Therefore, the F1 generation of offspring all are YyRr (Figure 12.16).

Figure 8.16

For the F2 generation, the law of segregation requires that each gamete receive either an R allele or an r allele along with either a Y allele or a y allele. The law of independent assortment states that a gamete into which an r allele sorted would be equally likely to contain either a Y allele or a y allele. Thus, there are four equally likely gametes that can be formed when the YyRr heterozygote is self-crossed, as follows: YR, Yr, yR, and yr. Arranging these gametes along the top and left of a 4 by 4 Punnett square (Figure 12.16) gives us 16 equally likely genotypic combinations. From these genotypes, we infer a phenotypic ratio of 9 round/yellow:3 round/green:3 wrinkled/yellow:1 wrinkled/green (Figure 12.16). These are the offspring ratios we would expect, assuming we performed the crosses with a large enough sample size. Because of independent assortment and dominance, the 9:3:3:1 dihybrid phenotypic ratio can be collapsed into two 3:1 ratios, characteristic of any monohybrid cross that follows a dominant and recessive pattern. Ignoring seed color and considering only seed texture in the above dihybrid cross, we would expect that three quarters of the F2 generation offspring would be round, and one quarter would be wrinkled. Similarly, isolating only seed color, we would assume that three quarters of the F2 offspring would be yellow and one quarter would be green. The sorting of alleles for texture and color are independent events, so we can apply the product rule. Therefore, the proportion of round and yellow F2 offspring is expected to be (3/4) Å~ (3/4) = 9/16, and the proportion of wrinkled and green offspring is expected to be (1/4) Å~ (1/4) = 1/16.

These proportions are identical to those obtained using a Punnett square. Round, green and wrinkled, yellow offspring can also be calculated using the product rule, as each of these genotypes includes one dominant and one recessive phenotype. Therefore, the proportion of each is calculated as (3/4) Å~ (1/4) = 3/16. The law of independent assortment also indicates that a cross between yellow, wrinkled (YYrr) and green, round (yyRR) parents would yield the same F1 and F2 offspring as in the YYRR x yyrr cross.

Linked Genes Violate the Law of Independent Assortment

Although all of Mendel’s pea characteristics behaved according to the law of independent assortment, we now know that some allele combinations are not inherited independently of each other. Genes that are located on separate nonhomologous chromosomes will always sort independently. However, each chromosome contains hundreds or thousands of genes, organized linearly on chromosomes like beads on a string. The segregation of alleles into gametes can be influenced by linkage, in which genes that are located physically close to each other on the same chromosome are more likely to be inherited as a pair. However, because of the process of recombination, or “crossover,” it is possible for two genes on the same chromosome to behave independently, or as if they are not linked. To understand this, let’s consider the biological basis of gene linkage and recombination.

Homologous chromosomes possess the same genes in the same linear order. The alleles may differ on homologous chromosome pairs, but the genes to which they correspond do not. In preparation for the first division of meiosis, homologous chromosomes replicate and synapse. Like genes on the homologs align with each other. At this stage, segments of homologous chromosomes exchange linear segments of genetic material (Figure 12.18). This process is called recombination, or crossover, and it is a common genetic process. Because the genes are aligned during recombination, the gene order is not altered. Instead, the result of recombination is that maternal and paternal alleles are combined onto the same chromosome. Across a given chromosome, several recombination events may occur, causing extensive shuffling of alleles.

Figure 8.18 The process of crossover, or recombination, occurs when two homologous chromosomes align during meiosis and exchange a segment of genetic material. Here, the alleles for gene C were exchanged. The result is two recombinant and two non-recombinant chromosomes.

When two genes are located in close proximity on the same chromosome, they are considered linked, and their alleles tend to be transmitted through meiosis together. To exemplify this, imagine a dihybrid cross involving flower color and plant height in which the genes are next to each other on the chromosome. If one homologous chromosome has alleles for tall plants and red flowers, and the other chromosome has genes for short plants and yellow flowers, then when the gametes are formed, the tall and red alleles will go together into a gamete and the short and yellow alleles will go into other gametes. These are called the parental genotypes because they have been inherited intact from the parents of the individual producing gametes. But unlike if the genes were on different chromosomes, there will be no gametes with tall and yellow alleles and no gametes with short and red alleles. If you create the Punnett square with these gametes, you will see that the classical Mendelian prediction of a 9:3:3:1 outcome of a dihybrid cross would not apply. As the distance between two genes increases, the probability of one or more crossovers between them increases, and the genes behave more like they are on separate chromosomes. Geneticists have used the proportion of recombinant gametes (the ones not like the parents) as a measure of how far apart genes are on a chromosome. Using this information, they have constructed elaborate maps of genes on chromosomes for well-studied organisms, including humans. Mendel’s seminal publication makes no mention of linkage, and many researchers have questioned whether he encountered linkage but chose not to publish those crosses out of concern that they would invalidate his independent assortment postulate. The garden pea has seven chromosomes, and some have suggested that his choice of seven characteristics was not a coincidence. However, even if the genes he examined were not located on separate chromosomes, it is possible that he simply did not observe linkage because of the extensive shuffling effects of recombination.

Figure 8.20 In mice, the mottled agouti coat color (A) is dominant to a solid coloration, such as black or gray. A gene at a separate locus (C) is responsible for pigment production. The recessive c allele does not produce pigment, and a mouse with the homozygous recessive cc genotype is albino regardless of the allele present at the A locus. Thus, the C gene is epistatic to the A gene. Epistasis can also occur when a dominant allele masks expression at a separate gene.

Fruit color in summer squash is expressed in this way. Homozygous recessive expression of the W gene (ww) coupled with homozygous dominant or heterozygous expression of the Y gene (YY or Yy) generates yellow fruit, and the wwyy genotype produces green fruit. However, if a dominant copy of the W gene is present in the homozygous or heterozygous form, the summer squash will produce white fruit regardless of the Y alleles. A cross between white heterozygotes for both genes (WwYy Å~ WwYy) would produce offspring with a phenotypic ratio of 12 white:3 yellow:1 green.

Finally, epistasis can be reciprocal such that either gene, when present in the dominant (or recessive) form, expresses the same phenotype. In the shepherd’s purse plant ( Capsella bursa-pastoris ), the characteristic of seed shape is controlled by two genes in a dominant epistatic relationship. When the genes A and B are both homozygous recessive (aabb), the seeds are ovoid. If the dominant allele for either of these genes is present, the result is triangular seeds. That is, every possible genotype other than aabb results in triangular seeds, and a cross between heterozygotes for both genes (AaBb x AaBb) would yield offspring with a phenotypic ratio of 15 triangular:1 ovoid.

For an excellent review of Mendel’s experiments and to perform your own crosses and identify patterns of inheritance, visit the Mendel’s Peas ( http://openstaxcollege.org/l/mendels_peas ) web lab.

Figure 8.21  Chromosomes are threadlike nuclear structures consisting of DNA and proteins that serve as the repositories for genetic information. The chromosomes depicted here were isolated from a fruit fly’s salivary gland, stained with dye, and visualized under a microscope. Akin to miniature bar codes, chromosomes absorb different dyes to produce characteristic banding patterns, which allows for their routine identification. (credit: modification of work by“LPLT”/Wikimedia Commons; scale-bar data from Matt Russell)

8.4 | Chromosomal Theory and Genetic Linkage

Long before chromosomes were visualized under a microscope, the father of modern genetics, Gregor Mendel, began studying heredity in 1843.With the improvement of microscopic techniques during the late 1800s, cell biologists could stain and visualize subcellular structures with dyes and observe their actions during cell division and meiosis. With each mitotic division, chromosomes replicated, condensed from an amorphous (no constant shape) nuclear mass into distinct X-shaped bodies (pairs of identical sister chromatids), and migrated to separate cellular poles.

The speculation that chromosomes might be the key to understanding heredity led several scientists to examine Mendel’s publications and re-evaluate his model in terms of the behavior of chromosomes during mitosis and meiosis. In 1902, Theodor Boveri observed that proper embryonic development of sea urchins does not occur unless chromosomes are present. That same year, Walter Sutton observed the separation of chromosomes into daughter cells during meiosis (Figure13.2). Together, these observations led to the development of the Chromosomal Theory of Inheritance, which identified chromosomes as the genetic material responsible for Mendelian inheritance.

Figure 8.22  (a) Walter Sutton and (b) Theodor Boveri are credited with developing the Chromosomal Theory ofInheritance, which states that chromosomes carry the unit of heredity (genes).

• During meiosis, homologous chromosome pairs migrate as discrete structures that are independent of other chromosome pairs.
• The sorting of chromosomes from each homologous pair into pre-gametes appears to be random.
• Each parent synthesizes gametes that contain only half of their chromosomal complement.
• Even though male and female gametes (sperm and egg) differ in size and morphology, they have the same number of chromosomes, suggesting equal genetic contributions from each parent.
• The gametic chromosomes combine during fertilization to produce offspring with the same chromosome number as their parents.

Despite compelling correlations between the behavior of chromosomes during meiosis and Mendel’s abstract laws, the Chromosomal Theory of Inheritance was proposed long before there was any direct evidence that traits were carried on chromosomes. Critics pointed out that individuals had far more independently segregating traits than they had chromosomes. It was only after several years of carrying out crosses with the fruit fly, Drosophila melanogaster , that Thomas Hunt Morgan provided experimental evidence to support the Chromosomal Theory of Inheritance.

Homologous Recombination

In 1909, Frans Janssen observed chiasmata—the point at which chromatids are in contact with each other and may exchange segments—prior to the first division of meiosis. He suggested that alleles become unlinked and chromosomes physically exchange segments. As chromosomes condensed and paired with their homologs, they appeared to interact at distinct points. Janssen suggested that these points corresponded to regions in which chromosome segments were exchanged. It is now known that the pairing and interaction between homologous chromosomes, known as synapsis, does more than simply organize the homologs for migration to separate daughter cells. When synapsed, homologous chromosomes undergo reciprocal physical exchanges at their arms in a process called homologous recombination, or more simply, “crossing over.”

To better understand the type of experimental results that researchers were obtaining at this time, consider a heterozygous individual that inherited dominant maternal alleles for two genes on the same chromosome (such as AB) and two recessive paternal alleles for those same genes (such as ab). If the genes are linked, one would expect this individual to produce gametes that are either AB or ab with a 1:1 ratio. If the genes are unlinked, the individual should produce AB, Ab, aB, and ab gametes with equal frequencies, according to the Mendelian concept of independent assortment. Because they correspond to new allele combinations, the genotypes Ab and aB are nonparental types that result from homologous recombination during meiosis. Parental types are progeny that exhibit the same allelic combination as their parents. Morgan and his colleagues, however, found that when such heterozygous individuals were test crossed to a homozygous recessive parent (AaBb ~ aabb), both parental and nonparental cases occurred. For example, 950 offspring might be recovered that were either AaBb or aabb, but 50 offspring would also be obtained that were either Aabb or aaBb. These results suggested that linkage occurred most often, but a significant minority of offspring were the products of recombination.

Figure 8.23  Inheritance patterns of unlinked and linked genes are shown.

Figure 8.24  This genetic map orders Drosophila genes on the basis of recombination frequency.

In 1931, Barbara McClintock and Harriet Creighton demonstrated the crossover of homologous chromosomes in corn plants. Weeks later, homologous recombination in Drosophila was demonstrated microscopically by Curt Stern. Stern observed several X-linked phenotypes that were associated with a structurally unusual and dissimilar X chromosome pair in which one X was missing a small terminal segment, and the other X was fused to a piece of the Y chromosome. By crossing flies, observing their offspring, and then visualizing the offspring’s chromosomes, Stern demonstrated that every time the offspring allele combination deviated from either of the parental combinations, there was a corresponding exchange of an X chromosome segment. Using mutant flies with structurally distinct X chromosomes was the key to observing the products of recombination because DNA sequencing and other molecular tools were not yet available. It is now known that homologous chromosomes regularly exchange segments in meiosis by reciprocally breaking and rejoining their DNA at precise locations.

Review Sturtevant’s process to create a genetic map on the basis of recombination frequencies here ( http://openstaxcollege.org/l/gene_crossover ) .

Mendel’s Mapped Traits

Homologous recombination is a common genetic process, yet Mendel never observed it. Had he investigated both linked and unlinked genes, it would have been much more difficult for him to create a unified model of his data on the basis of probabilistic calculations. Researchers who have since mapped the seven traits investigated by Mendel onto the seven chromosomes of the pea plant genome have confirmed that all of the genes he examined are either on separate chromosomes or are sufficiently far apart as to be statistically unlinked. Some have suggested that Mendel was enormously lucky to select only unlinked genes, whereas others question whether Mendel discarded any data suggesting linkage. In any case, Mendel consistently observed independent assortment because he examined genes that were effectively unlinked.

8.5 | Chromosomal Basis of Inherited Disorders

Inherited disorders can arise when chromosomes behave abnormally during meiosis. Chromosome disorders can be divided into two categories: abnormalities in chromosome number and chromosomal structural rearrangements. Because even small segments of chromosomes can span many genes, chromosomal disorders are characteristically dramatic and often fatal.

Identification of Chromosomes

The isolation and microscopic observation of chromosomes forms the basis of cytogenetics and is the primary method by which clinicians detect chromosomal abnormalities in humans. A karyotype is the number and appearance of chromosomes, and includes their length, banding pattern, and centromere position. To obtain a view of an individual’s karyotype, cytologists photograph the chromosomes and then cut and paste each chromosome into a chart, or karyogram, also known as an ideogram (Figure 13.5).

Figure 8.25 This karyotype is of a female human. Notice that homologous chromosomes are the same size, and have the same centromere positions and banding patterns. A human male would have an XY chromosome pair instead of the XX pair shown. (credit: Andreas Blozer et al)

In a given species, chromosomes can be identified by their number, size, centromere position, and banding pattern. In a human karyotype, autosomes or “body chromosomes” (all of the non–sex chromosomes) are generally organized in approximate order of size from largest (chromosome 1) to smallest (chromosome 22). The X and Y chromosomes are not autosomes. However, chromosome 21 is actually shorter than chromosome 22. This was discovered after the naming of Down syndrome as trisomy 21, reflecting how this disease results from possessing one extra chromosome 21 (three total). Not wanting to change the name of this important disease, chromosome 21 retained its numbering, despite describing the shortest set of chromosomes. The chromosome “arms” projecting from either end of the centromere may be designated as short or long, depending on their relative lengths. The short arm is abbreviated p (for “petite”), whereas the long arm is abbreviated q (because it follows “p” alphabetically). Each arm is further subdivided and denoted by a number. Using this naming system, locations on chromosomes can be described consistently in the scientific literature.

Geneticists Use Karyograms to Identify Chromosomal Aberrations

Although Mendel is referred to as the “father of modern genetics,” he performed his experiments with none of the tools that the geneticists of today routinely employ. One such powerful cytological technique is karyotyping, a method in which traits characterized by chromosomal abnormalities can be identified from a single cell. To observe an individual’s karyotype, a person’s cells (like white blood cells) are first collected from a blood sample or other tissue. In the laboratory, the isolated cells are stimulated to begin actively dividing. A chemical called colchicine is then applied to cells to arrest condensed chromosomes in metaphase. Cells are then made to swell using a hypotonic solution so the chromosomes spread apart. Finally, the sample is preserved in a fixative and applied to a slide.

The geneticist then stains chromosomes with one of several dyes to better visualize the distinct and reproducible banding patterns of each chromosome pair. Following staining, the chromosomes are viewed using bright-field microscopy. A common stain choice is the Giemsa stain. Giemsa staining results in approximately 400–800 bands (of tightly coiled DNA and condensed proteins) arranged along all of the 23 chromosome pairs; an experienced geneticist can identify each band. In addition to the banding patterns, chromosomes are further identified on the basis of size and centromere location. To obtain the classic depiction of the karyotype in which homologous pairs of chromosomes are aligned in numerical order from longest to shortest, the geneticist obtains a digital image, identifies each chromosome, and manually arranges the chromosomes into this pattern (Figure 12.25).

At its most basic, the karyogram may reveal genetic abnormalities in which an individual has too many or too few chromosomes per cell. Examples of this are Down Syndrome, which is identified by a third copy of chromosome 21, and Turner Syndrome, which is characterized by the presence of only one X chromosome in women instead of the normal two. Geneticists can also identify large deletions or insertions of DNA. For instance, Jacobsen Syndrome—which involves distinctive facial features as well as heart and bleeding defects—is identified by a deletion on chromosome 11. Finally, the karyotype can pinpoint translocations, which occur when a segment of genetic material breaks from one chromosome and reattaches to another chromosome or to a different part of the same chromosome. Translocations are implicated in certain cancers, including chronic myelogenous leukemia.

During Mendel’s lifetime, inheritance was an abstract concept that could only be inferred by performing crosses and observing the traits expressed by offspring. By observing a karyogram, today’s geneticists can actually visualize the chromosomal composition of an individual to confirm or predict genetic abnormalities in offspring, even before birth.

Disorders in Chromosome Number

Of all of the chromosomal disorders, abnormalities in chromosome number are the most obviously identifiable from a karyogram. Disorders of chromosome number include the duplication or loss of entire chromosomes, as well as changes in the number of complete sets of chromosomes. They are caused by nondisjunction, which occurs when pairs of homologous chromosomes or sister chromatids fail to separate during meiosis. Misaligned or incomplete synapsis, or a dysfunction of the spindle apparatus that facilitates chromosome migration, can cause nondisjunction. The risk of nondisjunction occurring increases with the age of the parents.

Nondisjunction can occur during either meiosis I or II, with differing results (Figure 13.6). If homologous chromosomes fail to separate during meiosis I, the result is two gametes that lack that particular chromosome and two gametes with two copies of the chromosome. If sister chromatids fail to separate during meiosis II, the result is one gamete that lacks that chromosome, two normal gametes with one copy of the chromosome, and one gamete with two copies of the chromosome.

An individual with the appropriate number of chromosomes for their species is called euploid; in humans, euploidy corresponds to 22 pairs of autosomes and one pair of sex chromosomes. An individual with an error in chromosome number is described as aneuploid, a term that includes monosomy (loss of one chromosome) or trisomy (gain of an extraneous chromosome). Monosomic human zygotes missing any one copy of an autosome invariably fail to develop to birth because they lack essential genes. This underscores the importance of “gene dosage” in humans. Most autosomal trisomies also fail to develop to birth; however, duplications of some of the smaller chromosomes (13, 15, 18, 21, or 22) can result in offspring that survive for several weeks to many years. Trisomic individuals suffer from a different type of genetic imbalance: an excess in gene dose. Individuals with an extra chromosome may synthesize an abundance of the gene products encoded by that chromosome. This extra dose (150 percent) of specific genes can lead to a number of functional challenges and often precludes development. The most common trisomy among viable births is that of chromosome 21, which corresponds to Down Syndrome. Individuals with this inherited disorder are characterized by short stature and stunted digits, facial distinctions that include a broad skull and large tongue, and significant developmental delays. The incidence of Down syndrome is correlated with maternal age; older women are more likely to become pregnant with fetuses carrying the trisomy 21 genotype ( Figure 8.27 ).

Figure 8.27 The incidence of having a fetus with trisomy 21 increases dramatically with maternal age. Visualize the addition of a chromosome that leads to Down syndrome in this video simulation (http://openstaxcollege.org/l/down_syndrome) .

An individual with more than the correct number of chromosome sets (two for diploid species) is called polyploid. For instance, fertilization of an abnormal diploid egg with a normal haploid sperm would yield a triploid zygote. Polyploid animals are extremely rare, with only a few examples among the flatworms, crustaceans, amphibians, fish, and lizards.

Polyploid animals are sterile because meiosis cannot proceed normally and instead produces mostly aneuploid daughter cells that cannot yield viable zygotes. Rarely, polyploid animals can reproduce asexually by haplodiploidy, in which an unfertilized egg divides mitotically to produce offspring. In contrast, polyploidy is very common in the plant kingdom, and polyploid plants tend to be larger and more robust than euploids of their species ( Figure 8.28 ).

Figure 8.28 As with many polyploid plants, this triploid orange daylily (Hemerocallis fulva) is particularly large and robust, and grows flowers with triple the number of petals of its diploid counterparts. (credit: Steve Karg)

Sex Chromosome Nondisjunction in Humans

Humans display dramatic deleterious effects with autosomal trisomies and monosomies. Therefore, it may seem counterintuitive that human females and males can function normally, despite carrying different numbers of the X chromosome. Rather than a gain or loss of autosomes, variations in the number of sex chromosomes are associated with relatively mild effects. In part, this occurs because of a molecular process called X inactivation. Early in development, when female mammalian embryos consist of just a few thousand cells (relative to trillions in the newborn), one X chromosome in each cell inactivates by tightly condensing into a quiescent (dormant) structure called a Barr body. The chance that an X chromosome (maternally or paternally derived) is inactivated in each cell is random, but once the inactivation occurs, all cells derived from that one will have the same inactive X chromosome or Barr body. By this process, females compensate for their double genetic dose of X chromosome. In so-called “tortoiseshell” cats, embryonic X inactivation is observed as color variegation (Figure 13.9). Females that are heterozygous for an X-linked coat color gene will express one of two different coat colors over different regions of their body, corresponding to whichever X chromosome is inactivated in the embryonic cell progenitor of that region.

Figure 8.29 In cats, the gene for coat color is located on the X chromosome. In the embryonic development of female cats, one of the two X chromosomes is randomly inactivated in each cell, resulting in a tortoiseshell pattern if the cat has two different alleles for coat color. Male cats, having only one X chromosome, never exhibit a tortoiseshell coat color. (credit: Michael Bodega)

An individual carrying an abnormal number of X chromosomes will inactivate all but one X chromosome in each of her cells. However, even inactivated X chromosomes continue to express a few genes, and X chromosomes must reactivate for the proper maturation of female ovaries. As a result, X-chromosomal abnormalities are typically associated with mild mental and physical defects, as well as sterility. If the X chromosome is absent altogether, the individual will not develop in utero.

Several errors in sex chromosome number have been characterized. Individuals with three X chromosomes, called triplo- X, are phenotypically female but express developmental delays and reduced fertility. The XXY genotype, corresponding to one type of Klinefelter syndrome, corresponds to phenotypically male individuals with small testes, enlarged breasts, and reduced body hair. More complex types of Klinefelter syndrome exist in which the individual has as many as five X chromosomes. In all types, every X chromosome except one undergoes inactivation to compensate for the excess genetic dosage. This can be seen as several Barr bodies in each cell nucleus. Turner syndrome, characterized as an X0 genotype (i.e., only a single sex chromosome), corresponds to a phenotypically female individual with short stature, webbed skin in the neck region, hearing and cardiac impairments, and sterility.

Duplications and Deletions

In addition to the loss or gain of an entire chromosome, a chromosomal segment may be duplicated or lost. Duplications and deletions often produce offspring that survive but exhibit physical and mental abnormalities. Duplicated chromosomal segments may fuse to existing chromosomes or may be free in the nucleus. Cri-du-chat (from the French for “cry of the cat”) is a syndrome associated with nervous system abnormalities and identifiable physical features that result from a deletion of most of 5p (the small arm of chromosome 5) ( Figure 8.30 ). Infants with this genotype emit a characteristic high-pitched cry on which the disorder’s name is based.

Figure 8.30 This individual with cri-du-chat syndrome is shown at two, four, nine, and 12 years of age. (credit: Paola Cerruti Mainardi)

Chromosomal Structural Rearrangements

Cytologists have characterized numerous structural rearrangements in chromosomes, but chromosome inversions and translocations are the most common. Both are identified during meiosis by the adaptive pairing of rearranged chromosomes with their former homologs to maintain appropriate gene alignment. If the genes carried on two homologs are not oriented correctly, a recombination event could result in the loss of genes from one chromosome and the gain of genes on the other. This would produce aneuploid gametes.

Chromosome Inversions

A chromosome inversion is the detachment, 180Åã rotation, and reinsertion of part of a chromosome. Inversions may occur

in nature as a result of mechanical shear, or from the action of transposable elements (special DNA sequences capable of facilitating the rearrangement of chromosome segments with the help of enzymes that cut and paste DNA sequences). Unless they disrupt a gene sequence, inversions only change the orientation of genes and are likely to have more mild effects than aneuploid errors. However, altered gene orientation can result in functional changes because regulators of gene expression could be moved out of position with respect to their targets, causing aberrant levels of gene products. An inversion can be pericentric and include the centromere, or paracentric and occur outside of the centromere ( Figure 8.31 ). A pericentric inversion that is asymmetric about the centromere can change the relative lengths of the chromosome arms, making these inversions easily identifiable.

Figure 8.31 Pericentric inversions include the centromere, and paracentric inversions do not. A pericentric inversion can change the relative lengths of the chromosome arms; a paracentric inversion cannot. When one homologous chromosome undergoes an inversion but the other does not, the individual is described as an inversion heterozygote. To maintain point-for-point synapsis during meiosis, one homolog must form a loop, and the other homolog must mold around it. Although this topology can ensure that the genes are correctly aligned, it also forces the homologs to stretch and can be associated with regions of imprecise synapsis (Figure 12.32).

Figure 8.32 When one chromosome undergoes an inversion but the other does not, one chromosome must form an inverted loop to retain point-for-point interaction during synapsis. This inversion pairing is essential to maintaining gene alignment during meiosis and to allow for recombination.

The Chromosome 18 Inversion

Not all structural rearrangements of chromosomes produce nonviable, impaired, or infertile individuals. In rare instances, such a change can result in the evolution of a new species. In fact, a pericentric inversion in chromosome 18 appears to have contributed to the evolution of humans. This inversion is not present in our closest genetic relatives, the chimpanzees. Humans and chimpanzees differ cytogenetically by pericentric inversions on several chromosomes and by the fusion of two separate chromosomes in chimpanzees that correspond to chromosome two in humans.

The pericentric chromosome 18 inversion is believed to have occurred in early humans following their divergence from a common ancestor with chimpanzees approximately five million years ago. Researchers characterizing this inversion have suggested that approximately 19,000 nucleotide bases were duplicated on 18p, and the duplicated region inverted and reinserted on chromosome 18 of an ancestral human. A comparison of human and chimpanzee genes in the region of this inversion indicates that two genes—ROCK1 and USP14—that are adjacent on chimpanzee chromosome 17 (which corresponds to human chromosome 18) are more distantly positioned on human chromosome 18. This suggests that one of the inversion breakpoints occurred between these two genes. Interestingly, humans and chimpanzees express USP14 at distinct levels in specific cell types, including cortical cells and fibroblasts. Perhaps the chromosome 18 inversion in an ancestral human repositioned specific genes and reset their expression levels in a useful way. Because both ROCK1 and USP14 encode cellular enzymes, a change in their expression could alter cellular function. It is not known how this inversion contributed to hominid evolution, but it appears to be a significant factor in the divergence of humans from other primates.

Translocations

A translocation occurs when a segment of a chromosome dissociates and reattaches to a different, non-homologous chromosome. Translocations can be benign or have devastating effects depending on how the positions of genes are altered with respect to regulatory sequences. Notably, specific translocations have been associated with several cancers and with schizophrenia. Reciprocal translocations result from the exchange of chromosome segments between two non-homologous chromosomes such that there is no gain or loss of genetic information ( Figure 8.33 ).

Figure 8.33 A reciprocal translocation occurs when a segment of DNA is transferred from one chromosome to another, nonhomologous chromosome. (credit: modification of work by National Human Genome Research/USA)

• Violaine Goidts et al., “Segmental duplication associated with the human-specific inversion of chromosome 18: a further example of the impact of segmental duplications on karyotype and genome evolution in primates,” Human Genetics. 115 (2004):116-122

allele gene variations that arise by mutation and exist at the same relative locations on homologous chromosomes

autosomes any of the non-sex chromosomes

codominance in a heterozygote, complete and simultaneous expression of both alleles for the same characteristic

continuous variation inheritance pattern in which a character shows a range of trait values with small gradations rather than large gaps between them

dihybrid result of a cross between two true-breeding parents that express different traits for two characteristics

dominant trait which confers the same physical appearance whether an individual has two copies of the trait or one copy of the dominant trait and one copy of the recessive trait

dominant lethal inheritance pattern in which an allele is lethal both in the homozygote and the heterozygote; this allele can only be transmitted if the lethality phenotype occurs after reproductive age

epistasis antagonistic interaction between genes such that one gene masks or interferes with the expression of another

genotype underlying genetic makeup, consisting of both physically visible and non-expressed alleles, of an organism

hemizygous presence of only one allele for a characteristic, as in X-linkage; hemizygosity makes descriptions of dominance and recessiveness irrelevant

heterozygous having two different alleles for a given gene on the homologous chromosome

homozygous having two identical alleles for a given gene on the homologous chromosome

hybridization process of mating two individuals that differ with the goal of achieving a certain characteristic in their offspring

incomplete dominance in a heterozygote, expression of two contrasting alleles such that the individual displays an intermediate phenotype

law of dominance in a heterozygote, one trait will conceal the presence of another trait for the same characteristic

law of independent assortment genes do not influence each other with regard to sorting of alleles into gametes; every possible combination of alleles is equally likely to occur

law of segregation paired unit factors (i.e., genes) segregate equally into gametes such that offspring have an equal likelihood of inheriting any combination of factors

linkage phenomenon in which alleles that are located in close proximity to each other on the same chromosome are more likely to be inherited together

monohybrid result of a cross between two true-breeding parents that express different traits for only one characteristic parental generation in a cross

phenotype observable traits expressed by an organism

recessive trait that appears “latent” or non-expressed when the individual also carries a dominant trait for that same

recessive lethal characteristic; when present as two identical copies, the recessive trait is expressed

sex-linked any gene on a sex chromosome

trait variation in the physical appearance of a heritable characteristic

X-linked gene present on the X, but not the Y chromosome

CHAPTER SUMMARY

8.1 mendel’s experiments and the laws of probability.

Working with garden pea plants, Mendel found that crosses between parents that differed by one trait produced F1 offspring that all expressed the traits of one parent. Observable traits are referred to as dominant, and non-expressed traits are described as recessive. When the offspring in Mendel’s experiment were self-crossed, the F2 offspring exhibited the dominant trait or the recessive trait in a 3:1 ratio, confirming that the recessive trait had been transmitted faithfully from the original P0 parent. Reciprocal crosses generated identical F1 and F2 offspring ratios. By examining sample sizes, Mendel showed that his crosses behaved reproducibly according to the laws of probability, and that the traits were inherited as independent events.

When true-breeding or homozygous individuals that differ for a certain trait are crossed, all of the offspring will be heterozygotes for that trait. If the traits are inherited as dominant and recessive, the F1 offspring will all exhibit the same phenotype as the parent homozygous for the dominant trait. If these heterozygous offspring are self-crossed, the resulting F2 offspring will be equally likely to inherit gametes carrying the dominant or recessive trait, giving rise to offspring of which one quarter are homozygous dominant, half are heterozygous, and one quarter are homozygous recessive. Because homozygous dominant and heterozygous individuals are phenotypically identical, the observed traits in the F2 offspring will exhibit a ratio of three dominant to one recessive. Alleles do not always behave in dominant and recessive patterns. Incomplete dominance describes situations in which the heterozygote exhibits a phenotype that is intermediate between the homozygous phenotypes. Codominance describes the simultaneous expression of both of the alleles in the heterozygote. Although diploid organisms can only have two alleles for any given gene, it is common for more than two alleles of a gene to exist in a population. In humans, as in many animals and some plants, females have two X chromosomes and males have one X and one Y chromosome. Genes that are present on the X but not the Y chromosome are said to be X-linked, such that males only inherit one allele for the gene, and females inherit two. Finally, some alleles can be lethal. Recessive lethal alleles are only lethal in homozygotes, but dominant lethal alleles are fatal in heterozygotes as well.

Mendel postulated that genes (characteristics) are inherited as pairs of alleles (traits) that behave in a dominant and recessive pattern. Alleles segregate into gametes such that each gamete is equally likely to receive either one of the two alleles present in a diploid individual. In addition, genes are assorted into gametes independently of one another. That is, alleles are generally not more likely to segregate into a gamete with a particular allele of another gene. A dihybrid cross demonstrates independent assortment when the genes in question are on different chromosomes or distant from each other on the same chromosome. For crosses involving more than two genes, use the forked line or probability methods to predict offspring genotypes and phenotypes rather than a Punnett square.

Although chromosomes sort independently into gametes during meiosis, Mendel’s law of independent assortment refers to genes, not chromosomes, and a single chromosome may carry more than 1,000 genes. When genes are located in close proximity on the same chromosome, their alleles tend to be inherited together. This results in offspring ratios that violate Mendel’s law of independent assortment. However, recombination serves to exchange genetic material on homologous chromosomes such that maternal and paternal alleles may be recombined on the same chromosome. This is why alleles on a given chromosome are not always inherited together. Recombination is a random event occurring anywhere on a chromosome. Therefore, genes that are far apart on the same chromosome are likely to still assort independently because of recombination events that occurred in the intervening chromosomal space.

Whether or not they are sorting independently, genes may interact at the level of gene products such that the expression of an allele for one gene masks or modifies the expression of an allele for a different gene. This is called epistasis.

REVIEW QUESTIONS

Mendel performed hybridizations by transferring pollen

from the _______ of the male plant to the female ova.

Which is one of the seven characteristics that Mendel

observed in pea plants?

a. flower size

b. seed texture

c. leaf shape

d. stem color

 Imagine you are performing a cross involving seed

color in garden pea plants. What F1 offspring would you

expect if you cross true-breeding parents with green seeds

and yellow seeds? Yellow seed color is dominant over

a. 100 percent yellow-green seeds

b. 100 percent yellow seeds

c. 50 percent yellow, 50 percent green seeds

d. 25 percent green, 75 percent yellow seeds

Consider a cross to investigate the pea pod texture trait,

involving constricted or inflated pods. Mendel found that

the traits behave according to a dominant/recessive pattern

in which inflated pods were dominant. If you performed

this cross and obtained 650 inflated-pod plants in the F2

generation, approximately how many constricted-pod

plants would you expect to have?

The observable traits expressed by an organism are

described as its ________.

a. phenotype

b. genotype

A recessive trait will be observed in individuals that

are ________ for that trait.

a. heterozygous

b. homozygous or heterozygous

c. homozygous

If black and white true-breeding mice are mated and

the result is all gray offspring, what inheritance pattern

would this be indicative of?

a. dominance

b. codominance

c. multiple alleles

d. incomplete dominance

The ABO blood groups in humans are expressed as

the IA, IB, and i alleles. The IA allele encodes the A blood

group antigen, IB encodes B, and i encodes O. Both A and

B are dominant to O. If a heterozygous blood type A

parent (IAi) and a heterozygous blood type B parent (IBi)

mate, one quarter of their offspring will have AB blood

type (IAIB) in which both antigens are expressed equally.

Therefore, ABO blood groups are an example of:

a. multiple alleles and incomplete dominance

b. codominance and incomplete dominance

c. incomplete dominance only

d. multiple alleles and codominance

In a mating between two individuals that are

heterozygous for a recessive lethal allele that is expressed

in utero, what genotypic ratio (homozygous

dominant:heterozygous:homozygous recessive) would you

expect to observe in the offspring?

X-linked recessive traits in humans (or in Drosophila)

are observed ________.

a. in more males than females

b. in more females than males

c. in males and females equally

d. in different distributions depending on the trait

The first suggestion that chromosomes may physically

exchange segments came from the microscopic

identification of ________.

a. synapsis

b. sister chromatids

c. chiasmata

Which recombination frequency corresponds to

independent assortment and the absence of linkage?

Which recombination frequency corresponds to perfect

linkage and violates the law of independent assortment?

Which of the following codes describes position 12 on

the long arm of chromosome 13?

In agriculture, polyploid crops (like coffee,

strawberries, or bananas) tend to produce ________.

a. more uniformity

b. more variety

c. larger yields

d. smaller yields

Assume a pericentric inversion occurred in one of two

homologs prior to meiosis. The other homolog remains

normal. During meiosis, what structure—if any—would

these homologs assume in order to pair accurately along

their lengths?

a. V formation

b. cruciform

d. pairing would not be possible

8. The genotype XXY corresponds to

a. Klinefelter syndrome

b. Turner syndrome

c. Triplo-X

d. Jacob syndrome

Abnormalities in the number of X chromosomes tends to have milder phenotypic effects than the same abnormalities in autosomes because of ________.

a. deletions

b. nonhomologous recombination

c. synapsis

d. X inactivation

By definition, a pericentric inversion includes the ________.

a. centromere

c. telomere

CRITICAL THINKING QUESTIONS

Describe one of the reasons why the garden pea was an excellent choice of model system for studying inheritance.

How would you perform a reciprocal cross for the characteristic of stem height in the garden pea?

The gene for flower position in pea plants exists as axial or terminal alleles. Given that axial is dominant to terminal, list all of the possible F1 and F2 genotypes and phenotypes from a cross involving parents that are homozygous for each trait. Express genotypes with conventional genetic abbreviations.

Use a Punnett square to predict the offspring in a cross between a dwarf pea plant (homozygous recessive) and a tall pea plant (heterozygous). What is the phenotypic ratio of the offspring?

Can a human male be a carrier of red-green color blindness?

Explain epistatis in terms of its Greek-language roots “standing upon.”

Adapted from:

OpenStax, Biology . OpenStax. May 20, 2013. < http://cnx.org/content/col11448/latest/ >

“Download for free at http://cnx.org/content/col11448/latest/ .”

Human Biology Copyright © by Nancy Barrickman; Kathy Bell, DVM, MPH; and Chris Cowan, M.S. is licensed under a Creative Commons Attribution 4.0 International License , except where otherwise noted.

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5.15: Genetic Variation and Drift

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Learning Objectives

• Describe the different types of variation in a population

Individuals of a population often display different phenotypes, or express different alleles of a particular gene, referred to as polymorphisms. Populations with two or more variations of particular characteristics are called polymorphic. The distribution of phenotypes among individuals, known as the population variation, is influenced by a number of factors, including the population’s genetic structure and the environment (Figure 1). Understanding the sources of a phenotypic variation in a population is important for determining how a population will evolve in response to different evolutionary pressures.

Genetic Variance

Natural selection and some of the other evolutionary forces can only act on heritable traits, namely an organism’s genetic code. Because alleles are passed from parent to offspring, those that confer beneficial traits or behaviors may be selected for, while deleterious alleles may be selected against. Acquired traits, for the most part, are not heritable. For example, if an athlete works out in the gym every day, building up muscle strength, the athlete’s offspring will not necessarily grow up to be a body builder. If there is a genetic basis for the ability to run fast, on the other hand, this may be passed to a child.

Heritability is the fraction of phenotype variation that can be attributed to genetic differences, or genetic variance, among individuals in a population. The greater the hereditability of a population’s phenotypic variation, the more susceptible it is to the evolutionary forces that act on heritable variation.

The diversity of alleles and genotypes within a population is called genetic variance . When scientists are involved in the breeding of a species, such as with animals in zoos and nature preserves, they try to increase a population’s genetic variance to preserve as much of the phenotypic diversity as they can. This also helps reduce the risks associated with inbreeding , the mating of closely related individuals, which can have the undesirable effect of bringing together deleterious recessive mutations that can cause abnormalities and susceptibility to disease. For example, a disease that is caused by a rare, recessive allele might exist in a population, but it will only manifest itself when an individual carries two copies of the allele. Because the allele is rare in a normal, healthy population with unrestricted habitat, the chance that two carriers will mate is low, and even then, only 25 percent of their offspring will inherit the disease allele from both parents. While it is likely to happen at some point, it will not happen frequently enough for natural selection to be able to swiftly eliminate the allele from the population, and as a result, the allele will be maintained at low levels in the gene pool. However, if a family of carriers begins to interbreed with each other, this will dramatically increase the likelihood of two carriers mating and eventually producing diseased offspring, a phenomenon known as inbreeding depression .

Changes in allele frequencies that are identified in a population can shed light on how it is evolving. In addition to natural selection, there are other evolutionary forces that could be in play: genetic drift, gene flow, mutation, nonrandom mating, and environmental variances.

Genetic Drift

The theory of natural selection stems from the observation that some individuals in a population are more likely to survive longer and have more offspring than others; thus, they will pass on more of their genes to the next generation. A big, powerful male gorilla, for example, is much more likely than a smaller, weaker one to become the population’s silverback, the pack’s leader who mates far more than the other males of the group. The pack leader will father more offspring, who share half of his genes, and are likely to also grow bigger and stronger like their father. Over time, the genes for bigger size will increase in frequency in the population, and the population will, as a result, grow larger on average. That is, this would occur if this particular selection pressure , or driving selective force, were the only one acting on the population. In other examples, better camouflage or a stronger resistance to drought might pose a selection pressure.

Another way a population’s allele and genotype frequencies can change is genetic drift (Figure 2), which is simply the effect of chance. By chance, some individuals will have more offspring than others—not due to an advantage conferred by some genetically-encoded trait, but just because one male happened to be in the right place at the right time (when the receptive female walked by) or because the other one happened to be in the wrong place at the wrong time (when a fox was hunting).

Practice Question

Do you think genetic drift would happen more quickly on an island or on the mainland?

[practice-area rows=”2″][/practice-area] [reveal-answer q=”949142″]Show Answer[/reveal-answer] [hidden-answer a=”949142″]Genetic drift is likely to occur more rapidly on an island where smaller populations are expected to occur.[/hidden-answer]

Small populations are more susceptible to the forces of genetic drift. Large populations, on the other hand, are buffered against the effects of chance. If one individual of a population of 10 individuals happens to die at a young age before it leaves any offspring to the next generation, all of its genes—1/10 of the population’s gene pool—will be suddenly lost. In a population of 100, that’s only 1 percent of the overall gene pool; therefore, it is much less impactful on the population’s genetic structure.

Watch this animation of random sampling and genetic drift in action:

Bottleneck Effect

Genetic drift can also be magnified by natural events, such as a natural disaster that kills—at random—a large portion of the population. Known as the bottleneck effect , it results in a large portion of the genome suddenly being wiped out (Figure 3). In one fell swoop, the genetic structure of the survivors becomes the genetic structure of the entire population, which may be very different from the pre-disaster population.

Founder Effect

Another scenario in which populations might experience a strong influence of genetic drift is if some portion of the population leaves to start a new population in a new location or if a population gets divided by a physical barrier of some kind. In this situation, those individuals are unlikely to be representative of the entire population, which results in the founder effect. The founder effect occurs when the genetic structure changes to match that of the new population’s founding fathers and mothers. The founder effect is believed to have been a key factor in the genetic history of the Afrikaner population of Dutch settlers in South Africa, as evidenced by mutations that are common in Afrikaners but rare in most other populations. This is likely due to the fact that a higher-than-normal proportion of the founding colonists carried these mutations. As a result, the population expresses unusually high incidences of Huntington’s disease (HD) and Fanconi anemia (FA), a genetic disorder known to cause blood marrow and congenital abnormalities—even cancer.

Watch this short video to learn more about the founder and bottleneck effects. Note that the video has no audio.

A YouTube element has been excluded from this version of the text. You can view it online here: pb.libretexts.org/fob1/?p=94

Testing the Bottleneck Effect

Question: How do natural disasters affect the genetic structure of a population?

Background: When much of a population is suddenly wiped out by an earthquake or hurricane, the individuals that survive the event are usually a random sampling of the original group. As a result, the genetic makeup of the population can change dramatically. This phenomenon is known as the bottleneck effect.

Hypothesis: Repeated natural disasters will yield different population genetic structures; therefore, each time this experiment is run, the results will vary.

Test the hypothesis: Count out the original population using different colored beads. For example, red, blue, and yellow beads might represent red, blue, and yellow individuals. After recording the number of each individual in the original population, place them all in a bottle with a narrow neck that will only allow a few beads out at a time. Then, pour 1/3 of the bottle’s contents into a bowl. This represents the surviving individuals after a natural disaster kills a majority of the population. Count the number of the different colored beads in the bowl, and record it. Then, place all of the beads back in the bottle and repeat the experiment four more times.

Analyze the data: Compare the five populations that resulted from the experiment. Do the populations all contain the same number of different colored beads, or do they vary? Remember, these populations all came from the same exact parent population.

Form a conclusion: Most likely, the five resulting populations will differ quite dramatically. This is because natural disasters are not selective—they kill and spare individuals at random. Now think about how this might affect a real population. What happens when a hurricane hits the Mississippi Gulf Coast? How do the seabirds that live on the beach fare?

Another important evolutionary force is gene flow : the flow of alleles in and out of a population due to the migration of individuals or gametes (Figure 4). While some populations are fairly stable, others experience more flux. Many plants, for example, send their pollen far and wide, by wind or by bird, to pollinate other populations of the same species some distance away. Even a population that may initially appear to be stable, such as a pride of lions, can experience its fair share of immigration and emigration as developing males leave their mothers to seek out a new pride with genetically unrelated females. This variable flow of individuals in and out of the group not only changes the gene structure of the population, but it can also introduce new genetic variation to populations in different geological locations and habitats.

Mutations are changes to an organism’s DNA and are an important driver of diversity in populations. Species evolve because of the accumulation of mutations that occur over time. The appearance of new mutations is the most common way to introduce novel genotypic and phenotypic variance. Some mutations are unfavorable or harmful and are quickly eliminated from the population by natural selection. Others are beneficial and will spread through the population. Whether or not a mutation is beneficial or harmful is determined by whether it helps an organism survive to sexual maturity and reproduce. Some mutations do not do anything and can linger, unaffected by natural selection, in the genome. Some can have a dramatic effect on a gene and the resulting phenotype.

Nonrandom Mating

If individuals nonrandomly mate with their peers, the result can be a changing population. There are many reasons nonrandom mating occurs. One reason is simple mate choice; for example, female peahens may prefer peacocks with bigger, brighter tails. Traits that lead to more matings for an individual become selected for by natural selection. One common form of mate choice, called assortative mating , is an individual’s preference to mate with partners who are phenotypically similar to themselves.

Another cause of nonrandom mating is physical location. This is especially true in large populations spread over large geographic distances where not all individuals will have equal access to one another. Some might be miles apart through woods or over rough terrain, while others might live immediately nearby.

Environmental Variance

Genes are not the only players involved in determining population variation. Phenotypes are also influenced by other factors, such as the environment (Figure 5). A beachgoer is likely to have darker skin than a city dweller, for example, due to regular exposure to the sun, an environmental factor. Some major characteristics, such as sex, are determined by the environment for some species. For example, some turtles and other reptiles have temperature-dependent sex determination (TSD). TSD means that individuals develop into males if their eggs are incubated within a certain temperature range, or females at a different temperature range.

Geographic separation between populations can lead to differences in the phenotypic variation between those populations. Such geographical variation is seen between most populations and can be significant. One type of geographic variation, called a cline , can be seen as populations of a given species vary gradually across an ecological gradient. Species of warm-blooded animals, for example, tend to have larger bodies in the cooler climates closer to the earth’s poles, allowing them to better conserve heat. This is considered a latitudinal cline. Alternatively, flowering plants tend to bloom at different times depending on where they are along the slope of a mountain, known as an altitudinal cline.

If there is gene flow between the populations, the individuals will likely show gradual differences in phenotype along the cline. Restricted gene flow, on the other hand, can lead to abrupt differences, even speciation.

Contributors and Attributions

• Biology. Provided by : OpenStax CNX. Located at : http://cnx.org/contents/[email protected] . License : CC BY: Attribution . License Terms : Download for free at http://cnx.org/contents/[email protected]
• Random sampling genetic drift. Authored by : Professor marginalia. Located at : https://commons.wikimedia.org/wiki/File:Random_sampling_genetic_drift.gif . License : CC BY-SA: Attribution-ShareAlike
• Founder and Bottleneck Effect (Evolution). Authored by : Greg Korchnak. Located at : https://youtu.be/hEYV9WEvwaI . License : All Rights Reserved . License Terms : Standard YouTube License

Module 12: Development and Inheritance

Patterns of inheritance, learning objectives.

By the end of this section, you will be able to:

• Differentiate between genotype and phenotype
• Describe how alleles determine a person’s traits
• Summarize Mendel’s experiments and relate them to human genetics
• Explain the inheritance of autosomal dominant and recessive and sex-linked genetic disorders

We have discussed the events that lead to the development of a newborn. But what makes each newborn unique? The answer lies, of course, in the DNA in the sperm and oocyte that combined to produce that first diploid cell, the human zygote.

From Genotype to Phenotype

Each human body cell has a full complement of DNA stored in 23 pairs of chromosomes. The image below shows the pairs in a systematic arrangement called a karyotype . Among these is one pair of chromosomes, called the sex chromosomes , that determines the sex of the individual (XX in females, XY in males). The remaining 22 chromosome pairs are called autosomal chromosomes . Each of these chromosomes carries hundreds or even thousands of genes, each of which codes for the assembly of a particular protein—that is, genes are “expressed” as proteins. An individual’s complete genetic makeup is referred to as his or her genotype . The characteristics that the genes express, whether they are physical, behavioral, or biochemical, are a person’s phenotype .

You inherit one chromosome in each pair—a full complement of 23—from each parent. This occurs when the sperm and oocyte combine at the moment of your conception. Homologous chromosomes—those that make up a complementary pair—have genes for the same characteristics in the same location on the chromosome. Because one copy of a gene, an allele , is inherited from each parent, the alleles in these complementary pairs may vary. Take for example an allele that encodes for dimples. A child may inherit the allele encoding for dimples on the chromosome from the father and the allele that encodes for smooth skin (no dimples) on the chromosome from the mother.

Figure 1. Each pair of chromosomes contains hundreds to thousands of genes. The banding patterns are nearly identical for the two chromosomes within each pair, indicating the same organization of genes. As is visible in this karyotype, the only exception to this is the XY sex chromosome pair in males. (credit: National Human Genome Research Institute)

Although a person can have two identical alleles for a single gene (a homozygous state), it is also possible for a person to have two different alleles (a heterozygous state). The two alleles can interact in several different ways. The expression of an allele can be dominant, for which the activity of this gene will mask the expression of a nondominant, or recessive, allele. Sometimes dominance is complete; at other times, it is incomplete. In some cases, both alleles are expressed at the same time in a form of expression known as codominance.

In the simplest scenario, a single pair of genes will determine a single heritable characteristic. However, it is quite common for multiple genes to interact to confer a feature. For instance, eight or more genes—each with their own alleles—determine eye color in humans. Moreover, although any one person can only have two alleles corresponding to a given gene, more than two alleles commonly exist in a population. This phenomenon is called multiple alleles. For example, there are three different alleles that encode ABO blood type; these are designated I A , I B , and i.

Over 100 years of theoretical and experimental genetics studies, and the more recent sequencing and annotation of the human genome, have helped scientists to develop a better understanding of how an individual’s genotype is expressed as their phenotype. This body of knowledge can help scientists and medical professionals to predict, or at least estimate, some of the features that an offspring will inherit by examining the genotypes or phenotypes of the parents. One important application of this knowledge is to identify an individual’s risk for certain heritable genetic disorders. However, most diseases have a multigenic pattern of inheritance and can also be affected by the environment, so examining the genotypes or phenotypes of a person’s parents will provide only limited information about the risk of inheriting a disease. Only for a handful of single-gene disorders can genetic testing allow clinicians to calculate the probability with which a child born to the two parents tested may inherit a specific disease.

Mendel’s Theory of Inheritance

Our contemporary understanding of genetics rests on the work of a nineteenth-century monk. Working in the mid-1800s, long before anyone knew about genes or chromosomes, Gregor Mendel discovered that garden peas transmit their physical characteristics to subsequent generations in a discrete and predictable fashion. When he mated, or crossed, two pure-breeding pea plants that differed by a certain characteristic, the first-generation offspring all looked like one of the parents. For instance, when he crossed tall and dwarf pure-breeding pea plants, all of the offspring were tall. Mendel called tallness dominant because it was expressed in offspring when it was present in a purebred parent. He called dwarfism recessive because it was masked in the offspring if one of the purebred parents possessed the dominant characteristic. Note that tallness and dwarfism are variations on the characteristic of height. Mendel called such a variation a trait . We now know that these traits are the expression of different alleles of the gene encoding height.

Mendel performed thousands of crosses in pea plants with differing traits for a variety of characteristics. And he repeatedly came up with the same results—among the traits he studied, one was always dominant, and the other was always recessive. (Remember, however, that this dominant–recessive relationship between alleles is not always the case; some alleles are codominant, and sometimes dominance is incomplete.)

Using his understanding of dominant and recessive traits, Mendel tested whether a recessive trait could be lost altogether in a pea lineage or whether it would resurface in a later generation. By crossing the second-generation offspring of purebred parents with each other, he showed that the latter was true: recessive traits reappeared in third-generation plants in a ratio of 3:1 (three offspring having the dominant trait and one having the recessive trait). Mendel then proposed that characteristics such as height were determined by heritable “factors” that were transmitted, one from each parent, and inherited in pairs by offspring.

In the language of genetics, Mendel’s theory applied to humans says that if an individual receives two dominant alleles, one from each parent, the individual’s phenotype will express the dominant trait. If an individual receives two recessive alleles, then the recessive trait will be expressed in the phenotype. Individuals who have two identical alleles for a given gene, whether dominant or recessive, are said to be homozygous for that gene (homo- = “same”). Conversely, an individual who has one dominant allele and one recessive allele is said to be heterozygous for that gene (hetero- = “different” or “other”). In this case, the dominant trait will be expressed, and the individual will be phenotypically identical to an individual who possesses two dominant alleles for the trait.

It is common practice in genetics to use capital and lowercase letters to represent dominant and recessive alleles. Using Mendel’s pea plants as an example, if a tall pea plant is homozygous, it will possess two tall alleles ( TT ). A dwarf pea plant must be homozygous because its dwarfism can only be expressed when two recessive alleles are present ( tt ). A heterozygous pea plant ( Tt ) would be tall and phenotypically indistinguishable from a tall homozygous pea plant because of the dominant tall allele. Mendel deduced that a 3:1 ratio of dominant to recessive would be produced by the random segregation of heritable factors (genes) when crossing two heterozygous pea plants. In other words, for any given gene, parents are equally likely to pass down either one of their alleles to their offspring in a haploid gamete, and the result will be expressed in a dominant–recessive pattern if both parents are heterozygous for the trait.

Because of the random segregation of gametes, the laws of chance and probability come into play when predicting the likelihood of a given phenotype. Consider a cross between an individual with two dominant alleles for a trait ( AA ) and an individual with two recessive alleles for the same trait ( aa ). All of the parental gametes from the dominant individual would be A , and all of the parental gametes from the recessive individual would be a . All of the offspring of that second generation, inheriting one allele from each parent, would have the genotype Aa , and the probability of expressing the phenotype of the dominant allele would be 4 out of 4, or 100 percent.

This seems simple enough, but the inheritance pattern gets interesting when the second-generation Aa individuals are crossed. In this generation, 50 percent of each parent’s gametes are A and the other 50 percent are a . By Mendel’s principle of random segregation, the possible combinations of gametes that the offspring can receive are AA , Aa , aA (which is the same as Aa ), and aa . Because segregation and fertilization are random, each offspring has a 25 percent chance of receiving any of these combinations. Therefore, if an Aa × Aa cross were performed 1000 times, approximately 250 (25 percent) of the offspring would be AA ; 500 (50 percent) would be Aa (that is, Aa plus aA ); and 250 (25 percent) would be aa . The genotypic ratio for this inheritance pattern is 1:2:1. However, we have already established that AA and Aa (and aA ) individuals all express the dominant trait (i.e., share the same phenotype), and can therefore be combined into one group. The result is Mendel’s third-generation phenotype ratio of 3:1.

Figure 2. In the formation of gametes, it is equally likely that either one of a pair alleles from one parent will be passed on to the offspring. This figure follows the possible combinations of alleles through two generations following a first-generation cross of homozygous dominant and homozygous recessive parents. The recessive phenotype, which is masked in the second generation, has a 1 in 4, or 25 percent, chance of reappearing in the third generation.

Mendel’s observation of pea plants also included many crosses that involved multiple traits, which prompted him to formulate the principle of independent assortment. The law states that the members of one pair of genes (alleles) from a parent will sort independently from other pairs of genes during the formation of gametes. Applied to pea plants, that means that the alleles associated with the different traits of the plant, such as color, height, or seed type, will sort independently of one another. This holds true except when two alleles happen to be located close to one other on the same chromosome. Independent assortment provides for a great degree of diversity in offspring.

Mendelian genetics represent the fundamentals of inheritance, but there are two important qualifiers to consider when applying Mendel’s findings to inheritance studies in humans. First, as we’ve already noted, not all genes are inherited in a dominant–recessive pattern. Although all diploid individuals have two alleles for every gene, allele pairs may interact to create several types of inheritance patterns, including incomplete dominance and codominance.

Secondly, Mendel performed his studies using thousands of pea plants. He was able to identify a 3:1 phenotypic ratio in second-generation offspring because his large sample size overcame the influence of variability resulting from chance. In contrast, no human couple has ever had thousands of children. If we know that a man and woman are both heterozygous for a recessive genetic disorder, we would predict that one in every four of their children would be affected by the disease. In real life, however, the influence of chance could change that ratio significantly. For example, if a man and a woman are both heterozygous for cystic fibrosis, a recessive genetic disorder that is expressed only when the individual has two defective alleles, we would expect one in four of their children to have cystic fibrosis. However, it is entirely possible for them to have seven children, none of whom is affected, or for them to have two children, both of whom are affected. For each individual child, the presence or absence of a single gene disorder depends on which alleles that child inherits from his or her parents.

Autosomal Dominant Inheritance

In the case of cystic fibrosis, the disorder is recessive to the normal phenotype. However, a genetic abnormality may be dominant to the normal phenotype. When the dominant allele is located on one of the 22 pairs of autosomes (non-sex chromosomes), we refer to its inheritance pattern as autosomal dominant . An example of an autosomal dominant disorder is neurofibromatosis type I, a disease that induces tumor formation within the nervous system that leads to skin and skeletal deformities. Consider a couple in which one parent is heterozygous for this disorder (and who therefore has neurofibromatosis), Nn , and one parent is homozygous for the normal gene, nn . The heterozygous parent would have a 50 percent chance of passing the dominant allele for this disorder to his or her offspring, and the homozygous parent would always pass the normal allele. Therefore, four possible offspring genotypes are equally likely to occur: Nn , Nn , nn , and nn . That is, every child of this couple would have a 50 percent chance of inheriting neurofibromatosis. This inheritance pattern is shown in the table below, in a form called a Punnett square , named after its creator, the British geneticist Reginald Punnett.

Figure 3. Inheritance pattern of an autosomal dominant disorder, such as neurofibromatosis, is shown in a Punnett square.

Other genetic diseases that are inherited in this pattern are achondroplastic dwarfism, Marfan syndrome, and Huntington’s disease. Because autosomal dominant disorders are expressed by the presence of just one gene, an individual with the disorder will know that he or she has at least one faulty gene. The expression of the disease may manifest later in life, after the childbearing years, which is the case in Huntington’s disease (discussed in more detail later in this section).

Autosomal Recessive Inheritance

When a genetic disorder is inherited in an autosomal recessive pattern, the disorder corresponds to the recessive phenotype. Heterozygous individuals will not display symptoms of this disorder, because their unaffected gene will compensate. Such an individual is called a carrier . Carriers for an autosomal recessive disorder may never know their genotype unless they have a child with the disorder.

An example of an autosomal recessive disorder is cystic fibrosis (CF), which we introduced earlier. CF is characterized by the chronic accumulation of a thick, tenacious mucus in the lungs and digestive tract. Decades ago, children with CF rarely lived to adulthood. With advances in medical technology, the average lifespan in developed countries has increased into middle adulthood. CF is a relatively common disorder that occurs in approximately 1 in 2000 Caucasians. A child born to two CF carriers would have a 25 percent chance of inheriting the disease. This is the same 3:1 dominant:recessive ratio that Mendel observed in his pea plants would apply here. The pattern is shown in the image below, using a diagram that tracks the likely incidence of an autosomal recessive disorder on the basis of parental genotypes.

On the other hand, a child born to a CF carrier and someone with two unaffected alleles would have a 0 percent probability of inheriting CF, but would have a 50 percent chance of being a carrier. Other examples of autosome recessive genetic illnesses include the blood disorder sickle-cell anemia, the fatal neurological disorder Tay–Sachs disease, and the metabolic disorder phenylketonuria.

Figure 4. The inheritance pattern of an autosomal recessive disorder with two carrier parents reflects a 3:1 probability of expression among offspring. (credit: U.S. National Library of Medicine)

X-linked Dominant or Recessive Inheritance

An X-linked transmission pattern involves genes located on the X chromosome of the 23rd pair. Recall that a male has one X and one Y chromosome. When a father transmits a Y chromosome, the child is male, and when he transmits an X chromosome, the child is female. A mother can transmit only an X chromosome, as both her sex chromosomes are X chromosomes.

X-linked Dominant Inheritance

When an abnormal allele for a gene that occurs on the X chromosome is dominant over the normal allele, the pattern is described as X-linked dominant . This is the case with vitamin D–resistant rickets: an affected father would pass the disease gene to all of his daughters, but none of his sons, because he donates only the Y chromosome to his sons. If it is the mother who is affected, all of her children—male or female—would have a 50 percent chance of inheriting the disorder because she can only pass an X chromosome on to her children. For an affected female, the inheritance pattern would be identical to that of an autosomal dominant inheritance pattern in which one parent is heterozygous and the other is homozygous for the normal gene.

Figure 5. Click for a larger image. A chart of X-linked dominant inheritance patterns differs depending on whether (a) the father or (b) the mother is affected with the disease. (credit: U.S. National Library of Medicine)

X-linked Recessive Inheritance

X-linked recessive inheritance is much more common because females can be carriers of the disease yet still have a normal phenotype. Diseases transmitted by X-linked recessive inheritance include color blindness, the blood-clotting disorder hemophilia, and some forms of muscular dystrophy. For an example of X-linked recessive inheritance, consider parents in which the mother is an unaffected carrier and the father is normal. None of the daughters would have the disease because they receive a normal gene from their father. However, they have a 50 percent chance of receiving the disease gene from their mother and becoming a carrier. In contrast, 50 percent of the sons would be affected.

With X-linked recessive diseases, males either have the disease or are genotypically normal—they cannot be carriers. Females, however, can be genotypically normal, a carrier who is phenotypically normal, or affected with the disease. A daughter can inherit the gene for an X-linked recessive illness when her mother is a carrier or affected, or her father is affected. The daughter will be affected by the disease only if she inherits an X-linked recessive gene from both parents. As you can imagine, X-linked recessive disorders affect many more males than females. For example, color blindness affects at least 1 in 20 males, but only about 1 in 400 females.

Figure 6. Given two parents in which the father is normal and the mother is a carrier of an X-linked recessive disorder, a son would have a 50 percent probability of being affected with the disorder, whereas daughters would either be carriers or entirely unaffected. (credit: U.S. National Library of Medicine)

Other Inheritance Patterns

Incomplete dominance.

Not all genetic disorders are inherited in a dominant–recessive pattern. In incomplete dominance , the offspring express a heterozygous phenotype that is intermediate between one parent’s homozygous dominant trait and the other parent’s homozygous recessive trait. An example of this can be seen in snapdragons when red-flowered plants and white-flowered plants are crossed to produce pink-flowered plants. In humans, incomplete dominance occurs with one of the genes for hair texture. When one parent passes a curly hair allele (the incompletely dominant allele) and the other parent passes a straight-hair allele, the effect on the offspring will be intermediate, resulting in hair that is wavy.

Codominance

Codominance is characterized by the equal, distinct, and simultaneous expression of both parents’ different alleles. This pattern differs from the intermediate, blended features seen in incomplete dominance. A classic example of codominance in humans is ABO blood type. People are blood type A if they have an allele for an enzyme that facilitates the production of surface antigen A on their erythrocytes. This allele is designated I A . In the same manner, people are blood type B if they express an enzyme for the production of surface antigen B. People who have alleles for both enzymes ( I A and I B ) produce both surface antigens A and B. As a result, they are blood type AB. Because the effect of both alleles (or enzymes) is observed, we say that the I A and I B alleles are codominant. There is also a third allele that determines blood type. This allele ( i ) produces a nonfunctional enzyme. People who have two i alleles do not produce either A or B surface antigens: they have type O blood. If a person has I A and i alleles, the person will have blood type A. Notice that it does not make any difference whether a person has two I A alleles or one I A and one i allele. In both cases, the person is blood type A. Because I A masks i , we say that I A is dominant to i . The following table summarizes the expression of blood type.

Lethal Alleles

Certain combinations of alleles can be lethal, meaning they prevent the individual from developing in utero, or cause a shortened life span. In recessive lethal inheritance patterns, a child who is born to two heterozygous (carrier) parents and who inherited the faulty allele from both would not survive. An example of this is Tay–Sachs, a fatal disorder of the nervous system. In this disorder, parents with one copy of the allele for the disorder are carriers. If they both transmit their abnormal allele, their offspring will develop the disease and will die in childhood, usually before age 5.

Dominant lethal inheritance patterns are much more rare because neither heterozygotes nor homozygotes survive. Of course, dominant lethal alleles that arise naturally through mutation and cause miscarriages or stillbirths are never transmitted to subsequent generations. However, some dominant lethal alleles, such as the allele for Huntington’s disease, cause a shortened life span but may not be identified until after the person reaches reproductive age and has children. Huntington’s disease causes irreversible nerve cell degeneration and death in 100 percent of affected individuals, but it may not be expressed until the individual reaches middle age. In this way, dominant lethal alleles can be maintained in the human population. Individuals with a family history of Huntington’s disease are typically offered genetic counseling, which can help them decide whether or not they wish to be tested for the faulty gene.

A mutation is a change in the sequence of DNA nucleotides that may or may not affect a person’s phenotype. Mutations can arise spontaneously from errors during DNA replication, or they can result from environmental insults such as radiation, certain viruses, or exposure to tobacco smoke or other toxic chemicals. Because genes encode for the assembly of proteins, a mutation in the nucleotide sequence of a gene can change amino acid sequence and, consequently, a protein’s structure and function. Spontaneous mutations occurring during meiosis are thought to account for many spontaneous abortions (miscarriages).

Chromosomal Disorders

Sometimes a genetic disease is not caused by a mutation in a gene, but by the presence of an incorrect number of chromosomes. For example, Down syndrome is caused by having three copies of chromosome 21. This is known as trisomy 21. The most common cause of trisomy 21 is chromosomal nondisjunction during meiosis. The frequency of nondisjunction events appears to increase with age, so the frequency of bearing a child with Down syndrome increases in women over 36. The age of the father matters less because nondisjunction is much less likely to occur in a sperm than in an egg.

Whereas Down syndrome is caused by having three copies of a chromosome, Turner syndrome is caused by having just one copy of the X chromosome. This is known as monosomy. The affected child is always female. Women with Turner syndrome are sterile because their sexual organs do not mature.

Career Connections: Genetic Counselor

Given the intricate orchestration of gene expression, cell migration, and cell differentiation during prenatal development, it is amazing that the vast majority of newborns are healthy and free of major birth defects. When a woman over 35 is pregnant or intends to become pregnant, or her partner is over 55, or if there is a family history of a genetic disorder, she and her partner may want to speak to a genetic counselor to discuss the likelihood that their child may be affected by a genetic or chromosomal disorder. A genetic counselor can interpret a couple’s family history and estimate the risks to their future offspring.

For many genetic diseases, a DNA test can determine whether a person is a carrier. For instance, carrier status for Fragile X, an X-linked disorder associated with mental retardation, or for cystic fibrosis can be determined with a simple blood draw to obtain DNA for testing. A genetic counselor can educate a couple about the implications of such a test and help them decide whether to undergo testing. For chromosomal disorders, the available testing options include a blood test, amniocentesis (in which amniotic fluid is tested), and chorionic villus sampling (in which tissue from the placenta is tested). Each of these has advantages and drawbacks. A genetic counselor can also help a couple cope with the news that either one or both partners is a carrier of a genetic illness, or that their unborn child has been diagnosed with a chromosomal disorder or other birth defect.

To become a genetic counselor, one needs to complete a 4-year undergraduate program and then obtain a Master of Science in Genetic Counseling from an accredited university. Board certification is attained after passing examinations by the American Board of Genetic Counseling. Genetic counselors are essential professionals in many branches of medicine, but there is a particular demand for preconception and prenatal genetic counselors.

Chapter Review

There are two aspects to a person’s genetic makeup. Their genotype refers to the genetic makeup of the chromosomes found in all their cells and the alleles that are passed down from their parents. Their phenotype is the expression of that genotype, based on the interaction of the paired alleles, as well as how environmental conditions affect that expression.

Working with pea plants, Mendel discovered that the factors that account for different traits in parents are discretely transmitted to offspring in pairs, one from each parent. He articulated the principles of random segregation and independent assortment to account for the inheritance patterns he observed. Mendel’s factors are genes, with differing variants being referred to as alleles and those alleles being dominant or recessive in expression. Each parent passes one allele for every gene on to offspring, and offspring are equally likely to inherit any combination of allele pairs. When Mendel crossed heterozygous individuals, he repeatedly found a 3:1 dominant–recessive ratio. He correctly postulated that the expression of the recessive trait was masked in heterozygotes but would resurface in their offspring in a predictable manner.

Human genetics focuses on identifying different alleles and understanding how they express themselves. Medical researchers are especially interested in the identification of inheritance patterns for genetic disorders, which provides the means to estimate the risk that a given couple’s offspring will inherit a genetic disease or disorder. Patterns of inheritance in humans include autosomal dominance and recessiveness, X-linked dominance and recessiveness, incomplete dominance, codominance, and lethality. A change in the nucleotide sequence of DNA, which may or may not manifest in a phenotype, is called a mutation.

Answer the question(s) below to see how well you understand the topics covered in the previous section.

Critical Thinking Questions

• Explain why it was essential that Mendel perform his crosses using a large sample size?
• How can a female carrier of an X-linked recessive disorder have a daughter who is affected?
• By using large sample sizes, Mendel minimized the effect of random variability resulting from chance. This allowed him to identify true ratios corresponding to dominant–recessive inheritance.
• The only way an affected daughter could be born is if the female carrier mated with a male who was affected. In this case, 50 percent of the daughters would be affected. Alternatively, but exceedingly unlikely, the daughter could become affected by a spontaneous mutation.

allele: alternative forms of a gene that occupy a specific locus on a specific gene

autosomal chromosome: in humans, the 22 pairs of chromosomes that are not the sex chromosomes (XX or XY)

autosomal dominant: pattern of dominant inheritance that corresponds to a gene on one of the 22 autosomal chromosomes

autosomal recessive: pattern of recessive inheritance that corresponds to a gene on one of the 22 autosomal chromosomes

carrier: heterozygous individual who does not display symptoms of a recessive genetic disorder but can transmit the disorder to his or her offspring

codominance: pattern of inheritance that corresponds to the equal, distinct, and simultaneous expression of two different alleles

dominant: describes a trait that is expressed both in homozygous and heterozygous form

dominant lethal: inheritance pattern in which individuals with one or two copies of a lethal allele do not survive in utero or have a shortened life span

genotype: complete genetic makeup of an individual

heterozygous: having two different alleles for a given gene

homozygous: having two identical alleles for a given gene

incomplete dominance: pattern of inheritance in which a heterozygous genotype expresses a phenotype intermediate between dominant and recessive phenotypes

karyotype: systematic arrangement of images of chromosomes into homologous pairs

mutation: change in the nucleotide sequence of DNA

phenotype: physical or biochemical manifestation of the genotype; expression of the alleles

Punnett square: grid used to display all possible combinations of alleles transmitted by parents to offspring and predict the mathematical probability of offspring inheriting a given genotype

recessive: describes a trait that is only expressed in homozygous form and is masked in heterozygous form

recessive lethal: inheritance pattern in which individuals with two copies of a lethal allele do not survive in utero or have a shortened life span

sex chromosomes: pair of chromosomes involved in sex determination; in males, the XY chromosomes; in females, the XX chromosomes

trait: variation of an expressed characteristic

X-linked: pattern of inheritance in which an allele is carried on the X chromosome of the 23rd pair

X-linked dominant: pattern of dominant inheritance that corresponds to a gene on the X chromosome of the 23rd pair

X-linked recessive: pattern of recessive inheritance that corresponds to a gene on the X chromosome of the 23rd pair

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