genotype and phenotype
The term genotype is used to describe the totality of the genes of an individual. Because the totality of an individual's genes is not known, the term, in practice, is usually used to describe a very small subset of genes of interest in a breeding program or research. Conventionally, a genotype is written with an uppercase letter (H, G) indicating the dominant allele (expressed over the alternative allele), while a lower case letter (h, g) indicates the recessive allele. A plant that has two identical alleles for genes is homozygous at that locus (e.g. AA, aa, GG, gg) and is called a homozygote. If it has different alleles for a gene, it is heterozygous at these loci (e.g. Aa, Gg) and is called a heterozygote. Certain plant breeding methods are designed to produce products that are homozygous (breed true – most or all of the loci are homozygous) whereas others (e.g. hybrids) depend on heterozygosity for success.
The term phenotype refers to the observable effect of a genotype (the genetic makeup of an individual). Because genes are expressed in an environment, a phenotype is the result of the interaction between a genotype and its environment (i.e. phenotype = genotype + environment, or symbolically, P = G + E). In Chapter 23, a more complete form of this equation will be introduced as P = G + E + GE + error, where GE represents the interaction between the environment and the genotype. This interaction effect helps plant breeders in the cultivar release decision making process (see Chapter 23).
5.9.3 Predicting genotype and phenotype
Based upon Mendel's laws of inheritance, statistical probability analysis can be applied to determine the outcome of a cross, given the genotype of the parents and gene action (dominance/recessivity). A genetic grid called a Punnett square (Figure 5.13) facilitates the analysis. For example, a monohybrid cross in which the genotypes of interest are AA × aa, where A is dominant over a, will produce a hybrid genotype Aa in the F1 (first filial generation) with a AA phenotype. However, in the F2 (F1 × F1), the Punnett square shows a genotypic ratio of 1AA: 2Aa: 1aa, and a phenotypic ratio of 3 : 1, because of dominance. A dihybrid cross (involving simultaneous analysis of two different genes) is more complex but conceptually like a monohybrid cross (only one gene of interest) analysis. An analysis of a dihybrid cross PPRR × pprr, using the Punnett square is illustrated in Figure 5.12. An alternative method of genetic analysis of a cross is by the branch diagram or forked line method (Figure 5.14).
Figure 5.14 The branch diagram method may also be used to predict the phenotypic and genotypic ratios in the F2 population.
Predicting the outcome of a cross is important to plant breeders. One of the critical steps in a hybrid program is to authenticate the F1 product. The breeder must be certain that the F1 truly is a successful cross and not a product of selfing. If a selfed product is advanced, the breeding program will be a total waste of resources. To facilitate the process, breeders may include a genetic marker in their program. If two plants are crossed, for example, one with purple flowers and the other white flowers, we expect the F1 plant to have purple flowers because of dominance of purple over white flowers. If the F1 plant has white flowers, it is proof that the cross was unsuccessful (i.e. the product of the “cross” is actually from selfing).
5.9.4 Distinguishing between heterozygous and homozygous individuals
In a segregating population where genotypes PP and Pp produce the same phenotype (because of dominance), it is necessary, sometimes, to know the exact genotype of a plant. There are two procedures that are commonly used to accomplish this task.
1 Test crossDeveloped by Mendel, a test cross entails crossing the plant with the dominant allele but unknown genotype with a homozygous recessive individual (Figure 5.15). If the unknown genotype is PP, crossing it with the genotype pp will produce all Pp offspring. However, if the unknown is Pp then a test cross will produce offspring segregating 50 : 50 for Pp: pp. The test cross also supports Mendel's postulate that separate genes control purple and white flowers.
2 Progeny testUnlike a test cross, a progeny test does not include a cross with a special parent but selfing of the F2. Each F2 plant is harvested and separately bagged and then, subsequently planted. In the F3, plants that are homozygous dominant will produce progeny that is uniform for the trait, whereas plants that are heterozygous will produce a segregating progeny row.
Figure 5.15 The test cross. Crossing a homozygous dominant genotype with a homozygous recessive genotype always produces all heterozygotes (a). However, crossing a heterozygote with a homozygous recessive produces both homozygotes and heterozygotes.
Plant breeders use the progeny test for a number of purposes. In breeding methodologies in which selection is based on phenotype, a progeny test will allow a breeder to select superior plants from among a genetically mixed population. Following an environmental stress, biotic or abiotic, a breeder may use a progeny test to identify superior individuals and further ascertain if the phenotypic variation is due to genetic effects or just caused by environment factors.
5.10 Complex inheritance
Just how lucky was Mendel in his experiments that yielded his landmark results? This question has been widely discussed among scientists over the years. Mendel selected traits whose inheritance patterns enabled him to avoid certain complex inheritance patterns that would have made his results and interpretations more challenging. The inheritance of traits such as those studied by Mendel is described as simple (simply inherited) traits or having Mendelian inheritance. There are other numerous traits that have complex inheritance patterns that cannot be predicted by Mendelian ratios. Several factors are responsible for the observation of non‐Mendelian ratios as discussed next.
5.10.1 Incomplete dominance and codominance
Mendel worked with traits that exhibited complete dominance. Post‐Mendelian studies revealed that frequently, the masking of one trait by another is only partial (called incomplete dominance or partial dominance). A cross between a red‐flowered (RR) and white‐flowered (rr) snapdragon produces pink‐flowered plants (Rr). The genotypic ratio remains 1 : 2 : 1, but a lack of complete dominance also makes the phenotypic ratio 1 : 2 : 1 (instead of the 3 : 1 expected for complete dominance).
Another situation in which there is no dominance
