“co‐adapted” gene complexes to produce a fully balanced phenotype, which is then protected from further change by genetic linkage. The breeding system will determine whether the newly constituted gene combinations will be maintained. Whereas inbreeding (e.g. selfing) would produce a homozygous population that will resist further change (until crossed), outbreeding tends to produce heterozygous combinations. In heterozygous populations, alleles that exhibit dominance in the direction of expression targeted by the breeder will be favored over other alleles. Hence, directional selection leads to the establishment of dominance and/or genic interaction (epistasis).
3.7 Effect of mating system on selection
Four mating systems are generally recognized. They may be grouped into two broad categories as random mating and non‐random mating (comprising genetic assortative mating, phenotypic assortative mating, and disassortative mating).
3.7.1 Random mating
In plants, random mating occurs when each female gamete has an equal chance of being fertilized by any male gamete of the same plant, or with any other plant of the population, and further, there is an equal chance for seed production. As can be seen from the previous statement, it is not possible to achieve true random mating in plant breeding since selection is involved. Consequently, it is more realistic to describe the system of mating as random mating with selection. Whereas true random mating does not change gene frequencies, existing variability in the population or genetic correlation between close relatives, random mating with selection changes gene frequencies and the mean of the population, with little or no effect on homozygosity, population variance, or genetic correlation between close relatives in a large population. Small populations are prone to random fluctuation in gene frequency (genetic drift) and inbreeding, factors that reduce heterozygosity in a population. Random mating does not fix genes, with or without selection. If the goal of the breeder is to preserve desirable alleles (e.g. in germplasm composites), random mating will be an effective method of breeding.
3.7.2 Non‐random mating
Non‐random mating has two basic forms: (i) mating occurs between individuals that are related to each other by ancestral descent (promotes an increase in homozygosity at all loci), and (ii) individuals mate preferentially with respect to their genotypes at any particular locus of interest. If mating occurs such that the mating pair has the same phenotype more often than would occur by chance, it is said to be assortative mating. The reverse is true in disassortative mating, which occurs in species with self‐incompatibility or sterility problems, promoting heterozygosity.
Genetic assortative mating
Genetic assortative mating or inbreeding entails mating individuals that are closely related by ancestry, the closest being selfing (self‐fertilization). A genetic consequence of genetic assortative mating is the exposure of cryptic genetic variability that was inaccessible to selection and was being protected by heterozygosity (i.e. heterozygous advantage). Also, repeated selfing results in homozygosity and brings about fixation of types. This mating system is effective if the goal of the breeder is to develop homozygous lines (e.g. developing inbred lines for hybrid seed breeding or development of synthetics).
Pheotypic assortative mating
Mating may also be done on the basis of phenotypic resemblance. Called phenotypic assortative mating, the breeder selects and mates individuals on the basis of their resemblance to each other compared to the rest of the population. The effect of this action is the development of two extreme phenotypes. A breeder may choose this mating system if the goal is to develop an extreme phenotype.
Disassortative mating
Disassortative mating may also be genetic or phenotypic. Genetic disassortative mating entails mating individuals that are less closely related than they would under random mating. A breeder may use this system to cross different strains. In phenotypic disassortative mating, the breeder may select individuals with contrasting phenotypes for mating. Phenotypic disassortative mating is a conservative mating system that may be used to maintain genetic diversity in the germplasm from which the breeder may obtain desirable genes for breeding as needed. It maintains heterozygosity in the population and reduces genetic correlation between relatives.
3.8 Concept of inbreeding
As previously indicated, plant breeding is a special case of evolution, whereby a mixture of natural and especially artificial selection operates, rather than natural selection alone. The Hardy‐Weinberg equilibrium is not satisfied in plant breeding because of factors including non‐random mating. Outcrossing promotes random mating, but breeding methods impose certain mating schemes that encourage non‐random mating, especially inbreeding. Inbreeding is measured by the coefficient of inbreeding (F), which is the probability of identity of alleles by descent. The range of F is 0 (no inbreeding; random mating) to 1 (prolonged selfing). It can be shown mathematically that
If F = 0, then the equation reduces to the familiar p 2 + 2pq + q 2 . However, if F = 1, it becomes p : 0 : q. The results show that any inbreeding leads to homozygosis (all or nearly all loci homozygous), with extreme inbreeding leading to a complete absence of heterozygosis (all or nearly all loci heterozygous).
Differential fitness is a factor that mitigates against the realization of the Hardy‐Weinberg equilibrium. According to Darwin, the more progeny left, on average, by a genotype in relation to the progeny left by other genotypes, the fitter it is. It can be shown that the persistence of alleles in the population depends on whether they are dominant, intermediate, or recessive in gene action. An unfit (deleterious) recessive allele is fairly quickly reduced in frequency but declines slowly thereafter. On the other hand, an unfit dominant allele is rapidly eliminated from the population, while an intermediate allele is reduced more rapidly than a recessive allele because the former is open to selection in the heterozygote. The consequence of these outcomes is that unfit dominant or intermediate alleles are rare in cross‐breeding populations, while unfit recessive alleles persist because they are protected by their recessiveness. The point that will be made later but is worth noting here is that inbreeding exposes unfit recessive alleles (they become homozygous and are expressed) to selection and potential elimination from the population. It follows that inbreeding will expose any unfit allele, dominant or recessive. Consequently, species that are inbreeding would have opportunity to purge out unfit alleles and hence carry less genetic unfitness load (i.e. have more allele fitness) than outcrossing species. Furthermore, inbreeders (self‐pollinated species) are more tolerant of inbreeding whereas outcrossing species are intolerant of inbreeding.
Whereas outcrossing species have more heterozygous loci and carry more unfitness load, there are cases in which the heterozygote is fitter than either homozygote. Called overdominance, this phenomenon is exploited in hybrid breeding (see Chapter 18).
3.9 Inbreeding and its implications in plant breeding
The point has already been made that the methods used by plant breeders depend on the natural means of reproduction of the species.
