Identifying Links Between Genotype and Phenotype Using Marker Loci and Candidate Genes

Abstract

The elucidation of the causal links between variation at the genetic level and the emergent phenotype has been at the heart of theoretical and empirical studies in quantitative and population genetics since the rediscovery of Mendel’s work and the synthesis of Mendelism, Darwinism, and Biometry through population genetics (Provine, 1971). Wright (1980, 1982) has summarized the historical emergence of four predominant interpretations to the relationship between genotype and phenotype (Figure 1). The first relationship (Figure 1A) represents a one to one mapping of genotype to phenotype. This relationship applies to genes of major effect, the traditional Mendelian view of inheritance (Haldane, 1932). Kimura’s (1983) neutral theory of evolution is depicted in relationship (Figure 1C), where variation at the genotype has no relationship to variation seen at the phenotypic level. Figures 1B and 1D represent the predominant views of the relationships between genotype and phenotype. Relationship (1B) represents multiple genes with minor additive effects on phenotypic variation, a view forcefully put forth by Fisher (1930). Relationship (1D) represents genic relationships with pleiotropic effects producing a maze of interaction influencing the phenotype (Wright, 1931; Wright, 1932). This chapter outlines the uses of molecular techniques to identify loci, genes, alleles, and mutations associated with variation at the phenotypic level.