Estimating Effects and Variance Components in Models of Quantitative Genetics in an Era of Sequenced Genomes

Abstract

As in many other areas of research in genetics, the availability of sequenced genomes in samples of individuals has revolutionized the study of quantitative traits, because researches have developed statistical evidence regarding the lo- cations of genomic regions, loci, that have been implicated with the expression of a quantitative trait or traits. Therefore, in cases in which it is possible to develop operational definitions of at least two alleles at each locus, genomic regions, it becomes possible to identify the genotype of each individual with re- spect to a set of loci that have been shown in other experiments to influence the expression of a quantitative trait. As will be shown in this paper, by knowing the genotype of each individual in a sample with respect to a set of identified loci, it is now possible to directly estimate effects that are measures of not only intra-allelic interactions at each locus under consideration but also various types of epistatic effects that are measures of interactions among alleles at different loci, governing the inheritance of a quantitative trait. These straight forward methods of estimation differ from those used in classical quantitative genetics, because such effects and corresponding variance components could be estimated indirectly, using analysis of variance procedures or some version of general lin- ear models that have been and are widely in statistical genetics. The direct method of estimation described in this paper, show promise towards shifting the working paradigm that has been used in classical models of the genetics of quantitative traits involving the estimation of variance components to a more direct approach and simpler approach.