Estimation of Variance Components in Finite Polygenic Models and Complex Pedigrees

• Main Author: Lahti, Katharine Gage
• Other Authors: Dairy Science, Hoeschele, Ina, Vinson, William E., Hallerman, Eric M., Notter, David R.
• Format: Thesis
• Language: unknown
• Published: Virginia Tech 1998
• Subjects: nonadditive genetic variance; finite polygenic model; Bayesian methods; DML
• Online Access: http://hdl.handle.net/10919/46496; http://scholar.lib.vt.edu/theses/available/etd-51798-163045/

Various models of the genetic architecture of quantitative traits have been considered to provide the basis for increased genetic progress. The finite polygenic model (FPM), which contains a finite number of unlinked polygenic loci, is proposed as an improvement to the infinitesimal model (IM) for estimating both additive and dominance variance for a wide range of genetic models. Analysis under an additive five-loci FPM by either a deterministic Maximum Likelihood (DML) or a Markov chain Monte Carlo (MCMC) Bayesian method (BGS) produced accurate estimates of narrow-sense heritability (0.48 to 0.50 with true values of h2 = 0.50) for phenotypic data from a five-generation, 6300-member pedigree simulated without selection under either an IM, FPMs containing five or forty loci with equal homozygote difference, or a FPM with eighteen loci of diminishing homozygote difference. However, reducing the analysis to a three- or four-loci FPM resulted in some biased estimates of heritability (0.53 to 0.55 across all genetic models for the 3-loci BGS analysis and 0.47 to 0.48 for the 40-loci FPM and the infinitesimal model for both the 3- and 4-loci DML analyses). The practice of cutting marriage and inbreeding loops utilized by the DML method expectedly produced overestimates of additive genetic variance (55.4 to 66.6 with a true value of sigma squared sub a = 50.0 across all four genetic models) for the same pedigree structure under selection, while the BGS method was mostly unaffected by selection, except for slight overestimates of additive variance (55.0 and 58.8) when analyzing the 40-loci FPM and the infinitesimal model, the two models with the largest numbers of loci. Changes to the BGS method to accommodate estimation of dominance variance by sampling genotypes at individual loci are explored. Analyzing the additive data sets with the BGS method, assuming a five-loci FPM including both additive and dominance effects, resulted in accurate estimates of additive genetic variance (50.8 to 52.2 for true sigma squared sub ...