Accuracy of Genomic Selection Using Different Methods to Define Haplotypes

TLDR

Genomic selection predicts juvenile animal breeding values from many marker haplotype effects across the genome. The study compares the accuracy of four genomic selection models across varying marker densities for traits with heritabilities of 50 % and 10 %. Models estimated effects of single SNPs, two‑marker haplotypes, and 2‑ or 10‑marker haplotypes incorporating linkage disequilibrium and linkage analysis, using 119–2,343 simulated SNPs on a 3‑Mb genome. For the 10 % heritability trait, model accuracies were similar with no clear winner, whereas for the 50 % heritability trait the HAP_IBD10 model achieved the highest accuracies across all marker densities, confirming that genomic selection is markedly more accurate than traditional selection, particularly for low‑heritability traits.

Abstract

Abstract Genomic selection uses total breeding values for juvenile animals, predicted from a large number of estimated marker haplotype effects across the whole genome. In this study the accuracy of predicting breeding values is compared for four different models including a large number of markers, at different marker densities for traits with heritabilities of 50 and 10%. The models estimated the effect of (1) each single-marker allele [single-nucleotide polymorphism (SNP)1], (2) haplotypes constructed from two adjacent marker alleles (SNP2), and (3) haplotypes constructed from 2 or 10 markers, including the covariance between haplotypes by combining linkage disequilibrium and linkage analysis (HAP_IBD2 and HAP_IBD10). Between 119 and 2343 polymorphic SNPs were simulated on a 3-M genome. For the trait with a heritability of 10%, the differences between models were small and none of them yielded the highest accuracies across all marker densities. For the trait with a heritability of 50%, the HAP_IBD10 model yielded the highest accuracies of estimated total breeding values for juvenile and phenotyped animals at all marker densities. It was concluded that genomic selection is considerably more accurate than traditional selection, especially for a low-heritability trait.