Strategy for applying genome‐wide selection in dairy cattle

TLDR

Genome‑wide SNP genotyping provides dense markers at roughly 1‑cM intervals, enabling inference of four possible sire haplotypes for each adjacent SNP pair. The study compared a genomic‑estimated breeding value strategy, calculable at birth with high accuracy, to traditional progeny testing in a Canadian‑like dairy cattle scenario. Interval effects were jointly estimated as random factors, and an animal’s genomic EBV was obtained by summing the estimated haplotype effects across all intervals. The genomic EBV achieved ~80% accuracy, cut bull‑proving costs by 92%, doubled genetic gain, and indicates genome‑wide selection could become a popular livestock improvement tool.

Abstract

Summary Animals can be genotyped for thousands of single nucleotide polymorphisms (SNPs) at one time, where the SNPs are located at roughly 1‐cM intervals throughout the genome. For each contiguous pair of SNPs there are four possible haplotypes that could be inherited from the sire. The effects of each interval on a trait can be estimated for all intervals simultaneously in a model where interval effects are random factors. Given the estimated effects of each haplotype for every interval in the genome, and given an animal's genotype, a ‘genomic’ estimated breeding value is obtained by summing the estimated effects for that genotype. The accuracy of that estimator of breeding values is around 80%. Because the genomic estimated breeding values can be calculated at birth, and because it has a high accuracy, a strategy that utilizes these advantages was compared with a traditional progeny testing strategy under a typical Canadian‐like dairy cattle situation. Costs of proving bulls were reduced by 92% and genetic change was increased by a factor of 2. Genome‐wide selection may become a popular tool for genetic improvement in livestock.