Reliabilities of Genomic Prediction for Young Stock Survival Traits Using 54K SNP Chip Augmented With Additional Single-Nucleotide Polymorphisms Selected From Imputed Whole-Genome Sequencing Data.

Goutam Sahana,Mogens Sandø Lund,Guosheng Su,Grum Gebreyesus

doi:10.3389/fgene.2021.667300

Abstract

This study investigated effects of integrating single-nucleotide polymorphisms (SNPs) selected based on previous genome-wide association studies (GWASs), from imputed whole-genome sequencing (WGS) data, in the conventional 54K chip on genomic prediction reliability of young stock survival (YSS) traits in dairy cattle. The WGS SNPs included two groups of SNP sets that were selected based on GWAS in the Danish Holstein for YSS index (YSS_SNPs, n = 98) and SNPs chosen as peaks of quantitative trait loci for the traits of Nordic total merit index in Denmark–Finland–Sweden dairy cattle populations (DFS_SNPs, n = 1,541). Additionally, the study also investigated the possibility of improving genomic prediction reliability for survival traits by modeling the SNPs within recessive lethal haplotypes (LET_SNP, n = 130) detected from the 54K chip in the Nordic Holstein. De-regressed proofs (DRPs) were obtained from 6,558 Danish Holstein bulls genotyped with either 54K chip or customized LD chip that includes SNPs in the standard LD chip and some of the selected WGS SNPs. The chip data were subsequently imputed to 54K SNP together with the selected WGS SNPs. Genomic best linear unbiased prediction (GBLUP) models were implemented to predict breeding values through either pooling the 54K and selected WGS SNPs together as one genetic component (a one-component model) or considering 54K SNPs and selected WGS SNPs as two separate genetic components (a two-component model). Across all the traits, inclusion of each of the selected WGS SNP sets led to negligible improvements in prediction accuracies (0.17 percentage points on average) compared to prediction using only 54K. Similarly, marginal improvement in prediction reliability was obtained when all the selected WGS SNPs were included (0.22 percentage points). No further improvement in prediction reliability was observed when considering random regression on genotype code of recessive lethal alleles in the model including both groups of the WGS SNPs. Additionally, there was no difference in prediction reliability from integrating the selected WGS SNP sets through the two-component model compared to the one-component GBLUP.

Highlights

Young stock mortality represents a major economic loss for dairy farmers due, for instance, to fewer heifers available for replacement in the production system, fewer male calves for slaughter, higher veterinarian cost, and cost related to disposal of dead calf
Proportion of the Genetic Variance Explained by the Different Single-Nucleotide Polymorphism Sets
An average gain in reliability of 16 percentage points was obtained using relationships derived from the 54K single-nucleotide polymorphisms (SNPs) compared to using relationships derived from pedigree

Summary

Introduction

Young stock mortality represents a major economic loss for dairy farmers due, for instance, to fewer heifers available for replacement in the production system, fewer male calves for slaughter, higher veterinarian cost, and cost related to disposal of dead calf. In the Nordic countries, annual total loss due to dairy calf mortality (including stillbirth) is estimated to be approximately €70 million (Østerårs et al, 2007). Part of the variation in young stock mortality is genetic with reported heritability estimates ranging from 0.00 to 0.08 (e.g., Hansen et al, 2003; Fuerst-Waltl and Sørensen, 2010; Henderson et al, 2011). In the Nordic countries, young stock survival (YSS) in calves is included in the Nordic total merit (NTM) index (NAV).. There are possibilities to improve the reliability of genomic prediction models by incorporating causative variants (if known) or markers highly correlated with them (de Los Campos et al, 2013)

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