Improvement of genomic prediction by integrating additional single nucleotide polymorphisms selected from imputed whole genome sequencing data

The availability of whole genome sequencing (WGS) data enables the discovery of causative single nucleotide polymorphisms (SNPs) or SNPs in high linkage disequilibrium with causative SNPs. This study investigated effects of integrating SNPs selected from imputed WGS data into the data of 54K chip on genomic prediction in Danish Jersey. The WGS SNPs, mainly including peaks of quantitative trait loci, structure variants, regulatory regions of genes, and SNPs within genes with strong effects predicted with variant effect predictor, were selected in previous analyses for dairy breeds in Denmark–Finland–Sweden (DFS) and France (FRA). Animals genotyped with 54K chip, standard LD chip, and customized LD chip which covered selected WGS SNPs and SNPs in the standard LD chip, were imputed to 54K together with DFS and FRA SNPs. Genomic best linear unbiased prediction (GBLUP) and Bayesian four-distribution mixture models considering 54K and selected WGS SNPs as one (a one-component model) or two separate genetic components (a two-component model) were used to predict breeding values. For milk production traits and mastitis, both DFS (0.025) and FRA (0.029) sets of additional WGS SNPs improved reliabilities, and inclusions of all selected WGS SNPs generally achieved highest improvements of reliabilities (0.034). A Bayesian four-distribution model yielded higher reliabilities than a GBLUP model for milk and protein, but extra gains in reliabilities from using selected WGS SNPs were smaller for a Bayesian four-distribution model than a GBLUP model. Generally, no significant difference was observed between one-component and two-component models, except for using GBLUP models for milk.