Haplotype-assisted genomic evaluations in Nordic Red Dairy Cattle

Abstract

In admixed populations originating from different base breeds, such as the Nordic Red Dairy Cattle, identity by state of haplotypes instead of single nucleotide polymorphisms (SNP) is a better surrogate for identity by descent. Therefore, haplotypes are expected to be more useful in recovering genetic relationships among animals and linkage disequilibrium between markers and quantitative trait loci (QTL). The objective of this study was to improve the prediction accuracy in genomic evaluations by the use of haplotypes of short chromosomal segments. In the first step, around 38,000 SNPs from a 50K chip were simultaneously scanned for QTL signals with BayesB. Based on these results, the SNPs with the strongest QTL signals were then pre-selected and haplotype blocks were constructed around these. In the second step, we estimated the relative variances for the pre-selected haplotypes with BayesA. In the final step, mixed model equations of the evaluation model were solved to estimate haplotype effects. Here, a pre-defined proportion of the genetic variance was assigned to a pedigree-based animal effect and the rest to haplotypes. The accuracies of several combinations for the number and the length of haplotype blocks were assessed by calculation of genome-enhanced breeding values and validation test reliabilities (R2). For three production traits (milk, protein, fat) and fertility, the highest R2 observed were 0.48, 0.41, 0.42 and 0.33, respectively. For milk and protein, we observed an improvement over G-BLUP of 3 and 1 percentage points, respectively. For fat and fertility, the highest R2 were the same as for GBLUP. Further analysis using only single SNPs instead of haplotype blocks yielded similar results. This may indicate a need to choose an alternative approach to pre-select haplotype blocks.