Managing genetic groups in single-step genomic evaluations applied on female fertility traits in Nordic Red Dairy cattle

Abstract

Joint Nordic (Denmark, Finland, Sweden) genetic evaluations of female fertility traits are currently based on a multi-trait multi-lactation animal model for two trait groups. This enables straightforward re-evaluation of the fertility model with genomic information by the single-step (ssGBLUP). ssGBLUP was applied for the first trait group and Nordic Red Dairy cattle data. The ssGBLUP used the same model and variance components as the routine animal model evaluation (BLUP). In addition to BLUP, four genomic evaluations were performed. The first two evaluations were ssGBLUP₀ and ssGBLUP_QP where either the pedigree relationships, or pedigree and genomic relationships, were accounted in the phantom parent group equations, respectively. Further development of the ssGBLUP_QP model was in the third model to include inbreeding coefficients into the pedigree relationship matrix also, and in the fourth model to approximate genomic relationship matrix with APY algorithm. The performance of BLUP and ssGBLUP were studied using Interbull GEBV validation test tailored to multi-trait single step evaluations. Convergence of iterative solver was slow in the BLUP evaluation and extremely slow in ssGBLUP₀ evaluation. Convergence of the ssGBLUP₀ evaluation was significantly improved by considering effect of genomic relationships in PPG equations, including inbreeding coefficients into the pedigree relationship matrix and applying APY. With these modifications, the number of iterations with ssGBLUP was comparable to animal model, although each iteration round took much longer time. Increase in validation reliability due to genomic information was moderate or high depending on the trait. Thus, the routine Nordic fertility evaluation using ssGBLUP was found feasible after the inbreeding coefficients and PPG had been correctly accounted.