Genomic-polygenic and polygenic predictions for milk yield, fat yield, and age at first calving in Thai multibreed dairy population using genic and functional sets of genotypes

Abstract The objectives of this research were to estimate genomic-polygenic and polygenic variance components and parameters, and to compare prediction accuracies and rankings of animals for 305-d milk yield (MY), 305-d fat yield (FY), and age at first calving (AFC) using three genomic-polygenic models and a polygenic model (PM). Data came from 8361 first-lactation cows from the Thai multibreed dairy population. The genomic-polygenic models utilized the complete set of SNP from GeneSeek GGP80k (ssGBLUP), a genic set composed of SNP associated with MY, FY, and AFC located inside or within 2500 bp of genes in the NCBI database (ssGBLUPS1), and a functional set was a subset of the genic set that included only those SNP that were present in enriched pathways involving these traits (ssGBLUPS2). The 3-trait ssGBLUP, ssGBLUPS1, ssGBLUPS2, and PM included contemporary group (herd-year-season) and heterosis as fixed effects, and animal additive genetic and residual as random effects. REML genomic-polygenic and polygenic variance components and parameters were estimated with program AIREMLF90. MY and FY ssGBLUP heritabilities were higher than PM (0.25 vs. 0.15 for MY, 0.18 vs. 0.14 for FY), but lower than PM for AFC (0.16 vs. 0.19). Genetic correlations were positive between MY and FY (0.65 for ssGBLUP; 0.72 for PM), and negative between MY and AFC (−0.11 for ssGBLUP; −0.08 for PM) and between FY and AFC (−0.17 for ssGBLUP; −0.22 for PM). Accuracies of the EBV for MY, FY, and AFC from ssGBLUP and ssGBLUPS1 were similar and higher than those from ssGBLUPS2 and PM. ssGBLUP and ssGBLUPS1 EBV yielded the highest rank correlations of all pairs of models among sires, cows, and all animals for all traits. The similarity between EBV accuracies and rank correlations from ssGBLUP and ssGBLUPS1 indicated that the set of SNP markers in the genic set could be a feasible alternative to the complete SNP set from GeneSeek GGP80k for genomic-polygenic evaluation and selection of animals in the Thai multibreed dairy population. However, an annual reassessment of the set of SNP markers included in the genic set would be advisable as additional phenotypic, pedigree, and genotypic information becomes available in future years.