Identification of SNP markers associated with milk and fat yields in multibreed dairy cattle using two genetic group structures

The objective of this research was to determine the correspondence between significant SNP for first-lactation 305-d milk and 305-d fat yields and associated genes from mixed models accounting for population structure using all additive relationships among animals and genetic groups constructed with either SNP genotypic information or with expected breed composition in the Thai multibreed dairy cattle population. The dataset contained 2410 MY and 912 FY from 2410 first-lactation cows with complete pedigree information genotyped with GeneSeek Genomic Profiler 9K. SNP genotypes located in autosomes and the X chromosome, with call rates larger than 90%, minor allele frequencies (MAF) larger than 0.01, and P-values for Hardy-Weinberg Equilibrium tests larger than 0.00001 were used in the research. Significant SNP for MY and FY were identified using two mixed models that differed only in their definition of genetic groups. Model 1 (M1) defined genetic groups in terms of breed composition and model 2 (M2) in terms of SNP genotypic information. Fixed effects in M1 and M2 were contemporary group (herd-year-season), genetic group, heterosis, and calving age. Random effects were animal additive genetic and residual. Significant SNP markers were used to identify genes using R package Map2NCBI. Molecular function and biological processes of genes identified by significant SNP markers located inside or within 2500 bp of these genes were obtained via program PANTHER. Both models yielded identically high correlations between number of significant SNP and number of genes per chromosome for MY (r = 0.97) and FY (r = 0.99). Over 60% of genes associated with MY and FY were involved in binding and catalytic activities. Similarly, over 50% of genes associated with MY and FY participated in cellular and metabolic processes. Larger numbers of significant SNP and genes were identified with M2 for MY and with M1 for FY. However, considering both traits, M1 identified more significant SNP and genes than M2 for MY and FY in this Thai multibreed dairy population. Genes associated with MY and FY were primarily involved in binding and catalytic activities as well as in cellular and metabolic processes. Genes identified to be important for MY and FY in the Thai multibreed population differed substantially from those identified in Bos taurus breeds in temperate environments indicating the need to continue to conduct studies with high-density genotyping chips that identify sets of genes relevant to MY and FY in populations of different breed composition under a variety of environmental conditions.