Validation of single nucleotide polymorphisms associated with milk production traits in dairy cattle.

Single nucleotide polymorphism (SNP) associations with milk production traits found to be significant in different screening experiments, including SNP in genes hypothesized to be in gene pathways affecting milk production, were tested in a validation population to confirm their association. In total, 423 SNP were genotyped across 411 Holstein bulls, and their association with 6 milk production traits--Australian Selection Index (indicating the profitability of an animal's milk production), protein, fat, and milk yields, and protein and fat composition--were tested using single SNP regressions. Seventy-two SNP were significantly associated with one or more of the traits; their effects were in the same direction as in the screening experiment and therefore their association was considered validated. An over-representation of SNP (43 of the 423) on chromosome 20 was observed, including a SNP in the growth hormone receptor gene previously published as having an association with protein composition and protein and milk yields. The association with protein composition was confirmed in this experiment, but not the association with protein and milk yields. A multiple SNP regression analysis for all SNP on chromosome 20 was performed for all 6 traits, which revealed that this mutation was not significantly associated with any of the milk production traits and that at least 2 other quantitative trait loci were present on chromosome 20.