Identification of Genetic Effects of and Genes with Milk Production Traits of Holstein Cattle in China.

With the development of high-throughput sequencing, RNA sequencing has been widely used in the identification of candidate genes for complex traits in livestock, and the functional genes and mutations with large genetic effects on milk production traits can provide molecular information for marker-assisted selection to increase the selection accuracy and accelerate genetic gain in dairy cattle. Our previous study on the liver transcriptome of Holstein cows found that acyl-CoA dehydrogenase () and interferon regulatory factor 6 () are differentially expressed between dry and peak lactation periods, as well as that they are involved in lipid metabolism and the proliferation and differentiation of mammary epithelial cells. Thus, the two genes were considered candidates for milk traits. Hence, this study further collected 1186 Holstein cows from 110 sire families to investigate their genetic associations with milk yield and composition traits. By resequencing the entire exons and 2000 bp of the 5' and 3' flanking regions of the two genes, we identified eight SNPs in and eight SNPs in . Subsequent single-locus association analyses showed that the eight SNPs in were all significantly associated with milk fat yield, fat percentage, and protein yield ( values ≤ 0.0001-0.0414), and the eight SNPs in were associated with milk, fat, and protein yields in the first or second lactation ( values ≤ 0.0001-0.0467). Using Haploview 4.2, one haplotype block with eight of the SNPs in (D' = 0.99-1.00) and two haplotype blocks in with three of the SNPs in each were observed (D' = 0.98-1.00). Similarly, the haplotype combinations of were significantly associated with milk yield, fat percentage, fat yield, and protein yield in the two lactations ( values ≤ 0.0001-0.0125), and those of were associated with five milk traits ( values ≤ 0.0001-0.0263). Furthermore, with the JASPAR software, it was predicted that the SNPs 19:g.26933503T>C in and 16:g.73501985G>A in changed the transcription factor binding sites of ZEB1, PLAGL2, and RHOXF1, implying their impacts on the expressions of the corresponding genes. Our findings demonstrated that the and genes have significant genetic effects on milk yield and composition traits, and the valuable SNPs might be used as genetic markers for genomic selection programs in dairy cattle.