Single Nucleotide Polymorphisms of ALDH18A1 and MAT2A Genes and Their Genetic Associations with Milk Production Traits of Chinese Holstein Cows

Our preliminary work had suggested two genes, aldehyde dehydrogenase 18 family member A1 (ALDH18A1) and methionine adenosyltransferase 2A (MAT2A), related to amino acid synthesis and metabolism as candidates affecting milk traits by analyzing the liver transcriptome and proteome of dairy cows at different lactation stages. In this study, the single nucleotide polymorphisms (SNPs) of ALDH18A1 and MAT2A genes were identified and their genetic effects and underlying causative mechanisms on milk production traits in dairy cattle were analyzed, with the aim of providing effective genetic information for the molecular breeding of dairy cows. By resequencing the entire coding and partial flanking regions of ALDH18A1 and MAT2A, we found eight SNPs located in ALDH18A1 and two in MAT2A. Single-SNP association analysis showed that most of the 10 SNPs of these two genes were significantly associated with the milk yield traits, 305-day milk yield, fat yield, and protein yield in the first and second lactations (corrected p ≤ 0.0488). Using Haploview 4.2, we found that the seven SNPs of ALDH18A1 formed two haplotype blocks; subsequently, the haplotype-based association analysis showed that both haplotypes were significantly associated with 305-day milk yield, fat yield, and protein yield (corrected p ≤ 0.014). Furthermore, by Jaspar and Genomatix software, we found that 26:g.17130318 C>A and 11:g.49472723G>C, respectively, in the 5′ flanking region of ALDH18A1 and MAT2A genes changed the transcription factor binding sites (TFBSs), which might regulate the expression of corresponding genes to affect the phenotypes of milk production traits. Therefore, these two SNPs were considered as potential functional mutations, but they also require further verification. In summary, ALDH18A1 and MAT2A were proved to probably have genetic effects on milk production traits, and their valuable SNPs might be used as candidate genetic markers for dairy cattle’s genomic selection (GS).