A post-GWAS confirming the genetic effects and functional polymorphisms of AGPAT3 gene on milk fatty acids in dairy cattle

Abstract Background People are paying more attention to the healthy and balanced diet with improvement of their living standards. Milk fatty acids (FAs) have been reported that they were related some atherosclerosis coronary heart diseases in human. In our previous genome-wide association study (GWAS) on milk FAs dairy cattle, 83 significant single nucleotide polymorphisms (SNPs) detected. Among them, two SNPs, ARS-BFGL-NGS-109493 BTA-56389-no-rs associated C18index ( P = 0.0459), located upstream 1-acylglycerol-3-phosphate O-acyltransferase 3 AGPAT3 ) gene. is involved glycerol-lipid, glycerol-phospholipid metabolism phospholipase D signaling pathways. Hence, it was inferred as a candidate gene for FAs. The aim this further confirm genetic effects FA traits cattle. Results Through re-sequencing complete coding region, 3000 bp 5′ 3′ regulatory regions gene, total 17 SNPs identified, including four one untranslated region (UTR), three introns, UTR, eight region. By linkage disequilibrium (LD) analysis Haploview4.1 software, haplotype blocks observed formed by 12 identified respectively. Using SAS9.2, we performed locus-based haplotype-based 24 1065 Chinese Holstein cows, discovered all significantly C6:0, C8:0 C10:0 < 0.0001–0.0384). Further, Genomatix, predicted (g.146702957G > A, g.146704373A G, g.146704618A G g.146704699G A) changed transcription factor binding sites (TFBSs) factors SMARCA3, REX1, VMYB, BRACH, NKX26, ZBED4, SP1, USF1, ARNT FOXA1. Out validated impact transcriptional activity performing luciferase assay alleles A both increased activities promoter compared 0.0004). Conclusions conclusion, findings first demonstrated associations potential causal mutations