A post-GWAS confirming theSCDgene associated with milk medium- and long-chain unsaturated fatty acids in Chinese Holstein population

Abstract

The stearoyl-CoA desaturase (delta-9-desaturase) gene encodes a key enzyme in the cellular biosynthesis of monounsaturated fatty acids. In our initial genome-wide association study (GWAS) of Chinese Holstein cows, 19 SNPs fell in a 1.8-Mb region (20.3-22.1 Mb) on chromosome 26 underlying the SCD gene and were highly significantly associated with C14:1 or C14 index. The aims of this study were to verify whether the SCD gene has significant genetic effects on milk fatty acid composition in dairy cattle. By resequencing the entire coding region of the bovine SCD gene, a total of six variations were identified, including three coding variations (g.10153G>A, g.10213T>C and g.10329C>T) and three intronic variations (g.6926A>G, g.8646G>A and g.16158G>C). The SNP in exon 3, g.10329C>T, was predicted to result in an amino acid replacement from alanine (GCG) to valine (GTG) in the SCD protein. An association study for 16 milk fatty acids using 346 Chinese Holstein cows with accurate phenotypes and genotypes was performed using the mixed animal model with the proc mixed procedure in sas 9.2. All six detected SNPs were revealed to be associated with six medium- and long-chain unsaturated fatty acids (P = 0.0457 to P < 0.0001), specifically for C14:1 and C14 index (P = 0.0005 to P < 0.0001). Subsequently, strong linkage disequilibrium (D' = 0.88-1.00) was observed among all six SNPs in SCD and the five SNPs (rs41623887, rs109923480, rs42090224, rs42092174 and rs42091426) within the 1.8-Mb region identified in our previous GWAS, indicating that the significant association of the SCD gene with milk fatty acid content traits reduced the observed significant 1.8-Mb chromosome region in GWAS. Haplotype-based analysis revealed significant associations of the haplotypes encompassing the six SCD SNPs and one SNP (rs109923480) in a GWAS with C14:1, C14 index, C16:1 and C16 index (P = 0.0011 to P < 0.0001). In summary, our findings provide replicate evidence for our previous GWAS and demonstrate that variants in the SCD gene are significantly associated with milk fatty acid composition in dairy cattle, which provides clear evidence for an increased understanding of milk fatty acid synthesis and enhances opportunities to improve milk-fat composition in dairy cattle.

Identification of genetic associations of ECHS1 gene with milk fatty acid traits in dairy cattle

“…), six in SCD1 (Li et al . ) and 11 in ECHS1 identified in this study. Previously, the LD between the SNP‐chip variants (Li et al .…”

“…The Chinese Holstein cows used in this study were completely different from those used in the study by Li et al . (, ), but also the SNPs identified by Li et al . (, ) were not genotyped in this study.…”

“…(, ), but also the SNPs identified by Li et al . (, ) were not genotyped in this study. Thus, we calculated the LD among the 13 SNPs in ECHS1 and 24 SNPs in SCD1 using 1577 Holsteins with worldwide correlation from the database of the 1000 Bull Genomes Project (Daetwyler et al .…”

“…) and the identified SNPs of the SCD1 gene (Li et al . ) was estimated using the common 346 Chinese Holstein cows in these two investigations (Li et al . , ).…”

“…) was estimated using the common 346 Chinese Holstein cows in these two investigations (Li et al . , ). The Chinese Holstein cows used in this study were completely different from those used in the study by Li et al .…”