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

Abstract

Our previous genome-wide association study identified 83 genome-wide significant SNPs and 20 novel promising candidate genes for milk fatty acids in Chinese Holstein. Among them, the enoyl-CoA hydratase, short chain 1 (ECHS1) and enoyl-CoA hydratase and 3hydroxyacyl CoA dehydrogenase (EHHADH) genes were located near two SNPs and one SNP respectively, and they play important roles in fatty acid metabolism pathways. We herein validated whether the two genes have genetic effects on milk fatty acid traits in dairy cattle. By re-sequencing the full-length coding region, partially adjacent introns and 3000 bp up/ downstream flanking sequences, we identified 12 SNPs in ECHS1: two in exons, four in the 3 0 flanking region and six in introns. The g.25858322C>T SNP results in an amino acid replacement from leucine to phenylalanine and changes the secondary structure of the ECHS1 protein, and single-locus association analysis showed that it was significantly associated with three milk fatty acids (P = 0.0002-0.0013). The remaining 11 SNPs were found to be significantly associated with at least one milk fatty acid (P = <0.0001-0.0040). Also, we found that two haplotype blocks, consisting of nine and two SNPs respectively, were significantly associated with eight milk fatty acids (P = <0.0001-0.0125). However, none of polymorphisms was observed in the EHHADH gene. In conclusion, our findings are the first to indicate that the ECHS1 gene has a significant genetic impact on long-chain unsaturated and medium-chain saturated fatty acid traits in dairy cattle, although the biological mechanism is still undetermined and requires further in-depth validation.

A Post-GWAS Confirming the Genetic Effects and Functional Polymorphisms of AGPAT3 Gene on Milk Fatty Acids in Dairy Cattle

“…In this study, a total of 1,065 Chinese Holstein cows were used as descripted in a previous research [18], which milk samples were collected in Beijing Dairy Cattle Center (www.bdcc.com.cn) to measure milk FA contents. With the gas chromatography method, a total of 16 kinds of milk FAs (C6:0, C8:0, C10:0, C11:0, C12:0, C13:0, C14:0, C14:1, C15:0, C16:0, C16:1, C17:0, C17:1, C18:0, C18:1cis-9 and C20:0) was measured [15].…”

“…With the gas chromatography method, a total of 16 kinds of milk FAs (C6:0, C8:0, C10:0, C11:0, C12:0, C13:0, C14:0, C14:1, C15:0, C16:0, C16:1, C17:0, C17:1, C18:0, C18:1cis-9 and C20:0) was measured [15]. In addition, we calculated ve index including C14index, C16index, C17index, C18index and total index as the descriptions in a previous study [18], and summarized SFA and UFA, and SFA/UFA were obtained as well.…”

“…Based on the genomic sequence of bovine AGPAT3 gene (Gene ID: 506607), 14 pairs of primers (Table S1) were designed by the Primer 3 version 4.0 (http://bioinfo.ut.ee/primer3-0.4.0/) and were synthesized in the Beijing Genomics Institute (Beijing, China) to amplify all the exons with partial adjacent intron region, and 3,000 bp of 5' and 3' regulatory regions. As previously descripted [18], two DNA pools were constructed and the polymerase chain reaction (PCR) ampli cations were performed with each DNA pool as template. To identify potential polymorphisms, the PCR ampli cation products were bi-directionally sequenced with an ABI3730XL DNA analyzer (Applied Biosystems, Foster, CA, USA).…”

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

“…In this study, a total of 1,065Chinese Holstein cows were used as descripted in a previous research [15], which milk samples werecollected in Beijing Dairy Cattle Center (www.bdcc.com.cn) to measure milk FA contents. With the gas chromatography method, a total of 16 milk FAs (C6:0, C8:0, C10:0, C11:0, C12:0, C13:0, C14:0, C14:1, C15:0, C16:0, C16:1, C17:0, C17:1, C18:0, C18:1cis-9 and C20:0) were measured as the weight proportion of total fat weight [12].…”

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

“…Based on the genomic sequence of bovine AGPAT3 gene (Gene ID: 506607), 14 pairs of primers (Table S1) were designed by the Primer 3 version 4.0 (http://bioinfo.ut.ee/primer3-0.4.0/) and were synthesized in the Beijing Genomics Institute (Beijing, China) to amplify all the exons with partial adjacent intron region, and 3,000 bp of 5' and 3' regulatory regions. As previously descripted [15], two DNA pools were constructed and the polymerase chain reaction (PCR) ampli cations were performed with each DNA pool as template. To identify potential polymorphisms, the PCR ampli cation products were bi-directionally sequenced with an ABI3730XL DNA analyzer (Applied Biosystems, Foster, CA, USA).…”