背景:氨基酸是蛋白质的基本成分,是评估肉质的重要指标。随着基因组学的快速发展,影响畜禽氨基酸含量的候选区域和基因已经逐渐被揭示。因此,全基因组关联研究(GWAS)可用于筛选与鸭肉中氨基酸含量相关的候选基因座。
结果:在当前的研究中,在358只鸭胸肌中检测到16种氨基酸的含量。Glu占总氨基酸含量的比例相对较高,比例为0.14。然而,Met含量的比例相对较低,在0.03。通过比较分析,男性和女性在3种氨基酸上存在显著差异,包括Ser,Met,还有Phe.此外,通过GWAS分析,12个SNP与Pro含量显著相关,这些SNP由7个蛋白质编码基因注释;8个显著的SNP与Tyr含量相关,这些SNP由6个蛋白质编码基因注释。同时,对具有显著信号的这些区域进行连锁不平衡(LD)分析。结果表明,3号染色体55-56Mbp区域的三个SNP与影响Pro含量(r2>0.6)的前导SNP(chr3:55526954)高度相关。同样,LD分析表明,在13号染色体的21.2-21.6Mbp区域中存在三个SNP,与前导SNP(chr13:21421661)高度相关(r2>0.6)。此外,通过对所有候选基因的功能富集分析。GO富集分析结果表明,几个显著的GO项目与氨基酸转运功能有关,包括氨基酸跨膜转运和谷氨酰胺转运。结果进一步表明这些候选基因与氨基酸转运密切相关。其中,关键候选基因包括SLC38A1。对于KEGG富集分析,CACNA2D3和CACNA1D基因被显著的途径所覆盖。
结论:在这项研究中,GWAS分析发现总共28个影响氨基酸含量的显著SNP。通过基因注释,共筛选了20个候选基因.此外,通过LD分析和富集分析,我们认为SERAC1、CACNA2D3和SLC38A1基因是影响鸭胸肌氨基酸含量的重要候选基因。
BACKGROUND: Amino acids are the basic components of protein and an important index to evaluate meat quality. With the rapid development of genomics, candidate regions and genes affecting amino acid content in livestock and poultry have been gradually revealed. Hence, genome-wide association study (GWAS) can be used to screen candidate loci associated with amino acid content in duck meat.
RESULTS: In the current study, the content of 16 amino acids was detected in 358 duck breast muscles. The proportion of Glu to the total amino acid content was relatively high, and the proportion was 0.14. However, the proportion of Met content was relatively low, at just 0.03. By comparative analysis, significant differences were found between males and females in 3 amino acids, including Ser, Met, and Phe. In addition, 12 SNPs were significantly correlated with Pro content by GWAS analysis, and these SNPs were annotated by 7 protein-coding genes; 8 significant SNPs were associated with Tyr content, and these SNPs were annotated by 6 protein-coding genes. At the same time, linkage disequilibrium (LD) analysis was performed on these regions with significant signals. The results showed that three SNPs in the 55-56 Mbp region of chromosome 3 were highly correlated with the leader SNP (chr3:55526954) that affected Pro content (r2 > 0.6). Similarly, LD analysis showed that there were three SNPs in the 21.2-21.6 Mbp region of chromosome 13, which were highly correlated with leader SNP (chr13:21421661) (r2 > 0.6). Moreover, Through functional enrichment analysis of all candidate genes. The results of GO enrichment analysis showed that several significant GO items were associated with amino acid transport function, including amino acid transmembrane transport and glutamine transport. The results further indicate that these candidate genes are closely associated with amino acid transport. Among them, key candidate genes include SLC38A1. For KEGG enrichment analysis, CACNA2D3 and CACNA1D genes were covered by significant pathways.
CONCLUSIONS: In this study, GWAS analysis found a total of 28 significant SNPs affecting amino acid content. Through gene annotation, a total of 20 candidate genes were screened. In addition, Through LD analysis and enrichment analysis, we considered that SERAC1, CACNA2D3 and SLC38A1 genes are important candidate genes affecting amino acid content in duck breast muscle.