Faculty of Animal Science and Technology, Yunnan Agricultural University, No. 95 of Jinhei Road, Kunming, 650201, Yunnan, China.
Faculty of Animal Science, Xichang University, Xichang, 615000, Sichuan, China.
BMC Genomics. 2022 Aug 15;23(1):594. doi: 10.1186/s12864-022-08827-8.
Carcass backfat thickness (BFT), carcass lean percentage (CLP) and carcass fat percentage (CFP) are important to the commercial pig industry. Nevertheless, the genetic architecture of BFT, CLP and CFP is still elusive. Here, we performed a genome-wide association study (GWAS) based on specific-locus amplified fragment sequencing (SLAF-seq) to analyze seven fatness-related traits, including five BFTs, CLP, and CFP on 223 four-way crossbred pigs.
A total of 227, 921 highly consistent single nucleotide polymorphisms (SNPs) evenly distributed throughout the genome were used to perform GWAS. Using the mixed linear model (MLM), a total of 20 SNP loci significantly related to these traits were identified on ten Sus scrofa chromosomes (SSC), of which 10 SNPs were located in previously reported quantitative trait loci (QTL) regions. On SSC7, two SNPs (SSC7:29,503,670 and rs1112937671) for average backfat thickness (ABFT) exceeded 1% and 10% Bonferroni genome-wide significance levels, respectively. These two SNP loci were located within an intron region of the COL21A1 gene, which was a protein-coding gene that played an important role in the porcine backfat deposition by affecting extracellular matrix (ECM) remodeling. In addition, based on the other three significant SNPs on SSC7, five candidate genes, ZNF184, ZNF391, HMGA1, GRM4 and NUDT3 were proposed to influence BFT. On SSC9, two SNPs for backfat thickness at 6-7 ribs (67RBFT) and one SNP for CLP were in the same locus region (19 kb interval). These three SNPs were located in the PGM2L1 gene, which encoded a protein that played an indispensable role in glycogen metabolism, glycolysis and gluconeogenesis as a key enzyme. Finally, one significant SNP on SSC14 for CLP was located within the PLBD2 gene, which participated in the lipid catabolic process.
A total of two regions on SSC7 and SSC9 and eight potential candidate genes were found for fatness-related traits in pigs. The results of this GWAS based on SLAF-seq will greatly advance our understanding of the genetic architecture of BFT, CLP, and CFP traits. These identified SNP loci and candidate genes might serve as a biological basis for improving the important fatness-related traits of pigs.
胴体背膘厚（BFT）、胴体瘦肉率（CLP）和胴体脂肪率（CFP）对商业养猪业很重要。然而，BFT、CLP 和 CFP 的遗传结构仍然难以捉摸。在这里，我们基于特异位点扩增片段测序（SLAF-seq）进行了全基因组关联研究（GWAS），以分析 223 头四元杂交猪的 7 个与脂肪有关的性状，包括 5 个 BFT、CLP 和 CFP。
总共使用 227921 个高度一致的均匀分布在基因组中的单核苷酸多态性（SNP）进行 GWAS。使用混合线性模型（MLM），在 10 个Sus scrofa 染色体（SSC）上总共鉴定到与这些性状相关的 20 个 SNP 位点，其中 10 个 SNP 位于先前报道的数量性状位点（QTL）区域。在 SSC7 上，两个 SNP（SSC7：29503670 和 rs1112937671）的平均背膘厚（ABFT）分别超过 1%和 10%的 Bonferroni 全基因组显著水平。这两个 SNP 位点位于 COL21A1 基因的内含子区域内，该基因是一个蛋白质编码基因，通过影响细胞外基质（ECM）重塑，对猪背膘沉积起着重要作用。此外，基于 SSC7 上的另外三个显著 SNP，提出了五个候选基因 ZNF184、ZNF391、HMGA1、GRM4 和 NUDT3 来影响 BFT。在 SSC9 上，两个 SNP 位于 6-7 肋的背膘厚（67RBFT）和一个 SNP 位于 CLP 的同一基因座区域（19 kb 间隔）。这三个 SNP 位于 PGM2L1 基因内，该基因编码的蛋白质作为一种关键酶，在糖原代谢、糖酵解和糖异生中起着不可或缺的作用。最后，一个位于 SSC14 上与 CLP 相关的显著 SNP 位于 PLBD2 基因内，该基因参与脂质分解代谢过程。
总共在 SSC7 和 SSC9 上发现了两个区域和八个潜在的候选基因与猪的脂肪相关性状有关。基于 SLAF-seq 的这项 GWAS 将极大地提高我们对 BFT、CLP 和 CFP 性状遗传结构的理解。这些鉴定的 SNP 位点和候选基因可能为提高猪的重要脂肪相关性状提供生物学基础。
