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利用140万个单核苷酸多态性(SNP)芯片进行全基因组关联研究揭示中国二花脸猪骨骼肌糖酵解潜力的遗传结构

Genetic architecture for skeletal muscle glycolytic potential in Chinese Erhualian pigs revealed by a genome-wide association study using 1.4M SNP array.

作者信息

Xie Xinke, Huang Cong, Huang Yizhong, Zou Xiaoxiao, Zhou Runxin, Ai Huashui, Huang Lusheng, Ma Junwu

机构信息

National Key Laboratory for Swine Genetic Improvement and Production Technology, Ministry of Science and Technology of China, Jiangxi Agricultural University, Nanchang, China.

出版信息

Front Genet. 2023 Mar 17;14:1141411. doi: 10.3389/fgene.2023.1141411. eCollection 2023.

Abstract

Muscle glycolytic potential (GP) is a key factor affecting multiple meat quality traits. It is calculated based on the contents of residual glycogen and glucose (RG), glucose-6-phosphate (G6P), and lactate (LAT) contents in muscle. However, the genetic mechanism of glycolytic metabolism in skeletal muscle of pigs remains poorly understood. With a history of more than 400 years and some unique characteristics, the Erhualian pig is called the "giant panda" (very precious) in the world's pig species by Chinese animal husbandry. Here, we performed a genome-wide association study (GWAS) using 1.4M single nucleotide polymorphisms (SNPs) chips for longissimus RG, G6P, LAT, and GP levels in 301 purebred Erhualian pigs. We found that the average GP value of Erhualian was unusually low (68.09 μmol/g), but the variation was large (10.4-112.7 μmol/g). The SNP-based heritability estimates for the four traits ranged from 0.16-0.32. In total, our GWAS revealed 31 quantitative trait loci (QTLs), including eight for RG, nine for G6P, nine for LAT, five for GP. Of these loci, eight were genome-wide significant ( < 3.8 × 10), and six loci were common to two or three traits. Multiple promising candidate genes such as , , , , and were identified. The genotype combinations of the five GP-associated SNPs also showed significant effect on other meat quality traits. These results not only provide insights into the genetic architecture of GP related traits in Erhualian, but also are useful for pig breeding programs involving this breed.

摘要

肌肉糖酵解潜力(GP)是影响多种肉质性状的关键因素。它是根据肌肉中残余糖原和葡萄糖(RG)、葡萄糖-6-磷酸(G6P)以及乳酸(LAT)的含量来计算的。然而,猪骨骼肌糖酵解代谢的遗传机制仍知之甚少。二花脸猪有着400多年的历史且具有一些独特特征,被中国畜牧业称为世界猪种中的“大熊猫”(非常珍贵)。在此,我们利用140万个单核苷酸多态性(SNP)芯片,对301头纯种二花脸猪的背最长肌RG、G6P、LAT和GP水平进行了全基因组关联研究(GWAS)。我们发现二花脸猪的平均GP值异常低(68.09μmol/g),但变异范围很大(10.4 - 112.7μmol/g)。这四个性状基于SNP的遗传力估计值在0.16 - 0.32之间。总体而言,我们的GWAS揭示了31个数量性状位点(QTL),包括8个与RG相关的、9个与G6P相关的、9个与LAT相关的、5个与GP相关的。在这些位点中,8个在全基因组水平上具有显著性(<3.8×10),6个位点在两个或三个性状中是共有的。鉴定出了多个有前景的候选基因,如 、 、 、 、 和 。五个与GP相关的SNP的基因型组合对其他肉质性状也显示出显著影响。这些结果不仅为二花脸猪中与GP相关性状的遗传结构提供了见解,也对涉及该品种猪的育种计划具有参考价值。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/37ad/10064215/1cb1b7c249ee/fgene-14-1141411-g001.jpg

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