整合基因组学和转录组学揭示了影响华西牛腰肌面积的候选基因。

Integrating genomics and transcriptomics reveals candidate genes affecting loin muscle area in Huaxi cattle.

作者信息

Xue Qingqing, Du Lili, Deng Tianyu, Liang Mang, Li Keanning, Qian Li, Qiu Shiyuan, Chen Yan, Gao Xue, Xu Lingyang, Wang Zezhao, Zheng Caihong, Zhang Lupei, Li Junya, Gao Huijiang

机构信息

Department of College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, China.

Department of Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China.

出版信息

PLoS One. 2025 May 9;20(5):e0322026. doi: 10.1371/journal.pone.0322026. eCollection 2025.

DOI:10.1371/journal.pone.0322026

PMID:40344088

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC12064012/

Abstract

Loin muscle area (LMA) is an indicator of carcass composition and is related to weight gain, animal musculature and meat quality traits. Therefore, integrating multi-omics data to reveal candidate genes affecting LMA has attracted extensive attention. We used the combined analysis method of GWAS and RNA-seq to find the candidate genes that affect the size of LMA. The association of 770K SNPs with the LMA captured four significant SNPs within or near three genes. Additionally, seven overlapping genes regarding LMA were determined via the analysis of differentially expressed genes (DEGs) and weighted gene co-expression network analysis (WGCNA). There is an overlapping gene (CD93) between the results of GWAS and DEGs. Through functional enrichment analysis of the above genes, candidate genes were identified as THBD, CD93, RIMS2, PLP1, SNCA, and NDUFS8, and it was found that they mainly affected the size of LMA by affecting muscle fiber diameter, muscle cell development, differentiation, and function. The findings provide valuable molecular insights into the mechanisms that influence LMA content in beef cattle.

摘要

腰部肌肉面积（LMA）是胴体组成的一个指标，与体重增加、动物肌肉组织和肉质性状相关。因此，整合多组学数据以揭示影响LMA的候选基因已引起广泛关注。我们使用全基因组关联研究（GWAS）和RNA测序（RNA-seq）的联合分析方法来寻找影响LMA大小的候选基因。77万个单核苷酸多态性（SNP）与LMA的关联在三个基因内部或附近捕获到四个显著的SNP。此外，通过对差异表达基因（DEG）和加权基因共表达网络分析（WGCNA）确定了七个与LMA相关的重叠基因。GWAS和DEG的结果之间存在一个重叠基因（CD93）。通过对上述基因的功能富集分析，确定候选基因为血栓调节蛋白（THBD）、CD93、RIMS2、髓鞘蛋白脂蛋白1（PLP1）、突触核蛋白α（SNCA）和NADH泛醌氧化还原酶核心亚基8（NDUFS8），并且发现它们主要通过影响肌纤维直径、肌肉细胞发育、分化和功能来影响LMA的大小。这些发现为影响肉牛LMA含量的机制提供了有价值的分子见解。