Zhou Meng, Ling Chenjin, Xiao Hui, Zhang Zhiyan
National Key Laboratory for Swine Genetic Improvement and Germplasm Innovation Technology, Jiangxi Agricultural University, Nanchang 330045, China.
Animals (Basel). 2025 Apr 24;15(9):1209. doi: 10.3390/ani15091209.
Understanding the genetic regulation of gene expression and splicing in muscle tissues is critical for elucidating the molecular mechanisms of meat quality traits. In this study, we integrated large-scale whole-genome sequencing and strand-specific RNA-seq data from 582 F2 hybrid pigs (White Duroc × Erhualian) to characterize the expression and splicing quantitative trait loci (eQTLs/sQTL) in muscle. We identified 11,058 cis-eQTL-associated genes (eGenes) and 5139 cis-sQTL-associated genes (sGenes), of which 29% of eGenes and 80% of sGenes were previously unreported in the PigGTEx database. Functional analyses revealed distinct genomic features: eQTLs were enriched near transcription start sites (TSSs) and associated with active TSS-proximal transcribed regions and enhancers, whereas sQTLs clustered at splice junctions, underscoring their distinct roles in gene expression and splicing regulation. Colocalization analysis of e/sQTLs with GWAS signals prioritized as a key candidate gene (PPH4 > 0.9) for glycogen metabolism. Notably, we confirmed that an sQTL-driven alternative splicing event in exon 10 of was significantly correlated with phenotypic variation ( = -0.39, = 9.5 × 10). Collectively, this study provides novel insights into the genetic regulation of gene expression and alternative splicing in porcine muscle tissue, advancing our understanding of the molecular mechanisms underlying economically important meat quality traits.
了解肌肉组织中基因表达和剪接的遗传调控对于阐明肉质性状的分子机制至关重要。在本研究中，我们整合了来自582头F2杂交猪（大白杜洛克×二花脸）的大规模全基因组测序和链特异性RNA-seq数据，以表征肌肉中的表达和剪接定量性状位点（eQTLs/sQTL）。我们鉴定出11,058个顺式eQTL相关基因（eGenes）和5,139个顺式sQTL相关基因（sGenes），其中29%的eGenes和80%的sGenes在PigGTEx数据库中此前未被报道。功能分析揭示了不同的基因组特征：eQTLs在转录起始位点（TSSs）附近富集，并与活跃的TSS近端转录区域和增强子相关，而sQTLs聚集在剪接连接处，突出了它们在基因表达和剪接调控中的不同作用。e/sQTLs与GWAS信号的共定位分析将 优先作为糖原代谢的关键候选基因（PPH4>0.9）。值得注意的是，我们证实 外显子10中一个由sQTL驱动的可变剪接事件与表型变异显著相关（ = -0.39， = 9.5×10）。总体而言，本研究为猪肌肉组织中基因表达和可变剪接的遗传调控提供了新的见解，推进了我们对经济上重要的肉质性状潜在分子机制的理解。
