Identification of the putative regulatory regions and candidate genes associated with backfat thickness and intramuscular fat content traits in Xiang pigs.

Backfat thickness (BFT) and intramuscular fat (IMF) content reflect fat deposition and meat quality in pigs. Numerous genetic variations contribute to differences in BFT and IMF for different pig breeds. However, limited information is available on the genetic variants associated with IMF deposition in Xiang pigs. To identify the putative regulatory regions and candidate genes associated with BFT and IMF traits in Xiang pigs, we integrated the whole genomic DNA genotyping and RNA-sequencing data in Longissimus thoracis muscle from F2 individuals of Large White × Xiang pig cross and performed the expression quantitative trait loci (eQTL) analyses. We identified a total of 64,419 significant cis-variant-eGene, including 33,288 eSNPs, 7,910 eInDels, and 5,940 eSVs. Among them, 1,156 cis-eQTL loci overlapped with QTL for IMF and BFT, affecting the expressions of 541 genes, including 54 transcription factors. Enrichment analysis revealed that key candidate genes were significantly associated with lipid metabolism pathways, such as mTOR and PPAR signaling. Overlap analysis demonstrated that several eQTLs exhibited dual regulatory effects on gene expression. Notable eQTL hotspots included eSNP 12:52760182_T, eInDel 2:6807484-6,807,485, and three eSV sites, with the P2RY6 gene significantly associated with multiple variants. Our results indicated that many regions across the pig genome that affected gene expression level (eQTL) and overlapped with QTL regions associated with the fat store and lipid metabolism for IMF and BFT. These findings enhance our understanding of the genetic mechanisms underlying fat deposition in Xiang pigs and provide a theoretical framework for future functional studies and genomic selection.