Integrating GWAS and RNA-Seq Reveals QTLs and Candidate Genes for Fat Deposition in Large White × Tongcheng Crossbred...

Fat deposition traits are crucial economic characteristics that directly influence production efficiency in pigs. To better understand the genetic mechanisms underlying fat deposition, four traits including backfat thickness (BF), caul fat rate (CFR), leaf fat rate (LFR), and internal fat rate (IFR) were measured in 421 Large White × Tongcheng crossbred pigs. A GWAS analysis identified 666, 15, 22, and 61 SNPs significantly associated with BF, LFR, CFR, and IFR, respectively. Bayesian fine-mapping revealed a major QTL on SSC7 (29.62-30.62 Mb) that influences all four fatness traits and harbors the candidate gene HMGA1 and NUDT3. Additionally, a QTL on SSC5 (28.67-30.52 Mb) was associated with BF and contains the candidate gene TBK1, while a QTL on SSC18 (8.01-9.88 Mb) associated with CFR includes AGK and TBXAS1. Integration of transcriptome, 3D genomic, and epigenomic data identified rs703100168 on SSC7 as a candidate functional SNP to control HMGA1 expression and regulate fat deposition in pigs. These findings provide valuable candidate genes and genetic variants for improving fatness traits in pig breeding programs.