Integrating Genome-Wide Association Study with RNA-Sequencing Reveals HDAC9 as a Candidate Gene Influencing Loin Muscle Area in Beijing Black Pigs

SIMPLE SUMMARY: In this study, the genomic variants associated with LMA in Beijing Black pigs revealed a total of 329 differentially expressed genes relating to LMA. Integrating a GWAS with RNA sequencing revealed HDAC9 as a crucial candidate gene for this trait. KEGG analysis using RNA-seq data indicated that the DEGs were mainly enriched in the JAK/STAT and oxytocin signaling pathways. We believe that our study makes a significant contribution to the literature because, although many candidate genes related to LMA have been reported, the molecular markers and candidate genes for LMA in Beijing Black pigs have not been identified. ABSTRACT: Loin muscle area (LMA) is an important meat production trait and plays a key role in determining carcass leanness. Genome-wide association study (GWAS) and RNA sequencing (RNA-seq) analysis were used to identify candidate LMA genes in Beijing Black pigs, a popular breed among consumers in northern China. Ten single nucleotide polymorphisms (SNPs) in sus scrofa chromosome (SSC) 9 were significantly associated with LMA. These SNPs were mapped to a 2.90 Mb (84.94–87.84 Mb) region. A total of 11 annotated genes were mapped on this region, namely MEOX2, CRPPA, SOSTDC1, LRRC72, ANKMY2, BZW2, TSPAN13, AGR2, AHR, SNX13, and HDAC9. In addition, RNA-seq analysis was performed between the high- and low-LMA groups, and 329 differentially expressed genes (DEGs) were identified. Further, Kyoto Encyclopedia of Genes and Genomes analysis based on DEGs revealed that the JAK/STAT signaling pathway and oxytocin signaling pathway may be responsible for LMA. Both GWAS and RNA-seq analysis identified the HDAC9 gene, indicating that it may be an important candidate gene affecting LMA in Beijing Black pigs. The findings provide valuable molecular insights into the mechanisms that influence LMA content in pigs, which can be utilized in targeted approaches to enhance meat quality and commercial profitability.