Integration of multiomics data identifies candidate genes influencing pH levels in Beijing Black pigs

Abstract

pH value is a crucial index used to evaluate pork quality due to its direct impact on specific meat characteristics. This study investigated the genetic mechanisms influencing pH values through measurements taken from the longissimus dorsi muscle of Beijing Black pigs at 2 h (pH_2h) and 24 h (pH_24h) postmortem. A total of 614 Beijing Black pigs were subsequently genotyped using the Illumina Porcine 50K SNP Chip. Heritability estimates for pH_2h and pH_24h were found to be 0.19 and 0.25, respectively, with a genetic correlation of 0.53. Furthermore, we conducted both a genome-wide association study (GWAS) and an RNA sequencing (RNA-seq) analysis, the latter of which identified differentially expressed genes (DEGs) between high and low pH groups. We identified 31, 6, and 32 single-nucleotide polymorphisms in the pH_2h, pH_24h, and pH_2–24h traits, respectively. The GWAS results revealed the presence of the SYT5 gene in both the pH_2h and pH_2–24h traits, while the SNX13 gene was simultaneously identified in the pH_24h and pH_2–24h traits. The RNA-seq results also found SYT5 to be highly expressed, while SNX13 did not exhibit differential expression. Moreover, Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses based on the DEGs revealed potential links between pH levels and the glycogen metabolic process as well as associations with the regulation of cell proliferation and calcium ion transmembrane transport. Ultimately, SYT5 and SNX13 emerged as key candidate genes affecting pH values at 2 and 24 h, respectively. These findings contribute to a better understanding of the genetic mechanisms affecting pork quality and safety and offer insights for enhancing meat quality through genetic improvement.