Genome-Wide Association Analysis of Muscle pH in Texel Sheep × Altay Sheep F(2) Resource Population

SIMPLE SUMMARY: pH was one of the main factors affecting meat storage/shelf life, and was also directly related to meat freshness, taste and overall quality. To extend storage/shelf life, pH-related candidate genes were mined to provide new opportunities for genetic improvement. We obtained candidate genes related to pH through a genome-wide association analysis to provide research directions for extending meat storage/shelf life. ABSTRACT: pH was one of the important meat quality traits, which was an important factor affecting the storage/shelf life and quality of meat in meat production. In order to find a way to extend the storage/shelf life, the pH values (pH(45min), pH(24h), pH(48h) and pH(72h)) of the longissimus dorsi muscles in F(2) individuals of 462 Texel sheep × Altay sheep were determined, genotyping was performed using Illumina Ovine SNP 600 K BeadChip and whole genome resequencing technology, a genome-wide association analysis (GWAS) was used to screen the candidate genes and molecular markers for pH values related to the quality traits of mutton, and the effects of population stratification were detected by Q–Q plots. The results showed that the pH population stratification analysis did not find significant systemic bias, and there was no obvious population stratification effect. The results of the association analysis showed that 28 SNPs significantly associated with pH reached the level of genomic significance. The candidate gene associated with pH(45min) was identified as the CCDC92 gene by gene annotation and a search of the literature. Candidate genes related to pH(24h) were KDM4C, TGFB2 and GOT2 genes. The candidate genes related to pH(48h) were MMP12 and MMP13 genes. The candidate genes related to pH(72h) were HILPDA and FAT1 genes. Further bioinformatics analyses showed 24 gene ontology terms and five signaling pathways that were significantly enriched (p ≤ 0.05). Many terms and pathways were related to cellular components, processes of protein modification, the activity of protein dimerization and hydrolase activity. These identified SNPs and genes could provide useful information about meat and the storage/shelf life of meat, thereby extending the storage/shelf life and quality of meat.