Genome-Wide Association Analysis of Muscle pH in Texel Sheep × Altay Sheep F2 Resource Population

Yilong Zhao; Sangang He; Jinfeng Huang; Mingjun Liu

doi:10.3390/ani13132162

Genome-Wide Association Analysis of Muscle pH in Texel Sheep × Altay Sheep F₂ Resource Population

Animals (Basel). 2023 Jun 30;13(13):2162. doi: 10.3390/ani13132162.

Authors

Yilong Zhao^{1

2}, Sangang He³, Jinfeng Huang⁴, Mingjun Liu³

Affiliations

¹ College of Animal Science and Technology, Shihezi University, Shihezi 832000, China.
² College of Animal Science and Technology, Xinjiang Agricultural Vocational and Technical College, Changji 831100, China.
³ Biotechnology Institute, Xinjiang Academy of Animal Science, Urumqi 830013, China.
⁴ Changji Huamu Animal Clinic, Changji 831100, China.

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 F₂ 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.

Keywords: 600 K BeadChip; GWAS; SNP; pH; sheep; whole genome resequencing.

Grants and funding

This research was funded by the Xinjiang Uygur Autonomous Region Innovation Environment (talent, base) Construction Project in 2021—Natural Science Foundation project (2021D01A112) for supporting this study.