Mining 2 key candidate genes for pork tenderness in large White pigs based on GWAS, colocalization analysis, SMR and TWAS

Pork tenderness is a critical determinant of meat quality and is primarily assessed by shear force measurement. In this study, the shear force of the longissimus dorsi muscle was measured in 413 Large White pigs. A genome-wide association study (GWAS) based on imputed data identified multiple loci significantly associated with shear force on chromosomes 5, 8, 13, and 14. Comparison with the PigQTLdb indicated that these four QTLs have not been previously reported. By integrating GWAS results with transcriptomic data from the pigGTEx database, analyses including colocalization, TWAS, and SMR were performed, leading to the identification of two candidate genes, GRM2 and NISCH. PheWAS results showed that NISCH was significantly correlated with palmitoleic acid content, consistent with the positive correlation between palmitoleic acid and shear force in this population. GRM2 was significantly associated with backfat thickness. These results suggest a potential genetic association between fatty acid metabolism and pork tenderness.