Identification of new candidate genes affecting drip loss in pigs based on genomics and transcriptomics data

Drip loss (DL) is a crucial trait for evaluating muscle quality in pigs. In this study, Chinese Suhuai pigs with DL records were genotyped using the Neogen GGP Porcine 80 K single-nucleotide polymorphism (SNP) array to identify quantitative trait locus (QTL) affecting DL and dissect candidate genes for this trait. The SNP-chip data was imputed to the level of whole-genome sequence (iWGS). Through genome-wide association studies (GWAS) based on iWGS data, significant SNPs were detected on Sus scrofa chromosomes (SSC) 4, SSC13, and SSC14 for DL, involving 37 candidate genes such as AACS, CRB4, and OXSM. Notably, 3 QTL regions (SSC4, SSC13, and SSC14) were newly identified in this study, which were SSC4: 65.2 to 66.1 Mb, SSC13:12.46 to 12.48 Mb and SSC14: 20.7 to 20.9 Mb respectively. Additionally, RNA sequencing (RNA-seq) was conducted on muscle tissues from individual pigs with extremely high and low genomic estimated breeding values of DL, identifying 21 differentially expressed genes (DEGs). Integrating these DEGs with quantitative trait transcriptome (QTT) analysis results from our Suhuai pig muscle tissue transcriptome data pinpointed 6 DEGs strongly linked to DL: GALNT15, TBC1D1, MLLT11, PPARGC1A, NREP, and CNTFR. Integration of candidate genes identified by GWAS with the results of QTT analysis revealed that the expression of GWAS-identified genes NCOA2, HPF1, and CLCN3 was significantly correlated with DL. Functional enrichment analysis, combining the 37 candidate genes identified by GWAS and the 6 DEGs co-identified by RNA-seq and QTT analyses, suggested that GALNT15, TBC1D1, PPARGC1A, AACS, CBR4, and OXSM genes may be functionally related to pork DL, thereby positioning them as important candidate genes. These genes (NCOA2, HPF1, CLCN3, PPARGC1A, TBC1D1, GALNT15, CBR4, AACS, and OXSM) were newly identified candidate genes for DL. This research provides a foundation for improving meat quality traits through marker-assisted or genomic selection in pig breeding programs.