| Abstract: 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.© The Author(s) 2025. Published by Oxford University Press on behalf of the American Society of Animal Science.YuJianghuiJ0009-0008-3461-674XKey Laboratory of Pig Genetic Resources Evaluation and Utilization (Nanjing), Ministry of Agriculture and Rural Affairs, Institute of Swine Science, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China.TaoWeiWKey Laboratory of Pig Genetic Resources Evaluation and Utilization (Nanjing), Ministry of Agriculture and Rural Affairs, Institute of Swine Science, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China.AiXinjieXKey Laboratory of Pig Genetic Resources Evaluation and Utilization (Nanjing), Ministry of Agriculture and Rural Affairs, Institute of Swine Science, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China.LiuQianQKey Laboratory of Pig Genetic Resources Evaluation and Utilization (Nanjing), Ministry of Agriculture and Rural Affairs, Institute of Swine Science, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China.MaJinfengJKey Laboratory of Pig Genetic Resources Evaluation and Utilization (Nanjing), Ministry of Agriculture and Rural Affairs, Institute of Swine Science, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China.XuLimingL0009-0006-5610-9744Key Laboratory of Pig Genetic Resources Evaluation and Utilization (Nanjing), Ministry of Agriculture and Rural Affairs, Institute of Swine Science, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China.LiQiangQHuaiyin Xinhuai Pig Breeding Farm of Huaian City, Huaian, China.WangWenqiangWHuaian Academy of Nanjing Agricultural University, Huaian, China.HuangRuihuaRKey Laboratory of Pig Genetic Resources Evaluation and Utilization (Nanjing), Ministry of Agriculture and Rural Affairs, Institute of Swine Science, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China.Huaian Academy of Nanjing Agricultural University, Huaian, China.ZhaoQingboQKey Laboratory of Pig Genetic Resources Evaluation and Utilization (Nanjing), Ministry of Agriculture and Rural Affairs, Institute of Swine Science, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China.LiPinghuaP0000-0003-2148-2435Key Laboratory of Pig Genetic Resources Evaluation and Utilization (Nanjing), Ministry of Agriculture and Rural Affairs, Institute of Swine Science, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China.Huaian Academy of Nanjing Agricultural University, Huaian, China.engJournal ArticleUnited StatesJ Anim Sci80030020021-8812IMAnimalsQuantitative Trait LociSwinegeneticsphysiologyTranscriptomePolymorphism, Single NucleotideGenome-Wide Association StudyveterinaryGenomicsGene Expression ProfilingveterinaryDrip loss (DL) is an important trait of pork quality. In this study, we focused on pigs to identify quantitative trait loci (QTLs) and candidate genes that might impact DL based on genomics and transcriptomics data. We detected 3 QTL regions that could be linked to DL on Sus scrofa chromosomes (SSC) 4, SSC13, and SSC14 for DL based on genomics data. We also identified 6 differentially expressed genes significantly associated with the DL trait: GALNT15, TBC1D1, MLLT11, PPARGC1A, NREP, and CNTFR based on transcriptomics data. By integrating genomics data with transcriptomics data, we identified 3 key candidate genes for DL, i.e., NCOA2, HPF1, and CLCN3. These findings offer potential genetic markers and genes for improving pork quality through molecular breeding. |