Yu Jianghui, Tao Wei, Ai Xinjie, Liu Qian, Ma Jinfeng, Xu Liming, Li Qiang, Wang Wenqiang, Huang Ruihua, Zhao Qingbo, Li Pinghua
Key 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.
Huaiyin Xinhuai Pig Breeding Farm of Huaian City, Huaian, China.
J Anim Sci. 2025 Jan 4;103. doi: 10.1093/jas/skaf177.
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.
滴水损失（DL）是评估猪肌肉品质的关键性状。在本研究中，对有滴水损失记录的中国苏淮猪使用Neogen GGP猪80K单核苷酸多态性（SNP）芯片进行基因分型，以鉴定影响滴水损失的数量性状位点（QTL）并剖析该性状的候选基因。将SNP芯片数据推算到全基因组序列（iWGS）水平。通过基于iWGS数据的全基因组关联研究（GWAS），在猪1号染色体（SSC）4、SSC13和SSC14上检测到与滴水损失显著相关的SNP，涉及37个候选基因，如AACS、CRB4和OXSM。值得注意的是，本研究新鉴定出3个QTL区域（SSC4、SSC13和SSC14），分别为SSC4：65.2至66.1 Mb、SSC13：12.46至12.48 Mb和SSC14：20.7至20.9 Mb。此外，对滴水损失基因组估计育种值极高和极低的个体猪的肌肉组织进行了RNA测序（RNA-seq），鉴定出21个差异表达基因（DEG）。将这些DEG与我们苏淮猪肌肉组织转录组数据的数量性状转录组（QTT）分析结果相结合，确定了6个与滴水损失密切相关的DEG：GALNT15、TBC1D1、MLLT11、PPARGC1A、NREP和CNTFR。将GWAS鉴定的候选基因与QTT分析结果相结合，发现GWAS鉴定的基因NCOA2、HPF1和CLCN3的表达与滴水损失显著相关。功能富集分析结合GWAS鉴定的37个候选基因以及RNA-seq和QTT分析共同鉴定的6个DEG，表明GALNT15、TBC1D1、PPARGC1A、AACS、CBR4和OXSM基因可能在功能上与猪肉滴水损失相关，从而将它们定位为重要的候选基因。这些基因（NCOA2、HPF1、CLCN3、PPARGC1A、TBC1D1、GALNT15、CBR4、AACS和OXSM）是新鉴定出的滴水损失候选基因。本研究为通过标记辅助或基因组选择改善猪育种计划中的肉质性状提供了基础。
