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

IF 2.7 2区农林科学 Q1 AGRICULTURE, DAIRY & ANIMAL SCIENCE

Journal of animal science Pub Date : 2025-06-09 DOI:10.1093/jas/skaf177

Jianghui Yu, Wei Tao, Xinjie Ai, Qian Liu, Jinfeng Ma, Liming Xu, Qiang Li, Wenqiang Wang, Ruihua Huang, Qingbo Zhao, Pinghua Li

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引用次数: 0

Abstract

Drip loss (DL) is a crucial trait for evaluating muscle quality in pigs. In this study, Chinese Suhuai pigs with DL record 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, three QTL regions (SSC4, SSC13, and SSC14) were newly identified in this study, which were SSC4: 65.2~66.1 Mb, SSC13:12.46~12.48 Mb and SSC14: 20.7~20.9 Mb respectively. Additionally, RNA sequencing (RNA-seq) was conducted on muscle tissues from individual pigs with extremely high and low genomic estimated breeding values (GEBV) of drip loss, identifying 21 differentially expressed genes (DEGs). Integrating these DEGs with QTT analysis results from our Suhuai pig muscle tissue transcriptome data pinpointed six DEGs strongly linked to drip loss: 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 drip loss. Functional enrichment analysis, combining the 37 candidate genes identified by GWAS and the six 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 drip loss, 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 provide a foundation for improving meat quality traits through marker-assisted or genomic selection in pig breeding programs.

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基于基因组学和转录组学数据鉴定影响猪滴漏损失的新候选基因

滴漏损失（DL）是评价猪肌肉质量的重要指标。本研究采用Neogen®GGP猪80k单核苷酸多态性（SNP）阵列对中国苏怀猪进行基因分型，确定影响深度睡眠的数量性状位点（QTL），并解剖该性状的候选基因。snp芯片数据被归算到全基因组序列（iWGS）水平。通过基于iWGS数据的全基因组关联研究（GWAS），在苏斯scrofa染色体（SSC） 4、SSC13和SSC14上检测到DL的显著snp，涉及AACS、CRB4和OXSM等37个候选基因。值得注意的是，本研究新发现了3个QTL区域（SSC4、SSC13和SSC14），分别为SSC4: 65.2~66.1 Mb、SSC13:12.46~12.48 Mb和SSC14: 20.7~20.9 Mb。此外，对滴漏损失基因组估计值（GEBV）极高和极低的个体猪的肌肉组织进行RNA测序（RNA-seq），鉴定出21个差异表达基因（deg）。将这些基因与苏淮猪肌肉组织转录组数据的QTT分析结果相结合，确定了6个与滴漏密切相关的基因：GALNT15、TBC1D1、MLLT11、PPARGC1A、NREP和CNTFR。将GWAS鉴定的候选基因与QTT分析结果整合后发现，GWAS鉴定的基因NCOA2、HPF1和CLCN3的表达与滴漏损失显著相关。功能富集分析，结合GWAS鉴定的37个候选基因和RNA-seq和QTT分析共同鉴定的6个DEGs，提示GALNT15、TBC1D1、PPARGC1A、AACS、CBR4和OXSM基因可能在功能上与猪肉漏损相关，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）是新发现的DL候选基因。本研究为通过标记辅助选择或基因组选择提高猪的肉质性状提供了基础。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Journal of animal science 农林科学-奶制品与动物科学

CiteScore

4.80

自引率

12.10%

发文量

1589

审稿时长

3 months

期刊介绍： The Journal of Animal Science (JAS) is the premier journal for animal science and serves as the leading source of new knowledge and perspective in this area. JAS publishes more than 500 fully reviewed research articles, invited reviews, technical notes, and letters to the editor each year. Articles published in JAS encompass a broad range of research topics in animal production and fundamental aspects of genetics, nutrition, physiology, and preparation and utilization of animal products. Articles typically report research with beef cattle, companion animals, goats, horses, pigs, and sheep; however, studies involving other farm animals, aquatic and wildlife species, and laboratory animal species that address fundamental questions related to livestock and companion animal biology will be considered for publication.