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Journal of Integrative Agriculture
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Integrated analysis strategy of genome-wide functional gene mining and transcriptome analysis reveals MALSU1 gene underlying intramuscular fat in Bamei pigs

Tiantian Yuan1*, Yulin He1*, Minghao Cao2, Dong Li1, 3, Yulong Wang1, Lin Zhang1, Xiang Li1, Rongrong Ding1#, Gongshe Yang1, Taiyong Yu1#

1 Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Laboratory of Animal Fat Deposition & Muscle Development, College of Animal Science and Technology, Northwest A&F University, Yangling Shaanxi 712100, China

2 State Key Laboratory of Genetic Evolution & Animal Models and Yunnan Key Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China

3 Animal Breeding and Genomics, Wageningen University and Research, Wageningen, 6708PB, The Netherlands 

 Highlights 

Integrated genomic analysis identifies MALSU1 as a key gene for intramuscular fat in Bamei pigs.

MALSU1 promotes IMF deposition by inhibiting proliferation and promoting differentiation of adipocytes.

A functional missense mutation (p.Arg10Leu) was identified to alter MALSU1 protein structure and hydrophobicity, serves as a potential molecular marker for improving pork quality. 

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摘要  

八眉猪是中国西北地区的一个地方猪种,以其优异的肉质而闻名。然而,受外来品种引进及传统养殖模式改变的冲击,八眉猪正面临种质资源退化和遗传背景不清的严峻挑战。为了深入解析八眉猪优良肉质性状的遗传基础,并挖掘调控猪肌内脂肪沉积的关键基因,本研究开展了系统的多组学分析。为了揭示其优良性状背后的遗传基础,我们收集了61头八眉猪的全基因组测序数据,并整合了NCBI数据库中涵盖亚洲与欧洲家猪及野猪的427头个体的基因组数据,构建了包含488个体的全基因组变异数据集合。研究结果表明,八眉猪具有良好的保种现况,与西方猪种存在基因组差异。基于这一遗传差异,我们将选择信号分析与公共数据库(PigGTExPigBiobank PigQTL)相结合,鉴定到 MALSU1 是一个调控猪肌内脂肪沉积的新候选基因。MALSU1 的过表达和干扰实验表明,该基因通过抑制猪肌内脂肪原代细胞的增殖,促进其分化来调控肌内脂肪。RNA-seq 结果进一步揭示,MALSU1 通过抑制脂质代谢并促进脂质合成来调控肌内脂肪。有趣的是,我们在 MALSU1 基因的编码区鉴定到一个错义突变(p.Arg10Leu),通过Sanger测序验证与AlphaFold3蛋白质三维结构预测,我们发现该突变在高低肌内脂肪猪种中存在频率差异,显著改变了MALSU1蛋白结构。通过构建突变型过表达载体进行验证实验发现,该突变能够显著促进肌内前脂肪细胞的增殖,提示该位点可能是调节猪肌内脂肪沉积的关键变异。综上所述,本研究绘制了八眉猪的全基因组变异图谱,从基因组、表观组、转录组及细胞生物学多维度证实了肉质候选基因MALSU1及其关键突变位点具有调控猪肌内脂肪沉积的功能。研究成果不仅为八眉猪种质资源的保护提供了理论依据,也为未来猪肉品质改良的分子育种提供了重要的遗传标记。



Abstract  

The Bamei pigs (BM), an indigenous breed in Northwest China, is renowned for its superior meat quality. To uncover the genetic basis of its traits, we analyzed whole-genome sequencing data from 61 BM. Our results revealed that BM have a good genetic conservation status and distinct genomic divergence from Western breeds. We identified MALSU1 as a new candidate gene associated with intramuscular fat (IMF) by integrating selection signature analysis with public databases, such as PigGTEx, PigBiobank, and PigQTL. Overexpression and interference experiments of MALSU1 demonstrated that it regulates IMF by inhibiting the proliferation and promoting the differentiation of porcine intramuscular adipocyte primary cells. RNA-seq results further revealed that MALSU1 regulates IMF by inhibiting lipid metabolism and promoting lipid synthesis. Interestingly, a missense mutation (p.Arg10Leu) in the coding region of the MALSU1 gene was identified, which could promote the proliferation of intramuscular preadipocytes, suggesting an important role in IMF deposition.

Keywords:  Bamei pigs              intramuscular fat       MALSU1       population genetics  
Online: 19 December 2025  
Fund: 

This work was supported by the Biological Breeding-National Science and Technology Major Project (2023ZD04044), the National Key Research and Development Program of China (2021YFD1301200), and the Shaanxi Livestock and Poultry Breeding Double-chain Fusion Key Project (2022GD-TSLD-46). 

About author:  Tiantian Yuan, E-mail: ytt7586@163.com; Yulin He, E-mail: heyulin0924@163.com; #Correspondence Taiyong Yu, E-mail, yutaiyong310@nwsuaf.edu.cn; Rongrong Ding, E-mail: dingrongrong92@nwafu.edu.cn *These authors contributed equally to this study.

Cite this article: 

Tiantian Yuan, Yulin He, Minghao Cao, Dong Li, Yulong Wang, Lin Zhang, Xiang Li, Rongrong Ding, Gongshe Yang, Taiyong Yu. 2025. Integrated analysis strategy of genome-wide functional gene mining and transcriptome analysis reveals MALSU1 gene underlying intramuscular fat in Bamei pigs. Journal of Integrative Agriculture, Doi:10.1016/j.jia.2025.12.032

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