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二花脸猪和巴马香猪乳腺原基的ATAC-Seq与RNA-Seq整合分析鉴定出影响猪乳头数变异的候选基因

Integration ATAC-Seq and RNA-Seq Analysis of Mammary Placodes in Erhualian and Bamaxiang Pigs Identified Candidate Genes Influencing Pig Teat Number Variation.

作者信息

Liu Chenxi, Huang Ruihua, Jiang Nengjing, Zhou Wuduo, Liu Qian, Du Taoran, Zhang Qian, Ma Jinfeng, Zhao Qingbo, Li Pinghua

机构信息

Institute of Swine Science (Key Laboratory of Pig Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs (Nanjing)) Nanjing Agricultural University Nanjing People's Republic of China.

College of Animal Science and Technology Hunan Agricultural University Changsha People's Republic of China.

出版信息

Evol Appl. 2025 Jun 28;18(7):e70129. doi: 10.1111/eva.70129. eCollection 2025 Jul.

Abstract

Teat number is an important economic trait in pigs, affecting piglet health and survival. While numerous GWAS have identified candidate genes for teat number in Duroc, Landrace, and Large White pigs, the causal genes remain unclear, largely due to a lack of transcriptional and epigenetic studies on mammary placodes in 26-day-old pig embryos, a critical stage for teat formation. Erhualian and Bamaxiang pigs, derived from Chinese wild boars, serve as ideal models for studying genetic variation in teat number, with Erhualian averaging nearly 20 teats and Bamaxiang around 10. This study collected mammary placodes from these breeds at embryonic day 26 and performed ATAC-seq and RNA-seq to explore chromatin accessibility and gene expression. Results indicate widespread chromatin accessibility across mammary placodes. Of the 30,806 open chromatin regions (OCRs) identified, only 30 showed breed-specific differences, suggesting conserved accessibility patterns across breeds. OCRs are enriched in intergenic and promoter regions, and significantly overlap with QTL intervals for teat number. RNA-seq revealed 4432 differentially expressed genes between the two breeds, including and , indicating breed-specific gene expression patterns. Combining ATAC-seq and RNA-seq results identified three protein-coding genes (, , and ) near 48.80 Mb on SSC14 that are associated with teat number according to pheWAS and GWAS data. FISH analysis confirmed that is specifically expressed in epithelial cells of mammary placodes, and this region is under stronger selection in Erhualian pigs, suggesting its role in the breed's higher teat number. In conclusion, this study integrates ATAC-seq and RNA-seq to construct a chromatin accessibility and gene expression map of pig mammary placodes. It identifies , , and as key candidate genes driving teat number differences, providing insights for understanding QTL intervals and identifying causal genes linked to teat number in pigs.

摘要

乳头数量是猪的一个重要经济性状,影响仔猪的健康和存活。虽然众多全基因组关联研究(GWAS)已在杜洛克猪、长白猪和大白猪中鉴定出乳头数量的候选基因,但因果基因仍不明确,这主要是由于缺乏对26日龄猪胚胎乳腺基板的转录和表观遗传学研究,而这一阶段是乳头形成的关键时期。源自中国野猪的二花脸猪和巴马香猪是研究乳头数量遗传变异的理想模型,二花脸猪平均有近20个乳头,巴马香猪约有10个乳头。本研究在胚胎第26天收集了这些品种的乳腺基板,并进行了ATAC测序和RNA测序,以探索染色质可及性和基因表达。结果表明,乳腺基板中存在广泛的染色质可及性。在鉴定出的30806个开放染色质区域(OCR)中,只有30个显示出品种特异性差异,这表明不同品种间的可及性模式具有保守性。OCR在基因间和启动子区域富集,并且与乳头数量的数量性状位点(QTL)区间显著重叠。RNA测序揭示了两个品种之间有4432个差异表达基因,包括……,表明存在品种特异性的基因表达模式。结合ATAC测序和RNA测序结果,根据全基因组关联研究(GWAS)和表型全基因组关联研究(pheWAS)数据,在14号猪染色体(SSC14)上48.80 Mb附近鉴定出三个与乳头数量相关的蛋白质编码基因(……)。荧光原位杂交(FISH)分析证实,……在乳腺基板的上皮细胞中特异性表达,并且该区域在二花脸猪中受到更强的选择,这表明其在该品种较高乳头数量中的作用。总之,本研究整合了ATAC测序和RNA测序,构建了猪乳腺基板的染色质可及性和基因表达图谱。它鉴定出……作为驱动乳头数量差异的关键候选基因,为理解数量性状位点区间和鉴定与猪乳头数量相关的因果基因提供了见解。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2f3f/12205214/4f4c73e5864c/EVA-18-e70129-g001.jpg

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