The Meishan pig genome reveals structural variation-mediated gene expression and phenotypic divergence underlying Asian pig domestication

文献类型： 外文期刊

第一作者： Zhou, Rong

作者： Zhou, Rong;Yao, Wen-Ye;Xie, Chun-Di;Zeng, Zhi-Jie;Xu, Kui;Mu, Yulian;Li, Kui;Li, Shang-Tong;Chen, Zhiqiang;Wang, Di;Jiang, Wenkai;Li, Ruiqiang;Liang, Qiqi;Zeng, Zhi-Jie;Shen, Zhao-Ji;Shen, Zhao-Ji;Bao, Wenbin

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关键词： genome assembly; genome evolution; Meishan pig; structural variation

期刊名称：MOLECULAR ECOLOGY RESOURCES （ 影响因子：6.286； 五年影响因子：7.488 ）

ISSN： 1755-098X

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收录情况： SCI

摘要： There are wide genomic and phenotypic differences between Asian and European pig breeds, yet the current reference genome is the European Duroc pig genome. A high-quality pig genome is lacking for genetic analysis of agricultural traits in Asian pigs. Here, using a hybrid approach, a high-quality reference genome (MSCAAS v1) for the Asian Meishan breed is assembled with a contig N50 size of 48.05 Mb. MSCAAS v1 outperforms the Duroc genome as a reference genome for Asian breeds. Genomic comparison reveals 49,103 structural variations (SVs) between Meishan and Duroc, 4.02% of which are Asian-specific SVs (AP-SVs). Notably, a 30-Mb hotspot for AP-SVs on chromosome X enriched for genes associated with Asian-pig-specific phenotypes is present in Asian domestic pig breeds, but absent in Asian wild boars, suggesting that Asian domestic breeds share a common ancestor. Interbreed transcriptomics reveals transcriptional suppression roles of AP-SVs in multiple tissues. Finally, transcriptional regulation in the intron of IGF2R is reported, as genomic SV (274-bp deletion) in Tibetan pig limits its growth compared to domestic pig breeds. In summary, this study provides insights regarding the genetic changes underlying pig domestication and presents a benchmark-setting resource for the utilization of agricultural valuable loci in Asian pigs.

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