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The Meishan pig genome reveals structural variation‐mediated gene expression and phenotypic divergence underlying Asian pig domestication
Author(s) -
Zhou Rong,
Li ShangTong,
Yao WenYe,
Xie ChunDi,
Chen Zhiqiang,
Zeng ZhiJie,
Wang Di,
Xu Kui,
Shen ZhaoJi,
Mu Yulian,
Bao Wenbin,
Jiang Wenkai,
Li Ruiqiang,
Liang Qiqi,
Li Kui
Publication year - 2021
Publication title -
molecular ecology resources
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.96
H-Index - 136
eISSN - 1755-0998
pISSN - 1755-098X
DOI - 10.1111/1755-0998.13396
Subject(s) - biology , domestication , genome , genetics , gene , phenotype , reference genome , contig , evolutionary biology
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.