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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

作者： Zhou, Rong 1 ; Li, Shang-Tong 2 ; Yao, Wen-Ye 1 ; Xie, Chun-Di 1 ; Chen, Zhiqiang 3 ; Zeng, Zhi-Jie 1 ; Wang, Di 3 ; Xu, 1 ;

作者机构： 1.Chinese Acad Agr Sci, Minist Agr & Rural Affairs, Key Lab Anim Genet Breeding & Reprod, State Key Lab Anim Nutr,Inst Anim Sci, Beijing 100193, Peoples R China

2.Natl Inst Biol Sci NIBS, Beijing, Peoples R China

3.Novogene Bioinformat Inst, Beijing 100083, Peoples R China

4.Anhui Agr Univ, Coll Anim Sci & Technol, Hefei, Peoples R China

5.Foshan Univ, Coll Life Sci & Engn, Guangdong Prov Key Lab Anim Mol Design & Precise, Foshan, Peoples R China

6.Fulcrum Gene Sci & Technol Beijing Ltd, Beijing, Peoples R China

7.Yangzhou Univ, Coll Anim Sci & Technol, Yangzhou, Jiangsu, Peoples R China

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

年卷期：

页码：

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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