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Whole genome sequence analysis reveals genetic structure and X-chromosome haplotype structure in indigenous Chinese pigs

文献类型： 外文期刊

作者： Tong, Xiong 1 ; Hou, Lianjie 1 ; He, Weiming 2 ; Mei, Chugang 4 ; Huang, Bo 1 ; Zhang, Chi 2 ; Hu, Chingyuan 5 ; Wang, Ch 1 ;

作者机构： 1.South China Agr Univ, Coll Anim Sci, Guangdong Prov Key Lab Agroanim Genom & Mol Breed, Natl Engn Res Ctr Breeding Swine Ind, Guangzhou 510642, Guangdong, Peoples R China

2.BGI Shenzhen, BGI Genom, State Key Lab Agr Genom, Shenzhen 518083, Peoples R China

3.Guangdong Acad Agr Sci, Inst Anim Sci, State Key Lab Livestock & Poultry Breeding, Guangzhou 510640, Peoples R China

4.Northwest A&F Univ, Coll Anim Sci & Technol, Yangling 712100, Shaanxi, Peoples R China

5.Univ Hawaii Manoa, Dept Human Nutr Food & Anim Sci, 1955 East West Rd,AgSci 415J, Honolulu, HI 96822 USA

期刊名称：SCIENTIFIC REPORTS （ 影响因子：4.379； 五年影响因子：5.133 ）

ISSN： 2045-2322

年卷期： 2020 年 10 卷 1 期

页码：

收录情况： SCI

摘要： Chinese indigenous pigs exhibit considerable phenotypic diversity, but their population structure and the genetic basis of agriculturally important traits need further exploration. Here, we sequenced the whole genomes of 24 individual pigs representing 22 breeds distributed throughout China. For comparison with European and commercial breeds (one pig per breed), we included seven published pig genomes with our new genomes for analyses. Our results showed that breeds grouped together based on morphological classifications are not necessarily more genetically similar to each other than to breeds from other groups. We found that genetic material from European pigs likely introgressed into five Chinese breeds. We have identified two new subpopulations of domestic pigs that encompass morphology-based criteria in China. The Southern Chinese subpopulation comprises the classical South Chinese Type and part of the Central China Type. In contrast, the Northern Chinese subpopulation comprises the North China Type, the Lower Yangtze River Basin Type, the Southwest Type, the Plateau Type, and the remainder of the Central China Type. Eight haplotypes and two recombination sites were identified within a conserved 40.09Mb linkage-disequilibrium (LD) block on the X chromosome. Potential candidate genes (LEPR, FANCC, COL1A1, and PCCA) influencing body size were identified. Our findings provide insights into the phylogeny of Chinese indigenous pig breeds and benefit gene mining efforts to improve major economic traits.

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