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

Abstract 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...

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Autores principales:	Xiong Tong, Lianjie Hou, Weiming He, Chugang Mei, Bo Huang, Chi Zhang, Chingyuan Hu, Chong Wang
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2020
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/2deeadb104de448ca42847ce29edfd38
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spelling	oai:doaj.org-article:2deeadb104de448ca42847ce29edfd382021-12-02T17:52:23ZWhole genome sequence analysis reveals genetic structure and X-chromosome haplotype structure in indigenous Chinese pigs10.1038/s41598-020-66061-22045-2322https://doaj.org/article/2deeadb104de448ca42847ce29edfd382020-06-01T00:00:00Zhttps://doi.org/10.1038/s41598-020-66061-2https://doaj.org/toc/2045-2322Abstract 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 40.09 Mb 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.Xiong TongLianjie HouWeiming HeChugang MeiBo HuangChi ZhangChingyuan HuChong WangNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 10, Iss 1, Pp 1-10 (2020)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Xiong Tong Lianjie Hou Weiming He Chugang Mei Bo Huang Chi Zhang Chingyuan Hu Chong Wang Whole genome sequence analysis reveals genetic structure and X-chromosome haplotype structure in indigenous Chinese pigs
description	Abstract 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 40.09 Mb 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.
format	article
author	Xiong Tong Lianjie Hou Weiming He Chugang Mei Bo Huang Chi Zhang Chingyuan Hu Chong Wang
author_facet	Xiong Tong Lianjie Hou Weiming He Chugang Mei Bo Huang Chi Zhang Chingyuan Hu Chong Wang
author_sort	Xiong Tong
title	Whole genome sequence analysis reveals genetic structure and X-chromosome haplotype structure in indigenous Chinese pigs
title_short	Whole genome sequence analysis reveals genetic structure and X-chromosome haplotype structure in indigenous Chinese pigs
title_full	Whole genome sequence analysis reveals genetic structure and X-chromosome haplotype structure in indigenous Chinese pigs
title_fullStr	Whole genome sequence analysis reveals genetic structure and X-chromosome haplotype structure in indigenous Chinese pigs
title_full_unstemmed	Whole genome sequence analysis reveals genetic structure and X-chromosome haplotype structure in indigenous Chinese pigs
title_sort	whole genome sequence analysis reveals genetic structure and x-chromosome haplotype structure in indigenous chinese pigs
publisher	Nature Portfolio
publishDate	2020
url	https://doaj.org/article/2deeadb104de448ca42847ce29edfd38
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Whole genome sequence analysis reveals genetic structure and X-chromosome haplotype structure in indigenous Chinese pigs

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