Genome Re-Sequencing of Semi-Wild Soybean Reveals a Complex Soja Population Structure and Deep Introgression

Semi-wild soybean is a unique type of soybean that retains both wild and domesticated characteristics, which provides an important intermediate type for understanding the evolution of the subgenus Soja population in the Glycine genus. In this study, a semi-wild soybean line (Maliaodou) and a wild li...

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Main Authors:	Qiu, Jie, Wang, Yu, Wu, Sanling, Wang, Ying-Ying, Ye, Chu-Yu, Bai, Xuefei, Li, Zefeng, Yan, Chenghai, Wang, Weidi, Wang, Ziqiang, Shu, Qingyao, Xie, Jiahua, Lee, Suk-Ha, Fan, Longjiang
Format:	Online
Language:	English
Published:	Public Library of Science 2014
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4181298/

id	pubmed-4181298
recordtype	oai_dc
spelling	pubmed-41812982014-10-07 Genome Re-Sequencing of Semi-Wild Soybean Reveals a Complex Soja Population Structure and Deep Introgression Qiu, Jie Wang, Yu Wu, Sanling Wang, Ying-Ying Ye, Chu-Yu Bai, Xuefei Li, Zefeng Yan, Chenghai Wang, Weidi Wang, Ziqiang Shu, Qingyao Xie, Jiahua Lee, Suk-Ha Fan, Longjiang Research Article Semi-wild soybean is a unique type of soybean that retains both wild and domesticated characteristics, which provides an important intermediate type for understanding the evolution of the subgenus Soja population in the Glycine genus. In this study, a semi-wild soybean line (Maliaodou) and a wild line (Lanxi 1) collected from the lower Yangtze regions were deeply sequenced while nine other semi-wild lines were sequenced to a 3-fold genome coverage. Sequence analysis revealed that (1) no independent phylogenetic branch covering all 10 semi-wild lines was observed in the Soja phylogenetic tree; (2) besides two distinct subpopulations of wild and cultivated soybean in the Soja population structure, all semi-wild lines were mixed with some wild lines into a subpopulation rather than an independent one or an intermediate transition type of soybean domestication; (3) high heterozygous rates (0.19–0.49) were observed in several semi-wild lines; and (4) over 100 putative selective regions were identified by selective sweep analysis, including those related to the development of seed size. Our results suggested a hybridization origin for the semi-wild soybean, which makes a complex Soja population structure. Public Library of Science 2014-09-29 /pmc/articles/PMC4181298/ /pubmed/25265539 http://dx.doi.org/10.1371/journal.pone.0108479 Text en © 2014 Qiu et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Qiu, Jie Wang, Yu Wu, Sanling Wang, Ying-Ying Ye, Chu-Yu Bai, Xuefei Li, Zefeng Yan, Chenghai Wang, Weidi Wang, Ziqiang Shu, Qingyao Xie, Jiahua Lee, Suk-Ha Fan, Longjiang
spellingShingle	Qiu, Jie Wang, Yu Wu, Sanling Wang, Ying-Ying Ye, Chu-Yu Bai, Xuefei Li, Zefeng Yan, Chenghai Wang, Weidi Wang, Ziqiang Shu, Qingyao Xie, Jiahua Lee, Suk-Ha Fan, Longjiang Genome Re-Sequencing of Semi-Wild Soybean Reveals a Complex Soja Population Structure and Deep Introgression
author_facet	Qiu, Jie Wang, Yu Wu, Sanling Wang, Ying-Ying Ye, Chu-Yu Bai, Xuefei Li, Zefeng Yan, Chenghai Wang, Weidi Wang, Ziqiang Shu, Qingyao Xie, Jiahua Lee, Suk-Ha Fan, Longjiang
author_sort	Qiu, Jie
title	Genome Re-Sequencing of Semi-Wild Soybean Reveals a Complex Soja Population Structure and Deep Introgression
title_short	Genome Re-Sequencing of Semi-Wild Soybean Reveals a Complex Soja Population Structure and Deep Introgression
title_full	Genome Re-Sequencing of Semi-Wild Soybean Reveals a Complex Soja Population Structure and Deep Introgression
title_fullStr	Genome Re-Sequencing of Semi-Wild Soybean Reveals a Complex Soja Population Structure and Deep Introgression
title_full_unstemmed	Genome Re-Sequencing of Semi-Wild Soybean Reveals a Complex Soja Population Structure and Deep Introgression
title_sort	genome re-sequencing of semi-wild soybean reveals a complex soja population structure and deep introgression
description	Semi-wild soybean is a unique type of soybean that retains both wild and domesticated characteristics, which provides an important intermediate type for understanding the evolution of the subgenus Soja population in the Glycine genus. In this study, a semi-wild soybean line (Maliaodou) and a wild line (Lanxi 1) collected from the lower Yangtze regions were deeply sequenced while nine other semi-wild lines were sequenced to a 3-fold genome coverage. Sequence analysis revealed that (1) no independent phylogenetic branch covering all 10 semi-wild lines was observed in the Soja phylogenetic tree; (2) besides two distinct subpopulations of wild and cultivated soybean in the Soja population structure, all semi-wild lines were mixed with some wild lines into a subpopulation rather than an independent one or an intermediate transition type of soybean domestication; (3) high heterozygous rates (0.19–0.49) were observed in several semi-wild lines; and (4) over 100 putative selective regions were identified by selective sweep analysis, including those related to the development of seed size. Our results suggested a hybridization origin for the semi-wild soybean, which makes a complex Soja population structure.
publisher	Public Library of Science
publishDate	2014
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4181298/
_version_	1613139483157331968

Genome Re-Sequencing of Semi-Wild Soybean Reveals a Complex Soja Population Structure and Deep Introgression

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