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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Autores principales:	Jie Qiu, Yu Wang, Sanling Wu, Ying-Ying Wang, Chu-Yu Ye, Xuefei Bai, Zefeng Li, Chenghai Yan, Weidi Wang, Ziqiang Wang, Qingyao Shu, Jiahua Xie, Suk-Ha Lee, Longjiang Fan
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2014
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/03da1b4eef3949af8ac191f7717d903f
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spelling	oai:doaj.org-article:03da1b4eef3949af8ac191f7717d903f2021-11-25T05:58:48ZGenome re-sequencing of semi-wild soybean reveals a complex Soja population structure and deep introgression.1932-620310.1371/journal.pone.0108479https://doaj.org/article/03da1b4eef3949af8ac191f7717d903f2014-01-01T00:00:00Zhttps://doi.org/10.1371/journal.pone.0108479https://doaj.org/toc/1932-6203Semi-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.Jie QiuYu WangSanling WuYing-Ying WangChu-Yu YeXuefei BaiZefeng LiChenghai YanWeidi WangZiqiang WangQingyao ShuJiahua XieSuk-Ha LeeLongjiang FanPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 9, Iss 9, p e108479 (2014)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Jie Qiu Yu Wang Sanling Wu Ying-Ying Wang Chu-Yu Ye Xuefei Bai Zefeng Li Chenghai Yan Weidi Wang Ziqiang Wang Qingyao Shu Jiahua Xie Suk-Ha Lee Longjiang Fan 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.
format	article
author	Jie Qiu Yu Wang Sanling Wu Ying-Ying Wang Chu-Yu Ye Xuefei Bai Zefeng Li Chenghai Yan Weidi Wang Ziqiang Wang Qingyao Shu Jiahua Xie Suk-Ha Lee Longjiang Fan
author_facet	Jie Qiu Yu Wang Sanling Wu Ying-Ying Wang Chu-Yu Ye Xuefei Bai Zefeng Li Chenghai Yan Weidi Wang Ziqiang Wang Qingyao Shu Jiahua Xie Suk-Ha Lee Longjiang Fan
author_sort	Jie Qiu
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.
publisher	Public Library of Science (PLoS)
publishDate	2014
url	https://doaj.org/article/03da1b4eef3949af8ac191f7717d903f
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Genome re-sequencing of semi-wild soybean reveals a complex Soja population structure and deep introgression.

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