Identification and Validation of Candidate Genes Associated with Domesticated and Improved Traits in Soybean
Soybean, an important source of vegetable oils and proteins for humans, has undergone significant phenotypic changes during domestication and improvement. However, there is limited knowledge about genes related to these domesticated and improved traits, such as flowering time, seed development, alka...
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Series: | The Plant Genome |
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doaj-431a525e0f1441e1b616f3ef7f4cdb6d2020-11-25T03:51:03ZengWileyThe Plant Genome1940-33722016-07-019210.3835/plantgenome2015.09.0090plantgenome2015.09.0090Identification and Validation of Candidate Genes Associated with Domesticated and Improved Traits in SoybeanLing ZhouLonghai LuoJian-Fang ZuoLinfeng YangLi ZhangXuanmin GuangYuan NiuJianbo JianQing-Chun GengLiping LiangQijian SongJim M. DunwellZhenzhen WuJia WenYu-Qin LiuYuan-Ming ZhangSoybean, an important source of vegetable oils and proteins for humans, has undergone significant phenotypic changes during domestication and improvement. However, there is limited knowledge about genes related to these domesticated and improved traits, such as flowering time, seed development, alkaline-salt tolerance, and seed oil content (SOC). In this study, more than 106,000 single nucleotide polymorphisms (SNPs) were identified by restriction site associated DNA sequencing of 14 wild, 153 landrace, and 119 bred soybean accessions, and 198 candidate domestication regions (CDRs) were identified via multiple genetic diversity analyses. Of the 1489 candidate domestication genes (CDGs) within these CDRs, a total of 330 CDGs were related to the above four traits in the domestication, gene ontology (GO) enrichment, gene expression, and pathway analyses. Eighteen, 60, 66, and 10 of the 330 CDGs were significantly associated with the above four traits, respectively. Of 134 trait-associated CDGs, 29 overlapped with previous CDGs, 11 were consistent with candidate genes in previous trait association studies, and 66 were covered by the domesticated and improved quantitative trait loci or their adjacent regions, having six common CDGs, such as one functionally characterized gene (). Of the 68 seed size (SS) and SOC CDGs, 37 were further confirmed by gene expression analysis. In addition, eight genes were found to be related to artificial selection during modern breeding. Therefore, this study provides an integrated method for efficiently identifying CDGs and valuable information for domestication and genetic research.https://dl.sciencesocieties.org/publications/tpg/articles/9/2/plantgenome2015.09.0090 |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Ling Zhou Longhai Luo Jian-Fang Zuo Linfeng Yang Li Zhang Xuanmin Guang Yuan Niu Jianbo Jian Qing-Chun Geng Liping Liang Qijian Song Jim M. Dunwell Zhenzhen Wu Jia Wen Yu-Qin Liu Yuan-Ming Zhang |
spellingShingle |
Ling Zhou Longhai Luo Jian-Fang Zuo Linfeng Yang Li Zhang Xuanmin Guang Yuan Niu Jianbo Jian Qing-Chun Geng Liping Liang Qijian Song Jim M. Dunwell Zhenzhen Wu Jia Wen Yu-Qin Liu Yuan-Ming Zhang Identification and Validation of Candidate Genes Associated with Domesticated and Improved Traits in Soybean The Plant Genome |
author_facet |
Ling Zhou Longhai Luo Jian-Fang Zuo Linfeng Yang Li Zhang Xuanmin Guang Yuan Niu Jianbo Jian Qing-Chun Geng Liping Liang Qijian Song Jim M. Dunwell Zhenzhen Wu Jia Wen Yu-Qin Liu Yuan-Ming Zhang |
author_sort |
Ling Zhou |
title |
Identification and Validation of Candidate Genes Associated with Domesticated and Improved Traits in Soybean |
title_short |
Identification and Validation of Candidate Genes Associated with Domesticated and Improved Traits in Soybean |
title_full |
Identification and Validation of Candidate Genes Associated with Domesticated and Improved Traits in Soybean |
title_fullStr |
Identification and Validation of Candidate Genes Associated with Domesticated and Improved Traits in Soybean |
title_full_unstemmed |
Identification and Validation of Candidate Genes Associated with Domesticated and Improved Traits in Soybean |
title_sort |
identification and validation of candidate genes associated with domesticated and improved traits in soybean |
publisher |
Wiley |
series |
The Plant Genome |
issn |
1940-3372 |
publishDate |
2016-07-01 |
description |
Soybean, an important source of vegetable oils and proteins for humans, has undergone significant phenotypic changes during domestication and improvement. However, there is limited knowledge about genes related to these domesticated and improved traits, such as flowering time, seed development, alkaline-salt tolerance, and seed oil content (SOC). In this study, more than 106,000 single nucleotide polymorphisms (SNPs) were identified by restriction site associated DNA sequencing of 14 wild, 153 landrace, and 119 bred soybean accessions, and 198 candidate domestication regions (CDRs) were identified via multiple genetic diversity analyses. Of the 1489 candidate domestication genes (CDGs) within these CDRs, a total of 330 CDGs were related to the above four traits in the domestication, gene ontology (GO) enrichment, gene expression, and pathway analyses. Eighteen, 60, 66, and 10 of the 330 CDGs were significantly associated with the above four traits, respectively. Of 134 trait-associated CDGs, 29 overlapped with previous CDGs, 11 were consistent with candidate genes in previous trait association studies, and 66 were covered by the domesticated and improved quantitative trait loci or their adjacent regions, having six common CDGs, such as one functionally characterized gene (). Of the 68 seed size (SS) and SOC CDGs, 37 were further confirmed by gene expression analysis. In addition, eight genes were found to be related to artificial selection during modern breeding. Therefore, this study provides an integrated method for efficiently identifying CDGs and valuable information for domestication and genetic research. |
url |
https://dl.sciencesocieties.org/publications/tpg/articles/9/2/plantgenome2015.09.0090 |
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