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A reference-grade wild soybean genome

Efficient crop improvement depends on the application of accurate genetic information contained in diverse germplasm resources. Here we report a reference-grade genome of wild soybean accession W05, with a final assembled genome size of 1013.2 Mb and a contig N50 of 3.3 Mb. The analytical power of t...

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Autores principales: Xie, Min, Chung, Claire Yik-Lok, Li, Man-Wah, Wong, Fuk-Ling, Wang, Xin, Liu, Ailin, Wang, Zhili, Leung, Alden King-Yung, Wong, Tin-Hang, Tong, Suk-Wah, Xiao, Zhixia, Fan, Kejing, Ng, Ming-Sin, Qi, Xinpeng, Yang, Linfeng, Deng, Tianquan, He, Lijuan, Chen, Lu, Fu, Aisi, Ding, Qiong, He, Junxian, Chung, Gyuhwa, Isobe, Sachiko, Tanabata, Takanari, Valliyodan, Babu, Nguyen, Henry T., Cannon, Steven B., Foyer, Christine H., Chan, Ting-Fung, Lam, Hon-Ming
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6418295/
https://www.ncbi.nlm.nih.gov/pubmed/30872580
http://dx.doi.org/10.1038/s41467-019-09142-9
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author Xie, Min
Chung, Claire Yik-Lok
Li, Man-Wah
Wong, Fuk-Ling
Wang, Xin
Liu, Ailin
Wang, Zhili
Leung, Alden King-Yung
Wong, Tin-Hang
Tong, Suk-Wah
Xiao, Zhixia
Fan, Kejing
Ng, Ming-Sin
Qi, Xinpeng
Yang, Linfeng
Deng, Tianquan
He, Lijuan
Chen, Lu
Fu, Aisi
Ding, Qiong
He, Junxian
Chung, Gyuhwa
Isobe, Sachiko
Tanabata, Takanari
Valliyodan, Babu
Nguyen, Henry T.
Cannon, Steven B.
Foyer, Christine H.
Chan, Ting-Fung
Lam, Hon-Ming
author_facet Xie, Min
Chung, Claire Yik-Lok
Li, Man-Wah
Wong, Fuk-Ling
Wang, Xin
Liu, Ailin
Wang, Zhili
Leung, Alden King-Yung
Wong, Tin-Hang
Tong, Suk-Wah
Xiao, Zhixia
Fan, Kejing
Ng, Ming-Sin
Qi, Xinpeng
Yang, Linfeng
Deng, Tianquan
He, Lijuan
Chen, Lu
Fu, Aisi
Ding, Qiong
He, Junxian
Chung, Gyuhwa
Isobe, Sachiko
Tanabata, Takanari
Valliyodan, Babu
Nguyen, Henry T.
Cannon, Steven B.
Foyer, Christine H.
Chan, Ting-Fung
Lam, Hon-Ming
author_sort Xie, Min
collection PubMed
description Efficient crop improvement depends on the application of accurate genetic information contained in diverse germplasm resources. Here we report a reference-grade genome of wild soybean accession W05, with a final assembled genome size of 1013.2 Mb and a contig N50 of 3.3 Mb. The analytical power of the W05 genome is demonstrated by several examples. First, we identify an inversion at the locus determining seed coat color during domestication. Second, a translocation event between chromosomes 11 and 13 of some genotypes is shown to interfere with the assignment of QTLs. Third, we find a region containing copy number variations of the Kunitz trypsin inhibitor (KTI) genes. Such findings illustrate the power of this assembly in the analysis of large structural variations in soybean germplasm collections. The wild soybean genome assembly has wide applications in comparative genomic and evolutionary studies, as well as in crop breeding and improvement programs.
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spelling pubmed-64182952019-03-18 A reference-grade wild soybean genome Xie, Min Chung, Claire Yik-Lok Li, Man-Wah Wong, Fuk-Ling Wang, Xin Liu, Ailin Wang, Zhili Leung, Alden King-Yung Wong, Tin-Hang Tong, Suk-Wah Xiao, Zhixia Fan, Kejing Ng, Ming-Sin Qi, Xinpeng Yang, Linfeng Deng, Tianquan He, Lijuan Chen, Lu Fu, Aisi Ding, Qiong He, Junxian Chung, Gyuhwa Isobe, Sachiko Tanabata, Takanari Valliyodan, Babu Nguyen, Henry T. Cannon, Steven B. Foyer, Christine H. Chan, Ting-Fung Lam, Hon-Ming Nat Commun Article Efficient crop improvement depends on the application of accurate genetic information contained in diverse germplasm resources. Here we report a reference-grade genome of wild soybean accession W05, with a final assembled genome size of 1013.2 Mb and a contig N50 of 3.3 Mb. The analytical power of the W05 genome is demonstrated by several examples. First, we identify an inversion at the locus determining seed coat color during domestication. Second, a translocation event between chromosomes 11 and 13 of some genotypes is shown to interfere with the assignment of QTLs. Third, we find a region containing copy number variations of the Kunitz trypsin inhibitor (KTI) genes. Such findings illustrate the power of this assembly in the analysis of large structural variations in soybean germplasm collections. The wild soybean genome assembly has wide applications in comparative genomic and evolutionary studies, as well as in crop breeding and improvement programs. Nature Publishing Group UK 2019-03-14 /pmc/articles/PMC6418295/ /pubmed/30872580 http://dx.doi.org/10.1038/s41467-019-09142-9 Text en © The Author(s) 2019 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
spellingShingle Article
Xie, Min
Chung, Claire Yik-Lok
Li, Man-Wah
Wong, Fuk-Ling
Wang, Xin
Liu, Ailin
Wang, Zhili
Leung, Alden King-Yung
Wong, Tin-Hang
Tong, Suk-Wah
Xiao, Zhixia
Fan, Kejing
Ng, Ming-Sin
Qi, Xinpeng
Yang, Linfeng
Deng, Tianquan
He, Lijuan
Chen, Lu
Fu, Aisi
Ding, Qiong
He, Junxian
Chung, Gyuhwa
Isobe, Sachiko
Tanabata, Takanari
Valliyodan, Babu
Nguyen, Henry T.
Cannon, Steven B.
Foyer, Christine H.
Chan, Ting-Fung
Lam, Hon-Ming
A reference-grade wild soybean genome
title A reference-grade wild soybean genome
title_full A reference-grade wild soybean genome
title_fullStr A reference-grade wild soybean genome
title_full_unstemmed A reference-grade wild soybean genome
title_short A reference-grade wild soybean genome
title_sort reference-grade wild soybean genome
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6418295/
https://www.ncbi.nlm.nih.gov/pubmed/30872580
http://dx.doi.org/10.1038/s41467-019-09142-9
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