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Chromosome‐level reference genome and resequencing of 322 accessions reveal evolution, genomic imprint and key agronomic traits in adzuki bean

Liwei Chu Orcid Logo, Kai Yang, Chunhai Chen, Bo Zhao, Yanan Hou, Wanqiu Wang, Pu Zhao, Kaili Wang, Binhu Wang, Ying Xiao, Yongqiang Li, Yisong Li, Qijian Song, Biao Liu, Ruoxi Fan, Abhishek Bohra, Jianping Yu, Eva C. Sonnenschein Orcid Logo, Rajeev K Varshney Orcid Logo, Zhixi Tian Orcid Logo, Jianbo Jian, Ping Wan

Plant Biotechnology Journal, Volume: 22, Issue: 8, Pages: 2173 - 2185

Swansea University Author: Eva C. Sonnenschein Orcid Logo

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DOI (Published version): 10.1111/pbi.14337

Abstract

Adzuki bean (Vigna angularis) is an important legume crop cultivated in over 30 countries worldwide. We developed a high-quality chromosome-level reference genome of adzuki bean cultivar Jingnong6 by combining PacBio Sequel long-read sequencing with short-read and Hi-C technologies. The assembled ge...

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Published in: Plant Biotechnology Journal
ISSN: 1467-7644 1467-7652
Published: Wiley 2024
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We developed a high-quality chromosome-level reference genome of adzuki bean cultivar Jingnong6 by combining PacBio Sequel long-read sequencing with short-read and Hi-C technologies. The assembled genome covers 97.8% of the adzuki bean genome with a contig N50 of approximately 16 Mb and a total of 32 738 protein-coding genes. We also generated a comprehensive genome variation map of adzuki bean by whole-genome resequencing (WGRS) of 322 diverse adzuki beans accessions including both wild and cultivated. Furthermore, we have conducted comparative genomics and a genome-wide association study (GWAS) on key agricultural traits to investigate the evolution and domestication. GWAS identified several candidate genes, including VaCycA3;1, VaHB15, VaANR1 and VaBm, that exhibited significant associations with domestication traits. Furthermore, we conducted functional analyses on the roles of VaANR1 and VaBm in regulating seed coat colour. We provided evidence for the highest genetic diversity of wild adzuki (Vigna angularis var. nipponensis) in China with the presence of the most original wild adzuki bean, and the occurrence of domestication process facilitating transition from wild to cultigen. The present study elucidates the genetic basis of adzuki bean domestication traits and provides crucial genomic resources to support future breeding efforts in adzuki bean.</abstract><type>Journal Article</type><journal>Plant Biotechnology Journal</journal><volume>22</volume><journalNumber>8</journalNumber><paginationStart>2173</paginationStart><paginationEnd>2185</paginationEnd><publisher>Wiley</publisher><placeOfPublication/><isbnPrint/><isbnElectronic/><issnPrint>1467-7644</issnPrint><issnElectronic>1467-7652</issnElectronic><keywords>Adzuki bean, domestication, GWAS, agronomictraits, seed coat colour</keywords><publishedDay>1</publishedDay><publishedMonth>8</publishedMonth><publishedYear>2024</publishedYear><publishedDate>2024-08-01</publishedDate><doi>10.1111/pbi.14337</doi><url/><notes/><college>COLLEGE NANME</college><department>Biosciences Geography and Physics School</department><CollegeCode>COLLEGE CODE</CollegeCode><DepartmentCode>BGPS</DepartmentCode><institution>Swansea University</institution><apcterm>Another institution paid the OA fee</apcterm><funders>Beijing Municipal Natural Science Foundation. 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spelling v2 66578 2024-06-03 Chromosome‐level reference genome and resequencing of 322 accessions reveal evolution, genomic imprint and key agronomic traits in adzuki bean f6a4027578a15ea3e6453a54b849c686 0000-0001-6959-5100 Eva C. Sonnenschein Eva C. Sonnenschein true false 2024-06-03 BGPS Adzuki bean (Vigna angularis) is an important legume crop cultivated in over 30 countries worldwide. We developed a high-quality chromosome-level reference genome of adzuki bean cultivar Jingnong6 by combining PacBio Sequel long-read sequencing with short-read and Hi-C technologies. The assembled genome covers 97.8% of the adzuki bean genome with a contig N50 of approximately 16 Mb and a total of 32 738 protein-coding genes. We also generated a comprehensive genome variation map of adzuki bean by whole-genome resequencing (WGRS) of 322 diverse adzuki beans accessions including both wild and cultivated. Furthermore, we have conducted comparative genomics and a genome-wide association study (GWAS) on key agricultural traits to investigate the evolution and domestication. GWAS identified several candidate genes, including VaCycA3;1, VaHB15, VaANR1 and VaBm, that exhibited significant associations with domestication traits. Furthermore, we conducted functional analyses on the roles of VaANR1 and VaBm in regulating seed coat colour. We provided evidence for the highest genetic diversity of wild adzuki (Vigna angularis var. nipponensis) in China with the presence of the most original wild adzuki bean, and the occurrence of domestication process facilitating transition from wild to cultigen. The present study elucidates the genetic basis of adzuki bean domestication traits and provides crucial genomic resources to support future breeding efforts in adzuki bean. Journal Article Plant Biotechnology Journal 22 8 2173 2185 Wiley 1467-7644 1467-7652 Adzuki bean, domestication, GWAS, agronomictraits, seed coat colour 1 8 2024 2024-08-01 10.1111/pbi.14337 COLLEGE NANME Biosciences Geography and Physics School COLLEGE CODE BGPS Swansea University Another institution paid the OA fee Beijing Municipal Natural Science Foundation. Grant Number: KZ201710020013 National Natural Science Foundation of China. Grant Number: 31871697 National Key Research and Development Program of China. Grant Numbers: 2018YFD1000705, 2018YFD1000700 Food Futures Institute (Murdoch University) New varieties breeding and Experimental demonstration of adzuki bean. Grant Number: 2024115272-22 2024-07-24T13:07:33.2103685 2024-06-03T14:14:28.5895526 Faculty of Science and Engineering School of Biosciences, Geography and Physics - Biosciences Liwei Chu 0000-0001-5468-9542 1 Kai Yang 2 Chunhai Chen 3 Bo Zhao 4 Yanan Hou 5 Wanqiu Wang 6 Pu Zhao 7 Kaili Wang 8 Binhu Wang 9 Ying Xiao 10 Yongqiang Li 11 Yisong Li 12 Qijian Song 13 Biao Liu 14 Ruoxi Fan 15 Abhishek Bohra 16 Jianping Yu 17 Eva C. Sonnenschein 0000-0001-6959-5100 18 Rajeev K Varshney 0000-0002-4562-9131 19 Zhixi Tian 0000-0001-6051-9670 20 Jianbo Jian 21 Ping Wan 22 66578__30964__5a5fbdb0c4c944ba9ec1eae17be69125.pdf 66578.VoR.pdf 2024-07-24T13:06:15.8670193 Output 4490310 application/pdf Version of Record true Copyright 2024 The Authors. This is an open access article under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs License. true eng http://creativecommons.org/licenses/by-nc-nd/4.0/
title Chromosome‐level reference genome and resequencing of 322 accessions reveal evolution, genomic imprint and key agronomic traits in adzuki bean
spellingShingle Chromosome‐level reference genome and resequencing of 322 accessions reveal evolution, genomic imprint and key agronomic traits in adzuki bean
Eva C. Sonnenschein
title_short Chromosome‐level reference genome and resequencing of 322 accessions reveal evolution, genomic imprint and key agronomic traits in adzuki bean
title_full Chromosome‐level reference genome and resequencing of 322 accessions reveal evolution, genomic imprint and key agronomic traits in adzuki bean
title_fullStr Chromosome‐level reference genome and resequencing of 322 accessions reveal evolution, genomic imprint and key agronomic traits in adzuki bean
title_full_unstemmed Chromosome‐level reference genome and resequencing of 322 accessions reveal evolution, genomic imprint and key agronomic traits in adzuki bean
title_sort Chromosome‐level reference genome and resequencing of 322 accessions reveal evolution, genomic imprint and key agronomic traits in adzuki bean
author_id_str_mv f6a4027578a15ea3e6453a54b849c686
author_id_fullname_str_mv f6a4027578a15ea3e6453a54b849c686_***_Eva C. Sonnenschein
author Eva C. Sonnenschein
author2 Liwei Chu
Kai Yang
Chunhai Chen
Bo Zhao
Yanan Hou
Wanqiu Wang
Pu Zhao
Kaili Wang
Binhu Wang
Ying Xiao
Yongqiang Li
Yisong Li
Qijian Song
Biao Liu
Ruoxi Fan
Abhishek Bohra
Jianping Yu
Eva C. Sonnenschein
Rajeev K Varshney
Zhixi Tian
Jianbo Jian
Ping Wan
format Journal article
container_title Plant Biotechnology Journal
container_volume 22
container_issue 8
container_start_page 2173
publishDate 2024
institution Swansea University
issn 1467-7644
1467-7652
doi_str_mv 10.1111/pbi.14337
publisher Wiley
college_str Faculty of Science and Engineering
hierarchytype
hierarchy_top_id facultyofscienceandengineering
hierarchy_top_title Faculty of Science and Engineering
hierarchy_parent_id facultyofscienceandengineering
hierarchy_parent_title Faculty of Science and Engineering
department_str School of Biosciences, Geography and Physics - Biosciences{{{_:::_}}}Faculty of Science and Engineering{{{_:::_}}}School of Biosciences, Geography and Physics - Biosciences
document_store_str 1
active_str 0
description Adzuki bean (Vigna angularis) is an important legume crop cultivated in over 30 countries worldwide. We developed a high-quality chromosome-level reference genome of adzuki bean cultivar Jingnong6 by combining PacBio Sequel long-read sequencing with short-read and Hi-C technologies. The assembled genome covers 97.8% of the adzuki bean genome with a contig N50 of approximately 16 Mb and a total of 32 738 protein-coding genes. We also generated a comprehensive genome variation map of adzuki bean by whole-genome resequencing (WGRS) of 322 diverse adzuki beans accessions including both wild and cultivated. Furthermore, we have conducted comparative genomics and a genome-wide association study (GWAS) on key agricultural traits to investigate the evolution and domestication. GWAS identified several candidate genes, including VaCycA3;1, VaHB15, VaANR1 and VaBm, that exhibited significant associations with domestication traits. Furthermore, we conducted functional analyses on the roles of VaANR1 and VaBm in regulating seed coat colour. We provided evidence for the highest genetic diversity of wild adzuki (Vigna angularis var. nipponensis) in China with the presence of the most original wild adzuki bean, and the occurrence of domestication process facilitating transition from wild to cultigen. The present study elucidates the genetic basis of adzuki bean domestication traits and provides crucial genomic resources to support future breeding efforts in adzuki bean.
published_date 2024-08-01T13:07:32Z
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