Chromosome‐level reference genome and resequencing of 322 accessions reveal evolution, genomic imprint and key agronomic traits in adzuki bean
Summary 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 asse...
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| creator | Chu, Liwei Yang, Kai Chen, Chunhai Zhao, Bo Hou, Yanan Wang, Wanqiu Zhao, Pu Wang, Kaili Wang, Binhu Xiao, Ying Li, Yongqiang Li, Yisong Song, Qijian Liu, Biao Fan, Ruoxi Bohra, Abhishek Yu, Jianping Sonnenschein, Eva C. Varshney, Rajeev K Tian, Zhixi Jian, Jianbo Wan, Ping |
| description | Summary
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. |
| doi_str_mv | 10.1111/pbi.14337 |
| format | Article |
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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.</description><identifier>ISSN: 1467-7644</identifier><identifier>ISSN: 1467-7652</identifier><identifier>EISSN: 1467-7652</identifier><identifier>DOI: 10.1111/pbi.14337</identifier><identifier>PMID: 38497586</identifier><language>eng</language><publisher>England: John Wiley & Sons, Inc</publisher><subject>Adzuki bean ; agronomic traits ; Beans ; biotechnology ; China ; Chromosomes ; color ; Cultivars ; Cultivation ; Domestication ; Evolution ; Evolutionary genetics ; Gene sequencing ; Genes ; Genetic analysis ; Genetic diversity ; genetic variation ; genome ; Genome-wide association studies ; genome-wide association study ; Genomes ; Genomics ; Grain cultivation ; GWAS ; Legumes ; Phylogenetics ; Plant breeding ; Proteins ; seed coat ; seed coat colour ; Vigna angularis ; Vigna angularis var. nipponensis</subject><ispartof>Plant biotechnology journal, 2024-08, Vol.22 (8), p.2173-2185</ispartof><rights>2024 The Authors. published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.</rights><rights>2024 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.</rights><rights>2024. This work is published under http://creativecommons.org/licenses/by-nc-nd/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><cites>FETCH-LOGICAL-c3817-56e936e4e00ef310e0595bb3bf6288710bc21bd9d6f1e326ba955238cdb1382d3</cites><orcidid>0000-0002-4562-9131 ; 0000-0001-5468-9542 ; 0000-0001-6051-9670</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://onlinelibrary.wiley.com/doi/pdf/10.1111%2Fpbi.14337$$EPDF$$P50$$Gwiley$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://onlinelibrary.wiley.com/doi/full/10.1111%2Fpbi.14337$$EHTML$$P50$$Gwiley$$Hfree_for_read</linktohtml><link.rule.ids>314,776,780,860,1411,11541,27901,27902,45550,45551,46027,46451</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/38497586$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Chu, Liwei</creatorcontrib><creatorcontrib>Yang, Kai</creatorcontrib><creatorcontrib>Chen, Chunhai</creatorcontrib><creatorcontrib>Zhao, Bo</creatorcontrib><creatorcontrib>Hou, Yanan</creatorcontrib><creatorcontrib>Wang, Wanqiu</creatorcontrib><creatorcontrib>Zhao, Pu</creatorcontrib><creatorcontrib>Wang, Kaili</creatorcontrib><creatorcontrib>Wang, Binhu</creatorcontrib><creatorcontrib>Xiao, Ying</creatorcontrib><creatorcontrib>Li, Yongqiang</creatorcontrib><creatorcontrib>Li, Yisong</creatorcontrib><creatorcontrib>Song, Qijian</creatorcontrib><creatorcontrib>Liu, Biao</creatorcontrib><creatorcontrib>Fan, Ruoxi</creatorcontrib><creatorcontrib>Bohra, Abhishek</creatorcontrib><creatorcontrib>Yu, Jianping</creatorcontrib><creatorcontrib>Sonnenschein, Eva C.</creatorcontrib><creatorcontrib>Varshney, Rajeev K</creatorcontrib><creatorcontrib>Tian, Zhixi</creatorcontrib><creatorcontrib>Jian, Jianbo</creatorcontrib><creatorcontrib>Wan, Ping</creatorcontrib><title>Chromosome‐level reference genome and resequencing of 322 accessions reveal evolution, genomic imprint and key agronomic traits in adzuki bean</title><title>Plant biotechnology journal</title><addtitle>Plant Biotechnol J</addtitle><description>Summary
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.</description><subject>Adzuki bean</subject><subject>agronomic traits</subject><subject>Beans</subject><subject>biotechnology</subject><subject>China</subject><subject>Chromosomes</subject><subject>color</subject><subject>Cultivars</subject><subject>Cultivation</subject><subject>Domestication</subject><subject>Evolution</subject><subject>Evolutionary genetics</subject><subject>Gene sequencing</subject><subject>Genes</subject><subject>Genetic analysis</subject><subject>Genetic diversity</subject><subject>genetic variation</subject><subject>genome</subject><subject>Genome-wide association studies</subject><subject>genome-wide association study</subject><subject>Genomes</subject><subject>Genomics</subject><subject>Grain cultivation</subject><subject>GWAS</subject><subject>Legumes</subject><subject>Phylogenetics</subject><subject>Plant breeding</subject><subject>Proteins</subject><subject>seed coat</subject><subject>seed coat colour</subject><subject>Vigna angularis</subject><subject>Vigna angularis var. 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of 322 accessions reveal evolution, genomic imprint and key agronomic traits in adzuki bean</title><author>Chu, Liwei ; Yang, Kai ; Chen, Chunhai ; Zhao, Bo ; Hou, Yanan ; Wang, Wanqiu ; Zhao, Pu ; Wang, Kaili ; Wang, Binhu ; Xiao, Ying ; Li, Yongqiang ; Li, Yisong ; Song, Qijian ; Liu, Biao ; Fan, Ruoxi ; Bohra, Abhishek ; Yu, Jianping ; Sonnenschein, Eva C. ; Varshney, Rajeev K ; Tian, Zhixi ; Jian, Jianbo ; Wan, Ping</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c3817-56e936e4e00ef310e0595bb3bf6288710bc21bd9d6f1e326ba955238cdb1382d3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2024</creationdate><topic>Adzuki bean</topic><topic>agronomic traits</topic><topic>Beans</topic><topic>biotechnology</topic><topic>China</topic><topic>Chromosomes</topic><topic>color</topic><topic>Cultivars</topic><topic>Cultivation</topic><topic>Domestication</topic><topic>Evolution</topic><topic>Evolutionary genetics</topic><topic>Gene sequencing</topic><topic>Genes</topic><topic>Genetic analysis</topic><topic>Genetic diversity</topic><topic>genetic variation</topic><topic>genome</topic><topic>Genome-wide association studies</topic><topic>genome-wide association study</topic><topic>Genomes</topic><topic>Genomics</topic><topic>Grain cultivation</topic><topic>GWAS</topic><topic>Legumes</topic><topic>Phylogenetics</topic><topic>Plant breeding</topic><topic>Proteins</topic><topic>seed coat</topic><topic>seed coat colour</topic><topic>Vigna angularis</topic><topic>Vigna angularis var. nipponensis</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Chu, Liwei</creatorcontrib><creatorcontrib>Yang, Kai</creatorcontrib><creatorcontrib>Chen, Chunhai</creatorcontrib><creatorcontrib>Zhao, Bo</creatorcontrib><creatorcontrib>Hou, Yanan</creatorcontrib><creatorcontrib>Wang, Wanqiu</creatorcontrib><creatorcontrib>Zhao, Pu</creatorcontrib><creatorcontrib>Wang, 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Qijian</au><au>Liu, Biao</au><au>Fan, Ruoxi</au><au>Bohra, Abhishek</au><au>Yu, Jianping</au><au>Sonnenschein, Eva C.</au><au>Varshney, Rajeev K</au><au>Tian, Zhixi</au><au>Jian, Jianbo</au><au>Wan, Ping</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Chromosome‐level reference genome and resequencing of 322 accessions reveal evolution, genomic imprint and key agronomic traits in adzuki bean</atitle><jtitle>Plant biotechnology journal</jtitle><addtitle>Plant Biotechnol J</addtitle><date>2024-08</date><risdate>2024</risdate><volume>22</volume><issue>8</issue><spage>2173</spage><epage>2185</epage><pages>2173-2185</pages><issn>1467-7644</issn><issn>1467-7652</issn><eissn>1467-7652</eissn><abstract>Summary
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.</abstract><cop>England</cop><pub>John Wiley & Sons, Inc</pub><pmid>38497586</pmid><doi>10.1111/pbi.14337</doi><tpages>13</tpages><orcidid>https://orcid.org/0000-0002-4562-9131</orcidid><orcidid>https://orcid.org/0000-0001-5468-9542</orcidid><orcidid>https://orcid.org/0000-0001-6051-9670</orcidid><oa>free_for_read</oa></addata></record> |
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| subjects | Adzuki bean agronomic traits Beans biotechnology China Chromosomes color Cultivars Cultivation Domestication Evolution Evolutionary genetics Gene sequencing Genes Genetic analysis Genetic diversity genetic variation genome Genome-wide association studies genome-wide association study Genomes Genomics Grain cultivation GWAS Legumes Phylogenetics Plant breeding Proteins seed coat seed coat colour Vigna angularis Vigna angularis var. nipponensis |
| title | Chromosome‐level reference genome and resequencing of 322 accessions reveal evolution, genomic imprint and key agronomic traits in adzuki bean |
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