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Journal article
Chromosome-level reference genome and resequencing of 322 accessions reveal evolution, genomic imprint and key agronomic traits in adzuki bean
Plant biotechnology journal, Vol.22(8), pp.2173-2185
2024
PMID: 38497586
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 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.
Details
- Title
- Chromosome-level reference genome and resequencing of 322 accessions reveal evolution, genomic imprint and key agronomic traits in adzuki bean
- Authors/Creators
- Liwei Chu - Beijing University of AgricultureKai Yang - Beijing University of AgricultureChunhai Chen - BGI GroupBo Zhao - Beijing University of AgricultureYanan Hou - Beijing University of AgricultureWanqiu Wang - BGI GroupPu Zhao - Beijing University of AgricultureKaili Wang - Beijing University of AgricultureBinhu Wang - BGI GroupYing Xiao - College of Plant Science and Technology, Key Laboratory of New Technology in Agricultural Application, Beijing University of Agriculture, Beijing, ChinaYongqiang Li - Beijing University of AgricultureYisong Li - Beijing University of AgricultureQijian Song - Beltsville Agricultural Research CenterBiao Liu - Beijing University of AgricultureRuoxi Fan - Beijing University of AgricultureAbhishek Bohra - Murdoch UniversityJianping Yu - Beijing University of AgricultureEva C Sonnenschein - Swansea UniversityRajeev K Varshney - Murdoch UniversityZhixi Tian - Institute of Genetics and Developmental BiologyJianbo Jian - BGI GroupPing Wan - College of Plant Science and Technology, Key Laboratory of New Technology in Agricultural Application, Beijing University of Agriculture, Beijing, China
- Publication Details
- Plant biotechnology journal, Vol.22(8), pp.2173-2185
- Publisher
- Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.
- Grant note
- KZ201710020013 / Beijing Municipal Natural Science Foundation 31871697 / National Natural Science Foundation of China 2024115272-22 / New varieties breeding and Experimental demonstration of adzuki bean 2018YFD1000705 / National Key Research and Development Program of China 2018YFD1000700 / National Key Research and Development Program of China Food Futures Institute (Murdoch University)
- Identifiers
- 991005650756707891
- Copyright
- © 2024 The Authors.
- Murdoch Affiliation
- Food Futures Institute
- Language
- English
- Resource Type
- Journal article
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- Collaboration types
- Domestic collaboration
- International collaboration
- Citation topics
- 3 Agriculture, Environment & Ecology
- 3.4 Crop Science
- 3.4.96 QTL
- Web Of Science research areas
- Biotechnology & Applied Microbiology
- Plant Sciences
- ESI research areas
- Plant & Animal Science