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Jaiswal SK, Dakora FD. Seed-Coat Pigmentation Plays a Crucial Role in Partner Selection and N 2 Fixation in Legume-Root-Microbe Associations in African Soils. PLANTS (BASEL, SWITZERLAND) 2024; 13:1464. [PMID: 38891273 PMCID: PMC11175086 DOI: 10.3390/plants13111464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 05/17/2024] [Accepted: 05/22/2024] [Indexed: 06/21/2024]
Abstract
Legume-rhizobia symbiosis is the most important plant-microbe interaction in sustainable agriculture due to its ability to provide much needed N in cropping systems. This interaction is mediated by the mutual recognition of signaling molecules from the two partners, namely legumes and rhizobia. In legumes, these molecules are in the form of flavonoids and anthocyanins, which are responsible for the pigmentation of plant organs, such as seeds, flowers, fruits, and even leaves. Seed-coat pigmentation in legumes is a dominant factor influencing gene expression relating to N2 fixation and may be responsible for the different N2-fixing abilities observed among legume genotypes under field conditions in African soils. Common bean, cowpea, Kersting's groundnut, and Bambara groundnut landraces with black seed-coat color are reported to release higher concentrations of nod-gene-inducing flavonoids and anthocyanins compared with the Red and Cream landraces. Black seed-coat pigmentation is considered a biomarker for enhanced nodulation and N2 fixation in legumes. Cowpea, Bambara groundnut, and Kersting's bean with differing seed-coat colors are known to attract different soil rhizobia based on PCR-RFLP analysis of bacterial DNA. Even when seeds of the same legume with diverse seed-coat colors were planted together in one hole, the nodulating bradyrhizobia clustered differently in the PCR-RFLP dendrogram. Kersting's groundnut, Bambara groundnut, and cowpea with differing seed-coat colors were selectively nodulated by different bradyrhizobial species. The 16S rRNA amplicon sequencing also found significant selective influences of seed-coat pigmentation on microbial community structure in the rhizosphere of five Kersting's groundnut landraces. Seed-coat color therefore plays a dominant role in the selection of the bacterial partner in the legume-rhizobia symbiosis.
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Affiliation(s)
- Sanjay K. Jaiswal
- Department of Chemistry, Tshwane University of Technology, Arcadia Campus, Pretoria 0183, South Africa
| | - Felix D. Dakora
- Department of Chemistry, Tshwane University of Technology, Arcadia Campus, Pretoria 0183, South Africa
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Chu L, Yang K, Chen C, Zhao B, Hou Y, Wang W, Zhao P, Wang K, Wang B, Xiao Y, Li Y, Li Y, Song Q, Liu B, Fan R, Bohra A, Yu J, Sonnenschein EC, Varshney RK, Tian Z, Jian J, Wan P. Chromosome-level reference genome and resequencing of 322 accessions reveal evolution, genomic imprint and key agronomic traits in adzuki bean. PLANT BIOTECHNOLOGY JOURNAL 2024. [PMID: 38497586 DOI: 10.1111/pbi.14337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 02/22/2024] [Accepted: 03/02/2024] [Indexed: 03/19/2024]
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.
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Affiliation(s)
- Liwei Chu
- College of Plant Science and Technology, Key Laboratory of New Technology in Agricultural Application, Beijing University of Agriculture, Beijing, China
- College of Life and Health, Dalian University, Dalian, Liaoning, China
| | - Kai Yang
- College of Plant Science and Technology, Key Laboratory of New Technology in Agricultural Application, Beijing University of Agriculture, Beijing, China
| | | | - Bo Zhao
- College of Plant Science and Technology, Key Laboratory of New Technology in Agricultural Application, Beijing University of Agriculture, Beijing, China
| | - Yanan Hou
- College of Plant Science and Technology, Key Laboratory of New Technology in Agricultural Application, Beijing University of Agriculture, Beijing, China
| | | | - Pu Zhao
- College of Plant Science and Technology, Key Laboratory of New Technology in Agricultural Application, Beijing University of Agriculture, Beijing, China
| | - Kaili Wang
- College of Plant Science and Technology, Key Laboratory of New Technology in Agricultural Application, Beijing University of Agriculture, Beijing, China
| | - Binhu Wang
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Ying Xiao
- College of Plant Science and Technology, Key Laboratory of New Technology in Agricultural Application, Beijing University of Agriculture, Beijing, China
| | - Yongqiang Li
- College of Plant Science and Technology, Key Laboratory of New Technology in Agricultural Application, Beijing University of Agriculture, Beijing, China
| | - Yisong Li
- College of Plant Science and Technology, Key Laboratory of New Technology in Agricultural Application, Beijing University of Agriculture, Beijing, China
| | - Qijian Song
- Soybean Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, USDA-ARS, Beltsville, Maryland, USA
| | - Biao Liu
- College of Plant Science and Technology, Key Laboratory of New Technology in Agricultural Application, Beijing University of Agriculture, Beijing, China
| | - Ruoxi Fan
- College of Plant Science and Technology, Key Laboratory of New Technology in Agricultural Application, Beijing University of Agriculture, Beijing, China
| | - Abhishek Bohra
- WA State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, Western Australia, Australia
| | - Jianping Yu
- College of Plant Science and Technology, Key Laboratory of New Technology in Agricultural Application, Beijing University of Agriculture, Beijing, China
| | | | - Rajeev K Varshney
- WA State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, Western Australia, Australia
| | - Zhixi Tian
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Jianbo Jian
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Ping Wan
- College of Plant Science and Technology, Key Laboratory of New Technology in Agricultural Application, Beijing University of Agriculture, Beijing, China
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Wang Z, Zhao W, Huang Y, Zhao P, Yang K, Wan P, Chu L. Progress in Adzuki Bean Seed Coat Colour Studies. PLANTS (BASEL, SWITZERLAND) 2023; 12:3242. [PMID: 37765406 PMCID: PMC10536511 DOI: 10.3390/plants12183242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 08/28/2023] [Accepted: 08/30/2023] [Indexed: 09/29/2023]
Abstract
Seed coat colour is an important quality trait, domestication trait, and morphological marker, and it is closely associated with flavonoid and anthocyanin metabolism pathways. The seed coat colour of the adzuki bean, an important legume crop, influences the processing quality, the commodity itself, and its nutritional quality. In this review, a genetic analysis of different seed coat colours, gene mapping, metabolite content determination, and varietal improvement in adzuki bean are summarized. It provides further insight into gene mapping and cloning of seed coat colour genes and varietal improvements in adzuki beans.
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Affiliation(s)
- Zhen Wang
- Schools of Life and Health, Dalian University, No. 10 Xuefu Street, Dalian 116622, China; (Z.W.)
| | - Wei Zhao
- Schools of Life and Health, Dalian University, No. 10 Xuefu Street, Dalian 116622, China; (Z.W.)
| | - Yufei Huang
- Schools of Life and Health, Dalian University, No. 10 Xuefu Street, Dalian 116622, China; (Z.W.)
| | - Pu Zhao
- Key Laboratory of New Technology in Agricultural Application, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
| | - Kai Yang
- Key Laboratory of New Technology in Agricultural Application, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
| | - Ping Wan
- Key Laboratory of New Technology in Agricultural Application, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
| | - Liwei Chu
- Schools of Life and Health, Dalian University, No. 10 Xuefu Street, Dalian 116622, China; (Z.W.)
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Dwivedi SL, Chapman MA, Abberton MT, Akpojotor UL, Ortiz R. Exploiting genetic and genomic resources to enhance productivity and abiotic stress adaptation of underutilized pulses. Front Genet 2023; 14:1193780. [PMID: 37396035 PMCID: PMC10311922 DOI: 10.3389/fgene.2023.1193780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Accepted: 06/07/2023] [Indexed: 07/04/2023] Open
Abstract
Underutilized pulses and their wild relatives are typically stress tolerant and their seeds are packed with protein, fibers, minerals, vitamins, and phytochemicals. The consumption of such nutritionally dense legumes together with cereal-based food may promote global food and nutritional security. However, such species are deficient in a few or several desirable domestication traits thereby reducing their agronomic value, requiring further genetic enhancement for developing productive, nutritionally dense, and climate resilient cultivars. This review article considers 13 underutilized pulses and focuses on their germplasm holdings, diversity, crop-wild-crop gene flow, genome sequencing, syntenic relationships, the potential for breeding and transgenic manipulation, and the genetics of agronomic and stress tolerance traits. Recent progress has shown the potential for crop improvement and food security, for example, the genetic basis of stem determinacy and fragrance in moth bean and rice bean, multiple abiotic stress tolerant traits in horse gram and tepary bean, bruchid resistance in lima bean, low neurotoxin in grass pea, and photoperiod induced flowering and anthocyanin accumulation in adzuki bean have been investigated. Advances in introgression breeding to develop elite genetic stocks of grass pea with low β-ODAP (neurotoxin compound), resistance to Mungbean yellow mosaic India virus in black gram using rice bean, and abiotic stress adaptation in common bean, using genes from tepary bean have been carried out. This highlights their potential in wider breeding programs to introduce such traits in locally adapted cultivars. The potential of de-domestication or feralization in the evolution of new variants in these crops are also highlighted.
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Affiliation(s)
| | - Mark A. Chapman
- Biological Sciences, University of Southampton, Southampton, United Kingdom
| | | | | | - Rodomiro Ortiz
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
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Takahashi Y, Nasu H, Nakayama S, Tomooka N. Domestication of azuki bean and soybean in Japan: From the insight of archeological and molecular evidence. BREEDING SCIENCE 2023; 73:117-131. [PMID: 37404345 PMCID: PMC10316305 DOI: 10.1270/jsbbs.22074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 01/05/2023] [Indexed: 07/06/2023]
Abstract
Domestication of azuki bean and soybean has enabled them to acquire non-dormant seeds, non-shattering pods, and larger seed size. Seed remains of the Jomon period recently discovered at archeological sites in the Central Highlands of Japan (6,000-4,000 BP) suggest that the use of azuki bean and soybean and their increase in seed size began earlier in Japan than in China and Korea; molecular phylogenetic studies indicate that azuki bean and soybean originated in Japan. Recent identification of domestication genes indicate that the domestication traits of azuki bean and soybean were established by different mechanisms. Analyses of domestication related genes using DNA extracted from the seed remains would reveal further details about their domestication processes.
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Affiliation(s)
- Yu Takahashi
- Research Center of Genetic Resources, National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-8602, Japan
| | - Hiroo Nasu
- Faculty of Biosphere-Geosphere Science, Okayama University of Science, Okayama 700-0005, Japan
| | - Seiji Nakayama
- Research Institute of Cultural Properties, Teikyo University, Fuefuki, Yamanashi 406-0032, Japan
| | - Norihiko Tomooka
- Research Center of Genetic Resources, National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-8602, Japan
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Tayade R, Rana V, Shafiqul M, Nabi RBS, Raturi G, Dhar H, Thakral V, Kim Y. Genome-Wide Identification of Aquaporin Genes in Adzuki Bean ( Vigna angularis) and Expression Analysis under Drought Stress. Int J Mol Sci 2022; 23:ijms232416189. [PMID: 36555833 PMCID: PMC9782098 DOI: 10.3390/ijms232416189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 12/15/2022] [Accepted: 12/16/2022] [Indexed: 12/23/2022] Open
Abstract
The adzuki bean Vigna angularis (Wild.) is an important leguminous crop cultivated mainly for food purposes in Asian countries; it represents a source of carbohydrates, digestible proteins, minerals, and vitamins. Aquaporins (AQPs) are crucial membrane proteins involved in the transmembrane diffusion of water and small solutes in all living organisms, including plants. In this study, we used the whole genome sequence of the adzuki bean for in silico analysis to comprehensively identify 40 Vigna angularis aquaporin (VaAQP) genes and reveal how these plants react to drought stress. VaAQPs were compared with AQPs from other closely-related leguminous plants, and the results showed that mustard (Brassica rapa) (59), barrel medic (Medicago truncatula) (46), soybean (Glycine max) (66), and common bean (Phaseolus vulgaris L.) (41) had more AQP genes. Phylogenetic analysis revealed that forty VaAQPs belong to five subfamilies, with the VaPIPs (fifteen) subfamily the largest, followed by the VaNIPs (ten), VaTIPs (ten), VaSIPs (three), and VaXIPs (two) subfamilies. Furthermore, all AQP subcellular locations were found at the plasma membrane, and intron-exon analysis revealed a relationship between the intron number and gene expression, duplication, evolution, and diversity. Among the six motifs identified, motifs one, two, five, and six were prevalent in VaTIP, VaNIP, VaPIP, and VaXIP, while motifs one, three, and four were not observed in VaPIP1-3 and VaPIP1-4. Under drought stress, two of the VaAQPs (VaPIP2-1 and VaPIP2-5) showed significantly higher expression in the root tissue while the other two genes (VaPIP1-1 and VaPIP1-7) displayed variable expression in leaf tissue. This finding revealed that the selected VaAQPs might have unique molecular functions linked with the uptake of water under drought stress or in the exertion of osmoregulation to transport particular substrates rather than water to protect plants from drought. This study presents the first thorough investigation of VaAQPs in adzuki beans, and it reveals the transport mechanisms and related physiological processes that may be utilized for the development of drought-tolerant adzuki bean cultivars.
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Affiliation(s)
- Rupesh Tayade
- Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Varnika Rana
- National Agri-Food Biotechnology Institute (NABI), Mohali 140306, India
| | - Mohammad Shafiqul
- Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Rizwana Begum Syed Nabi
- Department of Southern Area Crop Science, National Institute of Crop Science, Rural Development Administration, Miryang 50424, Republic of Korea
| | - Gaurav Raturi
- National Agri-Food Biotechnology Institute (NABI), Mohali 140306, India
| | - Hena Dhar
- National Agri-Food Biotechnology Institute (NABI), Mohali 140306, India
| | - Vandana Thakral
- National Agri-Food Biotechnology Institute (NABI), Mohali 140306, India
| | - Yoonha Kim
- Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea
- Correspondence: ; Tel./Fax: +82-53-950-5710
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Desta KT, Yoon H, Shin MJ, Lee S, Wang XH, Choi YM, Yi JY. Variability of Anthocyanin Concentrations, Total Metabolite Contents and Antioxidant Activities in Adzuki Bean Cultivars. Antioxidants (Basel) 2022; 11:antiox11061134. [PMID: 35740028 PMCID: PMC9220110 DOI: 10.3390/antiox11061134] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 06/05/2022] [Accepted: 06/07/2022] [Indexed: 11/20/2022] Open
Abstract
In this study, adzuki bean cultivars including Arari, Chilbopat, Geomguseul, and Hongeon were recently cultivated, and the concentrations of seven individual anthocyanins were determined in their seed coats for the first time. Moreover, the variations of total saponin content (TSC), total phenolic content (TPC), 1,1-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging activity, Trolox equivalent antioxidant capacity (TEAC), and ferric reducing antioxidant power (FRAP) between defatted and undefatted extracts of whole seeds, seed coats, and dehulled seeds of each were analyzed. The anthocyanins were detected only in the black seed-coated cultivars and delphinidin-3-O-glucoside was dominant in both Geomguseul (12.46 mg/g) and Chilbopat (10.88 mg/g) followed by delphinidin-3-O-galactoside. TSC and TPC were in the ranges of 16.20−944.78 mg DE/g and 0.80−57.35 mg GAE/g, respectively, and each decreased in the order of seed coats > whole seeds > dehulled seeds regardless of extract type. The antioxidant activities also showed similar patterns of variation. Geomguseul seed coats outweighed the remaining cultivars in terms of TPC and FRAP activity (p < 0.05). Generally, significant variations of metabolite contents and antioxidant activities were observed between cultivars and across their seed parts (p < 0.05). Thence, black seed-coated adzuki beans could be excellent sources of anthocyanins and antioxidants.
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Zhao P, Chu L, Wang K, Zhao B, Li Y, Yang K, Wan P. Analyses on the pigment composition of different seed coat colors in adzuki bean. Food Sci Nutr 2022; 10:2611-2619. [PMID: 35959271 PMCID: PMC9361439 DOI: 10.1002/fsn3.2866] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 03/13/2022] [Accepted: 03/20/2022] [Indexed: 12/20/2022] Open
Abstract
Seed coat color is an important quality and domestication trait. The adzuki bean has more than a dozen seed coat colors closely associated with the anthocyanin and flavonoid metabolism pathways. In this study, we explored the pigment composition of 10 different seed coat color adzuki beans including red, black mottle on red, black mottle on gray, golden, green, black, ivory, brown, and light brown. The results showed that anthocyanins are the main pigment in adzuki bean seed coat. There were no carotenoid or pelargonidin derivatives in the seed coats of any accessions. Different colors of adzuki bean seed coat have different pigment compositions and the combination of procyanidins and anthocyanins affected seed coat color. The ivory seed coat had an extremely low proanthocyanidin and anthocyanin content. Only the green adzuki bean seed coats contained chlorophyll. Our results explain the pigment composition of the different seed coat colors and the combination of proanthocyanidins and anthocyanins affected seed coat color in adzuki bean. These results can provide a theoretical basis for the study of adzuki bean coloring mechanism.
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Affiliation(s)
- Pu Zhao
- Key Laboratory of New Technology in Agricultural Application College of Plant Science and Technology Beijing University of Agriculture Beijing China
| | - Liwei Chu
- Key Laboratory of New Technology in Agricultural Application College of Plant Science and Technology Beijing University of Agriculture Beijing China
- Institute of Modern Agricultural Research Dalian University Liaoning China
| | - Kaili Wang
- Key Laboratory of New Technology in Agricultural Application College of Plant Science and Technology Beijing University of Agriculture Beijing China
| | - Bo Zhao
- Key Laboratory of New Technology in Agricultural Application College of Plant Science and Technology Beijing University of Agriculture Beijing China
| | - Yisong Li
- Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture College of Bioscience and Resource Environment Beijing University of Agriculture Beijing China
| | - Kai Yang
- Key Laboratory of New Technology in Agricultural Application College of Plant Science and Technology Beijing University of Agriculture Beijing China
| | - Ping Wan
- Key Laboratory of New Technology in Agricultural Application College of Plant Science and Technology Beijing University of Agriculture Beijing China
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