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Ye A, Shen JN, Li Y, Lian X, Ma BG, Guo FB. Reconstruction of the genome-scale metabolic network model of Sinorhizobium fredii CCBAU45436 for free-living and symbiotic states. Front Bioeng Biotechnol 2024; 12:1377334. [PMID: 38590605 PMCID: PMC10999553 DOI: 10.3389/fbioe.2024.1377334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Accepted: 03/11/2024] [Indexed: 04/10/2024] Open
Abstract
Sinorhizobium fredii CCBAU45436 is an excellent rhizobium that plays an important role in agricultural production. However, there still needs more comprehensive understanding of the metabolic system of S. fredii CCBAU45436, which hinders its application in agriculture. Therefore, based on the first-generation metabolic model iCC541 we developed a new genome-scale metabolic model iAQY970, which contains 970 genes, 1,052 reactions, 942 metabolites and is scored 89% in the MEMOTE test. Cell growth phenotype predicted by iAQY970 is 81.7% consistent with the experimental data. The results of mapping the proteome data under free-living and symbiosis conditions to the model showed that the biomass production rate in the logarithmic phase was faster than that in the stable phase, and the nitrogen fixation efficiency of rhizobia parasitized in cultivated soybean was higher than that in wild-type soybean, which was consistent with the actual situation. In the symbiotic condition, there are 184 genes that would affect growth, of which 94 are essential; In the free-living condition, there are 143 genes that influence growth, of which 78 are essential. Among them, 86 of the 94 essential genes in the symbiotic condition were consistent with the prediction of iCC541, and 44 essential genes were confirmed by literature information; meanwhile, 30 genes were identified by DEG and 33 genes were identified by Geptop. In addition, we extracted four key nitrogen fixation modules from the model and predicted that sulfite reductase (EC 1.8.7.1) and nitrogenase (EC 1.18.6.1) as the target enzymes to enhance nitrogen fixation by MOMA, which provided a potential focus for strain optimization. Through the comprehensive metabolic model, we can better understand the metabolic capabilities of S. fredii CCBAU45436 and make full use of it in the future.
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Affiliation(s)
- Anqiang Ye
- Department of Respiratory and Critical Care Medicine, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, Wuhan University, Wuhan, China
| | - Jian-Ning Shen
- Department of Respiratory and Critical Care Medicine, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Yong Li
- Department of Respiratory and Critical Care Medicine, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Xiang Lian
- Department of Respiratory and Critical Care Medicine, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Bin-Guang Ma
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Feng-Biao Guo
- Department of Respiratory and Critical Care Medicine, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, Wuhan University, Wuhan, China
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Zhang Z, Zhang Z, Shan M, Amjad Z, Xue J, Zhang Z, Wang J, Guo Y. Genome-Wide Studies of FH Family Members in Soybean ( Glycine max) and Their Responses under Abiotic Stresses. PLANTS (BASEL, SWITZERLAND) 2024; 13:276. [PMID: 38256829 PMCID: PMC10820127 DOI: 10.3390/plants13020276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 01/10/2024] [Accepted: 01/15/2024] [Indexed: 01/24/2024]
Abstract
Formins or formin homology 2 (FH2) proteins, evolutionarily conserved multi-domain proteins in eukaryotes, serve as pivotal actin organizers, orchestrating the structure and dynamics of the actin cytoskeleton. However, a comprehensive investigation into the formin family and their plausible involvement in abiotic stress remains undocumented in soybean (Glycine max). In the current study, 34 soybean FH (GmFH)family members were discerned, their genomic distribution spanning the twenty chromosomes in a non-uniform pattern. Evolutionary analysis of the FH gene family across plant species delineated five discernible groups (Group I to V) and displayed a closer evolutionary relationship within Glycine soja, Glycine max, and Arabidopsis thaliana. Analysis of the gene structure of GmFH unveiled variable sequence lengths and substantial diversity in conserved motifs. Structural prediction in the promoter regions of GmFH gene suggested a large set of cis-acting elements associated with hormone signaling, plant growth and development, and stress responses. The investigation of the syntenic relationship revealed a greater convergence of GmFH genes with dicots, indicating a close evolutionary affinity. Transcriptome data unveiled distinctive expression patterns of several GmFH genes across diverse plant tissues and developmental stages, underscoring a spatiotemporal regulatory framework governing the transcriptional dynamics of GmFH gene. Gene expression and qRT-PCR analysis identified many GmFH genes with a dynamic pattern in response to abiotic stresses, revealing their potential roles in regulating plant stress adaptation. Additionally, protein interaction analysis highlighted an intricate web of interactions among diverse GmFH proteins. These findings collectively underscore a novel biological function of GmFH proteins in facilitating stress adaptation in soybeans.
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Affiliation(s)
- Zhenbiao Zhang
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Zhongqi Zhang
- Heze Academy of Agricultural Sciences, Heze 274000, China
| | - Muhammad Shan
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Zarmeena Amjad
- SINO_PAK Joint Research Laboratory, Institute of Plant Breeding and Biotechnology, MNS University of Agriculture, Multan 60000, Pakistan
| | - Jin Xue
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Zenglin Zhang
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Jie Wang
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Yongfeng Guo
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China
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3
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Wang Z, Han Q, Ji H. GmRj2/Rfg1 control of soybean-rhizobium-soil compatibility. TRENDS IN PLANT SCIENCE 2024; 29:7-9. [PMID: 37838520 DOI: 10.1016/j.tplants.2023.10.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 10/01/2023] [Accepted: 10/03/2023] [Indexed: 10/16/2023]
Abstract
Coordinated evolution and mutual adaptation of soybean-rhizobium-soil (SRS) are crucial for soybean distribution, but the genetic mechanism involved had remained unclear. In a recent study, Li et al. identified a natural variant of the GmRj2/Rfg1 gene that affected the ability of soybean to adapt to distinct soil types by controlling soybean-rhizobium interaction, thus unravelling the mystery of SRS compatibility.
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Affiliation(s)
- Zhijuan Wang
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qin Han
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430061, China; Laboratory of Risk Assessment for Oilseeds Products (Wuhan), Ministry of Agriculture, Wuhan 430061, China
| | - Hongtao Ji
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.
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4
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Nzepang DT, Gully D, Nguepjop JR, Zaiya Zazou A, Tossim HA, Sambou A, Rami JF, Hocher V, Fall S, Svistoonoff S, Fonceka D. Mapping of QTLs Associated with Biological Nitrogen Fixation Traits in Peanuts (Arachis hypogaea L.) Using an Interspecific Population Derived from the Cross between the Cultivated Species and Its Wild Ancestors. Genes (Basel) 2023; 14:genes14040797. [PMID: 37107555 PMCID: PMC10138160 DOI: 10.3390/genes14040797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 03/16/2023] [Accepted: 03/22/2023] [Indexed: 03/29/2023] Open
Abstract
Peanuts (Arachis hypogaea L.) are an allotetraploid grain legume mainly cultivated by poor farmers in Africa, in degraded soil and with low input systems. Further understanding nodulation genetic mechanisms could be a relevant option to facilitate the improvement of yield and lift up soil without synthetic fertilizers. We used a subset of 83 chromosome segment substitution lines (CSSLs) derived from the cross between a wild synthetic tetraploid AiAd (Arachis ipaensis × Arachis duranensis)4× and the cultivated variety Fleur11, and evaluated them for traits related to BNF under shade-house conditions. Three treatments were tested: without nitrogen; with nitrogen; and without nitrogen, but with added0 Bradyrhizobium vignae strain ISRA400. The leaf chlorophyll content and total biomass were used as surrogate traits for BNF. We found significant variations for both traits specially linked to BNF, and four QTLs (quantitative trait loci) were consistently mapped. At all QTLs, the wild alleles decreased the value of the trait, indicating a negative effect on BNF. A detailed characterization of the lines carrying those QTLs in controlled conditions showed that the QTLs affected the nitrogen fixation efficiency, nodule colonization, and development. Our results provide new insights into peanut nodulation mechanisms and could be used to target BNF traits in peanut breeding programs.
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Affiliation(s)
- Darius T. Nzepang
- Centre d’Etudes Régional pour l’Amélioration de l’Adaptation à la Sécheresse, CERAAS-Route de Khombole, Thiès BP 3320, Senegal
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
- Laboratoire Commun de Microbiologie (LCM) (IRD/ISRA/UCAD), Centre de Recherche de Bel Air, Dakar BP 1386, Senegal
- Laboratoire Mixte International Adaptation des Plantes et Microorganismes Associés aux Stress Environnementaux (LAPSE), Centre de Recherche de Bel Air, Dakar CP 18524, Senegal
- Dispositif de Recherche et de Formation en Partenariat, Innovation et Amélioration Variétale en Afrique de l’Ouest (IAVAO), CERAAS Route de Khombole, Thiès BP 3320, Senegal
| | - Djamel Gully
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
- Laboratoire Mixte International Adaptation des Plantes et Microorganismes Associés aux Stress Environnementaux (LAPSE), Centre de Recherche de Bel Air, Dakar CP 18524, Senegal
| | - Joël R. Nguepjop
- Centre d’Etudes Régional pour l’Amélioration de l’Adaptation à la Sécheresse, CERAAS-Route de Khombole, Thiès BP 3320, Senegal
- Dispositif de Recherche et de Formation en Partenariat, Innovation et Amélioration Variétale en Afrique de l’Ouest (IAVAO), CERAAS Route de Khombole, Thiès BP 3320, Senegal
- CIRAD, UMR AGAP, F-34398 Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Arlette Zaiya Zazou
- Institute of Agricultural Research for Development (IRAD) (IRAD), Maroua, Cameroon
| | - Hodo-Abalo Tossim
- Centre d’Etudes Régional pour l’Amélioration de l’Adaptation à la Sécheresse, CERAAS-Route de Khombole, Thiès BP 3320, Senegal
- Dispositif de Recherche et de Formation en Partenariat, Innovation et Amélioration Variétale en Afrique de l’Ouest (IAVAO), CERAAS Route de Khombole, Thiès BP 3320, Senegal
| | - Aissatou Sambou
- Centre d’Etudes Régional pour l’Amélioration de l’Adaptation à la Sécheresse, CERAAS-Route de Khombole, Thiès BP 3320, Senegal
- Dispositif de Recherche et de Formation en Partenariat, Innovation et Amélioration Variétale en Afrique de l’Ouest (IAVAO), CERAAS Route de Khombole, Thiès BP 3320, Senegal
| | - Jean-François Rami
- Dispositif de Recherche et de Formation en Partenariat, Innovation et Amélioration Variétale en Afrique de l’Ouest (IAVAO), CERAAS Route de Khombole, Thiès BP 3320, Senegal
- CIRAD, UMR AGAP, F-34398 Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Valerie Hocher
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
- Laboratoire Commun de Microbiologie (LCM) (IRD/ISRA/UCAD), Centre de Recherche de Bel Air, Dakar BP 1386, Senegal
- Laboratoire Mixte International Adaptation des Plantes et Microorganismes Associés aux Stress Environnementaux (LAPSE), Centre de Recherche de Bel Air, Dakar CP 18524, Senegal
| | - Saliou Fall
- Laboratoire Commun de Microbiologie (LCM) (IRD/ISRA/UCAD), Centre de Recherche de Bel Air, Dakar BP 1386, Senegal
- Laboratoire Mixte International Adaptation des Plantes et Microorganismes Associés aux Stress Environnementaux (LAPSE), Centre de Recherche de Bel Air, Dakar CP 18524, Senegal
| | - Sergio Svistoonoff
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
- Laboratoire Mixte International Adaptation des Plantes et Microorganismes Associés aux Stress Environnementaux (LAPSE), Centre de Recherche de Bel Air, Dakar CP 18524, Senegal
| | - Daniel Fonceka
- Centre d’Etudes Régional pour l’Amélioration de l’Adaptation à la Sécheresse, CERAAS-Route de Khombole, Thiès BP 3320, Senegal
- Dispositif de Recherche et de Formation en Partenariat, Innovation et Amélioration Variétale en Afrique de l’Ouest (IAVAO), CERAAS Route de Khombole, Thiès BP 3320, Senegal
- CIRAD, UMR AGAP, F-34398 Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
- Correspondence:
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Wang Z, Huang C, Niu Y, Yung WS, Xiao Z, Wong FL, Huang M, Wang X, Man CK, Sze CC, Liu A, Wang Q, Chen Y, Liu S, Wu C, Liu L, Hou W, Han T, Li MW, Lam HM. QTL analyses of soybean root system architecture revealed genetic relationships with shoot-related traits. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:4507-4522. [PMID: 36422673 DOI: 10.1007/s00122-022-04235-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 10/09/2022] [Indexed: 06/16/2023]
Abstract
The genetic basis of soybean root system architecture (RSA) and the genetic relationship between shoot and RSA were revealed by integrating data from recombinant inbred population grafting and QTL mapping. Variations in root system architecture (RSA) affect the functions of roots and thus play vital roles in plant adaptations and agricultural productivity. The aim of this study was to unravel the genetic relationship between RSA traits and shoot-related traits in soybean. This study characterized RSA variability at seedling stage in a recombinant inbred population, derived from a cross between cultivated soybean C08 and wild soybean W05, and performed high-resolution quantitative trait locus (QTL) mapping. In total, 34 and 41 QTLs were detected for RSA-related and shoot-related traits, respectively, constituting eight QTL clusters. Significant QTL correspondence was found between shoot biomass and RSA-related traits, consistent with significant correlations between these phenotypes. RSA-related QTLs also overlapped with selection regions in the genome, suggesting the cultivar RSA could be a partial consequence of domestication. Using reciprocal grafting, we confirmed that shoot-derived signals affected root development and the effects were controlled by multiple loci. Meanwhile, RSA-related QTLs were found to co-localize with four soybean flowering-time loci. Consistent with the phenotypes of the parental lines of our RI population, diminishing the function of flowering controlling E1 family through RNA interference (RNAi) led to reduced root growth. This implies that the flowering time-related genes within the RSA-related QTLs are actually contributing to RSA. To conclude, this study identified the QTLs that determine RSA through controlling root growth indirectly via regulating shoot functions, and discovered superior alleles from wild soybean that could be used to improve the root structure in existing soybean cultivars.
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Affiliation(s)
- Zhili Wang
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Cheng Huang
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
| | - Yongchao Niu
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Wai-Shing Yung
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Zhixia Xiao
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Fuk-Ling Wong
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Mingkun Huang
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, 332900, Jiangxi, China
| | - Xin Wang
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
| | - Chun-Kuen Man
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Ching-Ching Sze
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Ailin Liu
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Qianwen Wang
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Yinglong Chen
- The UWA Institute of Agriculture, & School of Agriculture and Environment, The University of Western Australia, Perth, WA6001, Australia
- State Key Laboratory of Soil Erosion and Dryland Farming On the Loess Plateau, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Shuo Liu
- State Key Laboratory of Soil Erosion and Dryland Farming On the Loess Plateau, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Cunxiang Wu
- Ministry of Agriculture and Rural Affairs Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, The Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, 100081, China
| | - Lifeng Liu
- Ministry of Agriculture and Rural Affairs Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, The Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, 100081, China
| | - Wensheng Hou
- Ministry of Agriculture and Rural Affairs Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, The Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, 100081, China
| | - Tianfu Han
- Ministry of Agriculture and Rural Affairs Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, The Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, 100081, China
| | - Man-Wah Li
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China.
| | - Hon-Ming Lam
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China.
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Kitaeva AB, Gorshkov AP, Kusakin PG, Sadovskaya AR, Tsyganova AV, Tsyganov VE. Tubulin Cytoskeleton Organization in Cells of Determinate Nodules. FRONTIERS IN PLANT SCIENCE 2022; 13:823183. [PMID: 35557719 PMCID: PMC9087740 DOI: 10.3389/fpls.2022.823183] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 03/23/2022] [Indexed: 06/15/2023]
Abstract
Plant cell differentiation is based on rearrangements of the tubulin cytoskeleton; this is also true for symbiotic nodules. Nevertheless, although for indeterminate nodules (with a long-lasting meristem) the organization of microtubules during nodule development has been studied for various species, for determinate ones (with limited meristem activity) such studies are rare. Here, we investigated bacteroid morphology and dynamics of the tubulin cytoskeleton in determinate nodules of four legume species: Glycine max, Glycine soja, Phaseolus vulgaris, and Lotus japonicus. The most pronounced differentiation of bacteroids was observed in G. soja nodules. In meristematic cells in incipient nodules of all analyzed species, the organization of both cortical and endoplasmic microtubules was similar to that described for meristematic cells of indeterminate nodules. In young infected cells in developing nodules of all four species, cortical microtubules formed irregular patterns (microtubules were criss-crossed) and endoplasmic ones were associated with infection threads and infection droplets. Surprisingly, in uninfected cells the patterns of cortical microtubules differed in nodules of G. max and G. soja on the one hand, and P. vulgaris and L. japonicus on the other. The first two species exhibited irregular patterns, while the remaining two exhibited regular ones (microtubules were oriented transversely to the longitudinal axis of cell) that are typical for uninfected cells of indeterminate nodules. In contrast to indeterminate nodules, in mature determinate nodules of all four studied species, cortical microtubules formed a regular pattern in infected cells. Thus, our analysis revealed common patterns of tubulin cytoskeleton in the determinate nodules of four legume species, and species-specific differences were associated with the organization of cortical microtubules in uninfected cells. When compared with indeterminate nodules, the most pronounced differences were associated with the organization of cortical microtubules in nitrogen-fixing infected cells. The revealed differences indicated a possible transition during evolution of infected cells from anisotropic growth in determinate nodules to isodiametric growth in indeterminate nodules. It can be assumed that this transition provided an evolutionary advantage to those legume species with indeterminate nodules, enabling them to host symbiosomes in their infected cells more efficiently.
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Affiliation(s)
- Anna B. Kitaeva
- Laboratory of Molecular and Cellular Biology, All-Russia Research Institute for Agricultural Microbiology, Saint Petersburg, Russia
| | - Artemii P. Gorshkov
- Laboratory of Molecular and Cellular Biology, All-Russia Research Institute for Agricultural Microbiology, Saint Petersburg, Russia
| | - Pyotr G. Kusakin
- Laboratory of Molecular and Cellular Biology, All-Russia Research Institute for Agricultural Microbiology, Saint Petersburg, Russia
| | | | - Anna V. Tsyganova
- Laboratory of Molecular and Cellular Biology, All-Russia Research Institute for Agricultural Microbiology, Saint Petersburg, Russia
| | - Viktor E. Tsyganov
- Laboratory of Molecular and Cellular Biology, All-Russia Research Institute for Agricultural Microbiology, Saint Petersburg, Russia
- Saint Petersburg Scientific Center RAS, Saint Petersburg, Russia
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7
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Impact of Fungi on Agriculture Production, Productivity, and Sustainability. Fungal Biol 2022. [DOI: 10.1007/978-981-16-8877-5_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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8
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Gebrai Y, Ghebremichael K, Mihelcic JR. A systems approach to analyzing food, energy, and water uses of a multifunctional crop: A review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 791:148254. [PMID: 34412387 DOI: 10.1016/j.scitotenv.2021.148254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 05/26/2021] [Accepted: 05/31/2021] [Indexed: 06/13/2023]
Abstract
Multifunctional crops can simultaneously contribute to multiple societal objectives. As a result, they represent an attractive means for improving rural livelihoods. Moringa oleifera is an example of a multifunctional crop that produces nutritious leaves with uses as food, fodder, and a biostimulant to enhance crop growth. It yields seeds containing a water purifying coagulant and oil with cosmetic uses and possible biofuel feedstock. Despite Moringa oleifera's (and other multifunctional crops') various Food-Energy-Water uses, optimizing the benefits of its multiple uses and livelihood improvements remains challenging. There is a need for holistic approaches capable of assessing the multifunctionality of agriculture and livelihood impacts. Therefore, this paper critically evaluates Moringa oleifera's Food-Energy-Water-Livelihood nexus applications to gain insight into the tradeoffs and synergies among its various applications using a systems thinking approach. A systems approach is proposed as a holistic thinking framework that can help navigate the complexity of a crop's multifunctionality. The "Success to the Successful" systems archetype was adopted to capture the competition between the need for leaf yields and seed yields. In areas where there is energy and water insecurity, Moringa oleifera seed production is recommended for its potential to coproduce oil, the water purifying coagulant, and a residue that can be applied as a fertilizer. In areas where food insecurity is an issue, focusing on leaf production would be beneficial due to its significance in augmenting food for human consumption, animal feed, and its use as a biostimulant to increase crop yields. A causal loop diagram was found to effectively map the interconnections among the various uses of Moringa oleifera and associated livelihood improvements. This framework provides stakeholders with a conceptual decision-making tool that can help maximize positive livelihood outcomes. This approach can also be applied for improved management of other multifunctional crops.
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Affiliation(s)
- Yoel Gebrai
- Department of Civil and Environmental Engineering, College of Engineering, University of South Florida, 4202 E Fowler Avenue, ENG 030, Tampa, FL 33620, United States of America
| | - Kebreab Ghebremichael
- Patel College of Global Sustainability, University of South Florida, 4202 E Fowler Avenue, CGS 238, Tampa, FL 33612, United States of America.
| | - James R Mihelcic
- Department of Civil and Environmental Engineering, College of Engineering, University of South Florida, 4202 E Fowler Avenue, ENG 030, Tampa, FL 33620, United States of America
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9
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Perkowski EA, Waring EF, Smith NG. Root mass carbon costs to acquire nitrogen are determined by nitrogen and light availability in two species with different nitrogen acquisition strategies. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:5766-5776. [PMID: 34114621 DOI: 10.1093/jxb/erab253] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 06/10/2021] [Indexed: 05/22/2023]
Abstract
Plant nitrogen acquisition requires carbon to be allocated belowground to build roots and sustain microbial associations. This carbon cost to acquire nitrogen varies by nitrogen acquisition strategy; however, the degree to which these costs vary due to nitrogen availability or demand has not been well tested under controlled conditions. We grew a species capable of forming associations with nitrogen-fixing bacteria (Glycine max) and a species not capable of forming such associations (Gossypium hirsutum) under four soil nitrogen levels to manipulate nitrogen availability and four light levels to manipulate nitrogen demand in a full-factorial greenhouse experiment. We quantified carbon costs to acquire nitrogen as the ratio of total root carbon to whole-plant nitrogen within each treatment combination. In both species, light availability increased carbon costs due to a larger increase in root carbon than whole-plant nitrogen, while nitrogen fertilization generally decreased carbon costs due to a larger increase in whole-plant nitrogen than root carbon. Nodulation data indicated that G. max shifted relative carbon allocation from nitrogen fixation to direct uptake with increased nitrogen fertilization. These findings suggest that carbon costs to acquire nitrogen are modified by changes in light and nitrogen availability in species with and without associations with nitrogen-fixing bacteria.
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Affiliation(s)
- Evan A Perkowski
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA
| | - Elizabeth F Waring
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA
- Department of Natural Sciences, Northeastern State University, Tahlequah, OK, USA
| | - Nicholas G Smith
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA
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10
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Fan K, Wong-Bajracharya J, Lin X, Ni M, Ku YS, Li MW, Tian CF, Chan TF, Lam HM. Differentially expressed microRNAs that target functional genes in mature soybean nodules. THE PLANT GENOME 2021; 14:e20103. [PMID: 33973410 DOI: 10.1002/tpg2.20103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Accepted: 03/29/2021] [Indexed: 06/12/2023]
Abstract
MicroRNAs (miRNAs) are important regulators of biological functions in plants. To find out what roles miRNAs play in regulating symbiotic nitrogen fixation (SNF) in soybean [Glycine max (L.) Merr.], we identified high-confidence differentially expressed (DE) miRNAs from uninoculated roots (UR), rhizobium-inoculated roots (IR), and nodules (NODs) of soybean by robust small RNA sequencing (sRNA-seq). Based on their predicted target messenger RNAs (mRNAs), the expression profiles of some of these DE miRNAs could be linked to nodule functions. In particular, several miRNAs associated with nutrient transportation genes were differentially expressed in IRs and mature NODs. MiR399b, specifically, was highly induced in IRs and NODs, as well as by inorganic phosphate (Pi) starvation. In composite soybean plants overexpressing miR399b, PHOSPHATE2 (PHO2), a known target of miR399b that inhibits the activities of high-affinity Pi transporters, was strongly repressed. In addition, the overexpression of miR399b in the roots of transgenic composite plants significantly improved whole-plant Pi and ureide concentrations and the overall growth in terms of leaf node numbers and whole-plant dry weight. Our findings suggest that the induction of miR399b in NODs could enhance nitrogen fixation and soybean growth, possibly via improving Pi uptake to achieve a better Pi-nitrogen balance to promote SNF in nodules.
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Affiliation(s)
- Kejing Fan
- School of Life Sciences and Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, HKSAR, Hong Kong
| | - Johanna Wong-Bajracharya
- School of Life Sciences and Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, HKSAR, Hong Kong
| | - Xiao Lin
- School of Life Sciences and Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, HKSAR, Hong Kong
| | - Meng Ni
- School of Life Sciences and Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, HKSAR, Hong Kong
| | - Yee-Shan Ku
- School of Life Sciences and Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, HKSAR, Hong Kong
| | - Man-Wah Li
- School of Life Sciences and Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, HKSAR, Hong Kong
| | - Chang Fu Tian
- State Key Laboratory of Agrobiotechnology, MOA Key Laboratory of Soil Microbiology, Rhizobium Research Center, and College of Biological Sciences, China Agricultural University, Beijing, China
| | - Ting-Fung Chan
- School of Life Sciences and Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, HKSAR, Hong Kong
| | - Hon-Ming Lam
- School of Life Sciences and Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, HKSAR, Hong Kong
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11
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Goyal RK, Mattoo AK, Schmidt MA. Rhizobial-Host Interactions and Symbiotic Nitrogen Fixation in Legume Crops Toward Agriculture Sustainability. Front Microbiol 2021; 12:669404. [PMID: 34177848 PMCID: PMC8226219 DOI: 10.3389/fmicb.2021.669404] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 04/29/2021] [Indexed: 11/13/2022] Open
Abstract
Symbiotic nitrogen fixation (SNF) process makes legume crops self-sufficient in nitrogen (N) in sharp contrast to cereal crops that require an external input by N-fertilizers. Since the latter process in cereal crops results in a huge quantity of greenhouse gas emission, the legume production systems are considered efficient and important for sustainable agriculture and climate preservation. Despite benefits of SNF, and the fact that chemical N-fertilizers cause N-pollution of the ecosystems, the focus on improving SNF efficiency in legumes did not become a breeder’s priority. The size and stability of heritable effects under different environment conditions weigh significantly on any trait useful in breeding strategies. Here we review the challenges and progress made toward decoding the heritable components of SNF, which is considerably more complex than other crop allelic traits since the process involves genetic elements of both the host and the symbiotic rhizobial species. SNF-efficient rhizobial species designed based on the genetics of the host and its symbiotic partner face the test of a unique microbiome for its success and productivity. The progress made thus far in commercial legume crops with relevance to the dynamics of host–rhizobia interaction, environmental impact on rhizobial performance challenges, and what collectively determines the SNF efficiency under field conditions are also reviewed here.
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Affiliation(s)
- Ravinder K Goyal
- Agriculture and Agri-Food Canada, Lacombe Research and Development Centre, Lacombe, AB, Canada
| | - Autar K Mattoo
- Sustainable Agricultural Systems Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville Agricultural Research Center, Beltsville, MD, United States
| | - Maria Augusta Schmidt
- Agriculture and Agri-Food Canada, Lacombe Research and Development Centre, Lacombe, AB, Canada
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12
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Togashi A, Oikawa S. Leaf productivity and persistence have been improved during soybean (Glycine max) domestication and evolution. JOURNAL OF PLANT RESEARCH 2021; 134:223-233. [PMID: 33576933 DOI: 10.1007/s10265-021-01263-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 01/31/2021] [Indexed: 06/12/2023]
Abstract
Artificial and natural selection improved the leaf photosynthetic rate of soybean (Glycine max (L.) Merr. subsp. max). This change may be accompanied by unconscious, undesired changes in other leaf traits, such as decreased leaf persistence, if a finite resource was shared by two or more leaf traits-i.e., if they were traded off. We investigated leaf traits related to productivity (leaf photosynthetic rate, leaf nitrogen content, and stomatal conductance) and those related to persistence (leaf lifespan, leaf mass per unit area, and leaf bulk density) in one wild soybean line and three domesticated soybean lines (a landrace, an old cultivar, and a modern cultivar) in a three year experiment. Some leaf trait values increased while others did not change significantly during domestication and evolution. These results indicate that productivity-related leaf traits and persistence-related leaf traits are not negatively correlated. It was also found that the changes in productivity-related leaf traits and persistence-related leaf traits occurred at different times. Our results indicate that the productivity-related leaf traits and the persistence-related leaf traits have been independently selected for in soybean, and that they were not traded off. Combination of high leaf productivity and high leaf persistence would lead to higher lifetime leaf carbon gain and increased soybean yield.
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Affiliation(s)
- Ayaka Togashi
- Graduate School of Science and Engineering, Ibaraki University, Mito, 310-0056, Japan
| | - Shimpei Oikawa
- Graduate School of Science and Engineering, Ibaraki University, Mito, 310-0056, Japan.
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13
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Yan H, Liu Q, Wen F, Bai B, Wen Y, Chen W, Lu W, Lin Y, Xia Q, Wang G. Characterization and potential application of an α-amylase (BmAmy1) selected during silkworm domestication. Int J Biol Macromol 2020; 167:1102-1112. [PMID: 33188814 DOI: 10.1016/j.ijbiomac.2020.11.064] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Revised: 11/07/2020] [Accepted: 11/09/2020] [Indexed: 01/06/2023]
Abstract
Efficient resource utilization plays a central role in the high productivity of domesticated plants and animals. Whether artificial selection acts on digestive enzymes in the domesticated silkworm (Bombyx mori), which is larger than its wild ancestor, Bombyx mandarina (B. mandarina), remains unknown. In this study, we present the characteristics of a novel alpha-amylase, BmAmy1, in B. mori. The activity of recombinant BmAmy1 was maximal at 35 °C and pH 9.0, and could be suppressed by amylase inhibitors from mulberry, the exclusive food source of silkworms. Three different transposable element fragments, which were independently inserted in the 5'-upstream regulatory region, might be responsible for the enhanced expression of BmAmy1 in different domesticated silkworm strains as revealed by dual-luciferase reporter assay. The BmAmy1 overexpression increased the weight of female and male B. mori by 11.9% and 6.8%, respectively, compared with non-transgenic controls. Our results emphasize that, by exploring the genetic mechanisms of human-selected traits, the domestication process could be further accelerated through genetic engineering and targeted breeding.
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Affiliation(s)
- Hao Yan
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400716, China; Chongqing Key Laboratory of Sericultural Science, Southwest University, Chongqing 400716, China; Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing 400716, China
| | - Qingsong Liu
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400716, China; Chongqing Key Laboratory of Sericultural Science, Southwest University, Chongqing 400716, China; Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing 400716, China
| | - Feng Wen
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400716, China; Chongqing Key Laboratory of Sericultural Science, Southwest University, Chongqing 400716, China; Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing 400716, China
| | - Bingchuan Bai
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400716, China; Chongqing Key Laboratory of Sericultural Science, Southwest University, Chongqing 400716, China; Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing 400716, China
| | - Yuchan Wen
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400716, China; Chongqing Key Laboratory of Sericultural Science, Southwest University, Chongqing 400716, China; Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing 400716, China
| | - Wenwen Chen
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400716, China; Chongqing Key Laboratory of Sericultural Science, Southwest University, Chongqing 400716, China; Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing 400716, China
| | - Wei Lu
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400716, China; Chongqing Key Laboratory of Sericultural Science, Southwest University, Chongqing 400716, China; Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing 400716, China
| | - Ying Lin
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400716, China; Chongqing Key Laboratory of Sericultural Science, Southwest University, Chongqing 400716, China; Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing 400716, China
| | - Qingyou Xia
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400716, China; Chongqing Key Laboratory of Sericultural Science, Southwest University, Chongqing 400716, China; Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing 400716, China
| | - Genhong Wang
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400716, China; Chongqing Key Laboratory of Sericultural Science, Southwest University, Chongqing 400716, China; Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing 400716, China.
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14
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Liu A, Ku YS, Contador CA, Lam HM. The Impacts of Domestication and Agricultural Practices on Legume Nutrient Acquisition Through Symbiosis With Rhizobia and Arbuscular Mycorrhizal Fungi. Front Genet 2020; 11:583954. [PMID: 33193716 PMCID: PMC7554533 DOI: 10.3389/fgene.2020.583954] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 09/08/2020] [Indexed: 12/03/2022] Open
Abstract
Legumes are unique among plants as they can obtain nitrogen through symbiosis with nitrogen-fixing rhizobia that form root nodules in the host plants. Therefore they are valuable crops for sustainable agriculture. Increasing nitrogen fixation efficiency is not only important for achieving better plant growth and yield, but it is also crucial for reducing the use of nitrogen fertilizer. Arbuscular mycorrhizal fungi (AMF) are another group of important beneficial microorganisms that form symbiotic relationships with legumes. AMF can promote host plant growth by providing mineral nutrients and improving the soil ecosystem. The trilateral legume-rhizobia-AMF symbiotic relationships also enhance plant development and tolerance against biotic and abiotic stresses. It is known that domestication and agricultural activities have led to the reduced genetic diversity of cultivated germplasms and higher sensitivity to nutrient deficiencies in crop plants, but how domestication has impacted the capability of legumes to establish beneficial associations with rhizospheric microbes (including rhizobia and fungi) is not well-studied. In this review, we will discuss the impacts of domestication and agricultural practices on the interactions between legumes and soil microbes, focusing on the effects on AMF and rhizobial symbioses and hence nutrient acquisition by host legumes. In addition, we will summarize the genes involved in legume-microbe interactions and studies that have contributed to a better understanding of legume symbiotic associations using metabolic modeling.
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Affiliation(s)
| | | | | | - Hon-Ming Lam
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
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15
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Liu J, Yu X, Qin Q, Dinkins RD, Zhu H. The Impacts of Domestication and Breeding on Nitrogen Fixation Symbiosis in Legumes. Front Genet 2020; 11:00973. [PMID: 33014021 PMCID: PMC7461779 DOI: 10.3389/fgene.2020.00973] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 07/31/2020] [Indexed: 01/12/2023] Open
Abstract
Legumes are the second most important family of crop plants. One defining feature of legumes is their unique ability to establish a nitrogen-fixing root nodule symbiosis with soil bacteria known as rhizobia. Since domestication from their wild relatives, crop legumes have been under intensive breeding to improve yield and other agronomic traits but with little attention paid to the belowground symbiosis traits. Theoretical models predict that domestication and breeding processes, coupled with high−input agricultural practices, might have reduced the capacity of crop legumes to achieve their full potential of nitrogen fixation symbiosis. Testing this prediction requires characterizing symbiosis traits in wild and breeding populations under both natural and cultivated environments using genetic, genomic, and ecological approaches. However, very few experimental studies have been dedicated to this area of research. Here, we review how legumes regulate their interactions with soil rhizobia and how domestication, breeding and agricultural practices might have affected nodulation capacity, nitrogen fixation efficiency, and the composition and function of rhizobial community. We also provide a perspective on how to improve legume-rhizobial symbiosis in sustainable agricultural systems.
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Affiliation(s)
- Jinge Liu
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, United States
| | - Xiaocheng Yu
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, United States
| | - Qiulin Qin
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, United States
| | - Randy D Dinkins
- Forage-Animal Production Research Unit, United States Department of Agriculture-Agricultural Research Service, Lexington, KY, United States
| | - Hongyan Zhu
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, United States
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16
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Lescano I. Determination of Ureides Content in Plant Tissues. Bio Protoc 2020; 10:e3642. [PMID: 33659312 DOI: 10.21769/bioprotoc.3642] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 04/14/2020] [Accepted: 04/16/2020] [Indexed: 11/02/2022] Open
Abstract
The ureides allantoin and allantoate are the main organic nitrogen compounds transported in several legumes, predominantly from N2 fixation. Moreover, recent studies point out a remarkable role for allantoin during several stress responses of plants other than legumes. The goal of this protocol is to determine ureides concentration in different plant tissues. Ureides are extracted from plant material by boiling it in phosphate buffer. The allantoin and allantoate present in the supernatants are subjected to alkaline-acidic hydrolysis to glyoxylate. The glyoxylate is converted into glycoxylic acid phenylhydrazone, that is then oxidized to red-colored 1,5-diphenylformazan. The absorbance of supernatants is measured using a spectrophotometer at 520 nm. Ureides concentration can be inferred by using a glyoxylate calibration curve. Ureide quantification of different tissues of Arabidopsis thaliana and soybean plants were carried out following this protocol.
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Affiliation(s)
- Ignacio Lescano
- Instituto Multidisciplinario de Biología Vegetal - Universidad Nacional de Córdoba, CONICET, Córdoba, Argentina
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17
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Liu S, Liao LL, Nie MM, Peng WT, Zhang MS, Lei JN, Zhong YJ, Liao H, Chen ZC. A VIT-like transporter facilitates iron transport into nodule symbiosomes for nitrogen fixation in soybean. THE NEW PHYTOLOGIST 2020; 226:1413-1428. [PMID: 32119117 DOI: 10.1111/nph.16506] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 02/17/2020] [Indexed: 06/10/2023]
Abstract
Effective legume-rhizobia symbiosis depends on efficient nutrient exchange. Rhizobia need to synthesize iron-containing proteins for symbiotic nitrogen fixation (SNF) in nodules, which depends on host plant-mediated iron uptake into the symbiosome. We functionally investigated a pair of vacuolar iron transporter like (VTL) genes, GmVTL1a/b, in soybean (Glycine max) and evaluated their contributions to SNF, including investigations of gene expression patterns, subcellular localization, and mutant phenotypes. Though both GmVTL1a/b genes were specifically expressed in the fixation zone of the nodule, GmVTL1a was the lone member to be localized at the tonoplast of tobacco protoplasts, and shown to facilitate ferrous iron transport in yeast. GmVTL1a targets the symbiosome in infected cells, as verified by in situ immunostaining. Two vtl1 knockout mutants had lower iron concentrations in nodule cell sap and peribacteroid units than in wild-type plants, suggesting that GmVTL1 knockout inhibited iron import into symbiosomes. Furthermore, GmVTL1 knockout minimally affected soybean growth under nonsymbiotic conditions, but dramatically impaired nodule development and SNF activity under nitrogen-limited and rhizobia-inoculation conditions, which eventually led to growth retardation. Taken together, these results demonstrate that GmVTL1a is indispensable for SNF in nodules as a transporter of ferrous iron from the infected root cell cytosol to the symbiosome.
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Affiliation(s)
- Sheng Liu
- Root Biology Center, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Li Li Liao
- Root Biology Center, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Miao Miao Nie
- Root Biology Center, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Wen Ting Peng
- Root Biology Center, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Meng Shi Zhang
- Root Biology Center, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jia Ning Lei
- Vector-borne Virus Research Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yong Jia Zhong
- Root Biology Center, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Hong Liao
- Root Biology Center, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zhi Chang Chen
- Root Biology Center, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
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18
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Metabolic Analyses of Nitrogen Fixation in the Soybean Microsymbiont Sinorhizobium fredii Using Constraint-Based Modeling. mSystems 2020; 5:5/1/e00516-19. [PMID: 32071157 PMCID: PMC7029217 DOI: 10.1128/msystems.00516-19] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Nitrogen is the most limiting macronutrient for plant growth, and rhizobia are important bacteria for agriculture because they can fix atmospheric nitrogen and make it available to legumes through the establishment of a symbiotic relationship with their host plants. In this work, we studied the nitrogen fixation process in the microsymbiont Sinorhizobium fredii at the genome level. A metabolic model was built using genome annotation and literature to reconstruct the symbiotic form of S. fredii. Genes controlling the nitrogen fixation process were identified by simulating gene knockouts. Additionally, the nitrogen-fixing capacities of S. fredii CCBAU45436 in symbiosis with cultivated and wild soybeans were evaluated. The predictions suggested an outperformance of S. fredii with cultivated soybean, consistent with published experimental evidence. The reconstruction presented here will help to understand and improve nitrogen fixation capabilities of S. fredii and will be beneficial for agriculture by reducing the reliance on fertilizer applications. Rhizobia are soil bacteria able to establish symbiosis with diverse host plants. Specifically, Sinorhizobium fredii is a soil bacterium that forms nitrogen-fixing root nodules in diverse legumes, including soybean. The strain S. fredii CCBAU45436 is a dominant sublineage of S. fredii that nodulates soybeans in alkaline-saline soils in the Huang-Huai-Hai Plain region of China. Here, we present a manually curated metabolic model of the symbiotic form of Sinorhizobium fredii CCBAU45436. A symbiosis reaction was defined to describe the specific soybean-microsymbiont association. The performance and quality of the reconstruction had a 70% score when assessed using a standardized genome-scale metabolic model test suite. The model was used to evaluate in silico single-gene knockouts to determine the genes controlling the nitrogen fixation process. One hundred forty-one of 541 genes (26%) were found to influence the symbiotic process, wherein 121 genes were predicted as essential and 20 others as having a partial effect. Transcriptomic profiles of CCBAU45436 were used to evaluate the nitrogen fixation capacity in cultivated versus in wild soybean inoculated with the microsymbiont. The model quantified the nitrogen fixation activities of the strain in these two hosts and predicted a higher nitrogen fixation capacity in cultivated soybean. Our results are consistent with published data demonstrating larger amounts of ureides and total nitrogen in cultivated soybean than in wild soybean. This work presents the first metabolic network reconstruction of S. fredii as an example of a useful tool for exploring the potential benefits of microsymbionts to sustainable agriculture and the ecosystem. IMPORTANCE Nitrogen is the most limiting macronutrient for plant growth, and rhizobia are important bacteria for agriculture because they can fix atmospheric nitrogen and make it available to legumes through the establishment of a symbiotic relationship with their host plants. In this work, we studied the nitrogen fixation process in the microsymbiont Sinorhizobium fredii at the genome level. A metabolic model was built using genome annotation and literature to reconstruct the symbiotic form of S. fredii. Genes controlling the nitrogen fixation process were identified by simulating gene knockouts. Additionally, the nitrogen-fixing capacities of S. fredii CCBAU45436 in symbiosis with cultivated and wild soybeans were evaluated. The predictions suggested an outperformance of S. fredii with cultivated soybean, consistent with published experimental evidence. The reconstruction presented here will help to understand and improve nitrogen fixation capabilities of S. fredii and will be beneficial for agriculture by reducing the reliance on fertilizer applications.
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19
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Kepler RM, Epp Schmidt DJ, Yarwood SA, Cavigelli MA, Reddy KN, Duke SO, Bradley CA, Williams MM, Buyer JS, Maul JE. Soil Microbial Communities in Diverse Agroecosystems Exposed to the Herbicide Glyphosate. Appl Environ Microbiol 2020; 86:e01744-19. [PMID: 31836576 PMCID: PMC7028976 DOI: 10.1128/aem.01744-19] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 11/24/2019] [Indexed: 11/20/2022] Open
Abstract
Despite glyphosate's wide use for weed control in agriculture, questions remain about the herbicide's effect on soil microbial communities. The existing scientific literature contains conflicting results, from no observable effect of glyphosate to the enrichment of agricultural pathogens such as Fusarium spp. We conducted a comprehensive field-based study to compare the microbial communities on the roots of plants that received a foliar application of glyphosate to adjacent plants that did not. The 2-year study was conducted in Beltsville, MD, and Stoneville, MS, with corn and soybean crops grown in a variety of organic and conventional farming systems. By sequencing environmental metabarcode amplicons, the prokaryotic and fungal communities were described, along with chemical and physical properties of the soil. Sections of corn and soybean roots were plated to screen for the presence of plant pathogens. Geography, farming system, and season were significant factors determining the composition of fungal and prokaryotic communities. Plots treated with glyphosate did not differ from untreated plots in overall microbial community composition after controlling for other factors. We did not detect an effect of glyphosate treatment on the relative abundance of organisms such as Fusarium spp.IMPORTANCE Increasing the efficiency of food production systems while reducing negative environmental effects remains a key societal challenge to successfully meet the needs of a growing global population. The herbicide glyphosate has become a nearly ubiquitous component of agricultural production across the globe, enabling an increasing adoption of no-till agriculture. Despite this widespread use, there remains considerable debate on the consequences of glyphosate exposure. In this paper, we examine the effect of glyphosate on soil microbial communities associated with the roots of glyphosate-resistant crops. Using metabarcoding techniques, we evaluated prokaryotic and fungal communities from agricultural soil samples (n = 768). No effects of glyphosate were found on soil microbial communities associated with glyphosate-resistant corn and soybean varieties across diverse farming systems.
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Affiliation(s)
- Ryan M Kepler
- Sustainable Agricultural Systems Laboratory, USDA-ARS, Beltsville, Maryland, USA
| | - Dietrich J Epp Schmidt
- Environmental Science and Technology Department, University of Maryland, College Park, Maryland, USA
| | - Stephanie A Yarwood
- Environmental Science and Technology Department, University of Maryland, College Park, Maryland, USA
| | - Michel A Cavigelli
- Sustainable Agricultural Systems Laboratory, USDA-ARS, Beltsville, Maryland, USA
| | - Krishna N Reddy
- Crop Production Systems Research Unit, USDA-ARS, Stoneville, Mississippi, USA
| | - Stephen O Duke
- Natural Products Utilization Research Unit, USDA-ARS, University of Mississippi, University, Mississippi, USA
| | - Carl A Bradley
- Department of Plant Pathology, University of Kentucky Research and Education Center, Princeton, Kentucky, USA
| | - Martin M Williams
- Global Change and Photosynthesis Research, USDA-ARS, Urbana, Illinois, USA
| | - Jeffrey S Buyer
- Sustainable Agricultural Systems Laboratory, USDA-ARS, Beltsville, Maryland, USA
| | - Jude E Maul
- Sustainable Agricultural Systems Laboratory, USDA-ARS, Beltsville, Maryland, USA
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20
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Kibido T, Kunert K, Makgopa M, Greve M, Vorster J. Improvement of rhizobium‐soybean symbiosis and nitrogen fixation under drought. Food Energy Secur 2020. [DOI: 10.1002/fes3.177] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Tsholofelo Kibido
- Department of Plant and Soil Sciences University of Pretoria Pretoria South Africa
- Forestry and Agricultural Biotechnology Institute University of Pretoria Pretoria South Africa
| | - Karl Kunert
- Department of Plant and Soil Sciences University of Pretoria Pretoria South Africa
- Forestry and Agricultural Biotechnology Institute University of Pretoria Pretoria South Africa
| | - Matome Makgopa
- Department of Plant and Soil Sciences University of Pretoria Pretoria South Africa
| | - Michelle Greve
- Department of Plant and Soil Sciences University of Pretoria Pretoria South Africa
| | - Juan Vorster
- Department of Plant and Soil Sciences University of Pretoria Pretoria South Africa
- Forestry and Agricultural Biotechnology Institute University of Pretoria Pretoria South Africa
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21
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Current Progress in Nitrogen Fixing Plants and Microbiome Research. PLANTS 2020; 9:plants9010097. [PMID: 31940996 PMCID: PMC7020401 DOI: 10.3390/plants9010097] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 01/02/2020] [Accepted: 01/08/2020] [Indexed: 01/10/2023]
Abstract
In agroecosystems, nitrogen is one of the major nutrients limiting plant growth. To meet the increased nitrogen demand in agriculture, synthetic fertilizers have been used extensively in the latter part of the twentieth century, which have led to environmental challenges such as nitrate pollution. Biological nitrogen fixation (BNF) in plants is an essential mechanism for sustainable agricultural production and healthy ecosystem functioning. BNF by legumes and associative, endosymbiotic, and endophytic nitrogen fixation in non-legumes play major roles in reducing the use of synthetic nitrogen fertilizer in agriculture, increased plant nutrient content, and soil health reclamation. This review discusses the process of nitrogen-fixation in plants, nodule formation, the genes involved in plant-rhizobia interaction, and nitrogen-fixing legume and non-legume plants. This review also elaborates on current research efforts involved in transferring nitrogen-fixing mechanisms from legumes to non-legumes, especially to economically important crops such as rice, maize, and wheat at the molecular level and relevant other techniques involving the manipulation of soil microbiome for plant benefits in the non-legume root environment.
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Rehman HM, Cheung WL, Wong KS, Xie M, Luk CY, Wong FL, Li MW, Tsai SN, To WT, Chan LY, Lam HM. High-Throughput Mass Spectrometric Analysis of the Whole Proteome and Secretome From Sinorhizobium fredii Strains CCBAU25509 and CCBAU45436. Front Microbiol 2019; 10:2569. [PMID: 31798547 PMCID: PMC6865838 DOI: 10.3389/fmicb.2019.02569] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 10/23/2019] [Indexed: 01/11/2023] Open
Abstract
Sinorhizobium fredii is a dominant rhizobium on alkaline-saline land that can induce nitrogen-fixing symbiotic root nodules in soybean. Two S. fredii strains, CCBAU25509 and CCBAU45436, were used in this study to facilitate in-depth analyses of this species and its interactions with soybean. We have previously completed the full assembly of the genomes and detailed transcriptomic analyses for these two S. fredii strains, CCBAU25509 and CCBAU45436, that exhibit differential compatibility toward some soybean hosts. In this work, we performed high-throughput Orbitrap analyses of the whole proteomes and secretomes of CCBAU25509 and CCBAU45436 at different growth stages. Our proteomic data cover coding sequences in the chromosome, chromid, symbiotic plasmid, and other accessory plasmids. In general, we found higher levels of protein expression by genes in the chromosomal genome, whereas proteins encoded by the symbiotic plasmid were differentially accumulated in bacteroids. We identified secreted proteins from the extracellular medium, including seven and eight Nodulation Outer Proteins (Nops) encoded by the symbiotic plasmid of CCBAU25509 and CCBAU45436, respectively. Differential host restriction of CCBAU25509 and CCBAU45436 is regulated by the allelic type of the soybean Rj2(Rfg1) protein. Using sequencing data from this work and available in public databases, our analysis confirmed that the soybean Rj2(Rfg1) protein has three major allelic types (Rj2/rfg1, rj2/Rfg1, rj2/rfg1) that determine the host restriction of some Bradyrhizobium diazoefficiens and S. fredii strains. A mutant defective in the type 3 protein secretion system (T3SS) in CCBAU25509 allowed this strain to nodulate otherwise-incompatible soybeans carrying the rj2/Rfg1 allelic type, probably by disrupting Nops secretion. The allelic forms of NopP and NopI in S. fredii might be associated with the restriction imposed by Rfg1. By swapping the NopP between CCBAU25509 and CCBAU45436, we found that only the strains carrying NopP from CCBAU45436 could nodulate soybeans carrying the rj2/Rfg1 allelic type. However, no direct interaction between either forms of NopP and Rfg1 could be observed.
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Affiliation(s)
- Hafiz Mamoon Rehman
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Wai-Lun Cheung
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Kwong-Sen Wong
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Min Xie
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Ching-Yee Luk
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Fuk-Ling Wong
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Man-Wah Li
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Sau-Na Tsai
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Wing-Ting To
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Lok-Yi Chan
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Hon-Ming Lam
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
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23
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Hassani MA, Özkurt E, Seybold H, Dagan T, Stukenbrock EH. Interactions and Coadaptation in Plant Metaorganisms. ANNUAL REVIEW OF PHYTOPATHOLOGY 2019; 57:483-503. [PMID: 31348865 DOI: 10.1146/annurev-phyto-082718-100008] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Plants associate with a wide diversity of microorganisms. Some microorganisms engage in intimate associations with the plant host, collectively forming a metaorganism. Such close coexistence with plants requires specific adaptations that allow microorganisms to overcome plant defenses and inhabit plant tissues during growth and reproduction. New data suggest that the plant immune system has a broader role beyond pathogen recognition and also plays an important role in the community assembly of the associated microorganism. We propose that core microorganisms undergo coadaptation with their plant host, notably in response to the plant immune system allowing them to persist and propagate in their host. Microorganisms, which are vertically transmitted from generation to generation via plant seeds, putatively compose highly adapted species and may have plant-beneficial functions. The extent to which plant domestication has impacted the underlying genetics of plant-microbe associations remains poorly understood. We propose that the ability of domesticated plants to select and maintain advantageous microbial partners may have been affected. In this review, we discuss factors that impact plant metaorganism assembly and function. We underline the importance of microbe-microbe interactions in plant tissues, as they are still poorly studied but may have a great impact on plant health.
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Affiliation(s)
- M Amine Hassani
- Environmental Genomics, Max Planck Institute for Evolutionary Biology, 24306 Plön, Germany;
- Environmental Genomics, Christian-Albrechts University of Kiel, 24118 Kiel, Germany
| | - Ezgi Özkurt
- Environmental Genomics, Max Planck Institute for Evolutionary Biology, 24306 Plön, Germany;
- Environmental Genomics, Christian-Albrechts University of Kiel, 24118 Kiel, Germany
| | - Heike Seybold
- Environmental Genomics, Max Planck Institute for Evolutionary Biology, 24306 Plön, Germany;
- Environmental Genomics, Christian-Albrechts University of Kiel, 24118 Kiel, Germany
| | - Tal Dagan
- Institute of Microbiology, Christian-Albrechts University of Kiel, 24118 Kiel, Germany
| | - Eva H Stukenbrock
- Environmental Genomics, Max Planck Institute for Evolutionary Biology, 24306 Plön, Germany;
- Environmental Genomics, Christian-Albrechts University of Kiel, 24118 Kiel, Germany
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24
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Foyer CH, Siddique KHM, Tai APK, Anders S, Fodor N, Wong FL, Ludidi N, Chapman MA, Ferguson BJ, Considine MJ, Zabel F, Prasad PVV, Varshney RK, Nguyen HT, Lam HM. Modelling predicts that soybean is poised to dominate crop production across Africa. PLANT, CELL & ENVIRONMENT 2019; 42:373-385. [PMID: 30329164 DOI: 10.1111/pce.13466] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 10/08/2018] [Accepted: 10/14/2018] [Indexed: 05/22/2023]
Abstract
The superior agronomic and human nutritional properties of grain legumes (pulses) make them an ideal foundation for future sustainable agriculture. Legume-based farming is particularly important in Africa, where small-scale agricultural systems dominate the food production landscape. Legumes provide an inexpensive source of protein and nutrients to African households as well as natural fertilization for the soil. Although the consumption of traditionally grown legumes has started to decline, the production of soybeans (Glycine max Merr.) is spreading fast, especially across southern Africa. Predictions of future land-use allocation and production show that the soybean is poised to dominate future production across Africa. Land use models project an expansion of harvest area, whereas crop models project possible yield increases. Moreover, a seed change in farming strategy is underway. This is being driven largely by the combined cash crop value of products such as oils and the high nutritional benefits of soybean as an animal feed. Intensification of soybean production has the potential to reduce the dependence of Africa on soybean imports. However, a successful "soybean bonanza" across Africa necessitates an intensive research, development, extension, and policy agenda to ensure that soybean genetic improvements and production technology meet future demands for sustainable production.
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Affiliation(s)
- Christine H Foyer
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, UK
- School of Molecular Science, The University of Western Australia, Perth, Western Australia, Australia
| | - Kadambot H M Siddique
- The UWA Institute of Agriculture and School of Agriculture and Environment, The University of Western Australia, Perth, Western Australia, Australia
| | - Amos P K Tai
- Earth System Science Programme, The Chinese University of Hong Kong, Shatin, Hong Kong
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Sven Anders
- Department of Resource Economics and Environmental Sociology, University of Alberta, Edmonton, Alberta, Canada
| | - Nándor Fodor
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, UK
- Centre for Agricultural Research, Hungarian Academy of Sciences, Agricultural Institute, Martonvásár, Hungary
| | - Fuk-Ling Wong
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Ndiko Ludidi
- Department of Biotechnology and the DST/NRF Centre of Excellence in Food Security, University of the Western Cape, Bellville, South Africa
| | - Mark A Chapman
- Biological Sciences, University of Southampton, Southampton, UK
| | - Brett J Ferguson
- Centre for Integrative Legume Research, School of Agriculture and Food Sciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Michael J Considine
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, UK
- School of Molecular Science, The University of Western Australia, Perth, Western Australia, Australia
- The UWA Institute of Agriculture and School of Agriculture and Environment, The University of Western Australia, Perth, Western Australia, Australia
- The Department of Primary Industries and Regional Development, South Perth, Western Australia, Australia
| | - Florian Zabel
- Ludwig-Maximilians-Universität München, Munich, Germany
| | - P V Vara Prasad
- Department of Agronomy, College of Agriculture, Kansas State University, Manhattan, Kansas, USA
| | - Rajeev K Varshney
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, Telangana, India
| | - Henry T Nguyen
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, Missouri
| | - Hon-Ming Lam
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
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Ferguson BJ, Minamisawa K, Muñoz NB, Lam HM. Editorial: Metabolic Adjustments and Gene Expression Reprogramming for Symbiotic Nitrogen Fixation in Legume Nodules. FRONTIERS IN PLANT SCIENCE 2019; 10:898. [PMID: 31338104 PMCID: PMC6629857 DOI: 10.3389/fpls.2019.00898] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Accepted: 06/24/2019] [Indexed: 05/11/2023]
Affiliation(s)
- Brett James Ferguson
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD, Australia
- *Correspondence: Brett James Ferguson
| | | | | | - Hon-Ming Lam
- Center for Soybean Research of The State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
- Hon-Ming Lam
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26
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Guo R, Bai Z, Zhou J, Zhong X, Gu F, Liu Q, Li H. Tissue physiological metabolic adaptability in young and old leaves of reed (Phragmites communis) in Songnen grassland. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2018; 128:99-105. [PMID: 29772493 DOI: 10.1016/j.plaphy.2018.05.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 05/08/2018] [Accepted: 05/08/2018] [Indexed: 06/08/2023]
Abstract
Common reed (Phragmites communis) is widely distributed as the dominant plant species in the Songnen Plain of China. The aim of this study was to investigate different physiological adaptive mechanisms to salinity tolerance between young and old leaves. The profiles of 68 metabolites were measured and studied in reed leaves by gas chromatography-mass spectrometer. The nitrogen, carbon, and pigment contents showed stronger growth inhibition for older leaves with salinity stress. In young leaves, high K+ contents not only promoted cell growth, but also prevented influx of superfluous Na+ ions in cells; the Ca2+ accumulation in old leaves implied that Ca2+ triggered the SOS-Na+ exclusion system and reduced Na+ toxicity. Thus, the mechanism of enhanced tolerance differed between young and old leaves. The metabolite results indicated that the young and old leaves had different mechanisms of osmotic regulation; sugars/polyols and amino acids played important roles in developing salinity tolerance in young leaves but high contents of fatty acids were important for old leaves. These results implied dramatically enhanced sugars and amino acid synthesis but inhibited energy metabolism in young leaves. In contrast, fatty acid synthesis was enhanced in old leaves. The results extended our understanding of the differences in physiological metabolism in adaptive to the salt-alkalization of soil in Songnen grassland between young and old leaves of reeds.
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Affiliation(s)
- Rui Guo
- Key Laboratory of Dryland Agriculture, Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Zhenzi Bai
- Department of Infectious Diseases, China-Japan Union Hospital of Jilin University, Changchun 130033, China
| | - Ji Zhou
- Land Consolidation and Rehabilitation Centre, The Ministry of Land and Resources, Beijing 100000, China
| | - XiuLi Zhong
- Key Laboratory of Dryland Agriculture, Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - FengXue Gu
- Key Laboratory of Dryland Agriculture, Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Qi Liu
- Key Laboratory of Dryland Agriculture, Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - HaoRu Li
- Key Laboratory of Dryland Agriculture, Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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Forrester NJ, Ashman TL. The direct effects of plant polyploidy on the legume-rhizobia mutualism. ANNALS OF BOTANY 2018; 121:209-220. [PMID: 29182713 PMCID: PMC5808787 DOI: 10.1093/aob/mcx121] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 09/08/2017] [Indexed: 05/09/2023]
Abstract
BACKGROUND Polyploidy is known to significantly alter plant genomes, phenotypes and interactions with the abiotic environment, yet the impacts of polyploidy on plant-biotic interactions are less well known. A particularly important plant-biotic interaction is the legume-rhizobia mutualism, in which rhizobia fix atmospheric nitrogen in exchange for carbon provided by legume hosts. This mutualism regulates nutrient cycles in natural ecosystems and provides nitrogen to agricultural environments. Despite the ecological, evolutionary and agricultural importance of plant polyploidy and the legume-rhizobia mutualism, it is not yet fully understood whether plant polyploidy directly alters mutualism traits or the consequences on plant growth. SCOPE The aim was to propose a conceptual framework to understand how polyploidy might directly enhance the quantity and quality of rhizobial symbionts hosted by legume plants, resulting in increased host access to fixed nitrogen (N). Mechanistic hypotheses have been devised to examine how polyploidy can directly alter traits that impact the quantity (e.g. nodule number, nodule size, terminal bacteroid differentiation) and quality of symbionts (e.g. nodule environment, partner choice, host sanctions). To evaluate these hypotheses, an exhaustive review of studies testing the effects of plant polyploidy on the mutualism was conducted. In doing so, overall trends were synthesized, highlighting the limited understanding of the mechanisms that underlie variation in results achieved thus far, revealing striking gaps in knowledge and uncovering areas ripe for future research. CONCLUSIONS Plant polyploidy can immediately alter nodule size, N fixation rate and the identity of rhizobial symbionts hosted by polyploid legumes, but many of the mechanistic hypotheses proposed here, such as bacteroid number and enhancements of the nodule environment, remain unexplored. Although current evidence supports a role of plant polyploidy in enhancing key aspects of the legume-rhizobia mutualism, the underlying mechanisms and effects on host benefit from the mutualism remain unresolved.
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Affiliation(s)
- Nicole J Forrester
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
- For correspondence. E-mail
| | - Tia-Lynn Ashman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
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28
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Jemo M, Sulieman S, Bekkaoui F, Olomide OAK, Hashem A, Abd_Allah EF, Alqarawi AA, Tran LSP. Comparative Analysis of the Combined Effects of Different Water and Phosphate Levels on Growth and Biological Nitrogen Fixation of Nine Cowpea Varieties. FRONTIERS IN PLANT SCIENCE 2017; 8:2111. [PMID: 29312379 PMCID: PMC5742256 DOI: 10.3389/fpls.2017.02111] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 11/27/2017] [Indexed: 05/23/2023]
Abstract
Water deficit and phosphate (Pi) deficiency adversely affect growth and biological nitrogen fixation (BNF) of legume crops. In this study, we examined the impact of interaction between soil water conditions and available soil-Pi levels on growth, nodule development and BNF potential of nine cowpea varieties grown on dry savanna soils. In our experimental design, soils with different available soil-Pi levels, i.e., low, moderate, and high soil-Pi levels, collected from various farming fields were used to grow nine cowpea varieties under well-watered and water-deficit conditions. Significant and severe water deficit-damaging effects on BNF, nodulation, growth, levels of plant-nitrogen (N) and -phosphorus (P), as well as shoot relative water content and chlorophyll content of cowpea plants were observed. Under well-watered and high available soil-Pi conditions, cowpea varieties IT07K-304-9 and Dan'Ila exhibited significantly higher BNF potential and dry biomass, as well as plant-N and -P contents compared with other tested ones. Significant genotypic variations among the cowpeas were recorded under low available soil-Pi and water-deficit conditions in terms of the BNF potential. Principal component (PC) analysis revealed that varieties IT04K-339-1, IT07K-188-49, IT07K-304-9, and IT04K-405-5 were associated with PC1, which was better explained by performance for nodulation, plant biomass, plant-N, plant-P, and BNF potential under the combined stress of water deficit and Pi deficiency, thereby offering prospects for development of varieties with high growth and BNF traits that are adaptive to such stress conditions in the region. On another hand, variety Dan'Ila was significantly related to PC2 that was highly explained by the plant shoot/root ratio and chlorophyll content, suggesting the existence of physiological and morphological adjustments to cope with water deficit and Pi deficiency for this particular variety. Additionally, increases in soil-Pi availability led to significant reductions of water-deficit damage on dry biomass, plant-N and -P contents, and BNF potential of cowpea varieties. This finding suggests that integrated nutrient management strategies that allow farmers to access to Pi-based fertilizers may help reduce the damage of adverse water deficit and Pi deficiency caused to cowpea crop in the regions, where soils are predominantly Pi-deficient and drought-prone.
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Affiliation(s)
- Martin Jemo
- AgroBiosciences Division, Mohammed VI Polytechnic University (UM6P), Ben Guerir, Morocco
- Office Chérifien des Phosphates (OCP)-Africa, Casablanca, Morocco
| | - Saad Sulieman
- Department of Agronomy, Faculty of Agriculture, University of Khartoum, Shambat, Sudan
| | - Faouzi Bekkaoui
- AgroBiosciences Division, Mohammed VI Polytechnic University (UM6P), Ben Guerir, Morocco
| | | | - Abeer Hashem
- Botany and Microbiology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
- Mycology and Plant Disease Survey Department, Plant Pathology Research Institute, ARC, Giza, Egypt
| | - Elsayed Fathi Abd_Allah
- Plant Production Department, College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Abdulaziz A. Alqarawi
- Plant Production Department, College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Lam-Son Phan Tran
- Institute of Research and Development, Duy Tan University, Da Nang, Vietnam
- Signalling Pathway Research Unit, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
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29
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Kepler RM, Maul JE, Rehner SA. Managing the plant microbiome for biocontrol fungi: examples from Hypocreales. Curr Opin Microbiol 2017; 37:48-53. [PMID: 28441534 DOI: 10.1016/j.mib.2017.03.006] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 03/22/2017] [Indexed: 01/01/2023]
Abstract
Feeding an increasing global population requires continued improvements in agricultural efficiency and productivity. Meeting estimated future production levels requires the adoption of practices that increase output without environmental degradation associated with external inputs to supplement nutrition or control pests. Enriching the community of microbes associated with plants in agricultural systems for those providing ecosystem services such as pest control is one possible component towards achieving sustainable productivity increases. In this review we explore the current state of knowledge for Hypocreales fungi used in biological control. Advances in understanding the field ecology, diversity and genetic determinants of host range and virulence of hypocrealean fungi provide the means to improve their efficacy.
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Affiliation(s)
- Ryan M Kepler
- Sustainable Agricultural Systems Laboratory, 10300 Baltimore Ave, Bldg 001, Rm 123, Beltsville, MD 20705, United States.
| | - Jude E Maul
- Sustainable Agricultural Systems Laboratory, 10300 Baltimore Ave, Bldg 001, Rm 123, Beltsville, MD 20705, United States
| | - Stephen A Rehner
- USDA-ARS, Mycology and Nematology Genetic Diversity and Biology Laboratory, Beltsville, MD, 20705, United States
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30
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Muñoz N, Liu A, Kan L, Li MW, Lam HM. Potential Uses of Wild Germplasms of Grain Legumes for Crop Improvement. Int J Mol Sci 2017; 18:E328. [PMID: 28165413 PMCID: PMC5343864 DOI: 10.3390/ijms18020328] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2016] [Revised: 01/26/2017] [Accepted: 01/26/2017] [Indexed: 01/14/2023] Open
Abstract
Challenged by population increase, climatic change, and soil deterioration, crop improvement is always a priority in securing food supplies. Although the production of grain legumes is in general lower than that of cereals, the nutritional value of grain legumes make them important components of food security. Nevertheless, limited by severe genetic bottlenecks during domestication and human selection, grain legumes, like other crops, have suffered from a loss of genetic diversity which is essential for providing genetic materials for crop improvement programs. Illustrated by whole-genome-sequencing, wild relatives of crops adapted to various environments were shown to maintain high genetic diversity. In this review, we focused on nine important grain legumes (soybean, peanut, pea, chickpea, common bean, lentil, cowpea, lupin, and pigeonpea) to discuss the potential uses of their wild relatives as genetic resources for crop breeding and improvement, and summarized the various genetic/genomic approaches adopted for these purposes.
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Affiliation(s)
- Nacira Muñoz
- Centre for Soybean Research of the Partner State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China.
- Centro de Investigaciones Agropecuarias-INTA, Instituto de Fisiología y Recursos Genéticos Vegetales, Córdoba X5000, Argentina.
- Cátedra de Fisiología Vegetal, Facultad de Ciencias Exactas Físicas y Naturales, Universidad Nacional de Córdoba, Córdoba X5000, Argentina.
| | - Ailin Liu
- Centre for Soybean Research of the Partner State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China.
| | - Leo Kan
- Centre for Soybean Research of the Partner State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China.
| | - Man-Wah Li
- Centre for Soybean Research of the Partner State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China.
| | - Hon-Ming Lam
- Centre for Soybean Research of the Partner State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China.
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