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Mooney BC, van der Hoorn RAL. Novel structural insights at the extracellular plant-pathogen interface. CURRENT OPINION IN PLANT BIOLOGY 2024; 82:102629. [PMID: 39299144 DOI: 10.1016/j.pbi.2024.102629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2024] [Revised: 08/05/2024] [Accepted: 08/29/2024] [Indexed: 09/22/2024]
Abstract
Plant pathogens represent a critical threat to global agriculture and food security, particularly under the pressures of climate change and reduced agrochemical use. Most plant pathogens initially colonize the extracellular space or apoplast and understanding the host-pathogen interactions that occur here is vital for engineering sustainable disease resistance in crops. Structural biology has played important roles in elucidating molecular mechanisms underpinning plant-pathogen interactions but only few studies have reported structures of extracellular complexes. This article highlights these resolved extracellular complexes by describing the insights gained from the solved structures of complexes consisting of CERK1-chitin, FLS2-flg22-BAK1, RXEG1-XEG1-BAK1 and PGIP2-FpPG. Finally, we discuss the potential of AI-based structure prediction platforms like AlphaFold as an alternative hypothesis generator to rapidly advance our molecular understanding of plant pathology and develop novel strategies to increase crop resilience against disease.
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Somoza SC, Bonfante P, Giovannetti M. Breaking barriers: improving time and space resolution of arbuscular mycorrhizal symbiosis with single-cell sequencing approaches. Biol Direct 2024; 19:67. [PMID: 39154166 PMCID: PMC11330620 DOI: 10.1186/s13062-024-00501-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Accepted: 07/11/2024] [Indexed: 08/19/2024] Open
Abstract
The cell and molecular bases of arbuscular mycorrhizal (AM) symbiosis, a crucial plant-fungal interaction for nutrient acquisition, have been extensively investigated by coupling traditional RNA sequencing techniques of roots sampled in bulk, with methods to capture subsets of cells such as laser microdissection. These approaches have revealed central regulators of this complex relationship, yet the requisite level of detail to effectively untangle the intricacies of temporal and spatial development remains elusive.The recent adoption of single-cell RNA sequencing (scRNA-seq) techniques in plant research is revolutionizing our ability to dissect the intricate transcriptional profiles of plant-microbe interactions, offering unparalleled insights into the diversity and dynamics of individual cells during symbiosis. The isolation of plant cells is particularly challenging due to the presence of cell walls, leading plant researchers to widely adopt nuclei isolation methods. Despite the increased resolution that single-cell analyses offer, it also comes at the cost of spatial perspective, hence, it is necessary the integration of these approaches with spatial transcriptomics to obtain a comprehensive overview.To date, few single-cell studies on plant-microbe interactions have been published, most of which provide high-resolution cell atlases that will become crucial for fully deciphering symbiotic interactions and addressing future questions. In AM symbiosis research, key processes such as the mutual recognition of partners during arbuscule development within cortical cells, or arbuscule senescence and degeneration, remain poorly understood, and these advancements are expected to shed light on these processes and contribute to a deeper understanding of this plant-fungal interaction.
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Affiliation(s)
| | - Paola Bonfante
- Department of Life Sciences and Systems Biology, University of Torino, Torino, 10125, Italy
| | - Marco Giovannetti
- Department of Biology, University of Padova, Padova, 35131, Italy.
- Department of Life Sciences and Systems Biology, University of Torino, Torino, 10125, Italy.
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Li Y, Chen H, Gu L, Wu J, Zheng X, Fan Z, Pan D, Li JT, Shu W, Rosendahl S, Wang Y. Domestication of rice may have changed its arbuscular mycorrhizal properties by modifying phosphorus nutrition-related traits and decreasing symbiotic compatibility. THE NEW PHYTOLOGIST 2024; 243:1554-1570. [PMID: 38853449 DOI: 10.1111/nph.19901] [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: 01/29/2024] [Accepted: 05/27/2024] [Indexed: 06/11/2024]
Abstract
Modern cultivated rice (Oryza sativa) typically experiences limited growth benefits from arbuscular mycorrhizal (AM) symbiosis. This could be due to the long-term domestication of rice under favorable phosphorus conditions. However, there is limited understanding of whether and how the rice domestication has modified AM properties. This study compared AM properties between a collection of wild (Oryza rufipogon) and domesticated rice genotypes and investigated the mechanisms underlying their differences by analyzing physiological, genomic, transcriptomic, and metabolomic traits critical for AM symbiosis. The results revealed significantly lower mycorrhizal growth responses and colonization intensity in domesticated rice compared to wild rice, and this change of AM properties may be associated with the domestication modifications of plant phosphorus utilization efficiency at physiological and genomic levels. Domestication also resulted in a decrease in the activity of the mycorrhizal phosphorus acquisition pathway, which may be attributed to reduced mycorrhizal compatibility of rice roots by enhancing defense responses like root lignification and reducing carbon supply to AM fungi. In conclusion, rice domestication may have changed its AM properties by modifying P nutrition-related traits and reducing symbiotic compatibility. This study offers new insights for improving AM properties in future rice breeding programs to enhance sustainable agricultural production.
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Affiliation(s)
- Yingwei Li
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Hanwen Chen
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Ling Gu
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Jingwen Wu
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Xiutan Zheng
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Zhilan Fan
- Rice Research Institute, Guangdong Academy of Agricultural Science, Guangzhou, 510640, China
| | - Dajian Pan
- Rice Research Institute, Guangdong Academy of Agricultural Science, Guangzhou, 510640, China
| | - Jin-Tian Li
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Wensheng Shu
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Søren Rosendahl
- Department of Biology, University of Copenhagen, DK-2100, Copenhagen, Denmark
| | - Yutao Wang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
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Duan S, Feng G, Limpens E, Bonfante P, Xie X, Zhang L. Cross-kingdom nutrient exchange in the plant-arbuscular mycorrhizal fungus-bacterium continuum. Nat Rev Microbiol 2024:10.1038/s41579-024-01073-7. [PMID: 39014094 DOI: 10.1038/s41579-024-01073-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/14/2024] [Indexed: 07/18/2024]
Abstract
The association between plants and arbuscular mycorrhizal fungi (AMF) affects plant performance and ecosystem functioning. Recent studies have identified AMF-associated bacteria as cooperative partners that participate in AMF-plant symbiosis: specific endobacteria live inside AMF, and hyphospheric bacteria colonize the soil that surrounds the extraradical hyphae. In this Review, we describe the concept of a plant-AMF-bacterium continuum, summarize current advances and provide perspectives on soil microbiology. First, we review the top-down carbon flow and the bottom-up mineral flow (especially phosphorus and nitrogen) in this continuum, as well as how AMF-bacteria interactions influence the biogeochemical cycling of nutrients (for example, carbon, phosphorus and nitrogen). Second, we discuss how AMF interact with hyphospheric bacteria or endobacteria to regulate nutrient exchange between plants and AMF, and the possible molecular mechanisms that underpin this continuum. Finally, we explore future prospects for studies on the hyphosphere to facilitate the utilization of AMF and hyphospheric bacteria in sustainable agriculture.
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Affiliation(s)
- Shilong Duan
- State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, Beijing, China
| | - Gu Feng
- State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, Beijing, China
| | - Erik Limpens
- Laboratory of Molecular Biology, Wageningen University and Research, Wageningen, The Netherlands
| | - Paola Bonfante
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy.
| | - Xianan Xie
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China.
| | - Lin Zhang
- State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, Beijing, China.
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Jyoti SD, Singh G, Pradhan AK, Tarpley L, Septiningsih EM, Talukder SK. Rice breeding for low input agriculture. FRONTIERS IN PLANT SCIENCE 2024; 15:1408356. [PMID: 38974981 PMCID: PMC11224470 DOI: 10.3389/fpls.2024.1408356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Accepted: 05/24/2024] [Indexed: 07/09/2024]
Abstract
A low-input-based farming system can reduce the adverse effects of modern agriculture through proper utilization of natural resources. Modern varieties often need to improve in low-input settings since they are not adapted to these systems. In addition, rice is one of the most widely cultivated crops worldwide. Enhancing rice performance under a low input system will significantly reduce the environmental concerns related to rice cultivation. Traits that help rice to maintain yield performance under minimum inputs like seedling vigor, appropriate root architecture for nutrient use efficiency should be incorporated into varieties for low input systems through integrated breeding approaches. Genes or QTLs controlling nutrient uptake, nutrient assimilation, nutrient remobilization, and root morphology need to be properly incorporated into the rice breeding pipeline. Also, genes/QTLs controlling suitable rice cultivars for sustainable farming. Since several variables influence performance under low input conditions, conventional breeding techniques make it challenging to work on many traits. However, recent advances in omics technologies have created enormous opportunities for rapidly improving multiple characteristics. This review highlights current research on features pertinent to low-input agriculture and provides an overview of alternative genomics-based breeding strategies for enhancing genetic gain in rice suitable for low-input farming practices.
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Affiliation(s)
- Subroto Das Jyoti
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States
| | - Gurjeet Singh
- Texas A&M AgriLife Research Center, Beaumont, TX, United States
| | | | - Lee Tarpley
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States
- Texas A&M AgriLife Research Center, Beaumont, TX, United States
| | - Endang M. Septiningsih
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States
| | - Shyamal K. Talukder
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States
- Texas A&M AgriLife Research Center, Beaumont, TX, United States
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Han R, Yang Z, Wang C, Zhu S, Tang G, Shen X, Duanmu D, Cao Y, Huang R. Wild species rice OsCERK1DY-mediated arbuscular mycorrhiza symbiosis boosts yield and nutrient use efficiency in rice breeding. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2024; 44:22. [PMID: 38435473 PMCID: PMC10907559 DOI: 10.1007/s11032-024-01459-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Accepted: 02/20/2024] [Indexed: 03/05/2024]
Abstract
Meeting the ever-increasing food demands of a growing global population while ensuring resource and environmental sustainability presents significant challenges for agriculture worldwide. Arbuscular mycorrhizal symbiosis (AMS) has emerged as a potential solution by increasing the surface area of a plant's root system and enhancing the absorption of phosphorus, nitrogen nutrients, and water. Consequently, there is a longstanding hypothesis that rice varieties exhibiting more efficient AMS could yield higher outputs at reduced input costs, paving the way for the development of Green Super Rice (GSR). Our prior research study identified a variant, OsCERK1DY, derived from Dongxiang wild-type rice, which notably enhanced AMS efficiency in the rice cultivar "ZZ35." This variant represents a promising gene for enhancing yield and nutrient use efficiency in rice breeding. In this study, we conducted a comparative analysis of biomass, crop growth characteristics, yield attributes, and nutrient absorption at varying soil nitrogen levels in the rice cultivar "ZZ35" and its chromosome single-segment substitution line, "GJDN1." In the field, GJDN1 exhibited a higher AM colonization level in its roots compared with ZZ35. Notably, GJDN1 displayed significantly higher effective panicle numbers and seed-setting rates than ZZ35. Moreover, the yield of GJDN1 with 75% nitrogen was 14.27% greater than the maximum yield achieved using ZZ35. At equivalent nitrogen levels, GJDN1 consistently outperformed ZZ35 in chlorophyll (Chl) content, dry matter accumulation, major nutrient element accumulation, N agronomic efficiency (NAE), N recovery efficiency (NRE), and N partial factor productivity (NPFP). The performance of OsCERK1DY overexpression lines corroborated these findings. These results support a model wherein the heightened level of AMS mediated by OsCERK1DY contributes to increased nitrogen, phosphorus, and potassium accumulation. This enhancement in nutrient utilization promotes higher fertilizer efficiency, dry matter accumulation, and ultimately, rice yield. Consequently, the OsCERK1DY gene emerges as a robust candidate for improving yield, reducing fertilizer usage, and facilitating a transition towards greener, lower-carbon agriculture. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-024-01459-8.
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Affiliation(s)
- Ruicai Han
- Nanchang Subcenter of National Research Center for Rice Engineering, Key Laboratory of Rice Physiology and Genetics of Jiangxi Province, Rice Research Institute, Jiangxi Academy of Agriculture Science, Nanchang, 330200 People’s Republic of China
| | - Zhou Yang
- Nanchang Subcenter of National Research Center for Rice Engineering, Key Laboratory of Rice Physiology and Genetics of Jiangxi Province, Rice Research Institute, Jiangxi Academy of Agriculture Science, Nanchang, 330200 People’s Republic of China
| | - Chunquan Wang
- Jiangxi Biotech Vocational College, Nanchang, 330200 People’s Republic of China
| | - Shan Zhu
- Nanchang Subcenter of National Research Center for Rice Engineering, Key Laboratory of Rice Physiology and Genetics of Jiangxi Province, Rice Research Institute, Jiangxi Academy of Agriculture Science, Nanchang, 330200 People’s Republic of China
| | - Guoping Tang
- Nanchang Subcenter of National Research Center for Rice Engineering, Key Laboratory of Rice Physiology and Genetics of Jiangxi Province, Rice Research Institute, Jiangxi Academy of Agriculture Science, Nanchang, 330200 People’s Republic of China
| | - Xianhua Shen
- Nanchang Subcenter of National Research Center for Rice Engineering, Key Laboratory of Rice Physiology and Genetics of Jiangxi Province, Rice Research Institute, Jiangxi Academy of Agriculture Science, Nanchang, 330200 People’s Republic of China
| | - Deqiang Duanmu
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Yangrong Cao
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Renliang Huang
- Nanchang Subcenter of National Research Center for Rice Engineering, Key Laboratory of Rice Physiology and Genetics of Jiangxi Province, Rice Research Institute, Jiangxi Academy of Agriculture Science, Nanchang, 330200 People’s Republic of China
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Guigard L, Jobert L, Busset N, Moulin L, Czernic P. Symbiotic compatibility between rice cultivars and arbuscular mycorrhizal fungi genotypes affects rice growth and mycorrhiza-induced resistance. FRONTIERS IN PLANT SCIENCE 2023; 14:1278990. [PMID: 37941658 PMCID: PMC10628536 DOI: 10.3389/fpls.2023.1278990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 10/09/2023] [Indexed: 11/10/2023]
Abstract
Introduction Arbuscular mycorrhizal fungi (AMF) belong to the Glomeromycota clade and can form root symbioses with 80% of Angiosperms, including crops species such as wheat, maize and rice. By increasing nutrient availability, uptake and soil anchoring of plants, AMF can improve plant's growth and tolerance to abiotic stresses. AMF can also reduce symptoms and pathogen load on infected plants, both locally and systemically, through a phenomenon called mycorrhiza induced resistance (MIR). There is scarce information on rice mycorrhization, despite the high potential of this symbiosis in a context of sustainable water management in rice production systems. Methods We studied the symbiotic compatibility (global mycorrhization & arbuscules intensity) and MIR phenotypes between six rice cultivars from two subspecies (indica: IR64 & Phka Rumduol; japonica: Nipponbare, Kitaake, Azucena & Zhonghua 11) and three AMF genotypes (Funneliformis mosseae FR140 (FM), Rhizophagus irregularis DAOM197198 (RIR) & R. intraradices FR121 (RIN)). The impact of mycorrhization on rice growth and defence response to Xanthomonas oryzae pv oryzae (Xoo) infection was recorded via both phenotypic indexes and rice marker gene expression studies. Results All three AMF genotypes colonise the roots of all rice varieties, with clear differences in efficiency depending on the combination under study (from 27% to 84% for Phka Rumduol-RIN and Nipponbare-RIR combinations, respectively). Mycorrhization significantly (α=0.05) induced negative to beneficial effects on rice growth (impact on dry weight ranging from -21% to 227% on Azucena-FM and Kitaake-RIN combinations, respectively), and neutral to beneficial effects on the extent of Xoo symptoms on leaves (except for Azucena-RIN combination which showed a 68% increase of chlorosis). R. irregularis DAOM197198 was the most compatible AMF partner of rice, with high root colonisation intensity (84% of Nipponbare's roots hyphal colonisation), beneficial effects on rice growth (dry weight +28% (IR64) to +178% (Kitaake)) and decrease of Xoo-induced symptoms (-6% (Nipponbare) to -27% (IR64)). Transcriptomic analyses by RT-qPCR on leaves of two rice cultivars contrasting in their association with AMF show two different patterns of response on several physiological marker genes. Discussion Overall, the symbiotic compatibility between rice cultivars and AMF demonstrates adequate colonization, effectively restricting the nutrient starvation response and mitigating symptoms of phytopathogenic infection.
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Affiliation(s)
| | | | | | | | - Pierre Czernic
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
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Gao L, Kantar MB, Moxley D, Ortiz-Barrientos D, Rieseberg LH. Crop adaptation to climate change: An evolutionary perspective. MOLECULAR PLANT 2023; 16:1518-1546. [PMID: 37515323 DOI: 10.1016/j.molp.2023.07.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 06/20/2023] [Accepted: 07/26/2023] [Indexed: 07/30/2023]
Abstract
The disciplines of evolutionary biology and plant and animal breeding have been intertwined throughout their development, with responses to artificial selection yielding insights into the action of natural selection and evolutionary biology providing statistical and conceptual guidance for modern breeding. Here we offer an evolutionary perspective on a grand challenge of the 21st century: feeding humanity in the face of climate change. We first highlight promising strategies currently under way to adapt crops to current and future climate change. These include methods to match crop varieties with current and predicted environments and to optimize breeding goals, management practices, and crop microbiomes to enhance yield and sustainable production. We also describe the promise of crop wild relatives and recent technological innovations such as speed breeding, genomic selection, and genome editing for improving environmental resilience of existing crop varieties or for developing new crops. Next, we discuss how methods and theory from evolutionary biology can enhance these existing strategies and suggest novel approaches. We focus initially on methods for reconstructing the evolutionary history of crops and their pests and symbionts, because such historical information provides an overall framework for crop-improvement efforts. We then describe how evolutionary approaches can be used to detect and mitigate the accumulation of deleterious mutations in crop genomes, identify alleles and mutations that underlie adaptation (and maladaptation) to agricultural environments, mitigate evolutionary trade-offs, and improve critical proteins. Continuing feedback between the evolution and crop biology communities will ensure optimal design of strategies for adapting crops to climate change.
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Affiliation(s)
- Lexuan Gao
- CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Michael B Kantar
- Department of Tropical Plant & Soil Sciences, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Dylan Moxley
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Daniel Ortiz-Barrientos
- School of Biological Sciences and Australian Research Council Centre of Excellence for Plant Success in Nature and Agriculture, The University of Queensland, Brisbane, QLD, Australia
| | - Loren H Rieseberg
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada.
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Trinh J, Li T, Franco JY, Toruño TY, Stevens DM, Thapa SP, Wong J, Pineda R, de Dios EÁ, Kahn TL, Seymour DK, Ramadugu C, Coaker GL. Variation in microbial feature perception in the Rutaceae family with immune receptor conservation in citrus. PLANT PHYSIOLOGY 2023; 193:689-707. [PMID: 37144828 PMCID: PMC10686701 DOI: 10.1093/plphys/kiad263] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 03/27/2023] [Accepted: 04/09/2023] [Indexed: 05/06/2023]
Abstract
Although much is known about the responses of model plants to microbial features, we still lack an understanding of the extent of variation in immune perception across members of a plant family. In this work, we analyzed immune responses in Citrus and wild relatives, surveying 86 Rutaceae genotypes with differing leaf morphologies and disease resistances. We found that responses to microbial features vary both within and between members. Species in 2 subtribes, the Balsamocitrinae and Clauseninae, can recognize flagellin (flg22), cold shock protein (csp22), and chitin, including 1 feature from Candidatus Liberibacter species (csp22CLas), the bacterium associated with Huanglongbing. We investigated differences at the receptor level for the flagellin receptor FLAGELLIN SENSING 2 (FLS2) and the chitin receptor LYSIN MOTIF RECEPTOR KINASE 5 (LYK5) in citrus genotypes. We characterized 2 genetically linked FLS2 homologs from "Frost Lisbon" lemon (Citrus ×limon, responsive) and "Washington navel" orange (Citrus ×aurantium, nonresponsive). Surprisingly, FLS2 homologs from responsive and nonresponsive genotypes were expressed in Citrus and functional when transferred to a heterologous system. "Washington navel" orange weakly responded to chitin, whereas "Tango" mandarin (C. ×aurantium) exhibited a robust response. LYK5 alleles were identical or nearly identical between the 2 genotypes and complemented the Arabidopsis (Arabidopsis thaliana) lyk4/lyk5-2 mutant with respect to chitin perception. Collectively, our data indicate that differences in chitin and flg22 perception in these citrus genotypes are not the results of sequence polymorphisms at the receptor level. These findings shed light on the diversity of perception of microbial features and highlight genotypes capable of recognizing polymorphic pathogen features.
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Affiliation(s)
- Jessica Trinh
- Department of Plant Pathology, University of California, Davis, CA 95616, USA
| | - Tianrun Li
- Department of Plant Pathology, University of California, Davis, CA 95616, USA
| | - Jessica Y Franco
- Department of Plant Pathology, University of California, Davis, CA 95616, USA
| | - Tania Y Toruño
- Department of Plant Pathology, University of California, Davis, CA 95616, USA
| | - Danielle M Stevens
- Department of Plant Pathology, University of California, Davis, CA 95616, USA
| | - Shree P Thapa
- Department of Plant Pathology, University of California, Davis, CA 95616, USA
| | - Justin Wong
- Department of Plant Pathology, University of California, Davis, CA 95616, USA
| | - Rebeca Pineda
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
| | - Emmanuel Ávila de Dios
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
| | - Tracy L Kahn
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
| | - Danelle K Seymour
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
| | - Chandrika Ramadugu
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
| | - Gitta L Coaker
- Department of Plant Pathology, University of California, Davis, CA 95616, USA
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Malviya D, Singh P, Singh UB, Paul S, Kumar Bisen P, Rai JP, Verma RL, Fiyaz RA, Kumar A, Kumari P, Dei S, Ahmed MR, Bagyaraj DJ, Singh HV. Arbuscular mycorrhizal fungi-mediated activation of plant defense responses in direct seeded rice ( Oryza sativa L.) against root-knot nematode Meloidogyne graminicola. Front Microbiol 2023; 14:1104490. [PMID: 37200920 PMCID: PMC10185796 DOI: 10.3389/fmicb.2023.1104490] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 03/13/2023] [Indexed: 05/20/2023] Open
Abstract
Rhizosphere is the battlefield of beneficial and harmful (so called phytopathogens) microorganisms. Moreover, these microbial communities are struggling for their existence in the soil and playing key roles in plant growth, mineralization, nutrient cycling and ecosystem functioning. In the last few decades, some consistent pattern have been detected so far that link soil community composition and functions with plant growth and development; however, it has not been studied in detail. AM fungi are model organisms, besides potential role in nutrient cycling; they modulate biochemical pathways directly or indirectly which lead to better plant growth under biotic and abiotic stress conditions. In the present investigations, we have elucidated the AM fungi-mediated activation of plant defense responses against Meloidogyne graminicola causing root-knot disease in direct seeded rice (Oryza sativa L.). The study describes the multifarious effects of Funneliformis mosseae, Rhizophagus fasciculatus, and Rhizophagus intraradices inoculated individually or in combination under glasshouse conditions in rice plants. It was found that F. mosseae, R. fasciculatus and R. intraradices when applied individually or in combination modulated the biochemical and molecular mechanisms in the susceptible and resistant inbred lines of rice. AM inoculation significantly increased various plant growth attributes in plants with simultaneous decrease in the root-knot intensity. Among these, the combined application of F. mosseae, R. fasciculatus, and R. intraradices was found to enhance the accumulation and activities of biomolecules and enzymes related to defense priming as well as antioxidation in the susceptible and resistant inbred lines of rice pre-challenged with M. graminicola. The application of F. mosseae, R. fasciculatus and R. intraradices, induced the key genes involved in plant defense and signaling and it has been demonstrated for the first time. Results of the present investigation advocated that the application of F. mosseae, R. fasciculatus and R. intraradices, particularly a combination of all three, not only helped in the control of root-knot nematodes but also increased plant growth as well as enhances the gene expression in rice. Thus, it proved to be an excellent biocontrol as well as plant growth-promoting agent in rice even when the crop is under biotic stress of the root-knot nematode, M. graminicola.
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Affiliation(s)
- Deepti Malviya
- Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan, India
| | - Prakash Singh
- Department of Plant Breeding and Genetics, Veer Kunwar Singh College of Agriculture, Bihar Agricultural University, Dumraon, India
| | - Udai B Singh
- Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan, India
| | - Surinder Paul
- Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan, India
| | | | - Jai P Rai
- Department of Mycology and Plant Pathology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, India
| | - Ram Lakhan Verma
- Division of Crop Improvement, ICAR-National Rice Research Institute, Cuttack, India
| | - R Abdul Fiyaz
- Division of Crop Improvement, ICAR-Indian Institute of Rice Research, Hyderabad, India
| | - A Kumar
- Bihar Agricultural University, Bhagalpur, India
| | - Poonam Kumari
- Agrotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, India
| | | | - Mohd Reyaz Ahmed
- Department of Plant Pathology, Veer Kunwar Singh College of Agriculture, Bihar Agricultural University, Dumraon, India
| | - D J Bagyaraj
- Centre for Natural Biological Resources and Community Development, Bengaluru, India
| | - Harsh V Singh
- Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan, India
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11
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Xu L, Wang J, Xiao Y, Han Z, Chai J. Structural insight into chitin perception by chitin elicitor receptor kinase 1 of Oryza sativa. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:235-248. [PMID: 35568972 DOI: 10.1111/jipb.13279] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Accepted: 05/12/2022] [Indexed: 06/15/2023]
Abstract
Plants have developed innate immune systems to fight against pathogenic fungi by monitoring pathogenic signals known as pathogen-associated molecular patterns (PAMP) and have established endo symbiosis with arbuscular mycorrhizal (AM) fungi through recognition of mycorrhizal (Myc) factors. Chitin elicitor receptor kinase 1 of Oryza sativa subsp. Japonica (OsCERK1) plays a bifunctional role in mediating both chitin-triggered immunity and symbiotic relationships with AM fungi. However, it remains unclear whether OsCERK1 can directly recognize chitin molecules. In this study, we show that OsCERK1 binds to the chitin hexamer ((NAG)6 ) and tetramer ((NAG)4 ) directly and determine the crystal structure of the OsCERK1-(NAG)6 complex at 2 Å. The structure shows that one OsCERK1 is associated with one (NAG)6 . Upon recognition, chitin hexamer binds OsCERK1 by interacting with the shallow groove on the surface of LysM2. These structural findings, complemented by mutational analyses, demonstrate that LysM2 is crucial for recognition of both (NAG)6 and (NAG)4 . Altogether, these findings provide structural insights into the ability of OsCERK1 in chitin perception, which will lead to a better understanding of the role of OsCERK1 in mediating both immunity and symbiosis in rice.
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Affiliation(s)
- Li Xu
- Tsinghua-Peking Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Centre for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Jizong Wang
- Tsinghua-Peking Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Centre for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yu Xiao
- Tsinghua-Peking Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Centre for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Zhifu Han
- Tsinghua-Peking Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Centre for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Jijie Chai
- Tsinghua-Peking Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Centre for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Max Planck Institute for Plant Breeding Research, Cologne, 50829, Germany
- Institute of Biochemistry, University of Cologne, Cologne, 50674, Germany
- Cluster of Excellence in Plant Sciences (CEPLAS), Düsseldorf, 40225, Germany
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12
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Huang R, Li Z, Shen X, Choi J, Cao Y. The Perspective of Arbuscular Mycorrhizal Symbiosis in Rice Domestication and Breeding. Int J Mol Sci 2022; 23:ijms232012383. [PMID: 36293238 PMCID: PMC9604486 DOI: 10.3390/ijms232012383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 10/10/2022] [Accepted: 10/13/2022] [Indexed: 11/21/2022] Open
Abstract
In nature, symbiosis with arbuscular mycorrhizal (AM) fungi contributes to sustainable acquisition of phosphorus and other elements in over 80% of plant species; improving interactions with AM symbionts may mitigate some of the environmental problems associated with fertilizer application in grain crops such as rice. Recent developments of high-throughput genome sequencing projects of thousands of rice cultivars and the discovery of the molecular mechanisms underlying AM symbiosis suggest that interactions with AM fungi might have been an overlooked critical trait in rice domestication and breeding. In this review, we discuss genetic variation in the ability of rice to form AM symbioses and how this might have affected rice domestication. Finally, we discuss potential applications of AM symbiosis in rice breeding for more sustainable agriculture.
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Affiliation(s)
- Renliang Huang
- National Engineering Research Center of Rice (Nanchang), Key Laboratory of Rice Physiology and Genetics of Jiangxi Province, Rice Research Institute, Jiangxi Academy of Agriculture Science, Nanchang 330200, China
| | - Zheng Li
- State Key Laboratory of Agriculture Microbiology, Hubei Hongshan Laboratory, Huazhong Agriculture University, Wuhan 430000, China
| | - Xianhua Shen
- National Engineering Research Center of Rice (Nanchang), Key Laboratory of Rice Physiology and Genetics of Jiangxi Province, Rice Research Institute, Jiangxi Academy of Agriculture Science, Nanchang 330200, China
| | - Jeongmin Choi
- Crop Science Centre, Department of Plant Sciences, University of Cambridge, Lawrence Weaver Road, Cambridge CB3 0LE, UK
| | - Yangrong Cao
- State Key Laboratory of Agriculture Microbiology, Hubei Hongshan Laboratory, Huazhong Agriculture University, Wuhan 430000, China
- Correspondence:
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13
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Li Z, Henawy AR, Halema AA, Fan Q, Duanmu D, Huang R. A Wild Rice Rhizobacterium Burkholderiacepacia BRDJ Enhances Nitrogen Use Efficiency in Rice. Int J Mol Sci 2022; 23:10769. [PMID: 36142689 PMCID: PMC9503923 DOI: 10.3390/ijms231810769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 09/09/2022] [Accepted: 09/12/2022] [Indexed: 11/17/2022] Open
Abstract
Rice domestication has dramatically improved its agronomic traits, albeit with unavoidable significantly reduced genetic diversity. Dongxiang common wild rice, the wild rice species distributed in northernmost China, exhibits excellent resistance against stress and diseases and provides a rich genetic resource for rice breeding. Most of the studies focus on the function of the plant genes, often disregarding the role of the root microbes associated with the plants. In this work, we isolated a Burkholderia strain from the root of Dongxiang wild rice, which we identified as Burkholderia cepacia BRDJ, based on a phylogenetic analysis. This strain promoted the rice growth under greenhouse conditions. The grain yield was higher in a rice line containing a small genomic fragment derived from the Dongxiang wild rice, compared to the indica rice cultivar Zhongzao 35. This new strain also increased the plant biomass under limiting nitrogen conditions. Interestingly, this strain had a differential effect on indica and japonica rice varieties under full nitrogen supply conditions. By genome sequencing and comparison with another two B. cepacia strains, we observed enriched genes related with nitrogen fixation and phytohormone and volatiles biosynthesis that may account for the growth-promoting effects of the BRDJ. BRDJ has the potential to be used as a biofertilizer in promoting nitrogen use efficiency and overall growth in rice.
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Affiliation(s)
- Zheng Li
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- National Engineering Research Center of Rice (Nanchang), Key Laboratory of Rice Physiology and Genetics of Jiangxi Province, Rice Research Institute, Jiangxi Academy of Agriculture Sciences, Nanchang 330200, China
| | - Ahmed R. Henawy
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Department of Microbiology, Faculty of Agriculture, Cairo University, Giza 12613, Egypt
| | - Asmaa A. Halema
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Department of Genetics, Faculty of Agriculture, Cairo University, Giza 12613, Egypt
| | - Qiuling Fan
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Deqiang Duanmu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Renliang Huang
- National Engineering Research Center of Rice (Nanchang), Key Laboratory of Rice Physiology and Genetics of Jiangxi Province, Rice Research Institute, Jiangxi Academy of Agriculture Sciences, Nanchang 330200, China
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14
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Sangwan S, Prasanna R. Mycorrhizae Helper Bacteria: Unlocking Their Potential as Bioenhancers of Plant-Arbuscular Mycorrhizal Fungal Associations. MICROBIAL ECOLOGY 2022; 84:1-10. [PMID: 34417849 DOI: 10.1007/s00248-021-01831-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 07/27/2021] [Indexed: 06/13/2023]
Abstract
The dynamic interactions of plants and arbuscular mycorrhizal fungi (AMF) that facilitate the efficient uptake of minerals from soil and provide protection from various environmental stresses (biotic and abiotic) are now also attributed to a third component of the symbiosis. These are the less investigated mycorrhizae helper bacteria (MHB), which constitute a dense, active bacterial community, tightly associated with AMF, and involved in the development and functioning of AMF. Although AMF spores are known to host several bacteria in their spore walls and cytoplasm, their role in promoting the ecological fitness and establishment of AMF symbiosis by influencing spore germination, mycelial growth, root colonization, metabolic diversity, and biocontrol of soil borne diseases is now being deciphered. MHB also promote the functioning of arbuscular mycorrhizal symbiosis by triggering various plant growth factors, leading to better availability of nutrients in the soil and uptake by plants. In order to develop strategies to promote mycorrhization by AMF, and particularly to stimulate the ability to utilize phosphorus from the soil, there is a need to decipher crucial metabolic signalling pathways of MHB and elucidate their functional significance as mycorrhiza helper bacteria. MHB, also referred to as AMF bioenhancers, also improve agronomic efficiency and formulations using AMF along with enriched population of MHB are a promising option. This review covers the aspects related to the specificity and mechanisms of action of MHB, which positively impact the formation and functioning of AMF in mycorrhizal symbiosis, and the need to advocate MHB as AMF bioenhancers towards their inclusion in integrated nutrient management practices in sustainable agriculture.
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Affiliation(s)
- Seema Sangwan
- Division of Microbiology, ICAR Indian Agricultural Research Institute, New Delhi, 110012, India.
| | - Radha Prasanna
- Division of Microbiology, ICAR Indian Agricultural Research Institute, New Delhi, 110012, India
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15
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Bennett AE, Groten K. The Costs and Benefits of Plant-Arbuscular Mycorrhizal Fungal Interactions. ANNUAL REVIEW OF PLANT BIOLOGY 2022; 73:649-672. [PMID: 35216519 DOI: 10.1146/annurev-arplant-102820-124504] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The symbiotic interaction between plants and arbuscular mycorrhizal (AM) fungi is often perceived as beneficial for both partners, though a large ecological literature highlights the context dependency of this interaction. Changes in abiotic variables, such as nutrient availability, can drive the interaction along the mutualism-parasitism continuum with variable outcomes for plant growth and fitness. However, AM fungi can benefit plants in more ways than improved phosphorus nutrition and plant growth. For example, AM fungi can promote abiotic and biotic stress tolerance even when considered parasitic from a nutrient provision perspective. Other than being obligate biotrophs, very little is known about the benefits AM fungi gain from plants. In this review, we utilize both molecular biology and ecological approaches to expand our understanding of the plant-AM fungal interaction across disciplines.
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Affiliation(s)
- Alison E Bennett
- Department of Evolution, Ecology, and Organismal Biology, Ohio State University, Columbus, Ohio, USA;
| | - Karin Groten
- Max Planck Institute for Chemical Ecology, Jena, Germany;
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16
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Ndoye MS, Burridge J, Bhosale R, Grondin A, Laplaze L. Root traits for low input agroecosystems in Africa: Lessons from three case studies. PLANT, CELL & ENVIRONMENT 2022; 45:637-649. [PMID: 35037274 DOI: 10.1111/pce.14256] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 12/09/2021] [Indexed: 06/14/2023]
Abstract
In many regions across Africa, agriculture is largely based on low-input and small-holder farming systems that use little inorganic fertilisers and have limited access to irrigation and mechanisation. Improving agricultural practices and developing new cultivars adapted to these environments, where production already suffers from climate change, is a major priority for food security. Here, we illustrate how breeding for specific root traits could improve crop resilience in Africa using three case studies covering very contrasting low-input agroecosystems. We first review how greater basal root whorl number and longer and denser root hairs increased P acquisition efficiency and yield in common bean in South East Africa. We then discuss how water-saving strategies, root hair density and deep root growth could be targeted to improve sorghum and pearl millet yield in West Africa. Finally, we evaluate how breeding for denser root systems in the topsoil and interactions with arbuscular mycorrhizal fungi could be mobilised to optimise water-saving alternate wetting and drying practices in West African rice agroecosystems. We conclude with a discussion on how to evaluate the utility of root traits and how to make root trait selection feasible for breeders so that improved varieties can be made available to farmers through participatory approaches.
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Affiliation(s)
- Mame S Ndoye
- CERAAS, Thies Escale, Thies, Senegal
- LMI LAPSE, Centre de Recherche ISRA/IRD de Bel Air, Dakar, Senegal
- UMR DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
| | - James Burridge
- UMR DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
| | - Rahul Bhosale
- Future Food Beacon of Excellence and School of Biosciences, University of Nottingham, Nottingham, UK
| | - Alexandre Grondin
- CERAAS, Thies Escale, Thies, Senegal
- LMI LAPSE, Centre de Recherche ISRA/IRD de Bel Air, Dakar, Senegal
- UMR DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
| | - Laurent Laplaze
- LMI LAPSE, Centre de Recherche ISRA/IRD de Bel Air, Dakar, Senegal
- UMR DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
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17
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Thirkell TJ, Grimmer M, James L, Pastok D, Allary T, Elliott A, Paveley N, Daniell T, Field KJ. Variation in mycorrhizal growth response among a spring wheat mapping population shows potential to breed for symbiotic benefit. Food Energy Secur 2022; 11:e370. [PMID: 35865673 PMCID: PMC9286679 DOI: 10.1002/fes3.370] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 11/09/2021] [Accepted: 12/15/2021] [Indexed: 12/12/2022] Open
Affiliation(s)
- Tom J. Thirkell
- Plants, Photosynthesis and Soil School of Biosciences University of Sheffield Sheffield UK
| | | | | | - Daria Pastok
- School of Biology Centre for Plant Sciences University of Leeds Leeds UK
| | - Théa Allary
- Plants, Photosynthesis and Soil School of Biosciences University of Sheffield Sheffield UK
| | - Ashleigh Elliott
- School of Biology Centre for Plant Sciences University of Leeds Leeds UK
| | | | - Tim Daniell
- Plants, Photosynthesis and Soil School of Biosciences University of Sheffield Sheffield UK
| | - Katie J. Field
- Plants, Photosynthesis and Soil School of Biosciences University of Sheffield Sheffield UK
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18
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Das D, Paries M, Hobecker K, Gigl M, Dawid C, Lam HM, Zhang J, Chen M, Gutjahr C. PHOSPHATE STARVATION RESPONSE transcription factors enable arbuscular mycorrhiza symbiosis. Nat Commun 2022; 13:477. [PMID: 35078978 PMCID: PMC8789775 DOI: 10.1038/s41467-022-27976-8] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 12/21/2021] [Indexed: 01/19/2023] Open
Abstract
Arbuscular mycorrhiza (AM) is a widespread symbiosis between roots of the majority of land plants and Glomeromycotina fungi. AM is important for ecosystem health and functioning as the fungi critically support plant performance by providing essential mineral nutrients, particularly the poorly accessible phosphate, in exchange for organic carbon. AM fungi colonize the inside of roots and this is promoted at low but inhibited at high plant phosphate status, while the mechanistic basis for this phosphate-dependence remained obscure. Here we demonstrate that a major transcriptional regulator of phosphate starvation responses in rice PHOSPHATE STARVATION RESPONSE 2 (PHR2) regulates AM. Root colonization of phr2 mutants is drastically reduced, and PHR2 is required for root colonization, mycorrhizal phosphate uptake, and yield increase in field soil. PHR2 promotes AM by targeting genes required for pre-contact signaling, root colonization, and AM function. Thus, this important symbiosis is directly wired to the PHR2-controlled plant phosphate starvation response.
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Affiliation(s)
- Debatosh Das
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Research and Development Center for Fine Chemicals, Guizhou University, Guiyang, China
- CUHK Shenzhen Research Institute, No. 10 Yuexing 2nd Road, Nanshan, Shenzhen, China
| | - Michael Paries
- Plant Genetics, TUM School of Life Sciences, Technical University of Munich (TUM), Emil Ramann Str. 4, 85354, Freising, Germany
| | - Karen Hobecker
- Plant Genetics, TUM School of Life Sciences, Technical University of Munich (TUM), Emil Ramann Str. 4, 85354, Freising, Germany
| | - Michael Gigl
- Chair of Food Chemistry and Molecular Sensory Science, TUM School of Life Sciences, Technical University of Munich (TUM), Lise-Meitner-Str. 34, D-85354, Freising, Germany
| | - Corinna Dawid
- Chair of Food Chemistry and Molecular Sensory Science, TUM School of Life Sciences, Technical University of Munich (TUM), Lise-Meitner-Str. 34, D-85354, Freising, Germany
| | - Hon-Ming Lam
- CUHK Shenzhen Research Institute, No. 10 Yuexing 2nd Road, Nanshan, Shenzhen, China
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Jianhua Zhang
- CUHK Shenzhen Research Institute, No. 10 Yuexing 2nd Road, Nanshan, Shenzhen, China.
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong.
- Department of Biology, Hong Kong Baptist University, Shatin, Hong Kong.
| | - Moxian Chen
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Research and Development Center for Fine Chemicals, Guizhou University, Guiyang, China.
| | - Caroline Gutjahr
- Plant Genetics, TUM School of Life Sciences, Technical University of Munich (TUM), Emil Ramann Str. 4, 85354, Freising, Germany.
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19
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Das D, Paries M, Hobecker K, Gigl M, Dawid C, Lam HM, Zhang J, Chen M, Gutjahr C. PHOSPHATE STARVATION RESPONSE transcription factors enable arbuscular mycorrhiza symbiosis. Nat Commun 2022; 13:477. [PMID: 35078978 DOI: 10.1101/2021.11.05.467437] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 12/21/2021] [Indexed: 05/26/2023] Open
Abstract
Arbuscular mycorrhiza (AM) is a widespread symbiosis between roots of the majority of land plants and Glomeromycotina fungi. AM is important for ecosystem health and functioning as the fungi critically support plant performance by providing essential mineral nutrients, particularly the poorly accessible phosphate, in exchange for organic carbon. AM fungi colonize the inside of roots and this is promoted at low but inhibited at high plant phosphate status, while the mechanistic basis for this phosphate-dependence remained obscure. Here we demonstrate that a major transcriptional regulator of phosphate starvation responses in rice PHOSPHATE STARVATION RESPONSE 2 (PHR2) regulates AM. Root colonization of phr2 mutants is drastically reduced, and PHR2 is required for root colonization, mycorrhizal phosphate uptake, and yield increase in field soil. PHR2 promotes AM by targeting genes required for pre-contact signaling, root colonization, and AM function. Thus, this important symbiosis is directly wired to the PHR2-controlled plant phosphate starvation response.
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Affiliation(s)
- Debatosh Das
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Research and Development Center for Fine Chemicals, Guizhou University, Guiyang, China
- CUHK Shenzhen Research Institute, No. 10 Yuexing 2nd Road, Nanshan, Shenzhen, China
| | - Michael Paries
- Plant Genetics, TUM School of Life Sciences, Technical University of Munich (TUM), Emil Ramann Str. 4, 85354, Freising, Germany
| | - Karen Hobecker
- Plant Genetics, TUM School of Life Sciences, Technical University of Munich (TUM), Emil Ramann Str. 4, 85354, Freising, Germany
| | - Michael Gigl
- Chair of Food Chemistry and Molecular Sensory Science, TUM School of Life Sciences, Technical University of Munich (TUM), Lise-Meitner-Str. 34, D-85354, Freising, Germany
| | - Corinna Dawid
- Chair of Food Chemistry and Molecular Sensory Science, TUM School of Life Sciences, Technical University of Munich (TUM), Lise-Meitner-Str. 34, D-85354, Freising, Germany
| | - Hon-Ming Lam
- CUHK Shenzhen Research Institute, No. 10 Yuexing 2nd Road, Nanshan, Shenzhen, China
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Jianhua Zhang
- CUHK Shenzhen Research Institute, No. 10 Yuexing 2nd Road, Nanshan, Shenzhen, China.
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong.
- Department of Biology, Hong Kong Baptist University, Shatin, Hong Kong.
| | - Moxian Chen
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Research and Development Center for Fine Chemicals, Guizhou University, Guiyang, China.
| | - Caroline Gutjahr
- Plant Genetics, TUM School of Life Sciences, Technical University of Munich (TUM), Emil Ramann Str. 4, 85354, Freising, Germany.
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20
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Panneerselvam P, Saha S, Senapati A, Nayak AK, Kumar U, Mitra D. New generation post-emergence herbicides and their impact on arbuscular mycorrhizae fungal association in rice. CURRENT RESEARCH IN MICROBIAL SCIENCES 2021; 2:100067. [PMID: 34841357 PMCID: PMC8610324 DOI: 10.1016/j.crmicr.2021.100067] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 07/26/2021] [Accepted: 08/24/2021] [Indexed: 11/18/2022] Open
Abstract
To prevent weed invasion in direct seeded rice cultivation, several new generation post emergence herbicides viz. bispyribac sodium, flucetosulfuron, ethoxysulfuron, fenoxaprop-p ethyl, penoxsulam, fenoxaprop-p-ethyl plus ethoxysulfuron and cyhalofop‑butyl plus penoxsulam are widely used in sub-tropical rice ecosystems of Eastern India. The main objective of this study was to know whether application of above listed post emergence herbicides at recommended (n1) and double recommended dose (n2) has any negative impact on arbuscular mycorrhizal fungal (AMF) association in rice plants. Further, the effects of herbicides on soil microbial properties viz. microbial biomass carbon (MBC), fluroscein diacetate (FDA), dehydrogenase (DHA), acid phosphatase (AcP) and alkaline phosphatase (AkP) activities were analyzed using unsupervised and supervised learning methods. Results indicated that among different herbicides evaluated only application of penoxsulam significantly (p<0.05) reduced the AMF root colonization (58.0%) at recommended dose (n1) compared to only AMF (70.3%) application. Whereas, application of bispyribac sodium (both n1 and n2 dose) enhanced AMF sporulation (1100 spores/100 g) and root colonization (86.68%) compared to other herbicides application. Unsupervised learning approaches through PCA found that application of bispyribac sodium enhanced both above ground plant growth responses and soil microbial properties, but penoxsulam had negative impact. But, the combined application of penoxsulam and cyhalofop‑butyl did not show any negative impact on AMF association in rice plants. This study concluded that selection of right type of post-emergence herbicides are very important to minimize the harmful effect or enhance AMF association in rice plants.
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Key Words
- AMF
- AMF, arbuscular mycorrhizal fungi
- AMFc, percentage of colonization
- AMFs, AMF sporulation density
- AcP, acid phosphatase activity
- AkP, alkaline phosphatase activity
- Application
- BIOm, dry plant biomass
- DHA, dehydrogenase activity
- DSR, direct seeding of rice
- EC, emulsifiable concentrate
- Environmental sustainability
- MEG, monoethylene glycol
- PCA, principal component analysis
- PEG 300, polyethylene glycol
- PG, propylene glycol
- Post emergence herbicides
- RL, root length
- Rice
- SC, Suspension concentrates
- SOC, soil organic carbon
- Sl, plant height
- Soil
- WDG, water dispersible granule
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21
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Wang Y, Bao X, Li S. Effects of Arbuscular Mycorrhizal Fungi on Rice Growth Under Different Flooding and Shading Regimes. Front Microbiol 2021; 12:756752. [PMID: 34764946 PMCID: PMC8577809 DOI: 10.3389/fmicb.2021.756752] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 10/06/2021] [Indexed: 11/24/2022] Open
Abstract
Arbuscular mycorrhizal fungi (AMF) are present in paddy fields, where they suffer from periodic soil flooding and sometimes shading stress, but their interaction with rice plants in these environments is not yet fully explained. Based on two greenhouse experiments, we examined rice-growth response to AMF under different flooding and/or shading regimes to survey the regulatory effects of flooding on the mycorrhizal responses of rice plants under different light conditions. AMF had positive or neutral effects on the growth and yields of both tested rice varieties under non-flooding conditions but suppressed them under all flooding and/or shading regimes, emphasizing the high importance of flooding and shading conditions in determining the mycorrhizal effects. Further analyses indicated that flooding and shading both reduced the AMF colonization and extraradical hyphal density (EHD), implying a possible reduction of carbon investment from rice to AMF. The expression profiles of mycorrhizal P pathway marker genes (GintPT and OsPT11) suggested the P delivery from AMF to rice roots under all flooding and shading conditions. Nevertheless, flooding and shading both decreased the mycorrhizal P benefit of rice plants, as indicated by the significant decrease of mycorrhizal P responses (MPRs), contributing to the negative mycorrhizal effects on rice production. The expression profiles of rice defense marker genes OsPR1 and OsPBZ1 suggested that regardless of mycorrhizal growth responses (MGRs), AMF colonization triggered the basal defense response, especially under shading conditions, implying the multifaceted functions of AMF symbiosis and their effects on rice performance. In conclusion, this study found that flooding and shading both modulated the outcome of AMF symbiosis for rice plants, partially by influencing the mycorrhizal P benefit. This finding has important implications for AMF application in rice production.
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Affiliation(s)
- Yutao Wang
- Key Laboratory of Ecology and Environmental Science in Guangdong Higher Education and Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Xiaozhe Bao
- Key Laboratory of Ecology and Environmental Science in Guangdong Higher Education and Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Shaoshan Li
- Key Laboratory of Ecology and Environmental Science in Guangdong Higher Education and Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
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Rhizospheric microbiome: Bio-based emerging strategies for sustainable agriculture development and future perspectives. Microbiol Res 2021; 254:126901. [PMID: 34700186 DOI: 10.1016/j.micres.2021.126901] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 10/16/2021] [Accepted: 10/21/2021] [Indexed: 12/12/2022]
Abstract
In the light of intensification of cropping practices and changing climatic conditions, nourishing a growing global population requires optimizing environmental sustainability and reducing ecosystem impacts of food production. The use of microbiological systems to ameliorate the agricultural production in a sustainable and eco-friendly way is widespread accepted as a future key-technology. However, the multitude of interaction possibilities between the numerous beneficial microbes and plants in their habitat calls for systematic analysis and management of the rhizospheric microbiome. This review exploits present and future strategies for rhizospheric microbiome management with the aim to generate a comprehensive understanding of the known tools and techniques. Significant information on the structure and dynamics of rhizospheric microbiota of isolated microbial communities is now available. These microbial communities have beneficial effects including increased plant growth, essential nutrient acquisition, pathogens tolerance, and increased abiotic as well as biotic stress tolerance such as drought, temperature, salinity and antagonistic activities against the phyto-pathogens. A better and comprehensive understanding of the various effects and microbial interactions can be gained by application of molecular approaches as extraction of DNA/RNA and other biochemical markers to analyze microbial soil diversity. Novel techniques like interactome network analysis and split-ubiquitin system framework will enable to gain more insight into communication and interactions between the proteins from microbes and plants. The aim of the analysis tasks leads to the novel approach of Rhizosphere microbiome engineering. The capability of forming the rhizospheric microbiome in a defined way will allow combining several microbes (e.g. bacteria and fungi) for a given environment (soil type and climatic zone) in order to exert beneficial influences on specific plants. This integration will require a large-scale effort among academic researchers, industry researchers and farmers to understand and manage interactions of plant-microbiomes within modern farming systems, and is clearly a multi-domain approach and can be mastered only jointly by microbiology, mathematics and information technology. These innovations will open up a new avenue for designing and implementing intensive farming microbiome management approaches to maximize resource productivity and stress tolerance of agro-ecosystems, which in return will create value to the increasing worldwide population, for both food production and consumption.
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Andrea Genre. THE NEW PHYTOLOGIST 2021; 231:1316-1317. [PMID: 34263952 DOI: 10.1111/nph.17424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 04/22/2021] [Indexed: 06/13/2023]
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Gourion B, Ratet P. Avoidance of detrimental defense responses in beneficial plant-microbe interactions. Curr Opin Biotechnol 2021; 70:266-272. [PMID: 34252756 DOI: 10.1016/j.copbio.2021.06.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 06/07/2021] [Accepted: 06/15/2021] [Indexed: 12/21/2022]
Abstract
In the environment microbes interact with plants and provide them with benefits that include protection against biotic and abiotic stresses as well as improved nutrition. However, plants are also exposed to parasites and pathogens. To manage appropriate responses, evolution has resulted in improved tolerance of plants to beneficial microbes while keeping the ability to recognize detrimental ones and to develop defense responses. Here we review the mechanisms involved in these interactions. We also discuss how the interactions might be handled to improve crop resistance to pathogens without losing the ability to establish beneficial interactions.
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Affiliation(s)
- Benjamin Gourion
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Pascal Ratet
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405, Orsay, France; Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405, Orsay, France.
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Cui D, Tang C, Lu H, Li J, Ma X, A X, Han B, Yang Y, Dong C, Zhang F, Dai L, Han L. Genetic differentiation and restricted gene flow in rice landraces from Yunnan, China: effects of isolation-by-distance and isolation-by-environment. RICE (NEW YORK, N.Y.) 2021; 14:54. [PMID: 34131824 PMCID: PMC8206287 DOI: 10.1186/s12284-021-00497-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 05/25/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Understanding and identifying the factors responsible for genetic differentiation is of fundamental importance for efficient utilization and conservation of traditional rice landraces. In this study, we examined the spatial genetic differentiation of 594 individuals sampled from 28 locations in Yunnan Province, China, covering a wide geographic distribution and diverse growing conditions. All 594 accessions were studied using ten unlinked target genes and 48 microsatellite loci, and the representative 108 accessions from the whole collection were sampled for resequencing. RESULTS The genetic diversity of rice landraces was quite different geographically and exhibited a geographical decline from south to north in Yunnan, China. Population structure revealed that the rice landraces could be clearly differentiated into japonica and indica groups, respectively. In each group, the rice accessions could be further differentiated corresponded to their geographic locations, including three subgroups from northern, southern and middle locations. We found more obvious internal geographic structure in the japonica group than in the indica group. In the japonica group, we found that genetic and phenotypic differentiation were strongly related to geographical distance, suggesting a pattern of isolation by distance (IBD); this relationship remained highly significant when we controlled for environmental effects, where the likelihood of gene flow is inversely proportional to the distance between locations. Moreover, the gene flow also followed patterns of isolation by environment (IBE) whereby gene flow rates are higher in similar environments. We detected 314 and 216 regions had been differentially selected between Jap-N and Jap-S, Ind-N and Ind-S, respectively, and thus referred to as selection signatures for different geographic subgroups. We also observed a number of significant and interesting associations between loci and environmental factors, which implies adaptation to local environment. CONCLUSIONS Our findings highlight the influence of geographical isolation and environmental heterogeneity on the pattern of the gene flow, and demonstrate that both geographical isolation and environment drives adaptive divergence play dominant roles in the genetic differentiation of the rice landraces in Yunnan, China as a result of limited dispersal.
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Affiliation(s)
- Di Cui
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun Nandajie, 100081 Beijing, China
| | - Cuifeng Tang
- Institute of Biotech and Germplasm Resources, Yunnan Academy of Agricultural Sciences, No. 9 Xueyunlu, 650205 Kunming, Yunnan, China
| | - Hongfeng Lu
- Novogene Bioinformatics Institute, 100083 Beijing, China
| | - Jinmei Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun Nandajie, 100081 Beijing, China
| | - Xiaoding Ma
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun Nandajie, 100081 Beijing, China
| | - Xinxiang A
- Institute of Biotech and Germplasm Resources, Yunnan Academy of Agricultural Sciences, No. 9 Xueyunlu, 650205 Kunming, Yunnan, China
| | - Bing Han
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun Nandajie, 100081 Beijing, China
| | - Yayun Yang
- Institute of Biotech and Germplasm Resources, Yunnan Academy of Agricultural Sciences, No. 9 Xueyunlu, 650205 Kunming, Yunnan, China
| | - Chao Dong
- Institute of Biotech and Germplasm Resources, Yunnan Academy of Agricultural Sciences, No. 9 Xueyunlu, 650205 Kunming, Yunnan, China
| | - Feifei Zhang
- Institute of Biotech and Germplasm Resources, Yunnan Academy of Agricultural Sciences, No. 9 Xueyunlu, 650205 Kunming, Yunnan, China
| | - Luyuan Dai
- Institute of Biotech and Germplasm Resources, Yunnan Academy of Agricultural Sciences, No. 9 Xueyunlu, 650205 Kunming, Yunnan, China
| | - Longzhi Han
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun Nandajie, 100081 Beijing, China
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Thoms D, Liang Y, Haney CH. Maintaining Symbiotic Homeostasis: How Do Plants Engage With Beneficial Microorganisms While at the Same Time Restricting Pathogens? MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2021; 34:462-469. [PMID: 33534602 DOI: 10.1094/mpmi-11-20-0318-fi] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
This article is part of the Top 10 Unanswered Questions in MPMI invited review series.That plants recruit beneficial microbes while simultaneously restricting pathogens is critical to their survival. Plants must exclude pathogens; however, most land plants are able to form mutualistic symbioses with arbuscular mycorrhizal fungi. Plants also associate with the complex microbial communities that form the microbiome. The outcome of each symbiotic interaction-whether a specific microbe is pathogenic, commensal, or mutualistic-relies on the specific interplay of host and microbial genetics and the environment. Here, we discuss how plants use metabolites as a gate to select which microbes can be symbiotic. Once present, we discuss how plants integrate multiple inputs to initiate programs of immunity or mutualistic symbiosis and how this paradigm may be expanded to the microbiome. Finally, we discuss how environmental signals are integrated with immunity to fine-tune a thermostat that determines whether a plant engages in mutualism, resistance to pathogens, and shapes associations with the microbiome. Collectively, we propose that the plant immune thermostat is set to select for and tolerate a largely nonharmful microbiome while receptor-mediated decision making allows plants to detect and dynamically respond to the presence of potential pathogens or mutualists.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- David Thoms
- Department of Microbiology and Immunology, The University of British Columbia, Vancouver, V6T 1Z3 Canada
- Michael Smith Laboratories, The University of British Columbia, Vancouver, V6T 1Z4 Canada
| | - Yan Liang
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Cara H Haney
- Department of Microbiology and Immunology, The University of British Columbia, Vancouver, V6T 1Z3 Canada
- Michael Smith Laboratories, The University of British Columbia, Vancouver, V6T 1Z4 Canada
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French E, Kaplan I, Iyer-Pascuzzi A, Nakatsu CH, Enders L. Emerging strategies for precision microbiome management in diverse agroecosystems. NATURE PLANTS 2021; 7:256-267. [PMID: 33686226 DOI: 10.1038/s41477-020-00830-9] [Citation(s) in RCA: 84] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 12/08/2020] [Indexed: 05/18/2023]
Abstract
Substantial efforts to characterize the structural and functional diversity of soil, plant and insect-associated microbial communities have illuminated the complex interacting domains of crop-associated microbiomes that contribute to agroecosystem health. As a result, plant-associated microorganisms have emerged as an untapped resource for combating challenges to agricultural sustainability. However, despite growing interest in maximizing microbial functions for crop production, resource efficiency and stress resistance, research has struggled to harness the beneficial properties of agricultural microbiomes to improve crop performance. Here, we introduce the historical arc of agricultural microbiome research, highlighting current progress and emerging strategies for intentional microbiome manipulation to enhance crop performance and sustainability. We synthesize current practices and limitations to managing agricultural microbiomes and identify key knowledge gaps in our understanding of microbe-assisted crop production. Finally, we propose research priorities that embrace a holistic view of crop microbiomes for achieving precision microbiome management that is tailored, predictive and integrative in diverse agricultural systems.
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Affiliation(s)
- Elizabeth French
- Department of Entomology, Purdue University, West Lafayette, IN, USA
| | - Ian Kaplan
- Department of Entomology, Purdue University, West Lafayette, IN, USA
| | - Anjali Iyer-Pascuzzi
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, USA
| | - Cindy H Nakatsu
- Department of Agronomy, Purdue University, West Lafayette, IN, USA
| | - Laramy Enders
- Department of Entomology, Purdue University, West Lafayette, IN, USA.
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Nasir F, Bahadur A, Lin X, Gao Y, Tian C. Novel insights into host receptors and receptor-mediated signaling that regulate arbuscular mycorrhizal symbiosis. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:1546-1557. [PMID: 33252650 DOI: 10.1093/jxb/eraa538] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 11/10/2020] [Indexed: 06/12/2023]
Abstract
More than 80% of land plant species benefit from symbiotic partnerships with arbuscular mycorrhizal (AM) fungi, which assist in nutrient acquisition and enhance the ability of host plants to adapt to environmental constraints. Host-generated plasma membrane-residing receptor-like kinases and the intracellular α/β-hydrolase DWARF14-LIKE, a putative karrikin receptor, detect the presence of AM fungi before physical contact between the host and fungus. Detection induces appropriate symbiotic responses, which subsequently enables a favorable environment for AM symbiosis to occur. To prevent hyper-colonization and maintain a mutually beneficial association, the host plant precisely monitors and controls AM colonization by receptor-like kinases, such as SUPER NUMERIC NODULES. Previous studies have elucidated how host plant receptors and receptor-mediated signaling regulate AM symbiosis, but the underlying molecular mechanisms remain poorly understood. The identification of a rice CHITIN ELICITOR RECEPTOR KINASE 1 interaction partner, MYC FACTOR RECEPTOR 1, and new insights into DWARF14-LIKE receptor- and SUPER NUMERIC NODULES receptor-mediated signaling have expanded our understanding of how host plant receptors and their corresponding signals regulate AM symbiosis. This review summarizes these and other recent relevant findings. The identified receptors and/or their signaling components could be manipulated to engineer crops with improved agronomic traits by conferring the ability to precisely control AM colonization.
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Affiliation(s)
- Fahad Nasir
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, Jilin Province, China
| | - Ali Bahadur
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Northwest Institute of Eco-environment and Resources, Chinese Academy of Sciences, Lanzhou, Gansu Province, China
| | - Xiaolong Lin
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, Jilin Province, China
| | - Yingzhi Gao
- Key Laboratory of Vegetation Ecology, Institute of Grassland Science, Northeast Normal University, Changchun, Jilin Province, China
| | - Chunjie Tian
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, Jilin Province, China
- Key Laboratory of Straw Biology and Utilization of the Ministry of Education, Jilin Agricultural University, Changchun, Jilin Province, China
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29
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Berger F, Gutjahr C. Factors affecting plant responsiveness to arbuscular mycorrhiza. CURRENT OPINION IN PLANT BIOLOGY 2021; 59:101994. [PMID: 33450718 DOI: 10.1016/j.pbi.2020.101994] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 12/14/2020] [Accepted: 12/18/2020] [Indexed: 06/12/2023]
Abstract
Arbuscular mycorrhiza (AM) is an ancient, widespread symbiosis between most land plants and fungi of the Glomeromycotina, which receives increasing interest for agricultural application because it can promote plant growth and yield. The ability of plants to react to AM with changes in morphology and/or performance in terms of yield is called 'AM responsiveness'. Its amplitude depends on the plant- fungal genotype combination and the abiotic and biotic environment. A molecular understanding of AM responsiveness is key for enabling rational application of AM in agriculture, for example through targeted breeding of AM-optimised crops. However, the genetic and mechanistic underpinnings of AM responsiveness variation remain still unknown. Here, we review current knowledge on AM responsiveness, with a focus on agricultural crops, and speculate on mechanisms that may contribute to the variation in AM response.
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Affiliation(s)
- Florian Berger
- Plant Genetics, TUM School of Life Sciences, Technical University of Munich (TUM), Emil-Ramann-Str. 4, 85354 Freising, Germany
| | - Caroline Gutjahr
- Plant Genetics, TUM School of Life Sciences, Technical University of Munich (TUM), Emil-Ramann-Str. 4, 85354 Freising, Germany.
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30
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Ramírez-Flores MR, Perez-Limon S, Li M, Barrales-Gamez B, Albinsky D, Paszkowski U, Olalde-Portugal V, Sawers RJH. The genetic architecture of host response reveals the importance of arbuscular mycorrhizae to maize cultivation. eLife 2020; 9:e61701. [PMID: 33211006 PMCID: PMC7676867 DOI: 10.7554/elife.61701] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Accepted: 10/30/2020] [Indexed: 12/15/2022] Open
Abstract
Arbuscular mycorrhizal fungi (AMF) are ubiquitous in cultivated soils, forming symbiotic relationships with the roots of major crop species. Studies in controlled conditions have demonstrated the potential of AMF to enhance the growth of host plants. However, it is difficult to estimate the actual benefit in the field, not least because of the lack of suitable AMF-free controls. Here we implement a novel strategy using the selective incorporation of AMF-resistance into a genetic mapping population to evaluate maize response to AMF. We found AMF to account for about one-third of the grain production in a medium input field, as well as to affect the relative performance of different plant genotypes. Characterization of the genetic architecture of the host response indicated a trade-off between mycorrhizal dependence and benefit. We identified several QTL linked to host benefit, supporting the feasibility of breeding crops to maximize profit from symbiosis with AMF.
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Affiliation(s)
- M Rosario Ramírez-Flores
- Departamento de Biotecnología y Bioquímica, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN)IrapuatoMexico
| | - Sergio Perez-Limon
- Laboratorio Nacional de Genómica para la Biodiversidad/Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados, Instituto Politécnico Nacional (CINVESTAV-IPN)IrapuatoMexico
| | - Meng Li
- Department of Plant Science, The Pennsylvania State UniversityState CollegeUnited States
| | - Benjamín Barrales-Gamez
- Laboratorio Nacional de Genómica para la Biodiversidad/Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados, Instituto Politécnico Nacional (CINVESTAV-IPN)IrapuatoMexico
| | - Doris Albinsky
- Crop Science Centre and Department of Plant Sciences, University of CambridgeCambridgeUnited Kingdom
| | - Uta Paszkowski
- Crop Science Centre and Department of Plant Sciences, University of CambridgeCambridgeUnited Kingdom
| | - Víctor Olalde-Portugal
- Departamento de Biotecnología y Bioquímica, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN)IrapuatoMexico
| | - Ruairidh JH Sawers
- Department of Plant Science, The Pennsylvania State UniversityState CollegeUnited States
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31
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Pang Z, Zhao Y, Xu P, Yu D. Microbial Diversity of Upland Rice Roots and Their Influence on Rice Growth and Drought Tolerance. Microorganisms 2020; 8:microorganisms8091329. [PMID: 32878310 PMCID: PMC7564600 DOI: 10.3390/microorganisms8091329] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 08/27/2020] [Accepted: 08/30/2020] [Indexed: 01/25/2023] Open
Abstract
Among abiotic stresses, drought is one of the most important factors limiting plant growth. To increase their drought tolerance and survival, most plants interact directly with a variety of microbes. Upland rice (Oryza sativa L.) is a rice ecotype that differs from irrigated ecotype rice; it is adapted to both drought-stress and aerobic conditions. However, its root microbial resources have not been explored. We isolated bacteria and fungi from roots of upland rice in Xishuangbanna, China. Four hundred sixty-two endophytic and rhizospheric isolates (337 bacteria and 125 fungi) were distributed. They were distributed among 43 genera on the basis of 16S rRNA and internal transcribed spacer (ITS) gene sequence analysis. Notably, these root microbes differed from irrigated rice root microbes in irrigated environments; for example, members of the Firmicutes phylum were enriched (by 28.54%) in the roots of the upland plants. The plant growth-promoting (PGP) potential of 217 isolates was investigated in vitro. The PGP ability of 17 endophytic and 10 rhizospheric isolates from upland rice roots was evaluated under well-irrigated and drought-stress conditions, and 9 fungal strains increased rice seedling shoot length, shoot and root fresh weight (FW), antioxidant capability, and proline (Pro) and soluble sugar contents. Our work suggests that fungi from upland rice roots can increase plant growth under irrigated and drought-stress conditions and can serve as effective microbial resources for sustainable agricultural production in arid regions.
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Affiliation(s)
- Zhiqiang Pang
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650223, China; (Z.P.); (Y.Z.)
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Menglun, Mengla, Yunnan 666303, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ying Zhao
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650223, China; (Z.P.); (Y.Z.)
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan 666303, China
| | - Peng Xu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650223, China; (Z.P.); (Y.Z.)
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Menglun, Mengla, Yunnan 666303, China
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, Menglun, Mengla, Yunnan 666303, China
- Correspondence: (P.X.); (D.Y.)
| | - Diqiu Yu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650223, China; (Z.P.); (Y.Z.)
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, China
- Correspondence: (P.X.); (D.Y.)
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32
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Gong BQ, Wang FZ, Li JF. Hide-and-Seek: Chitin-Triggered Plant Immunity and Fungal Counterstrategies. TRENDS IN PLANT SCIENCE 2020; 25:805-816. [PMID: 32673581 DOI: 10.1016/j.tplants.2020.03.006] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 03/01/2020] [Accepted: 03/10/2020] [Indexed: 05/05/2023]
Abstract
Fungal pathogens are major destructive microorganisms for land plants and pose growing challenges to global crop production. Chitin is a vital building block for fungal cell walls and also a broadly effective elicitor of plant immunity. Here we review the rapid progress in understanding chitin perception and signaling in plants and highlight similarities and differences of these processes between arabidopsis and rice. We also outline moonlight functions of CERK1, an indispensable chitin coreceptor conserved across the plant kingdom, which imply potential crosstalk between chitin signaling and symbiotic or biotic/abiotic stress signaling in plants via CERK1. Moreover, we summarize current knowledge about fungal counterstrategies for subverting chitin-triggered plant immunity and propose open questions and future directions in this field.
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Affiliation(s)
- Ben-Qiang Gong
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory of Biocontrol, MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Feng-Zhu Wang
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory of Biocontrol, MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Jian-Feng Li
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory of Biocontrol, MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China.
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33
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Lefebvre B. An opportunity to breed rice for improved benefits from the arbuscular mycorrhizal symbiosis? THE NEW PHYTOLOGIST 2020; 225:1404-1406. [PMID: 31823373 DOI: 10.1111/nph.16333] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Affiliation(s)
- Benoit Lefebvre
- LIPM, Université de Toulouse, INRA, CNRS, 31326, Castanet-Tolosan, France
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