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Slimani A, Ait-El-Mokhtar M, Ben-Laouane R, Boutasknit A, Anli M, Abouraicha EF, Oufdou K, Meddich A, Baslam M. Molecular and Systems Biology Approaches for Harnessing the Symbiotic Interaction in Mycorrhizal Symbiosis for Grain and Oil Crop Cultivation. Int J Mol Sci 2024; 25:912. [PMID: 38255984 PMCID: PMC10815302 DOI: 10.3390/ijms25020912] [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: 12/14/2023] [Revised: 01/09/2024] [Accepted: 01/09/2024] [Indexed: 01/24/2024] Open
Abstract
Mycorrhizal symbiosis, the mutually beneficial association between plants and fungi, has gained significant attention in recent years due to its widespread significance in agricultural productivity. Specifically, arbuscular mycorrhizal fungi (AMF) provide a range of benefits to grain and oil crops, including improved nutrient uptake, growth, and resistance to (a)biotic stressors. Harnessing this symbiotic interaction using molecular and systems biology approaches presents promising opportunities for sustainable and economically-viable agricultural practices. Research in this area aims to identify and manipulate specific genes and pathways involved in the symbiotic interaction, leading to improved cereal and oilseed crop yields and nutrient acquisition. This review provides an overview of the research frontier on utilizing molecular and systems biology approaches for harnessing the symbiotic interaction in mycorrhizal symbiosis for grain and oil crop cultivation. Moreover, we address the mechanistic insights and molecular determinants underpinning this exchange. We conclude with an overview of current efforts to harness mycorrhizal diversity to improve cereal and oilseed health through systems biology.
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Affiliation(s)
- Aiman Slimani
- Centre d’Agrobiotechnologie et Bioingénierie, Unité de Recherche Labellisée CNRST (Centre AgroBiotech-URL-CNRST-05), Cadi Ayyad University, Marrakesh 40000, Morocco
- Laboratory of Agro-Food, Biotechnologies and Valorization of Plant Bioresources (AGROBIOVAL), Department of Biology, Faculty of Science Semlalia, Cadi Ayyad University, Marrakesh 40000, Morocco
- Laboratory of Microbial Biotechnologies, Agrosciences, and Environment, Department of Biology, Faculty of Science Semlalia, Cadi Ayyad University, Marrakesh 40000, Morocco
| | - Mohamed Ait-El-Mokhtar
- Laboratory Biochemistry, Environment & Agri-Food URAC 36, Department of Biology, Faculty of Science and Techniques—Mohammedia, Hassan II University of Casablanca, Mohammedia 28800, Morocco
| | - Raja Ben-Laouane
- Laboratory of Environment and Health, Department of Biology, Faculty of Science and Techniques, Errachidia 52000, Morocco
| | - Abderrahim Boutasknit
- Centre d’Agrobiotechnologie et Bioingénierie, Unité de Recherche Labellisée CNRST (Centre AgroBiotech-URL-CNRST-05), Cadi Ayyad University, Marrakesh 40000, Morocco
- Laboratory of Agro-Food, Biotechnologies and Valorization of Plant Bioresources (AGROBIOVAL), Department of Biology, Faculty of Science Semlalia, Cadi Ayyad University, Marrakesh 40000, Morocco
- Department of Biology, Multidisciplinary Faculty of Nador, Mohamed First University, Nador 62700, Morocco
| | - Mohamed Anli
- Laboratory of Agro-Food, Biotechnologies and Valorization of Plant Bioresources (AGROBIOVAL), Department of Biology, Faculty of Science Semlalia, Cadi Ayyad University, Marrakesh 40000, Morocco
- Department of Life, Earth and Environmental Sciences, University of Comoros, Patsy University Center, Moroni 269, Comoros
| | - El Faiza Abouraicha
- Centre d’Agrobiotechnologie et Bioingénierie, Unité de Recherche Labellisée CNRST (Centre AgroBiotech-URL-CNRST-05), Cadi Ayyad University, Marrakesh 40000, Morocco
- Laboratory of Agro-Food, Biotechnologies and Valorization of Plant Bioresources (AGROBIOVAL), Department of Biology, Faculty of Science Semlalia, Cadi Ayyad University, Marrakesh 40000, Morocco
- Higher Institute of Nursing and Health Techniques (ISPITS), Essaouira 44000, Morocco
| | - Khalid Oufdou
- Laboratory of Microbial Biotechnologies, Agrosciences, and Environment, Department of Biology, Faculty of Science Semlalia, Cadi Ayyad University, Marrakesh 40000, Morocco
| | - Abdelilah Meddich
- Centre d’Agrobiotechnologie et Bioingénierie, Unité de Recherche Labellisée CNRST (Centre AgroBiotech-URL-CNRST-05), Cadi Ayyad University, Marrakesh 40000, Morocco
- Laboratory of Agro-Food, Biotechnologies and Valorization of Plant Bioresources (AGROBIOVAL), Department of Biology, Faculty of Science Semlalia, Cadi Ayyad University, Marrakesh 40000, Morocco
| | - Marouane Baslam
- Centre d’Agrobiotechnologie et Bioingénierie, Unité de Recherche Labellisée CNRST (Centre AgroBiotech-URL-CNRST-05), Cadi Ayyad University, Marrakesh 40000, Morocco
- Laboratory of Agro-Food, Biotechnologies and Valorization of Plant Bioresources (AGROBIOVAL), Department of Biology, Faculty of Science Semlalia, Cadi Ayyad University, Marrakesh 40000, Morocco
- GrowSmart, Seoul 03129, Republic of Korea
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Duc NH, Szentpéteri V, Mayer Z, Posta K. Distinct impact of arbuscular mycorrhizal isolates on tomato plant tolerance to drought combined with chronic and acute heat stress. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 201:107892. [PMID: 37490823 DOI: 10.1016/j.plaphy.2023.107892] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 06/17/2023] [Accepted: 07/10/2023] [Indexed: 07/27/2023]
Abstract
Arbuscular mycorrhizal (AM) fungi could mitigate individual drought and heat stress in host plants. However, there are still major gaps in our understanding of AM symbiosis response to the combined stresses. Here, we compared seven AM fungi, Rhizophagus irregularis, Funneliformis mosseae, Funneliformis geosporum, Funneliformis verruculosum, Funneliformis coronatum, Septoglomus deserticola, Septoglomus constrictum, distributed to many world regions in terms of their impacts on tomato endurance to combined drought and chronic heat as well as combined drought and heat shock. A multidisciplinary approach including morphometric, ecophysiological, biochemical, targeted metabolic (by ultrahigh-performance LC-MS), and molecular analyses was applied. The variation among AM fungi isolates in the enhancement in leaf water potential, stomatal conductance, photosynthetic activity, and maximal PSII photochemical efficiency, proline accumulation, antioxidant enzymes (POD, SOD, CAT), and lowered ROS markers (H2O2, MDA) in host plants under combined stresses were observed. S. constrictum inoculation could better enhanced the host plant physiology and biochemical parameters, while F. geosporum colonization less positively influenced the host plants than other treatments under both combined stresses. F. mosseae- and S. constrictum-associated plants showed the common AM-induced modifications and AM species-specific alterations in phytohormones (ABA, SA, JA, IAA), aquaporin (SlSIP1-2; SlTIP2-3; SlNIP2-1; SlPIP2-1) and abiotic stress-responsive genes (SlAREB1, SlLEA, SlHSP70, SlHSP90) in host plants under combined stresses. Altogether, mycorrhizal mitigation of the negative impacts of drought + prolonged heat and drought + acute heat, with the variation among different AM fungi isolates, depending on the specific combined stress and stress duration.
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Affiliation(s)
- Nguyen Hong Duc
- Department of Microbiology and Applied Biotechnology, Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences (MATE), Gödöllő, Hungary
| | - Viktor Szentpéteri
- Department of Microbiology and Applied Biotechnology, Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences (MATE), Gödöllő, Hungary; Agribiotechnology and Precision Breeding for Food Security National Laboratory, Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences (MATE), Gödöllő, Hungary
| | - Zoltán Mayer
- Department of Microbiology and Applied Biotechnology, Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences (MATE), Gödöllő, Hungary
| | - Katalin Posta
- Department of Microbiology and Applied Biotechnology, Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences (MATE), Gödöllő, Hungary; Agribiotechnology and Precision Breeding for Food Security National Laboratory, Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences (MATE), Gödöllő, Hungary.
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Yu H, Bai F, Ji C, Fan Z, Luo J, Ouyang B, Deng X, Xiao S, Bisseling T, Limpens E, Pan Z. Plant lysin motif extracellular proteins are required for arbuscular mycorrhizal symbiosis. Proc Natl Acad Sci U S A 2023; 120:e2301884120. [PMID: 37368927 PMCID: PMC10318984 DOI: 10.1073/pnas.2301884120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 05/15/2023] [Indexed: 06/29/2023] Open
Abstract
Arbuscular mycorrhizal fungi (AMF) can form a mutually beneficial symbiotic relationship with most land plants. They are known to secrete lysin motif (LysM) effectors into host root cells for successful colonization. Intriguingly, plants secrete similar types of LysM proteins; however, their role in plant-microbe interactions is unknown. Here, we show that Medicago truncatula deploys LysM extracellular (LysMe) proteins to facilitate symbiosis with AMF. Promoter analyses demonstrated that three M. truncatula LysMe genes MtLysMe1/2/3, are expressed in arbuscule-containing cells and those adjacent to intercellular hyphae. Localization studies showed that these proteins are targeted to the periarbuscular space between the periarbuscular membrane and the fungal cell wall of the branched arbuscule. M. truncatula mutants in which MtLysMe2 was knocked out via CRISPR/Cas9-targeted mutagenesis exhibited a significant reduction in AMF colonization and arbuscule formation, whereas genetically complemented transgenic plants restored wild-type level AMF colonization. In addition, knocking out the ortholog of MtLysMe2 in tomato resulted in a similar defect in AMF colonization. In vitro binding affinity precipitation assays suggested binding of MtLysMe1/2/3 with chitin and chitosan, while microscale thermophoresis (MST) assays revealed weak binding of these proteins with chitooligosaccharides. Moreover, application of purified MtLysMe proteins to root segments could suppress chitooctaose (CO8)-induced reactive oxygen species production and expression of reporter genes of the immune response without impairing chitotetraose (CO4)-triggered symbiotic responses. Taken together, our results reveal that plants, like their fungal partners, also secrete LysM proteins to facilitate symbiosis establishment.
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Affiliation(s)
- Huimin Yu
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan430070, China
| | - Fuxi Bai
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan430070, China
- Institute of Fruit and Tea, Hubei Academy of Agricultural Sciences, Wuhan430064, China
| | - Chuanya Ji
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan430070, China
| | - Zhengyan Fan
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan430070, China
| | - Jinying Luo
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan430070, China
| | - Bo Ouyang
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan430070, China
| | - Xiuxin Deng
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan430070, China
| | - Shunyuan Xiao
- Institute for Bioscience and Biotechnology Research and Department of Plant Sciences and Landscape Architecture, University of Maryland College Park, Rockville, MD20850
| | - Ton Bisseling
- Department of Plant Sciences, Laboratory of Molecular Biology, Wageningen University and Research6708 PB, Wageningen, the Netherlands
| | - Erik Limpens
- Department of Plant Sciences, Laboratory of Molecular Biology, Wageningen University and Research6708 PB, Wageningen, the Netherlands
| | - Zhiyong Pan
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan430070, China
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4
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Chang OC, Lin WY. Variation of growth and transcriptome responses to arbuscular mycorrhizal symbiosis in different foxtail millet lines. BOTANICAL STUDIES 2023; 64:16. [PMID: 37326894 DOI: 10.1186/s40529-023-00391-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 06/08/2023] [Indexed: 06/17/2023]
Abstract
BACKGROUND Arbuscular mycorrhizal fungi (AMF) have been applied to promote the growth of different crop species, but knowledge about the impacts of symbiosis on foxtail millet at the physiological and molecular levels have remained limited. In this study, we compared the mycorrhization phenotypes of one cultivar and three different landraces and performed a comprehensive transcriptomic analysis to assess the effects of genetic variation on the responses to symbiosis. RESULTS Our results showed that colonization by AMF did not enhance biomass accumulation but significantly increased grain production only in three lines. More than 2,000 genes were affected by AMF colonization in all lines. Most AM symbiosis-conserved genes were induced, but the induction levels varied between lines. Gene Ontology (GO) analysis showed that Biological Function terms related to nitrogen transport and assimilation were only enriched in TT8. Similarly, two of phosphate starvation-induced phosphate transporters were only simultaneously downregulated in TT8. In the other two lines, the enrichment of GO terms associated with cell wall reorganization and lignification was observed, though the effects were different. CONCLUSION This study reveals the impacts of genetic variation of millet lines on the responses to AM symbiosis and provides information regarding AMF application for millet production.
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Affiliation(s)
- Ou-Chi Chang
- Department of Agronomy, National Taiwan University, Taipei, 106319, Taiwan
| | - Wei-Yi Lin
- Department of Agronomy, National Taiwan University, Taipei, 106319, Taiwan.
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Ji C, Song F, He C, An J, Huang S, Yu H, Lu H, Xiao S, Bucher M, Pan Z. Integrated miRNA-mRNA analysis reveals candidate miRNA family regulating arbuscular mycorrhizal symbiosis of Poncirus trifoliata. PLANT, CELL & ENVIRONMENT 2023; 46:1805-1821. [PMID: 36760042 DOI: 10.1111/pce.14564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 01/19/2023] [Accepted: 02/09/2023] [Indexed: 05/04/2023]
Abstract
Over 70% land plants live in mutualistic symbiosis with arbuscular mycorrhizal (AM) fungi, and maintenance of symbiosis requires transcriptional and post-transcriptional regulation. The former has been widely studied, whereas the latter mediated by symbiotic microRNAs (miRNAs) remains obscure, especially in woody plants. Here, we performed high-throughput sequencing of the perennial woody citrus plant Poncirus trifoliata and identified 3750 differentially expressed genes (DEGs) and 42 miRNAs (DEmiRs) upon AM fungal colonization. By analyzing cis-regulatory elements in the promoters of the DEGs, we predicted 329 key AM transcription factors (TFs). A miRNA-mRNA regulatory network was then constructed by integrating these data. Several candidate miRNA families of P. trifoliata were identified whose members target known symbiotic genes, such as miR167h-AMT2;3 and miR156e-EXO70I, or key TFs, such as miR164d-NAC and miR477a-GRAS, thus are involved in AM symbiotic processes of fungal colonization, arbuscule development, nutrient exchange and phytohormone signaling. Finally, analysis of selected miRNA family revealed that a miR159b conserved in mycorrhizal plant species and a Poncirus-specific miR477a regulate AM symbiosis. The role of miR477a was likely to target GRAS family gene RAD1 in citrus plants. Our results not only revealed that miRNA-mRNA network analysis, especially miRNA-TF analysis, is effective in identifying miRNA family regulating AM symbiosis, but also shed light on miRNA-mediated post-transcriptional regulation of AM symbiosis in woody citrus plants.
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Affiliation(s)
- Chuanya Ji
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, China
| | - Fang Song
- Institute of Fruit and Tea, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Chuan He
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, China
| | - Jianyong An
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University, Wageningen, The Netherlands
| | - Shengyu Huang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, China
| | - Huimin Yu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, China
| | - Hang Lu
- Institute for Plant Sciences, Cologne Biocenter, Cluster of Excellence on Plant Sciences, University of Cologne, Cologne, Germany
| | - Shunyuan Xiao
- Department of Plant Science and Landscape Architecture, Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland, USA
| | - Marcel Bucher
- Institute for Plant Sciences, Cologne Biocenter, Cluster of Excellence on Plant Sciences, University of Cologne, Cologne, Germany
| | - Zhiyong Pan
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, China
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Zeng Z, Liu Y, Feng XY, Li SX, Jiang XM, Chen JQ, Shao ZQ. The RNAome landscape of tomato during arbuscular mycorrhizal symbiosis reveals an evolving RNA layer symbiotic regulatory network. PLANT COMMUNICATIONS 2023; 4:100429. [PMID: 36071667 PMCID: PMC9860192 DOI: 10.1016/j.xplc.2022.100429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 08/15/2022] [Accepted: 09/02/2022] [Indexed: 06/15/2023]
Abstract
Arbuscular mycorrhizal symbiosis (AMS) is an ancient plant-fungus relationship that is widely distributed in terrestrial plants. The formation of symbiotic structures and bidirectional nutrient exchange requires the regulation of numerous genes. However, the landscape of RNAome during plant AMS involving different types of regulatory RNA is poorly understood. In this study, a combinatorial strategy utilizing multiple sequencing approaches was used to decipher the landscape of RNAome in tomato, an emerging AMS model. The annotation of the tomato genome was improved by a multiple-platform sequencing strategy. A total of 3,174 protein-coding genes were upregulated during AMS, 42% of which were alternatively spliced. Comparative-transcriptome analysis revealed that genes from 24 orthogroups were consistently induced by AMS in eight phylogenetically distant angiosperms. Seven additional orthogroups were specifically induced by AMS in all surveyed dicot AMS host plants. However, these orthogroups were absent or not induced in monocots and/or non-AMS hosts, suggesting a continuously evolving AMS-responsive network in addition to a conserved core regulatory module. Additionally, we detected 587 lncRNAs, ten miRNAs, and 146 circRNAs that responded to AMS, which were incorporated to establish a tomato AMS-responsive, competing RNA-responsive endogenous RNA (ceRNA) network. Finally, a tomato symbiotic transcriptome database (TSTD, https://efg.nju.edu.cn/TSTD) was constructed to serve as a resource for deep deciphering of the AMS regulatory network. These results help elucidate the reconfiguration of the tomato RNAome during AMS and suggest a sophisticated and evolving RNA layer responsive network during AMS processes.
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Affiliation(s)
- Zhen Zeng
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Yang Liu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Xing-Yu Feng
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Sai-Xi Li
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Xing-Mei Jiang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Jian-Qun Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China.
| | - Zhu-Qing Shao
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China.
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Tominaga T, Miura C, Sumigawa Y, Hirose Y, Yamaguchi K, Shigenobu S, Mine A, Kaminaka H. Conservation and Diversity in Gibberellin-Mediated Transcriptional Responses Among Host Plants Forming Distinct Arbuscular Mycorrhizal Morphotypes. FRONTIERS IN PLANT SCIENCE 2021; 12:795695. [PMID: 34975984 PMCID: PMC8718060 DOI: 10.3389/fpls.2021.795695] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 11/12/2021] [Indexed: 06/01/2023]
Abstract
Morphotypes of arbuscular mycorrhizal (AM) symbiosis, Arum, Paris, and Intermediate types, are mainly determined by host plant lineages. It was reported that the phytohormone gibberellin (GA) inhibits the establishment of Arum-type AM symbiosis in legume plants. In contrast, we previously reported that GA promotes the establishment of Paris-type AM symbiosis in Eustoma grandiflorum, while suppressing Arum-type AM symbiosis in a legume model plant, Lotus japonicus. This raises a hitherto unexplored possibility that GA-mediated transcriptional reprogramming during AM symbiosis is different among plant lineages as the AM morphotypes are distinct. Here, our comparative transcriptomics revealed that several symbiosis-related genes were commonly upregulated upon AM fungal colonization in L. japonicus (Arum-type), Daucus carota (Intermediate-type), and E. grandiflorum (Paris-type). Despite of the similarities, the fungal colonization levels and the expression of symbiosis-related genes were suppressed in L. japonicus and D. carota but were promoted in E. grandiflorum in the presence of GA. Moreover, exogenous GA inhibited the expression of genes involved in biosynthetic process of the pre-symbiotic signal component, strigolactone, which resulted in the reduction of its endogenous accumulation in L. japonicus and E. grandiflorum. Additionally, differential regulation of genes involved in sugar metabolism suggested that disaccharides metabolized in AM roots would be different between L. japonicus and D. carota/E. grandiflorum. Therefore, this study uncovered the conserved transcriptional responses during mycorrhization regardless of the distinct AM morphotype. Meanwhile, we also found diverse responses to GA among phylogenetically distant AM host plants.
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Affiliation(s)
- Takaya Tominaga
- The United Graduate School of Agricultural Sciences, Tottori University, Tottori, Japan
| | - Chihiro Miura
- Faculty of Agriculture, Tottori University, Tottori, Japan
| | - Yuuka Sumigawa
- Faculty of Agriculture, Tottori University, Tottori, Japan
| | - Yukine Hirose
- Faculty of Agriculture, Tottori University, Tottori, Japan
| | - Katsushi Yamaguchi
- Functional Genomics Facility, NIBB Core Research Facilities, National Institute for Basic Biology, Okazaki, Japan
| | - Shuji Shigenobu
- Functional Genomics Facility, NIBB Core Research Facilities, National Institute for Basic Biology, Okazaki, Japan
| | - Akira Mine
- Laboratory of Plant Pathology, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
- JST, PRESTO, Kawaguchi, Japan
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Quo vadis: signaling molecules and small secreted proteins from mycorrhizal fungi at the early stage of mycorrhiza formation. Symbiosis 2021. [DOI: 10.1007/s13199-021-00793-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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9
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Peng T, Kang JL, Xiong XT, Cheng FT, Zhou XJ, Dai WS, Wang M, Li ZY, Su HN, Zhong BL. Integrated Transcriptomics and Metabolomics Analyses Provide Insights Into the Response of Chongyi Wild Mandarin to Candidatus Liberibacter Asiaticus Infection. FRONTIERS IN PLANT SCIENCE 2021; 12:748209. [PMID: 34721476 PMCID: PMC8551615 DOI: 10.3389/fpls.2021.748209] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 09/06/2021] [Indexed: 05/13/2023]
Abstract
Candidatus Liberibacter asiaticus (CLas) is the causative agent of Huanglongbing (HLB), which has caused great economic losses to the citrus industry. The molecular mechanism of the host response to CLas in wild citrus germplasm has been reported less. Eighteen weeks after inoculation via grafting, all the CLas-inoculated Chongyi wild mandarin (Citrus reticulata) were positive and showed severe anatomical aberrations, suggesting its susceptibility to HLB. Transcriptomics and metabolomics analyses of leaves, barks, and roots from mock-inoculated (control) and CLas-inoculated seedlings were performed. Comparative transcriptomics identified 3,628, 3,770, and 1,716 differentially expressed genes (DEGs) between CLas-infected and healthy tissues in the leaves, barks, and roots, respectively. The CLas-infected tissues had higher transcripts per kilobase per million values and more genes that reached their maximal expression, suggesting that HLB might cause an overall increase in transcript accumulation. However, HLB-triggered transcriptional alteration showed tissue specificity. In the CLas-infected leaves, many DEGs encoding immune receptors were downregulated. In the CLas-infected barks, nearly all the DEGs involved in signaling and plant-pathogen interaction were upregulated. In the CLas-infected roots, DEGs encoding enzymes or transporters involved in carotenoid biosynthesis and nitrogen metabolism were downregulated. Metabolomics identified 71, 62, and 50 differentially accumulated metabolites (DAMs) in the CLas-infected leaves, barks and roots, respectively. By associating DEGs with DAMs, nitrogen metabolism was the only pathway shared by the three infected tissues and was depressed in the CLas-infected roots. In addition, 26 genes were determined as putative markers of CLas infection, and a hypothesized model for the HLB susceptibility mechanism in Chongyi was proposed. Our study may shed light on investigating the molecular mechanism of the host response to CLas infection in wild citrus germplasm.
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Affiliation(s)
- Ting Peng
- National Navel Orange Engineering Research Center, College of Life Sciences, Gannan Normal University, Ganzhou, China
- *Correspondence: Ting Peng orcid.org/0000-0002-3084-6328
| | - Jing-Liang Kang
- National Navel Orange Engineering Research Center, College of Life Sciences, Gannan Normal University, Ganzhou, China
- China-USA Citrus Huanglongbing Joint Laboratory, Ganzhou, China
| | - Xin-Ting Xiong
- National Navel Orange Engineering Research Center, College of Life Sciences, Gannan Normal University, Ganzhou, China
| | - Fang-Ting Cheng
- National Navel Orange Engineering Research Center, College of Life Sciences, Gannan Normal University, Ganzhou, China
| | - Xiao-Juan Zhou
- National Navel Orange Engineering Research Center, College of Life Sciences, Gannan Normal University, Ganzhou, China
| | - Wen-Shan Dai
- National Navel Orange Engineering Research Center, College of Life Sciences, Gannan Normal University, Ganzhou, China
- China-USA Citrus Huanglongbing Joint Laboratory, Ganzhou, China
| | - Min Wang
- National Navel Orange Engineering Research Center, College of Life Sciences, Gannan Normal University, Ganzhou, China
- China-USA Citrus Huanglongbing Joint Laboratory, Ganzhou, China
| | - Zhong-Yang Li
- National Navel Orange Engineering Research Center, College of Life Sciences, Gannan Normal University, Ganzhou, China
| | - Hua-Nan Su
- National Navel Orange Engineering Research Center, College of Life Sciences, Gannan Normal University, Ganzhou, China
| | - Ba-Lian Zhong
- National Navel Orange Engineering Research Center, College of Life Sciences, Gannan Normal University, Ganzhou, China
- Ba-Lian Zhong
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Paparokidou C, Leake JR, Beerling DJ, Rolfe SA. Phosphate availability and ectomycorrhizal symbiosis with Pinus sylvestris have independent effects on the Paxillus involutus transcriptome. MYCORRHIZA 2021; 31:69-83. [PMID: 33200348 PMCID: PMC7782400 DOI: 10.1007/s00572-020-01001-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 10/29/2020] [Indexed: 06/11/2023]
Abstract
Many plant species form symbioses with ectomycorrhizal fungi, which help them forage for limiting nutrients in the soil such as inorganic phosphate (Pi). The transcriptional responses to symbiosis and nutrient-limiting conditions in ectomycorrhizal fungal hyphae, however, are largely unknown. An artificial system was developed to study ectomycorrhizal basidiomycete Paxillus involutus growth in symbiosis with its host tree Pinus sylvestris at different Pi concentrations. RNA-seq analysis was performed on P. involutus hyphae growing under Pi-limiting conditions, either in symbiosis or alone. We show that Pi starvation and ectomycorrhizal symbiosis have an independent effect on the P. involutus transcriptome. Notably, low Pi availability induces expression of newly identified putative high-affinity Pi transporter genes, while reducing the expression of putative organic acid transporters. Additionally, low Pi availability induces a close transcriptional interplay between P and N metabolism. GTP-related signalling was found to have a positive effect in the maintenance of ectomycorrhizal symbiosis, whereas multiple putative cytochrome P450 genes were found to be downregulated, unlike arbuscular mycorrhizal fungi. We provide the first evidence of global transcriptional changes induced by low Pi availability and ectomycorrhizal symbiosis in the hyphae of P. involutus, revealing both similarities and differences with better-characterized arbuscular mycorrhizal fungi.
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Affiliation(s)
| | - Jonathan R Leake
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - David J Beerling
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - Stephen A Rolfe
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK.
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Song F, Bai F, Wang J, Wu L, Jiang Y, Pan Z. Influence of Citrus Scion/Rootstock Genotypes on Arbuscular Mycorrhizal Community Composition under Controlled Environment Condition. PLANTS 2020; 9:plants9070901. [PMID: 32708770 PMCID: PMC7412222 DOI: 10.3390/plants9070901] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 07/13/2020] [Accepted: 07/14/2020] [Indexed: 01/01/2023]
Abstract
Citrus is vegetatively propagated by grafting for commercial production, and most rootstock cultivars of citrus have scarce root hairs, thus heavily relying on mutualistic symbiosis with arbuscular mycorrhizal fungi (AMF) for mineral nutrient uptake. However, the AMF community composition, and its differences under different citrus scion/rootstock genotypes, were largely unknown. In this study, we investigated the citrus root-associated AMF diversity and richness, and assessed the influence of citrus scion/rootstock genotypes on the AMF community composition in a controlled condition, in order to exclude interferences from environmental factors and agricultural practices. As a result, a total of 613,408 Glomeromycota tags were detected in the citrus roots, and 46 AMF species were annotated against the MAARJAM database. Of these, 39 species belonged to Glomus, indicating a dominant role of the Glomus AMF in the symbiosis with citrus. PCoA analysis indicated that the AMF community’s composition was significantly impacted by both citrus scion and rootstock genotypes, but total samples were clustered according to rootstock genotype rather than scion genotype. In addition, AMF α diversity was significantly affected merely by rootstock genotype. Thus, rootstock genotype might exert a greater impact on the AMF community than scion genotype. Taken together, this study provides a comprehensive insight into the AMF community in juvenile citrus plants, and reveals the important effects of citrus genotype on AMF community composition.
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Affiliation(s)
- Fang Song
- Institute of Fruit and Tea, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
| | - Fuxi Bai
- Institute of Fruit and Tea, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
| | - Juanjuan Wang
- Institute National Agro-Technical Extension and Service Center (NATESC), Ministry of Agriculture, Beijing 100000, China
| | - Liming Wu
- Institute of Fruit and Tea, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
| | - Yingchun Jiang
- Institute of Fruit and Tea, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
| | - Zhiyong Pan
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
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12
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Pawlowski ML, Vuong TD, Valliyodan B, Nguyen HT, Hartman GL. Whole-genome resequencing identifies quantitative trait loci associated with mycorrhizal colonization of soybean. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:409-417. [PMID: 31707439 DOI: 10.1007/s00122-019-03471-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 11/01/2019] [Indexed: 05/15/2023]
Abstract
KEY MESSAGE A whole-genome resequencing-derived SNP dataset identified six quantitative trait loci (QTL) significantly associated with colonization of soybean by an arbuscular mycorrhizal fungus (Rhizophagus intraradices). Candidate genes identified in these QTL regions include homologs to known nodulin protein families and other symbiosis-specific genes. Arbuscular mycorrhizal fungi (AMF) form associations with over 80% of all terrestrial plant species and assist their host plants by increasing their nutrient uptake, drought tolerance, and resilience against pathogens and pests. Genotypic variation of crop plants to AMF colonization has been identified in crops, including soybean; however, the genetics controlling levels of AMF colonization in soybean are unknown. The overall goal of our study was to identify genomic regions associated with mycorrhizal colonization in soybean using genome-wide association analysis. A diverse panel of 350 exotic soybean genotypes inoculated with Rhizophagus intraradices were microscopically evaluated for root colonization using a modified gridline intersect method. Root colonization differed significantly (P < 0.001) among genotypes and ranged from 11 to 70%. A whole-genome resequencing-derived SNP dataset identified six quantitative trait loci (QTL) significantly associated with R. intraradices colonization that explained 24% of the phenotypic variance. Candidate genes identified in these QTL regions include homologs to known nodulin protein families and other symbiosis-specific genes. The results showed there was a significant genetic component to the level of colonization by R. intraradices in soybean. This information may be useful in the development of AMF-sensitive soybean cultivars to enhance nutrient uptake, drought tolerance, and disease resistance in the crop.
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Affiliation(s)
- Michelle L Pawlowski
- Department of Crop Science, University of Illinois, 1101 W. Peabody Drive, Urbana, IL, 61801, USA
| | - Tri D Vuong
- Department of Plant Sciences, University of Missouri, Columbia, MO, USA
| | - Babu Valliyodan
- Department of Plant Sciences, University of Missouri, Columbia, MO, USA
| | - Henry T Nguyen
- Department of Plant Sciences, University of Missouri, Columbia, MO, USA
| | - Glen L Hartman
- Department of Crop Science, University of Illinois, 1101 W. Peabody Drive, Urbana, IL, 61801, USA.
- USDA, Agricultural Research Services, University of Illinois, 1101 W. Peabody Dr., Urbana, IL, USA.
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13
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Moradi Tarnabi Z, Iranbakhsh A, Mehregan I, Ahmadvand R. Impact of arbuscular mycorrhizal fungi (AMF) on gene expression of some cell wall and membrane elements of wheat ( Triticum aestivum L.) under water deficit using transcriptome analysis. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2020; 26:143-162. [PMID: 32153322 PMCID: PMC7036378 DOI: 10.1007/s12298-019-00727-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 09/30/2019] [Accepted: 10/18/2019] [Indexed: 05/26/2023]
Abstract
Mycorrhizal symbiotic relationship is one of the most common collaborations between plant roots and the arbuscular mycorrhizal fungi (AMF). The first barrier for establishing this symbiosis is plant cell wall which strongly provides protection against biotic and abiotic stresses. The aim of this study was to investigate the gene expression changes in cell wall of wheat root cv. Chamran after inoculation with AMF, Funneliformis mosseae under two different irrigation regimes. To carry out this investigation, total RNA was extracted from the roots of mycorrhizal and non-mycorrhizal plants, and analyzed using RNA-Seq in an Illumina Next-Seq 500 platform. The results showed that symbiotic association between wheat and AMF and irrigation not only affect transcription profile of the plant growth, but also cell wall and membrane components. Of the 114428 genes expressed in wheat roots, the most differentially expressed genes were related to symbiotic plants under water stress. The most differentially expressed genes were observed in carbohydrate metabolic process, lipid metabolic process, cellulose synthase activity, membrane transports, nitrogen compound metabolic process and chitinase activity related genes. Our results indicated alteration in cell wall and membrane composition due to mycorrhization and irrigation regimes might have a noteworthy effect on the plant tolerance to water deficit.
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Affiliation(s)
- Zahra Moradi Tarnabi
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Alireza Iranbakhsh
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Iraj Mehregan
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Rahim Ahmadvand
- Vegetable Research Department, Seed and Plant Improvement Institute, Agricultural Research, Education and Extension Organization, Karaj, Iran
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Pankievicz VCS, Irving TB, Maia LGS, Ané JM. Are we there yet? The long walk towards the development of efficient symbiotic associations between nitrogen-fixing bacteria and non-leguminous crops. BMC Biol 2019; 17:99. [PMID: 31796086 PMCID: PMC6889567 DOI: 10.1186/s12915-019-0710-0] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 10/18/2019] [Indexed: 01/09/2023] Open
Abstract
Nitrogen is an essential element of life, and nitrogen availability often limits crop yields. Since the Green Revolution, massive amounts of synthetic nitrogen fertilizers have been produced from atmospheric nitrogen and natural gas, threatening the sustainability of global food production and degrading the environment. There is a need for alternative means of bringing nitrogen to crops, and taking greater advantage of biological nitrogen fixation seems a logical option. Legumes are used in most cropping systems around the world because of the nitrogen-fixing symbiosis with rhizobia. However, the world's three major cereal crops-rice, wheat, and maize-do not associate with rhizobia. In this review, we will survey how genetic approaches in rhizobia and their legume hosts allowed tremendous progress in understanding the molecular mechanisms controlling root nodule symbioses, and how this knowledge paves the way for engineering such associations in non-legume crops. We will also discuss challenges in bringing these systems into the field and how they can be surmounted by interdisciplinary collaborations between synthetic biologists, microbiologists, plant biologists, breeders, agronomists, and policymakers.
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Affiliation(s)
| | - Thomas B Irving
- Department of Bacteriology, University of Wisconsin, Madison, WI, USA
| | - Lucas G S Maia
- Department of Bacteriology, University of Wisconsin, Madison, WI, USA
| | - Jean-Michel Ané
- Department of Agronomy, University of Wisconsin, Madison, WI, USA.
- Department of Bacteriology, University of Wisconsin, Madison, WI, USA.
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