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Singh D, Chaudhary P, Taunk J, Singh CK, Chinnusamy V, Sevanthi AM, Singh VJ, Pal M. Targeting Induced Local Lesions in Genomes (TILLING): advances and opportunities for fast tracking crop breeding. Crit Rev Biotechnol 2024; 44:817-836. [PMID: 37455414 DOI: 10.1080/07388551.2023.2231630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 06/01/2023] [Indexed: 07/18/2023]
Abstract
The intensification of food production via conventional crop breeding alone is inadequate to cater for global hunger. The development of precise and expeditious high throughput reverse genetics approaches has hugely benefited modern plant breeding programs. Targeting Induced Local Lesions in Genomes (TILLING) is one such reverse genetics approach which employs chemical/physical mutagenesis to create new genetic sources and identifies superior/novel alleles. Owing to technical limitations and sectional applicability of the original TILLING protocol, it has been timely modified. Successions include: EcoTILLING, Double stranded EcoTILLING (DEcoTILLING), Self-EcoTILLING, Individualized TILLING (iTILLING), Deletion-TILLING (De-TILLING), PolyTILLING, and VeggieTILLING. This has widened its application to a variety of crops and needs. They can characterize mutations in coding as well as non-coding regions and can overcome complexities associated with the large genomes. Combining next generation sequencing tools with the existing TILLING protocols has enabled screening of huge germplasm collections and mutant populations for the target genes. In silico TILLING platforms have transformed TILLING into an exciting breeding approach. The present review outlines these multifarious TILLING modifications for precise mutation detection and their application in advance breeding programmes together with relevant case studies. Appropriate use of these protocols will open up new avenues for crop improvement in the twenty first century.
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Affiliation(s)
- Dharmendra Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Priya Chaudhary
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Jyoti Taunk
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Chandan Kumar Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Viswanathan Chinnusamy
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | | | - Vikram Jeet Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Madan Pal
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
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Reyero-Saavedra R, Fuentes SI, Leija A, Jiménez-Nopala G, Peláez P, Ramírez M, Girard L, Porch TG, Hernández G. Identification and Characterization of Common Bean ( Phaseolus vulgaris) Non-Nodulating Mutants Altered in Rhizobial Infection. PLANTS (BASEL, SWITZERLAND) 2023; 12:1310. [PMID: 36986997 PMCID: PMC10059843 DOI: 10.3390/plants12061310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 03/07/2023] [Accepted: 03/12/2023] [Indexed: 06/19/2023]
Abstract
The symbiotic N2-fixation process in the legume-rhizobia interaction is relevant for sustainable agriculture. The characterization of symbiotic mutants, mainly in model legumes, has been instrumental for the discovery of symbiotic genes, but similar studies in crop legumes are scant. To isolate and characterize common bean (Phaseolus vulgaris) symbiotic mutants, an ethyl methanesulphonate-induced mutant population from the BAT 93 genotype was analyzed. Our initial screening of Rhizobium etli CE3-inoculated mutant plants revealed different alterations in nodulation. We proceeded with the characterization of three non-nodulating (nnod), apparently monogenic/recessive mutants: nnod(1895), nnod(2353) and nnod(2114). Their reduced growth in a symbiotic condition was restored when the nitrate was added. A similar nnod phenotype was observed upon inoculation with other efficient rhizobia species. A microscopic analysis revealed a different impairment for each mutant in an early symbiotic step. nnod(1895) formed decreased root hair curling but had increased non-effective root hair deformation and no rhizobia infection. nnod(2353) produced normal root hair curling and rhizobia entrapment to form infection chambers, but the development of the latter was blocked. nnod(2114) formed infection threads that did not elongate and thus did not reach the root cortex level; it occasionally formed non-infected pseudo-nodules. The current research is aimed at mapping the responsible mutated gene for a better understanding of SNF in this critical food crop.
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Affiliation(s)
- Rocío Reyero-Saavedra
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Cuernavaca 62210, Morelos, Mexico; (R.R.-S.); (S.I.F.); (A.L.); (G.J.-N.); (P.P.); (M.R.); (L.G.)
| | - Sara Isabel Fuentes
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Cuernavaca 62210, Morelos, Mexico; (R.R.-S.); (S.I.F.); (A.L.); (G.J.-N.); (P.P.); (M.R.); (L.G.)
| | - Alfonso Leija
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Cuernavaca 62210, Morelos, Mexico; (R.R.-S.); (S.I.F.); (A.L.); (G.J.-N.); (P.P.); (M.R.); (L.G.)
| | - Gladys Jiménez-Nopala
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Cuernavaca 62210, Morelos, Mexico; (R.R.-S.); (S.I.F.); (A.L.); (G.J.-N.); (P.P.); (M.R.); (L.G.)
| | - Pablo Peláez
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Cuernavaca 62210, Morelos, Mexico; (R.R.-S.); (S.I.F.); (A.L.); (G.J.-N.); (P.P.); (M.R.); (L.G.)
| | - Mario Ramírez
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Cuernavaca 62210, Morelos, Mexico; (R.R.-S.); (S.I.F.); (A.L.); (G.J.-N.); (P.P.); (M.R.); (L.G.)
| | - Lourdes Girard
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Cuernavaca 62210, Morelos, Mexico; (R.R.-S.); (S.I.F.); (A.L.); (G.J.-N.); (P.P.); (M.R.); (L.G.)
| | - Timothy G. Porch
- USDA-ARS, Tropical Agriculture Research Station, 2200 P.A. Campos Avenue, Suite 201, Mayaguez 00680, Puerto Rico;
| | - Georgina Hernández
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Cuernavaca 62210, Morelos, Mexico; (R.R.-S.); (S.I.F.); (A.L.); (G.J.-N.); (P.P.); (M.R.); (L.G.)
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Liu M, Kameoka H, Oda A, Maeda T, Goto T, Yano K, Soyano T, Kawaguchi M. The effects of ERN1 on gene expression during early rhizobial infection in Lotus japonicus. FRONTIERS IN PLANT SCIENCE 2023; 13:995589. [PMID: 36733592 PMCID: PMC9888413 DOI: 10.3389/fpls.2022.995589] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Accepted: 12/19/2022] [Indexed: 06/18/2023]
Abstract
Legumes develop root nodules in association with compatible rhizobia to overcome nitrogen deficiency. Rhizobia enter the host legume, mainly through infection threads, and induce nodule primordium formation in the root cortex. Multiple transcription factors have been identified to be involved in the regulation of the establishment of root nodule symbiosis, including ERF Required for Nodulation1 (ERN1). ERN1 is involved in a transcription network with CYCLOPS and NODULE INCEPTION (NIN). Mutation of ERN1 often results in misshapen root hair tips, deficient infection thread formation, and immature root nodules. ERN1 directly activates the expression of ENOD11 in Medicago truncatula to assist cell wall remodeling and Epr3 in Lotus japonicus to distinguish rhizobial exopolysaccharide signals. However, aside from these two genes, it remains unclear which genes are regulated by LjERN1 or what role LjERN1 plays during root nodule symbiosis. Thus, we conducted RNA sequencing to compare the gene expression profiles of wild-type L. japonicus and Ljern1-6 mutants. In total, 234 differentially expressed genes were identified as candidate LjERN1 target genes. These genes were found to be associated with cell wall remodeling, signal transduction, phytohormone metabolism, and transcription regulation, suggesting that LjERN1 is involved in multiple processes during the early stages of the establishment of root nodule symbiosis. Many of these candidate genes including RINRK1 showed decreased expression levels in Ljnin-2 mutants based on a search of a public database, suggesting that LjERN1 and LjNIN coordinately regulate gene expression. Our data extend the current understanding of the pleiotropic role of LjERN1 in root nodule symbiosis.
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Affiliation(s)
- Meng Liu
- Division of Symbiotic Systems, National Institute for Basic Biology, Okazaki, Aichi, Japan
- Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi, Japan
| | - Hiromu Kameoka
- Division of Symbiotic Systems, National Institute for Basic Biology, Okazaki, Aichi, Japan
| | - Akiko Oda
- Division of Symbiotic Systems, National Institute for Basic Biology, Okazaki, Aichi, Japan
| | - Taro Maeda
- Division of Symbiotic Systems, National Institute for Basic Biology, Okazaki, Aichi, Japan
| | - Takashi Goto
- Division of Symbiotic Systems, National Institute for Basic Biology, Okazaki, Aichi, Japan
- Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi, Japan
| | - Koji Yano
- Division of Symbiotic Systems, National Institute for Basic Biology, Okazaki, Aichi, Japan
| | - Takashi Soyano
- Division of Symbiotic Systems, National Institute for Basic Biology, Okazaki, Aichi, Japan
- Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi, Japan
| | - Masayoshi Kawaguchi
- Division of Symbiotic Systems, National Institute for Basic Biology, Okazaki, Aichi, Japan
- Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi, Japan
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Kohli PS, Pazhamala LT, Mani B, Thakur JK, Giri J. Root hair-specific transcriptome reveals response to low phosphorus in Cicer arietinum. FRONTIERS IN PLANT SCIENCE 2022; 13:983969. [PMID: 36267945 PMCID: PMC9577374 DOI: 10.3389/fpls.2022.983969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 08/16/2022] [Indexed: 06/16/2023]
Abstract
Root hairs (RH) are a single-cell extension of root epidermal cells. In low phosphorus (LP) availability, RH length and density increase thus expanding the total root surface area for phosphate (Pi) acquisition. However, details on genes involved in RH development and response to LP are missing in an agronomically important leguminous crop, chickpea. To elucidate this response in chickpea, we performed tissue-specific RNA-sequencing and analyzed the transcriptome modulation for RH and root without RH (Root-RH) under LP. Root hair initiation and cellular differentiation genes like RSL TFs and ROPGEFs are upregulated in Root-RH, explaining denser, and ectopic RH in LP. In RH, genes involved in tip growth processes and phytohormonal biosynthesis like cell wall synthesis and loosening (cellulose synthase A catalytic subunit, CaEXPA2, CaGRP2, and CaXTH2), cytoskeleton/vesicle transport, and ethylene biosynthesis are upregulated. Besides RH development, genes involved in LP responses like lipid and/or pectin P remobilization and acid phosphatases are induced in these tissues summarizing a complete molecular response to LP. Further, RH displayed preferential enrichment of processes involved in symbiotic interactions, which provide an additional benefit during LP. In conclusion, RH shows a multi-faceted response that starts with molecular changes for epidermal cell differentiation and RH initiation in Root-RH and later induction of tip growth and various LP responses in elongated RH.
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Affiliation(s)
| | | | - Balaji Mani
- National Institute of Plant Genome Research (NIPGR), New Delhi, India
| | - Jitendra Kumar Thakur
- National Institute of Plant Genome Research (NIPGR), New Delhi, India
- International Center of Genetic Engineering and Biotechnology, New Delhi, India
| | - Jitender Giri
- National Institute of Plant Genome Research (NIPGR), New Delhi, India
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Zorin EA, Kliukova MS, Afonin AM, Gribchenko ES, Gordon ML, Sulima AS, Zhernakov AI, Kulaeva OA, Romanyuk DA, Kusakin PG, Tsyganova AV, Tsyganov VE, Tikhonovich IA, Zhukov VA. A variable gene family encoding nodule-specific cysteine-rich peptides in pea ( Pisum sativum L.). FRONTIERS IN PLANT SCIENCE 2022; 13:884726. [PMID: 36186063 PMCID: PMC9515463 DOI: 10.3389/fpls.2022.884726] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 08/08/2022] [Indexed: 06/16/2023]
Abstract
Various legume plants form root nodules in which symbiotic bacteria (rhizobia) fix atmospheric nitrogen after differentiation into a symbiotic form named bacteroids. In some legume species, bacteroid differentiation is promoted by defensin-like nodule-specific cysteine-rich (NCR) peptides. NCR peptides have best been studied in the model legume Medicago truncatula Gaertn., while in many other legumes relevant information is still fragmentary. Here, we characterize the NCR gene family in pea (Pisum sativum L.) using genomic and transcriptomic data. We found 360 genes encoding NCR peptides that are expressed in nodules. The sequences of pea NCR genes and putative peptides are highly variable and differ significantly from NCR sequences of M. truncatula. Indeed, only one pair of orthologs (PsNCR47-MtNCR312) has been identified. The NCR genes in the pea genome are located in clusters, and the expression patterns of NCR genes from one cluster tend to be similar. These data support the idea of independent evolution of NCR genes by duplication and diversification in related legume species. We also described spatiotemporal expression profiles of NCRs and identified specific transcription factor (TF) binding sites in promoters of "early" and "late" NCR genes. Further, we studied the expression of NCR genes in nodules of Fix- mutants and predicted potential regulators of NCR gene expression, one among them being the TF ERN1 involved in the early steps of nodule organogenesis. In general, this study contributes to understanding the functions of NCRs in legume nodules and contributes to understanding the diversity and potential antibiotic properties of pea nodule-specific antimicrobial molecules.
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Affiliation(s)
- Evgeny A. Zorin
- All-Russia Research Institute for Agricultural Microbiology, Saint Petersburg, Russia
| | - Marina S. Kliukova
- All-Russia Research Institute for Agricultural Microbiology, Saint Petersburg, Russia
| | - Alexey M. Afonin
- All-Russia Research Institute for Agricultural Microbiology, Saint Petersburg, Russia
| | - Emma S. Gribchenko
- All-Russia Research Institute for Agricultural Microbiology, Saint Petersburg, Russia
| | - Mikhail L. Gordon
- All-Russia Research Institute for Agricultural Microbiology, Saint Petersburg, Russia
| | - Anton S. Sulima
- All-Russia Research Institute for Agricultural Microbiology, Saint Petersburg, Russia
| | | | - Olga A. Kulaeva
- All-Russia Research Institute for Agricultural Microbiology, Saint Petersburg, Russia
| | - Daria A. Romanyuk
- All-Russia Research Institute for Agricultural Microbiology, Saint Petersburg, Russia
| | - Pyotr G. Kusakin
- All-Russia Research Institute for Agricultural Microbiology, Saint Petersburg, Russia
| | - Anna V. Tsyganova
- All-Russia Research Institute for Agricultural Microbiology, Saint Petersburg, Russia
| | - Viktor E. Tsyganov
- All-Russia Research Institute for Agricultural Microbiology, Saint Petersburg, Russia
| | - Igor A. Tikhonovich
- All-Russia Research Institute for Agricultural Microbiology, Saint Petersburg, Russia
- Department of Genetics and Biotechnology, Faculty of Biology, Saint Petersburg State University, Saint Petersburg, Russia
| | - Vladimir A. Zhukov
- All-Russia Research Institute for Agricultural Microbiology, Saint Petersburg, Russia
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Jardinaud MF, Fromentin J, Auriac MC, Moreau S, Pecrix Y, Taconnat L, Cottret L, Aubert G, Balzergue S, Burstin J, Carrere S, Gamas P. MtEFD and MtEFD2: Two transcription factors with distinct neofunctionalization in symbiotic nodule development. PLANT PHYSIOLOGY 2022; 189:1587-1607. [PMID: 35471237 PMCID: PMC9237690 DOI: 10.1093/plphys/kiac177] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 03/21/2022] [Indexed: 05/31/2023]
Abstract
Rhizobium-legume nitrogen-fixing symbiosis involves the formation of a specific organ, the root nodule, which provides bacteria with the proper cellular environment for atmospheric nitrogen fixation. Coordinated differentiation of plant and bacterial cells is an essential step of nodule development, for which few transcriptional regulators have been characterized. Medicago truncatula ETHYLENE RESPONSE FACTOR REQUIRED FOR NODULE DIFFERENTIATION (MtEFD) encodes an APETALA2/ETHYLENE RESPONSIVE FACTOR (ERF) transcription factor, the mutation of which leads to both hypernodulation and severe defects in nodule development. MtEFD positively controls a negative regulator of cytokinin signaling, the RESPONSE REGULATOR 4 (MtRR4) gene. Here we showed that that the Mtefd-1 mutation affects both plant and bacterial endoreduplication in nodules, as well as the expression of hundreds of genes in young and mature nodules, upstream of known regulators of symbiotic differentiation. MtRR4 expressed with the MtEFD promoter complemented Mtefd-1 hypernodulation but not the nodule differentiation phenotype. Unexpectedly, a nonlegume homolog of MtEFD, AtERF003 in Arabidopsis (Arabidopsis thaliana), could efficiently complement both phenotypes of Mtefd-1, in contrast to the MtEFD paralog MtEFD2 expressed in the root and nodule meristematic zone. A domain swap experiment showed that MtEFD2 differs from MtEFD by its C-terminal fraction outside the DNA binding domain. Furthermore, clustered regularly interspaced short palindromic repeats-CRISPR associated protein 9 (CRISPR-Cas9) mutagenesis of MtEFD2 led to a reduction in the number of nodules formed in Mtefd-1, with downregulation of a set of genes, including notably NUCLEAR FACTOR-YA1 (MtNF-YA1) and MtNF-YB16, which are essential for nodule meristem establishment. We, therefore, conclude that nitrogen-fixing symbiosis recruited two proteins originally expressed in roots, MtEFD and MtEFD2, with distinct functions and neofunctionalization processes for each of them.
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Affiliation(s)
| | | | | | - Sandra Moreau
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | | | | | - Ludovic Cottret
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Grégoire Aubert
- Agroécologie, AgroSup Dijon, INRAE, Université Bourgogne Franche-Comté, Dijon, France
| | | | - Judith Burstin
- Agroécologie, AgroSup Dijon, INRAE, Université Bourgogne Franche-Comté, Dijon, France
| | - Sébastien Carrere
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
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Li Y, Pei Y, Shen Y, Zhang R, Kang M, Ma Y, Li D, Chen Y. Progress in the Self-Regulation System in Legume Nodule Development-AON (Autoregulation of Nodulation). Int J Mol Sci 2022; 23:ijms23126676. [PMID: 35743118 PMCID: PMC9224500 DOI: 10.3390/ijms23126676] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 06/13/2022] [Accepted: 06/14/2022] [Indexed: 12/24/2022] Open
Abstract
The formation and development of legumes nodules requires a lot of energy. Legumes must strictly control the number and activity of nodules to ensure efficient energy distribution. The AON system can limit the number of rhizobia infections and nodule numbers through the systemic signal pathway network that the aboveground and belowground parts participate in together. It can also promote the formation of nodules when plants are deficient in nitrogen. The currently known AON pathway includes four parts: soil NO3− signal and Rhizobium signal recognition and transmission, CLE-SUNN is the negative regulation pathway, CEP-CRA2 is the positive regulation pathway and the miR2111/TML module regulates nodule formation and development. In order to ensure the biological function of this important approach, plants use a variety of plant hormones, polypeptides, receptor kinases, transcription factors and miRNAs for signal transmission and transcriptional regulation. This review summarizes and discusses the research progress of the AON pathway in Legume nodule development.
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Visualization of the Crossroads between a Nascent Infection Thread and the First Cell Division Event in Phaseolus vulgaris Nodulation. Int J Mol Sci 2022; 23:ijms23095267. [PMID: 35563659 PMCID: PMC9105610 DOI: 10.3390/ijms23095267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 04/30/2022] [Accepted: 05/03/2022] [Indexed: 11/17/2022] Open
Abstract
The development of a symbiotic nitrogen-fixing nodule in legumes involves infection and organogenesis. Infection begins when rhizobia enter a root hair through an inward structure, the infection thread (IT), which guides the bacteria towards the cortical tissue. Concurrently, organogenesis takes place by inducing cortical cell division (CCD) at the infection site. Genetic analysis showed that both events are well-coordinated; however, the dynamics connecting them remain to be elucidated. To visualize the crossroads between IT and CCD, we benefited from the fact that, in Phaseolus vulgaris nodulation, where the first division occurs in subepidermal cortical cells located underneath the infection site, we traced a Rhizobium etli strain expressing DsRed, the plant cytokinesis marker YFP-PvKNOLLE, a nuclear stain and cell wall auto-fluorescence. We found that the IT exits the root hair to penetrate an underlying subepidermal cortical (S-E) cell when it is concluding cytokinesis.
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Rudaya ES, Kozyulina PY, Pavlova OA, Dolgikh AV, Ivanova AN, Dolgikh EA. Regulation of the Later Stages of Nodulation Stimulated by IPD3/CYCLOPS Transcription Factor and Cytokinin in Pea Pisum sativum L. PLANTS (BASEL, SWITZERLAND) 2021; 11:56. [PMID: 35009060 PMCID: PMC8747635 DOI: 10.3390/plants11010056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 12/15/2021] [Accepted: 12/22/2021] [Indexed: 11/16/2022]
Abstract
The IPD3/CYCLOPS transcription factor was shown to be involved in the regulation of nodule primordia development and subsequent stages of nodule differentiation. In contrast to early stages, the stages related to nodule differentiation remain less studied. Recently, we have shown that the accumulation of cytokinin at later stages may significantly impact nodule development. This conclusion was based on a comparative analysis of cytokinin localization between pea wild type and ipd3/cyclops mutants. However, the role of cytokinin at these later stages of nodulation is still far from understood. To determine a set of genes involved in the regulation of later stages of nodule development connected with infection progress, intracellular accommodation, as well as plant tissue and bacteroid differentiation, the RNA-seq analysis of pea mutant SGEFix--2 (sym33) nodules impaired in these processes compared to wild type SGE nodules was performed. To verify cytokinin's influence on late nodule development stages, the comparative RNA-seq analysis of SGEFix--2 (sym33) mutant plants treated with cytokinin was also conducted. Findings suggest a significant role of cytokinin in the regulation of later stages of nodule development.
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Affiliation(s)
- Elizaveta S. Rudaya
- All-Russia Research Institute for Agricultural Microbiology, Podbelsky chausse 3, Pushkin, 196608 St. Petersburg, Russia; (E.S.R.); (P.Y.K.); (O.A.P.); (A.V.D.)
| | - Polina Yu. Kozyulina
- All-Russia Research Institute for Agricultural Microbiology, Podbelsky chausse 3, Pushkin, 196608 St. Petersburg, Russia; (E.S.R.); (P.Y.K.); (O.A.P.); (A.V.D.)
| | - Olga A. Pavlova
- All-Russia Research Institute for Agricultural Microbiology, Podbelsky chausse 3, Pushkin, 196608 St. Petersburg, Russia; (E.S.R.); (P.Y.K.); (O.A.P.); (A.V.D.)
| | - Alexandra V. Dolgikh
- All-Russia Research Institute for Agricultural Microbiology, Podbelsky chausse 3, Pushkin, 196608 St. Petersburg, Russia; (E.S.R.); (P.Y.K.); (O.A.P.); (A.V.D.)
| | - Alexandra N. Ivanova
- Komarov Botanical Institute RAS, Prof. Popov St., 2, 197376 St. Petersburg, Russia;
- Faculty of Biology, St. Petersburg State University, Universitetskaya Emb. 7-9, 199034 St. Petersburg, Russia
| | - Elena A. Dolgikh
- All-Russia Research Institute for Agricultural Microbiology, Podbelsky chausse 3, Pushkin, 196608 St. Petersburg, Russia; (E.S.R.); (P.Y.K.); (O.A.P.); (A.V.D.)
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Circadian Rhythms in Legumes: What Do We Know and What Else Should We Explore? Int J Mol Sci 2021; 22:ijms22094588. [PMID: 33925559 PMCID: PMC8123782 DOI: 10.3390/ijms22094588] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 04/16/2021] [Accepted: 04/21/2021] [Indexed: 12/15/2022] Open
Abstract
The natural timing devices of organisms, commonly known as biological clocks, are composed of specific complex folding molecules that interact to regulate the circadian rhythms. Circadian rhythms, the changes or processes that follow a 24-h light–dark cycle, while endogenously programmed, are also influenced by environmental factors, especially in sessile organisms such as plants, which can impact ecosystems and crop productivity. Current knowledge of plant clocks emanates primarily from research on Arabidopsis, which identified the main components of the circadian gene regulation network. Nonetheless, there remain critical knowledge gaps related to the molecular components of circadian rhythms in important crop groups, including the nitrogen-fixing legumes. Additionally, little is known about the synergies and trade-offs between environmental factors and circadian rhythm regulation, especially how these interactions fine-tune the physiological adaptations of the current and future crops in a rapidly changing world. This review highlights what is known so far about the circadian rhythms in legumes, which include major as well as potential future pulse crops that are packed with nutrients, particularly protein. Based on existing literature, this review also identifies the knowledge gaps that should be addressed to build a sustainable food future with the reputed “poor man’s meat”.
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Chaulagain D, Frugoli J. The Regulation of Nodule Number in Legumes Is a Balance of Three Signal Transduction Pathways. Int J Mol Sci 2021; 22:1117. [PMID: 33498783 PMCID: PMC7866212 DOI: 10.3390/ijms22031117] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 01/19/2021] [Accepted: 01/21/2021] [Indexed: 12/02/2022] Open
Abstract
Nitrogen is a major determinant of plant growth and productivity and the ability of legumes to form a symbiotic relationship with nitrogen-fixing rhizobia bacteria allows legumes to exploit nitrogen-poor niches in the biosphere. But hosting nitrogen-fixing bacteria comes with a metabolic cost, and the process requires regulation. The symbiosis is regulated through three signal transduction pathways: in response to available nitrogen, at the initiation of contact between the organisms, and during the development of the nodules that will host the rhizobia. Here we provide an overview of our knowledge of how the three signaling pathways operate in space and time, and what we know about the cross-talk between symbiotic signaling for nodule initiation and organogenesis, nitrate dependent signaling, and autoregulation of nodulation. Identification of common components and points of intersection suggest directions for research on the fine-tuning of the plant's response to rhizobia.
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Affiliation(s)
| | - Julia Frugoli
- Department of Genetics & Biochemistry, Clemson University, Clemson, SC 29634, USA;
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12
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Xu S, Song S, Dong X, Wang X, Wu J, Ren Z, Wu X, Lu J, Yuan H, Wu X, Li X, Wang Z. GmbZIP1 negatively regulates ABA-induced inhibition of nodulation by targeting GmENOD40-1 in soybean. BMC PLANT BIOLOGY 2021; 21:35. [PMID: 33421994 PMCID: PMC7796624 DOI: 10.1186/s12870-020-02810-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 12/22/2020] [Indexed: 05/10/2023]
Abstract
BACKGROUND Abscisic acid (ABA) plays an important role in plant growth and adaptation through the ABA signaling pathway. The ABA-responsive element binding (AREB/ABF) family transcriptional factors are central regulators that integrate ABA signaling with various signaling pathways. It has long been known that ABA inhibits rhizobial infection and nodule formation in legumes, but the underlying molecular mechanisms remain elusive. RESULTS Here, we show that nodulation is very sensitive to ABA and exogenous ABA dramatically inhibits rhizobial infection and nodule formation in soybean. In addition, we proved that GmbZIP1, an AREB/ABF transcription factor, is a major regulator in both nodulation and plant response to ABA in soybean. GmbZIP1 was specifically expressed during nodule formation and development. Overexpression of GmbZIP1 resulted in reduced rhizobial infection and decreased nodule number. Furthermore, GmbZIP1 is responsive to ABA, and ectopic overexpression of GmbZIP1 increased sensitivity of Arabidopsis plants to ABA during seed germination and postgerminative growth, and conferred enhanced drought tolerance of plants. Remarkably, we found that GmbZIP1 directly binds to the promoter of GmENOD40-1, a marker gene for nodule formation, to repress its expression. CONCLUSION Our results identified GmbZIP1 as a node regulator that integrates ABA signaling with nodulation signaling to negatively regulate nodule formation.
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Affiliation(s)
- Shimin Xu
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, P.R. China
| | - Shanshan Song
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, P.R. China
| | - Xiaoxu Dong
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, P.R. China
| | - Xinyue Wang
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, P.R. China
| | - Jun Wu
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, P.R. China
| | - Ziyin Ren
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, P.R. China
| | - Xuesong Wu
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, P.R. China
| | - Jingjing Lu
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, P.R. China
| | - Huifang Yuan
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, P.R. China
| | - Xinying Wu
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, P.R. China
| | - Xia Li
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, P.R. China
| | - Zhijuan Wang
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, P.R. China.
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13
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Roy S, Liu W, Nandety RS, Crook A, Mysore KS, Pislariu CI, Frugoli J, Dickstein R, Udvardi MK. Celebrating 20 Years of Genetic Discoveries in Legume Nodulation and Symbiotic Nitrogen Fixation. THE PLANT CELL 2020; 32:15-41. [PMID: 31649123 PMCID: PMC6961631 DOI: 10.1105/tpc.19.00279] [Citation(s) in RCA: 320] [Impact Index Per Article: 80.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 09/17/2019] [Accepted: 10/24/2019] [Indexed: 05/13/2023]
Abstract
Since 1999, various forward- and reverse-genetic approaches have uncovered nearly 200 genes required for symbiotic nitrogen fixation (SNF) in legumes. These discoveries advanced our understanding of the evolution of SNF in plants and its relationship to other beneficial endosymbioses, signaling between plants and microbes, the control of microbial infection of plant cells, the control of plant cell division leading to nodule development, autoregulation of nodulation, intracellular accommodation of bacteria, nodule oxygen homeostasis, the control of bacteroid differentiation, metabolism and transport supporting symbiosis, and the control of nodule senescence. This review catalogs and contextualizes all of the plant genes currently known to be required for SNF in two model legume species, Medicago truncatula and Lotus japonicus, and two crop species, Glycine max (soybean) and Phaseolus vulgaris (common bean). We also briefly consider the future of SNF genetics in the era of pan-genomics and genome editing.
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Affiliation(s)
- Sonali Roy
- Noble Research Institute, Ardmore, Oklahoma 73401
| | - Wei Liu
- Noble Research Institute, Ardmore, Oklahoma 73401
| | | | - Ashley Crook
- College of Science, Clemson University, Clemson, South Carolina 29634
| | | | | | - Julia Frugoli
- College of Science, Clemson University, Clemson, South Carolina 29634
| | - Rebecca Dickstein
- Department of Biological Sciences and BioDiscovery Institute, University of North Texas, Denton Texas 76203
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14
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Liu M, Soyano T, Yano K, Hayashi M, Kawaguchi M. ERN1 and CYCLOPS coordinately activate NIN signaling to promote infection thread formation in Lotus japonicus. JOURNAL OF PLANT RESEARCH 2019; 132:641-653. [PMID: 31313020 DOI: 10.1007/s10265-019-01122-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 07/04/2019] [Indexed: 06/10/2023]
Abstract
Legumes engage in symbiosis with nitrogen-fixing soil bacteria, collectively called rhizobia, under nitrogen-limited conditions. In many legumes, the root invasion of rhizobia is mediated by infection threads (ITs), tubular invaginations of the host cell wall and plasma membrane, developed from infection foci of deformed root hairs. IT formation is regulated by a series of signal transduction in host root. Nodulation signals activate the host transcription factor (TF), CYCLOPS, which directly induces expression of two TF genes, ERF REQUIRED FOR NODULATION1 (ERN1) and NODULE INCEPTION (NIN), essential for IT development. Here, we explored the relationship among these three symbiotic TF genes in the model legume Lotus japonicus and examined how their interplay contributes to IT formation. qRT-PCR analysis showed that NIN expression induced by rhizobial infection was attenuated in ern1-1, and further declined in cyclops-3 ern1-1. ERN1 overexpression led to induction of NIN expression in cyclops-3 ern1-1 in the presence of rhizobia. Thus, in addition to CYCLOPS, ERN1 is able to increase the NIN expression level depending on infection. Furthermore, consistent with this transcriptional hierarchy, ectopic expression of ERN1 as well as NIN suppressed the IT-deficient cyclops-3 phenotype, but ERN1 failed to confer ITs in the nin-2 root. However, the ern1-1 symbiotic epidermal phenotype was not suppressed by the NIN ectopic expression. The cyclops-3 ern1-1 double mutant was less sensitive to rhizobial infection than the single mutants and defective in the symbiotic root hair response at earlier stages. This more severe phenotype of the double mutant suggests a role for ERN1 that independent of the CYCLOPS-mediated transcriptional regulation. We conclude that ERN1 is involved in regulating NIN expression in addition to CYCLOPS, and these TFs coordinately promote the symbiotic root hair response and IT development. Our data help to reveal the extensive role of ERN1 in root nodule symbiosis signaling.
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Affiliation(s)
- Meng Liu
- Division of Symbiotic Systems, National Institute for Basic Biology, Okazaki, Aichi, 444-8585, Japan
- Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi, 444-8585, Japan
| | - Takashi Soyano
- Division of Symbiotic Systems, National Institute for Basic Biology, Okazaki, Aichi, 444-8585, Japan
- Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi, 444-8585, Japan
| | - Koji Yano
- Division of Symbiotic Systems, National Institute for Basic Biology, Okazaki, Aichi, 444-8585, Japan
| | - Makoto Hayashi
- Center for Sustainable Resource Science, RIKEN, Yokohama, Kanagawa, 230-0045, Japan
| | - Masayoshi Kawaguchi
- Division of Symbiotic Systems, National Institute for Basic Biology, Okazaki, Aichi, 444-8585, Japan.
- Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi, 444-8585, Japan.
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15
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Liu CW, Breakspear A, Guan D, Cerri MR, Jackson K, Jiang S, Robson F, Radhakrishnan GV, Roy S, Bone C, Stacey N, Rogers C, Trick M, Niebel A, Oldroyd GED, de Carvalho-Niebel F, Murray JD. NIN Acts as a Network Hub Controlling a Growth Module Required for Rhizobial Infection. PLANT PHYSIOLOGY 2019; 179:1704-1722. [PMID: 30710053 PMCID: PMC6446755 DOI: 10.1104/pp.18.01572] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 01/20/2019] [Indexed: 05/22/2023]
Abstract
The symbiotic infection of root cells by nitrogen-fixing rhizobia during nodulation requires the transcription factor Nodule Inception (NIN). Our root hair transcriptomic study extends NIN's regulon to include Rhizobium Polar Growth and genes involved in cell wall modification, gibberellin biosynthesis, and a comprehensive group of nutrient (N, P, and S) uptake and assimilation genes, suggesting that NIN's recruitment to nodulation was based on its role as a growth module, a role shared with other NIN-Like Proteins. The expression of jasmonic acid genes in nin suggests the involvement of NIN in the resolution of growth versus defense outcomes. We find that the regulation of the growth module component Nodulation Pectate Lyase by NIN, and its function in rhizobial infection, are conserved in hologalegina legumes, highlighting its recruitment as a major event in the evolution of nodulation. We find that Nodulation Pectate Lyase is secreted to the infection chamber and the lumen of the infection thread. Gene network analysis using the transcription factor mutants for ERF Required for Nodulation1 and Nuclear Factor-Y Subunit A1 confirms hierarchical control of NIN over Nuclear Factor-Y Subunit A1 and shows that ERF Required for Nodulation1 acts independently to control infection. We conclude that while NIN shares functions with other NIN-Like Proteins, the conscription of key infection genes to NIN's control has made it a central regulatory hub for rhizobial infection.
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Affiliation(s)
- Cheng-Wu Liu
- Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Andrew Breakspear
- Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Dian Guan
- Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Marion R Cerri
- Laboratory of Plant Microbe Interactions, Institut National de la Recherche Agronomique, Centre National de la Recherche Scientifique, Université de Toulouse, 31326 Castanet-Tolosan, France
| | - Kirsty Jackson
- Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Suyu Jiang
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Centre of Excellence for Plant and Microbial Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Fran Robson
- Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Guru V Radhakrishnan
- Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Sonali Roy
- Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Caitlin Bone
- Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Nicola Stacey
- Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Christian Rogers
- Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom
- Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, United Kingdom
| | - Martin Trick
- Computational and Systems Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Andreas Niebel
- Laboratory of Plant Microbe Interactions, Institut National de la Recherche Agronomique, Centre National de la Recherche Scientifique, Université de Toulouse, 31326 Castanet-Tolosan, France
| | - Giles E D Oldroyd
- Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom
- Computational and Systems Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Fernanda de Carvalho-Niebel
- Laboratory of Plant Microbe Interactions, Institut National de la Recherche Agronomique, Centre National de la Recherche Scientifique, Université de Toulouse, 31326 Castanet-Tolosan, France
| | - Jeremy D Murray
- Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Centre of Excellence for Plant and Microbial Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
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16
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Suzaki T, Takeda N, Nishida H, Hoshino M, Ito M, Misawa F, Handa Y, Miura K, Kawaguchi M. LACK OF SYMBIONT ACCOMMODATION controls intracellular symbiont accommodation in root nodule and arbuscular mycorrhizal symbiosis in Lotus japonicus. PLoS Genet 2019; 15:e1007865. [PMID: 30605473 PMCID: PMC6317779 DOI: 10.1371/journal.pgen.1007865] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 11/30/2018] [Indexed: 11/19/2022] Open
Abstract
Nitrogen-fixing rhizobia and arbuscular mycorrhizal fungi (AMF) form symbioses with plant roots and these are established by precise regulation of symbiont accommodation within host plant cells. In model legumes such as Lotus japonicus and Medicago truncatula, rhizobia enter into roots through an intracellular invasion system that depends on the formation of a root-hair infection thread (IT). While IT-mediated intracellular rhizobia invasion is thought to be the most evolutionarily derived invasion system, some studies have indicated that a basal intercellular invasion system can replace it when some nodulation-related factors are genetically modified. In addition, intracellular rhizobia accommodation is suggested to have a similar mechanism as AMF accommodation. Nevertheless, our understanding of the underlying genetic mechanisms is incomplete. Here we identify a L. japonicus nodulation-deficient mutant, with a mutation in the LACK OF SYMBIONT ACCOMMODATION (LAN) gene, in which root-hair IT formation is strongly reduced, but intercellular rhizobial invasion eventually results in functional nodule formation. LjLAN encodes a protein that is homologous to Arabidopsis MEDIATOR 2/29/32 possibly acting as a subunit of a Mediator complex, a multiprotein complex required for gene transcription. We also show that LjLAN acts in parallel with a signaling pathway including LjCYCLOPS. In addition, the lan mutation drastically reduces the colonization levels of AMF. Taken together, our data provide a new factor that has a common role in symbiont accommodation process during root nodule and AM symbiosis. Symbiosis between plants and beneficial microbes such as nitrogen-fixing bacteria and arbuscular mycorrhizal fungi has enabled plant colonization of new environments. Root nodule symbiosis with nitrogen-fixing rhizobia enables sessile plants to survive in a nitrogen-deficient environment. To establish the symbiosis, host plant cells need to accommodate rhizobia during nodule development, a process mediated by a plant-derived intracellular structure called the infection thread (IT). In this study, we show that LACK OF SYMBIONT ACCOMMODATION (LAN) is involved in intracellular rhizobia accommodation in the model leguminous plant Lotus japonicus. LjLAN encodes a putative subunit of Mediator complex, a multiprotein complex that has a fundamental role as an activator of gene transcription. Mutation analysis suggests that LjLAN is required for root hair IT formation, which enables swift and efficient rhizobial accommodation. Moreover, we show that LjLAN is required for symbiosis with arbuscular mycorrhizal fungi. These data add a new component to the molecular mechanism relevant to the establishment of root nodule and arbuscular mycorrhizal symbiosis.
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Affiliation(s)
- Takuya Suzaki
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
- College of Biological Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
- Tsukuba Plant-Innovation Research Center, University of Tsukuba, Tsukuba, Ibaraki, Japan
- * E-mail:
| | - Naoya Takeda
- Graduate School of Science and Technology, Kwansei Gakuin University, Mita, Hyogo, Japan
| | - Hanna Nishida
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Motomi Hoshino
- College of Biological Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Momoyo Ito
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Fumika Misawa
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | | | - Kenji Miura
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
- College of Biological Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
- Tsukuba Plant-Innovation Research Center, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Masayoshi Kawaguchi
- National Institute for Basic Biology, Okazaki, Aichi, Japan
- School of Life Science, Graduate University for Advanced Studies, Okazaki, Aichi, Japan
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17
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Tsyganova AV, Tsyganov VE. Plant Genetic Control over Infection Thread Development during Legume-Rhizobium Symbiosis. Symbiosis 2018. [DOI: 10.5772/intechopen.70689] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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18
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Diédhiou I, Diouf D. Transcription factors network in root endosymbiosis establishment and development. World J Microbiol Biotechnol 2018; 34:37. [PMID: 29450655 DOI: 10.1007/s11274-018-2418-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 01/29/2018] [Indexed: 11/29/2022]
Abstract
Root endosymbioses are mutualistic interactions between plants and the soil microorganisms (Fungus, Frankia or Rhizobium) that lead to the formation of nitrogen-fixing root nodules and/or arbuscular mycorrhiza. These interactions enable many species to survive in different marginal lands to overcome the nitrogen-and/or phosphorus deficient environment and can potentially reduce the chemical fertilizers used in agriculture which gives them an economic, social and environmental importance. The formation and the development of these structures require the mediation of specific gene products among which the transcription factors play a key role. Three of these transcription factors, viz., CYCLOPS, NSP1 and NSP2 are well conserved between actinorhizal, legume, non-legume and mycorrhizal symbioses. They interact with DELLA proteins to induce the expression of NIN in nitrogen fixing symbiosis or RAM1 in mycorrhizal symbiosis. Recently, the small non coding RNA including micro RNAs (miRNAs) have emerged as major regulators of root endosymbioses. Among them, miRNA171 targets NSP2, a TF conserved in actinorhizal, legume, non-legume and mycorrhizal symbioses. This review will also focus on the recent advances carried out on the biological function of others transcription factors during the root pre-infection/pre-contact, infection or colonization. Their role in nodule formation and AM development will also be described.
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Affiliation(s)
- Issa Diédhiou
- Laboratoire Campus de Biotecnologies Végétales, Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop, Dakar-Fann, Senegal.
| | - Diaga Diouf
- Laboratoire Campus de Biotecnologies Végétales, Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop, Dakar-Fann, Senegal
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19
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Reid D, Liu H, Kelly S, Kawaharada Y, Mun T, Andersen SU, Desbrosses G, Stougaard J. Dynamics of Ethylene Production in Response to Compatible Nod Factor. PLANT PHYSIOLOGY 2018; 176:1764-1772. [PMID: 29187569 PMCID: PMC5813561 DOI: 10.1104/pp.17.01371] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 11/28/2017] [Indexed: 05/22/2023]
Abstract
Establishment of symbiotic nitrogen-fixation in legumes is regulated by the plant hormone ethylene, but it has remained unclear whether and how its biosynthesis is regulated by the symbiotic pathway. We established a sensitive ethylene detection system for Lotus japonicus and found that ethylene production increased as early as 6 hours after inoculation with Mesorhizobium loti This ethylene response was dependent on Nod factor production by compatible rhizobia. Analyses of nodulation mutants showed that perception of Nod factor was required for ethylene emission, while downstream transcription factors including CYCLOPS, NIN, and ERN1 were not required for this response. Activation of the nodulation signaling pathway in spontaneously nodulating mutants was also sufficient to elevate ethylene production. Ethylene signaling is controlled by EIN2, which is duplicated in L. japonicus We obtained a L. japonicus Ljein2a Ljein2b double mutant that exhibits complete ethylene insensitivity and confirms that these two genes act redundantly in ethylene signaling. Consistent with this redundancy, both LjEin2a and LjEin2b are required for negative regulation of nodulation and Ljein2a Ljein2b double mutants are hypernodulating and hyperinfected. We also identified an unexpected role for ethylene in the onset of nitrogen fixation, with the Ljein2a Ljein2b double mutant showing severely reduced nitrogen fixation. These results demonstrate that ethylene production is an early and sustained nodulation response that acts at multiple stages to regulate infection, nodule organogenesis, and nitrogen fixation in L. japonicus.
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Affiliation(s)
- Dugald Reid
- Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, 8000, Denmark
| | - Huijun Liu
- Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, 8000, Denmark
| | - Simon Kelly
- Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, 8000, Denmark
| | - Yasuyuki Kawaharada
- Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, 8000, Denmark
| | - Terry Mun
- Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, 8000, Denmark
| | - Stig U Andersen
- Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, 8000, Denmark
| | - Guilhem Desbrosses
- Laboratoire des Symbioses Tropicales et Méditerranéennes, Université Montpellier 2, IRD, CIRAD, SupAgro, INRA Montpellier Cedex 05 France
| | - Jens Stougaard
- Centre for Carbohydrate Recognition and Signalling, Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, 8000, Denmark
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20
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Jin Y, Chen Z, Yang J, Mysore KS, Wen J, Huang J, Yu N, Wang E. IPD3 and IPD3L Function Redundantly in Rhizobial and Mycorrhizal Symbioses. FRONTIERS IN PLANT SCIENCE 2018; 9:267. [PMID: 29616050 PMCID: PMC5865340 DOI: 10.3389/fpls.2018.00267] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 02/14/2018] [Indexed: 05/08/2023]
Abstract
Legume plants form symbiotic associations with either nitrogen-fixing bacteria or arbuscular mycorrhizal (AM) fungi, which are regulated by a set of common symbiotic signaling pathway genes. Central to the signaling pathway is the activation of the DMI3/IPD3 protein complex by Ca2+ oscillations, and the initiation of nodule organogenesis and mycorrhizal symbiosis. DMI3 is essential for rhizobial infection and nodule organogenesis; however, ipd3 mutants have been shown to be impaired only in infection thread formation but not in root nodule organogenesis in Medicago truncatula. We identified an IPD3-like (IPD3L) gene in the M. truncatula genome. A single ipd3l mutant exhibits a normal root nodule phenotype. The ipd3l/ipd3-2 double mutant is completely unable to initiate infection threads and nodule primordia. IPD3L can functionally replace IPD3 when expressed under the control of the IPD3 promoter, indicating functional redundancy between these two transcriptional regulators. We constructed a version of IPD3 that was phosphomimetic with respect to two conserved serine residues (IPD3-2D). This was sufficient to trigger root nodule organogenesis, but the increased multisite phosphorylation of IPD3 (IPD3-8D) led to low transcriptional activity, suggesting that the phosphorylation levels of IPD3 fine-tune its transcriptional activity in the root nodule symbiosis. Intriguingly, the phosphomimetic version of IPD3 triggers spontaneous root-like nodules on the roots of dmi3-1 and dmi2-1 (DMI2 is an LRR-containing receptor-like kinase gene which is required for Ca2+ spiking), but not on the roots of wild-type or ipd3l ipd3-2 plants. In addition, fully developed arbuscules were formed in the ipd3l ipd3-2 mutants but not the ccamk/dmi3-1 mutants. Collectively, our data indicate that, in addition to IPD3 and IPD3L, another new genetic component or other new phosphorylation sites of IPD3 function downstream of DMI3 in rhizobial and mycorrhizal symbioses.
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Affiliation(s)
- Yue Jin
- College of Life and Environment Sciences, Shanghai Normal University, Shanghai, China
| | - Zixuan Chen
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Jun Yang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- Collaborative Innovation Center of Crop Stress Biology, Institute of Plant Stress Biology, Henan University, Kaifeng, China
| | - Kirankumar S. Mysore
- Plant Biology Division, Samuel Roberts Noble Foundation, Ardmore, OK, United States
| | - Jiangqi Wen
- Plant Biology Division, Samuel Roberts Noble Foundation, Ardmore, OK, United States
| | - Jirong Huang
- College of Life and Environment Sciences, Shanghai Normal University, Shanghai, China
| | - Nan Yu
- College of Life and Environment Sciences, Shanghai Normal University, Shanghai, China
- *Correspondence: Nan Yu
| | - Ertao Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- Ertao Wang
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Gene Silencing of Argonaute5 Negatively Affects the Establishment of the Legume-Rhizobia Symbiosis. Genes (Basel) 2017; 8:genes8120352. [PMID: 29182547 PMCID: PMC5748670 DOI: 10.3390/genes8120352] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 11/20/2017] [Accepted: 11/22/2017] [Indexed: 11/24/2022] Open
Abstract
The establishment of the symbiosis between legumes and nitrogen-fixing rhizobia is finely regulated at the transcriptional, posttranscriptional and posttranslational levels. Argonaute5 (AGO5), a protein involved in RNA silencing, can bind both viral RNAs and microRNAs to control plant-microbe interactions and plant physiology. For instance, AGO5 regulates the systemic resistance of Arabidopsis against Potato Virus X as well as the pigmentation of soybean (Glycine max) seeds. Here, we show that AGO5 is also playing a central role in legume nodulation based on its preferential expression in common bean (Phaseolus vulgaris) and soybean roots and nodules. We also report that the expression of AGO5 is induced after 1 h of inoculation with rhizobia. Down-regulation of AGO5 gene in P. vulgaris and G. max causes diminished root hair curling, reduces nodule formation and interferes with the induction of three critical symbiotic genes: Nuclear Factor Y-B (NF-YB), Nodule Inception (NIN) and Flotillin2 (FLOT2). Our findings provide evidence that the common bean and soybean AGO5 genes play an essential role in the establishment of the symbiosis with rhizobia.
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Reid D, Nadzieja M, Novák O, Heckmann AB, Sandal N, Stougaard J. Cytokinin Biosynthesis Promotes Cortical Cell Responses during Nodule Development. PLANT PHYSIOLOGY 2017; 175:361-375. [PMID: 28733389 PMCID: PMC5580777 DOI: 10.1104/pp.17.00832] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 07/18/2017] [Indexed: 05/22/2023]
Abstract
Legume mutants have shown the requirement for receptor-mediated cytokinin signaling in symbiotic nodule organogenesis. While the receptors are central regulators, cytokinin also is accumulated during early phases of symbiotic interaction, but the pathways involved have not yet been fully resolved. To identify the source, timing, and effect of this accumulation, we followed transcript levels of the cytokinin biosynthetic pathway genes in a sliding developmental zone of Lotus japonicus roots. LjIpt2 and LjLog4 were identified as the major contributors to the first cytokinin burst. The genetic dependence and Nod factor responsiveness of these genes confirm that cytokinin biosynthesis is a key target of the common symbiosis pathway. The accumulation of LjIpt2 and LjLog4 transcripts occurs independent of the LjLhk1 receptor during nodulation. Together with the rapid repression of both genes by cytokinin, this indicates that LjIpt2 and LjLog4 contribute to, rather than respond to, the initial cytokinin buildup. Analysis of the cytokinin response using the synthetic cytokinin sensor, TCSn, showed that this response occurs in cortical cells before spreading to the epidermis in L. japonicus While mutant analysis identified redundancy in several biosynthesis families, we found that mutation of LjIpt4 limits nodule numbers. Overexpression of LjIpt3 or LjLog4 alone was insufficient to produce the robust formation of spontaneous nodules. In contrast, overexpressing a complete cytokinin biosynthesis pathway leads to large, often fused spontaneous nodules. These results show the importance of cytokinin biosynthesis in initiating and balancing the requirement for cortical cell activation without uncontrolled cell proliferation.
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Affiliation(s)
- Dugald Reid
- Centre for Carbohydrate Recognition and Signaling, Department of Molecular Biology and Genetics, Aarhus University, Aarhus C 8000, Denmark
| | - Marcin Nadzieja
- Centre for Carbohydrate Recognition and Signaling, Department of Molecular Biology and Genetics, Aarhus University, Aarhus C 8000, Denmark
| | - Ondřej Novák
- Laboratory of Growth Regulators, Faculty of Science, Palacký University and Institute of Experimental Botany, Czech Academy of Sciences, CZ-78371 Olomouc, Czech Republic
| | - Anne B Heckmann
- Centre for Carbohydrate Recognition and Signaling, Department of Molecular Biology and Genetics, Aarhus University, Aarhus C 8000, Denmark
| | - Niels Sandal
- Centre for Carbohydrate Recognition and Signaling, Department of Molecular Biology and Genetics, Aarhus University, Aarhus C 8000, Denmark
| | - Jens Stougaard
- Centre for Carbohydrate Recognition and Signaling, Department of Molecular Biology and Genetics, Aarhus University, Aarhus C 8000, Denmark
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23
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Martin FM, Uroz S, Barker DG. Ancestral alliances: Plant mutualistic symbioses with fungi and bacteria. Science 2017; 356:356/6340/eaad4501. [DOI: 10.1126/science.aad4501] [Citation(s) in RCA: 235] [Impact Index Per Article: 33.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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24
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Yano K, Aoki S, Liu M, Umehara Y, Suganuma N, Iwasaki W, Sato S, Soyano T, Kouchi H, Kawaguchi M. Function and evolution of a Lotus japonicus AP2/ERF family transcription factor that is required for development of infection threads. DNA Res 2017; 24:193-203. [PMID: 28028038 PMCID: PMC5397602 DOI: 10.1093/dnares/dsw052] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 10/25/2016] [Indexed: 01/05/2023] Open
Abstract
Legume-rhizobium symbiosis is achieved by two major events evolutionarily acquired: root hair infection and organogenesis. Infection thread (IT) development is a distinct element for rhizobial infection. Through ITs, rhizobia are efficiently transported from infection foci on root hairs to dividing meristematic cortical cells. To unveil this process, we performed genetic screening using Lotus japonicus MG-20 and isolated symbiotic mutant lines affecting nodulation, root hair morphology, and IT development. Map-based cloning identified an AP2/ERF transcription factor gene orthologous to Medicago truncatula ERN1. LjERN1 was activated in response to rhizobial infection and depended on CYCLOPS and NSP2. Legumes conserve an ERN1 homolog, ERN2, that functions redundantly with ERN1 in M. truncatula. Phylogenetic analysis showed that the lineages of ERN1 and ERN2 genes originated from a gene duplication event in the common ancestor of legume plants. However, genomic analysis suggested the lack of ERN2 gene in the L. japonicus genome, consistent with Ljern1 mutants exhibited a root hair phenotype that is observed in ern1/ern2 double mutants in M. truncatula. Molecular evolutionary analysis suggested that the nonsynonymous/synonymous rate ratios of legume ERN1 genes was almost identical to that of non-legume plants, whereas the ERN2 genes experienced a relaxed selective constraint.
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Affiliation(s)
- Koji Yano
- National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan
- Division of Symbiotic Systems, National Institute for Basic Biology, National Institute for Natural Sciences, Okazaki 444-8585, Japan
| | - Seishiro Aoki
- Department of General Systems Studies, Graduate School of Arts and Sciences, the University of Tokyo, Meguro-ku, Tokyo 153-8902, Japan
- Department of Biological Sciences, Graduate School of Science, the University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Meng Liu
- Division of Symbiotic Systems, National Institute for Basic Biology, National Institute for Natural Sciences, Okazaki 444-8585, Japan
- Department of Basic Biology, School of Life Science, Graduate University for Advanced Studies (SOKENDAI), Okazaki 444-8585, Japan and
| | - Yosuke Umehara
- National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan
| | - Norio Suganuma
- Department of Life Science, Aichi University of Education, Kariya, Aichi 448–8542, Japan
| | - Wataru Iwasaki
- Department of Biological Sciences, Graduate School of Science, the University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Shusei Sato
- Kazusa DNA Research Institute, Kisarazu, Chiba 292–0812, Japan
- Graduate School of Life Sciences, Tohoku University, Aoba-ku, Sendai 980-8577, Japan
| | - Takashi Soyano
- Division of Symbiotic Systems, National Institute for Basic Biology, National Institute for Natural Sciences, Okazaki 444-8585, Japan
- Department of Basic Biology, School of Life Science, Graduate University for Advanced Studies (SOKENDAI), Okazaki 444-8585, Japan and
| | - Hiroshi Kouchi
- National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan
| | - Masayoshi Kawaguchi
- Division of Symbiotic Systems, National Institute for Basic Biology, National Institute for Natural Sciences, Okazaki 444-8585, Japan
- Department of Basic Biology, School of Life Science, Graduate University for Advanced Studies (SOKENDAI), Okazaki 444-8585, Japan and
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Kang Y, Li M, Sinharoy S, Verdier J. A Snapshot of Functional Genetic Studies in Medicago truncatula. FRONTIERS IN PLANT SCIENCE 2016; 7:1175. [PMID: 27555857 PMCID: PMC4977297 DOI: 10.3389/fpls.2016.01175] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2016] [Accepted: 07/21/2016] [Indexed: 05/21/2023]
Abstract
In the current context of food security, increase of plant protein production in a sustainable manner represents one of the major challenges of agronomic research, which could be partially resolved by increased cultivation of legume crops. Medicago truncatula is now a well-established model for legume genomic and genetic studies. With the establishment of genomics tools and mutant populations in M. truncatula, it has become an important resource to answer some of the basic biological questions related to plant development and stress tolerance. This review has an objective to overview a decade of genetic studies in this model plant from generation of mutant populations to nowadays. To date, the three biological fields, which have been extensively studied in M. truncatula, are the symbiotic nitrogen fixation, the seed development, and the abiotic stress tolerance, due to their significant agronomic impacts. In this review, we summarize functional genetic studies related to these three major biological fields. We integrated analyses of a nearly exhaustive list of genes into their biological contexts in order to provide an overview of the forefront research advances in this important legume model plant.
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Affiliation(s)
- Yun Kang
- Plant Biology Division, The Samuel Roberts Noble FoundationArdmore, OK, USA
| | - Minguye Li
- University of Chinese Academy of SciencesBeijing, China
- Shanghai Plant Stress Center, Shanghai Institutes of Biological Sciences, Chinese Academy of SciencesShanghai, China
| | - Senjuti Sinharoy
- Department of Biotechnology, University of CalcuttaCalcutta, India
| | - Jerome Verdier
- Shanghai Plant Stress Center, Shanghai Institutes of Biological Sciences, Chinese Academy of SciencesShanghai, China
- *Correspondence: Jerome Verdier
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