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Meziadi C, Alvarez-Diaz JC, Thareau V, Gratias A, Marande W, Soler-Garzon A, Miklas PN, Pflieger S, Geffroy V. Fine-mapping and evolutionary history of R-BPMV, a dominant resistance gene to Bean pod mottle virus in Phaseolus vulgaris L. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 137:8. [PMID: 38092992 DOI: 10.1007/s00122-023-04513-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 11/21/2023] [Indexed: 12/18/2023]
Abstract
KEY MESSAGE R-BPMV is located within a recently expanded TNL cluster in the Phaseolus genus with suppressed recombination and known for resistance to multiple pathogens including potyviruses controlled by the I gene. Bean pod mottle virus (BPMV) is a comovirus that infects common bean and legumes in general. BPMV is distributed throughout the world and is a major threat on soybean, a closely related species of common bean. In common bean, BAT93 was reported to carry the R-BPMV resistance gene conferring resistance to BPMV and linked with the I resistance gene. To fine map R-BPMV, 182 recombinant inbred lines (RILs) derived from the cross BAT93 × JaloEEP558 were genotyped with polymerase chain reaction (PCR)-based markers developed using genome assemblies from G19833 and BAT93, as well as BAT93 BAC clone sequences. Analysis of RILs carrying key recombination events positioned R-BPMV to a target region containing at least 16 TIR-NB-LRR (TNL) sequences in BAT93. Because the I cluster presents a suppression of recombination and a large number of repeated sequences, none of the 16 TNLs could be excluded as R-BPMV candidate gene. The evolutionary history of the TNLs for the I cluster were reconstructed using microsynteny and phylogenetic analyses within the legume family. A single I TNL was present in Medicago truncatula and lost in soybean, mirroring the absence of complete BPMV resistance in soybean. Amplification of TNLs in the I cluster predates the divergence of the Phaseolus species, in agreement with the emergence of R-BPMV before the separation of the common bean wild centers of diversity. This analysis provides PCR-based markers useful in marker-assisted selection (MAS) and laid the foundation for cloning of R-BPMV resistance gene in order to transfer the resistance into soybean.
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Affiliation(s)
- Chouaïb Meziadi
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Université Evry, 91190, Gif Sur Yvette, France
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Cité, CNRS, INRAE, 91190, Gif Sur Yvette, Rue Noetzlin, 91405, Orsay, France
| | - Juan-Camilo Alvarez-Diaz
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Université Evry, 91190, Gif Sur Yvette, France
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Cité, CNRS, INRAE, 91190, Gif Sur Yvette, Rue Noetzlin, 91405, Orsay, France
| | - Vincent Thareau
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Université Evry, 91190, Gif Sur Yvette, France
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Cité, CNRS, INRAE, 91190, Gif Sur Yvette, Rue Noetzlin, 91405, Orsay, France
| | - Ariane Gratias
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Université Evry, 91190, Gif Sur Yvette, France
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Cité, CNRS, INRAE, 91190, Gif Sur Yvette, Rue Noetzlin, 91405, Orsay, France
| | | | - Alvaro Soler-Garzon
- Irrigated Agriculture Research and Extension Center, Washington State Univ, Prosser, WA, USA
| | - Phillip N Miklas
- Grain Legume Genetics and Physiology Research Unit, USDA ARS, Prosser, WA, USA
| | - Stéphanie Pflieger
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Université Evry, 91190, Gif Sur Yvette, France
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Cité, CNRS, INRAE, 91190, Gif Sur Yvette, Rue Noetzlin, 91405, Orsay, France
| | - Valérie Geffroy
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Université Evry, 91190, Gif Sur Yvette, France.
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Cité, CNRS, INRAE, 91190, Gif Sur Yvette, Rue Noetzlin, 91405, Orsay, France.
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Kim H, Ahn YJ, Lee H, Chung EH, Segonzac C, Sohn KH. Diversified host target families mediate convergently evolved effector recognition across plant species. CURRENT OPINION IN PLANT BIOLOGY 2023; 74:102398. [PMID: 37295296 DOI: 10.1016/j.pbi.2023.102398] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 05/13/2023] [Accepted: 05/15/2023] [Indexed: 06/12/2023]
Abstract
Recognition of pathogen effectors is a crucial step for triggering plant immunity. Resistance (R) genes often encode for nucleotide-binding leucine-rich repeat receptors (NLRs), and NLRs detect effectors from pathogens to trigger effector-triggered immunity (ETI). NLR recognition of effectors is observed in diverse forms where NLRs directly interact with effectors or indirectly detect effectors by monitoring host guardees/decoys (HGDs). HGDs undergo different biochemical modifications by diverse effectors and expand the effector recognition spectrum of NLRs, contributing robustness to plant immunity. Interestingly, in many cases of the indirect recognition of effectors, HGD families targeted by effectors are conserved across the plant species while NLRs are not. Notably, a family of diversified HGDs can activate multiple non-orthologous NLRs across plant species. Further investigation on HGDs would reveal the mechanistic basis of how the diversification of HGDs confers novel effector recognition by NLRs.
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Affiliation(s)
- Haseong Kim
- Plant Immunity Research Center, Seoul National University, Seoul, 08826, Republic of Korea
| | - Ye Jin Ahn
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, 37673, Republic of Korea
| | - Hyeonjung Lee
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, 37673, Republic of Korea
| | - Eui-Hwan Chung
- Department of Plant Biotechnology, Korea University, Seoul, 02841, Republic of Korea
| | - Cécile Segonzac
- Plant Immunity Research Center, Seoul National University, Seoul, 08826, Republic of Korea; Department of Agriculture, Forestry and Bioresources, Seoul National University, Seoul, 08826, Republic of Korea; Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826, Republic of Korea; Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Kee Hoon Sohn
- Plant Immunity Research Center, Seoul National University, Seoul, 08826, Republic of Korea; Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826, Republic of Korea; Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea; Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, Republic of Korea.
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Hu Y, Su C, Zhang Y, Li Y, Chen X, Shang H, Hu X. A Puccinia striiformis f. sp. tritici effector inhibits high-temperature seedling-plant resistance in wheat. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 112:249-267. [PMID: 35960661 DOI: 10.1111/tpj.15945] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Revised: 08/07/2022] [Accepted: 08/09/2022] [Indexed: 06/15/2023]
Abstract
Resistance to Pseudomonas syringae pv. maculicola 1 (RPM1)-induced protein kinase (RIPK) in Arabidopsis belongs to the receptor-like cytoplasmic kinase (RLCK) family and plays a vital role in immunity. However, the role of RLCKs in the high-temperature seedling-plant (HTSP) resistance of wheat (Triticum aestivum) to Puccinia striiformis f. sp. tritici (Pst), the stripe rust pathogen, remains unclear. Here, we identified a homologous gene of RIPK in wheat, namely TaRIPK. Expression of TaRIPK was induced by Pst inoculation and high temperatures. Silencing of TaRIPK reduced the expression level of TaRPM1, resulting in weaker HTSP resistance. Moreover, TaRIPK interacts with and phosphorylates papain-like cysteine protease 1 (TaPLCP1). Meanwhile, we found that the Pst-secreted protein PSTG_01766 targets TaPLCP1. Transient expression of PSTG_01766 inhibited basal immunity in tobacco (Nicotiana benthamiana) and wheat. The role of PSTG_01766 as an effector involved in HTSP resistance was further supported by host-induced gene silencing and bacterial type three secretion system-mediated delivery into wheat. PSTG_01766 inhibited the TaRIPK-induced phosphorylation of TaPLCP1. Furthermore, PSTG_01766 has the potential to influence the subcellular localization of TaPLCP1. Overall, we suggest that the TaRIPK-TaPLCP1-TaRPM1 module fits the guard model for disease resistance, participating in HTSP resistance. PSTG_01766 decreases HTSP resistance via targeting TaPLCP1. Guarded by wheat and attacked by Pst, TaPLCP1 may serve as a central hub of the defense response. Our findings improve the understanding of the molecular mechanism of wheat HTSP resistance, which may be an important strategy for controlling stripe rust in the face of global warming.
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Affiliation(s)
- Yangshan Hu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Chang Su
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yue Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yuxiang Li
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xianming Chen
- Agricultural Research Service, United States Department of Agriculture and Department of Plant Pathology, Washington State University, Pullman, WA, 99164-6430, USA
| | - Hongsheng Shang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xiaoping Hu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
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Wan WL, Kim ST, Castel B, Charoennit N, Chae E. Genetics of autoimmunity in plants: an evolutionary genetics perspective. THE NEW PHYTOLOGIST 2021; 229:1215-1233. [PMID: 32970825 DOI: 10.1111/nph.16947] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 08/12/2020] [Indexed: 05/14/2023]
Abstract
Autoimmunity in plants has been found in numerous hybrids as a form of hybrid necrosis and mutant panels. Uncontrolled cell death is a main cellular outcome of autoimmunity, which negatively impacts growth. Its occurrence highlights the vulnerable nature of the plant immune system. Genetic investigation of autoimmunity in hybrid plants revealed that extreme variation in the immune receptor repertoire is a major contributor, reflecting an evolutionary conundrum that plants face in nature. In this review, we discuss natural variation in the plant immune system and its contribution to fitness. The value of autoimmunity genetics lies in its ability to identify combinations of a natural immune receptor and its partner that are predisposed to triggering autoimmunity. The network of immune components for autoimmunity becomes instrumental in revealing mechanistic details of how immune receptors recognize cellular invasion and activate signaling. The list of autoimmunity-risk variants also allows us to infer evolutionary processes contributing to their maintenance in the natural population. Our approach to autoimmunity, which integrates mechanistic understanding and evolutionary genetics, has the potential to serve as a prognosis tool to optimize immunity in crops.
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Affiliation(s)
- Wei-Lin Wan
- Department of Biological Sciences, National University of Singapore, Singapore, 117558, Singapore
| | - Sang-Tae Kim
- Department of Life Sciences, The Catholic University of Korea, Bucheon, Gyeonggi-do, 14662, South Korea
| | - Baptiste Castel
- Department of Biological Sciences, National University of Singapore, Singapore, 117558, Singapore
| | - Nuri Charoennit
- Department of Biological Sciences, National University of Singapore, Singapore, 117558, Singapore
| | - Eunyoung Chae
- Department of Biological Sciences, National University of Singapore, Singapore, 117558, Singapore
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Foucher J, Ruh M, Préveaux A, Carrère S, Pelletier S, Briand M, Serre RF, Jacques MA, Chen NWG. Common bean resistance to Xanthomonas is associated with upregulation of the salicylic acid pathway and downregulation of photosynthesis. BMC Genomics 2020; 21:566. [PMID: 32811445 DOI: 10.21203/rs.3.rs-17010/v3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 08/05/2020] [Indexed: 05/28/2023] Open
Abstract
BACKGROUND Common bacterial blight (CBB) caused by Xanthomonas phaseoli pv. phaseoli and Xanthomonas citri pv. fuscans is one of the major threats to common bean crops (Phaseolus vulgaris L.). Resistance to CBB is particularly complex as 26 quantitative resistance loci to CBB have been described so far. To date, transcriptomic studies after CBB infection have been very scarce and the molecular mechanisms underlying susceptibility or resistance are largely unknown. RESULTS We sequenced and annotated the genomes of two common bean genotypes being either resistant (BAT93) or susceptible (JaloEEP558) to CBB. Reciprocal BLASTp analysis led to a list of 20,787 homologs between these genotypes and the common bean reference genome (G19833), which provides a solid dataset for further comparative analyses. RNA-Seq after inoculation with X. phaseoli pv. phaseoli showed that the susceptible genotype initiated a more intense and diverse biological response than the resistant genotype. Resistance was linked to upregulation of the salicylic acid pathway and downregulation of photosynthesis and sugar metabolism, while susceptibility was linked to downregulation of resistance genes and upregulation of the ethylene pathway and of genes involved in cell wall modification. CONCLUSIONS This study helps better understanding the mechanisms occurring during the early colonization phase of common bean by Xanthomonas and unveils new actors potentially important for resistance and susceptibility to CBB. We discuss the potential link between the pathways induced during bean colonization and genes induced by transcription activator-like effectors (TALEs), as illustrated in other Xanthomonas pathovars.
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Affiliation(s)
- Justine Foucher
- IRHS, INRAE, AGROCAMPUS OUEST, Université d'Angers, SFR4207 QUASAV, 42, rue Georges Morel, F-49071, Beaucouzé, France
| | - Mylène Ruh
- IRHS, INRAE, AGROCAMPUS OUEST, Université d'Angers, SFR4207 QUASAV, 42, rue Georges Morel, F-49071, Beaucouzé, France
| | - Anne Préveaux
- IRHS, INRAE, AGROCAMPUS OUEST, Université d'Angers, SFR4207 QUASAV, 42, rue Georges Morel, F-49071, Beaucouzé, France
| | - Sébastien Carrère
- CNRS, UMR 2594, Laboratoire des Interactions Plantes-Microorganismes (LIPM), F-31326, Castanet-Tolosan, France
| | - Sandra Pelletier
- IRHS, INRAE, AGROCAMPUS OUEST, Université d'Angers, SFR4207 QUASAV, 42, rue Georges Morel, F-49071, Beaucouzé, France
| | - Martial Briand
- IRHS, INRAE, AGROCAMPUS OUEST, Université d'Angers, SFR4207 QUASAV, 42, rue Georges Morel, F-49071, Beaucouzé, France
| | | | - Marie-Agnès Jacques
- IRHS, INRAE, AGROCAMPUS OUEST, Université d'Angers, SFR4207 QUASAV, 42, rue Georges Morel, F-49071, Beaucouzé, France
| | - Nicolas W G Chen
- IRHS, INRAE, AGROCAMPUS OUEST, Université d'Angers, SFR4207 QUASAV, 42, rue Georges Morel, F-49071, Beaucouzé, France.
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Foucher J, Ruh M, Préveaux A, Carrère S, Pelletier S, Briand M, Serre RF, Jacques MA, Chen NWG. Common bean resistance to Xanthomonas is associated with upregulation of the salicylic acid pathway and downregulation of photosynthesis. BMC Genomics 2020; 21:566. [PMID: 32811445 PMCID: PMC7437933 DOI: 10.1186/s12864-020-06972-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 08/05/2020] [Indexed: 02/08/2023] Open
Abstract
Background Common bacterial blight (CBB) caused by Xanthomonas phaseoli pv. phaseoli and Xanthomonas citri pv. fuscans is one of the major threats to common bean crops (Phaseolus vulgaris L.). Resistance to CBB is particularly complex as 26 quantitative resistance loci to CBB have been described so far. To date, transcriptomic studies after CBB infection have been very scarce and the molecular mechanisms underlying susceptibility or resistance are largely unknown. Results We sequenced and annotated the genomes of two common bean genotypes being either resistant (BAT93) or susceptible (JaloEEP558) to CBB. Reciprocal BLASTp analysis led to a list of 20,787 homologs between these genotypes and the common bean reference genome (G19833), which provides a solid dataset for further comparative analyses. RNA-Seq after inoculation with X. phaseoli pv. phaseoli showed that the susceptible genotype initiated a more intense and diverse biological response than the resistant genotype. Resistance was linked to upregulation of the salicylic acid pathway and downregulation of photosynthesis and sugar metabolism, while susceptibility was linked to downregulation of resistance genes and upregulation of the ethylene pathway and of genes involved in cell wall modification. Conclusions This study helps better understanding the mechanisms occurring during the early colonization phase of common bean by Xanthomonas and unveils new actors potentially important for resistance and susceptibility to CBB. We discuss the potential link between the pathways induced during bean colonization and genes induced by transcription activator-like effectors (TALEs), as illustrated in other Xanthomonas pathovars.
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Affiliation(s)
- Justine Foucher
- IRHS, INRAE, AGROCAMPUS OUEST, Université d'Angers, SFR4207 QUASAV, 42, rue Georges Morel, F-49071, Beaucouzé, France
| | - Mylène Ruh
- IRHS, INRAE, AGROCAMPUS OUEST, Université d'Angers, SFR4207 QUASAV, 42, rue Georges Morel, F-49071, Beaucouzé, France
| | - Anne Préveaux
- IRHS, INRAE, AGROCAMPUS OUEST, Université d'Angers, SFR4207 QUASAV, 42, rue Georges Morel, F-49071, Beaucouzé, France
| | - Sébastien Carrère
- CNRS, UMR 2594, Laboratoire des Interactions Plantes-Microorganismes (LIPM), F-31326, Castanet-Tolosan, France
| | - Sandra Pelletier
- IRHS, INRAE, AGROCAMPUS OUEST, Université d'Angers, SFR4207 QUASAV, 42, rue Georges Morel, F-49071, Beaucouzé, France
| | - Martial Briand
- IRHS, INRAE, AGROCAMPUS OUEST, Université d'Angers, SFR4207 QUASAV, 42, rue Georges Morel, F-49071, Beaucouzé, France
| | | | - Marie-Agnès Jacques
- IRHS, INRAE, AGROCAMPUS OUEST, Université d'Angers, SFR4207 QUASAV, 42, rue Georges Morel, F-49071, Beaucouzé, France
| | - Nicolas W G Chen
- IRHS, INRAE, AGROCAMPUS OUEST, Université d'Angers, SFR4207 QUASAV, 42, rue Georges Morel, F-49071, Beaucouzé, France.
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Tirnaz S, Zhang Y, Batley J. Genome-Wide Mining of Disease Resistance Gene Analogs Using Conserved Domains. Methods Mol Biol 2020; 2107:365-375. [PMID: 31893459 DOI: 10.1007/978-1-0716-0235-5_20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The production of legume crop species is severely affected by disease, imposing a significant yield loss annually worldwide. Plant resistance gene analogs (RGAs) play specific roles in plant resistance responses, and their identification and subsequent application in breeding programs help to reduce this yield loss. RGAs contain conserved domains and motifs, which can be used for their identification and classification. Nucleotide-binding site-leucine-rich repeat (NLR), receptor like kinase (RLK), and receptor like protein (RLP) genes are the main types of RGAs. Computational identification and characterization of RGAs has been performed successfully among different plant species. Here, we explain the computational workflow for genome-wide RGA identification in legumes.
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Affiliation(s)
- Soodeh Tirnaz
- School of Biological Sciences, University of Western Australia, Crawley, WA, Australia
| | - Yueqi Zhang
- School of Biological Sciences, University of Western Australia, Crawley, WA, Australia
| | - Jacqueline Batley
- School of Biological Sciences, University of Western Australia, Crawley, WA, Australia.
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Noman A, Aqeel M, Lou Y. PRRs and NB-LRRs: From Signal Perception to Activation of Plant Innate Immunity. Int J Mol Sci 2019; 20:ijms20081882. [PMID: 30995767 PMCID: PMC6514886 DOI: 10.3390/ijms20081882] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 04/02/2019] [Accepted: 04/10/2019] [Indexed: 12/11/2022] Open
Abstract
To ward off pathogens and pests, plants use a sophisticated immune system. They use pattern-recognition receptors (PRRs), as well as nucleotide-binding and leucine-rich repeat (NB-LRR) domains, for detecting nonindigenous molecular signatures from pathogens. Plant PRRs induce local and systemic immunity. Plasma-membrane-localized PRRs are the main components of multiprotein complexes having additional transmembrane and cytosolic kinases. Topical research involving proteins and their interactive partners, along with transcriptional and posttranscriptional regulation, has extended our understanding of R-gene-mediated plant immunity. The unique LRR domain conformation helps in the best utilization of a surface area and essentially mediates protein–protein interactions. Genome-wide analyses of inter- and intraspecies PRRs and NB-LRRs offer innovative information about their working and evolution. We reviewed plant immune responses with relevance to PRRs and NB-LRRs. This article focuses on the significant functional diversity, pathogen-recognition mechanisms, and subcellular compartmentalization of plant PRRs and NB-LRRs. We highlight the potential biotechnological application of PRRs and NB-LRRs to enhance broad-spectrum disease resistance in crops.
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Affiliation(s)
- Ali Noman
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310027, China.
- Department of Botany, Government College University, Faisalabad 38000, Pakistan.
| | - Muhammad Aqeel
- State Key Laboratory of Grassland Agro-ecosystems, School of Life Science, Lanzhou University, Lanzhou 730000, China.
| | - Yonggen Lou
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310027, China.
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Neupane S, Ma Q, Mathew FM, Varenhorst AJ, Andersen EJ, Nepal MP. Evolutionary Divergence of TNL Disease-Resistant Proteins in Soybean (Glycine max) and Common Bean (Phaseolus vulgaris). Biochem Genet 2018; 56:397-422. [PMID: 29500532 DOI: 10.1007/s10528-018-9851-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 02/21/2018] [Indexed: 10/17/2022]
Abstract
Disease-resistant genes (R genes) encode proteins that are involved in protecting plants from their pathogens and pests. Availability of complete genome sequences from soybean and common bean allowed us to perform a genome-wide identification and analysis of the Toll interleukin-1 receptor-like nucleotide-binding site leucine-rich repeat (TNL) proteins. Hidden Markov model (HMM) profiling of all protein sequences resulted in the identification of 117 and 77 regular TNL genes in soybean and common bean, respectively. We also identified TNL gene homologs with unique domains, and signal peptides as well as nuclear localization signals. The TNL genes in soybean formed 28 clusters located on 10 of the 20 chromosomes, with the majority found on chromosome 3, 6 and 16. Similarly, the TNL genes in common bean formed 14 clusters located on five of the 11 chromosomes, with the majority found on chromosome 10. Phylogenetic analyses of the TNL genes from Arabidopsis, soybean and common bean revealed less divergence within legumes relative to the divergence between legumes and Arabidopsis. Syntenic blocks were found between chromosomes Pv10 and Gm03, Pv07 and Gm10, as well as Pv01 and Gm14. The gene expression data revealed basal level expression and tissue specificity, while analysis of available microRNA data showed 37 predicted microRNA families involved in targeting the identified TNL genes in soybean and common bean.
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Affiliation(s)
- Surendra Neupane
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, USA
| | - Qin Ma
- Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD, USA
| | - Febina M Mathew
- Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD, USA
| | - Adam J Varenhorst
- Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD, USA
| | - Ethan J Andersen
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, USA
| | - Madhav P Nepal
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, USA.
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Chen NWG, Thareau V, Ribeiro T, Magdelenat G, Ashfield T, Innes RW, Pedrosa-Harand A, Geffroy V. Common Bean Subtelomeres Are Hot Spots of Recombination and Favor Resistance Gene Evolution. FRONTIERS IN PLANT SCIENCE 2018; 9:1185. [PMID: 30154814 PMCID: PMC6102362 DOI: 10.3389/fpls.2018.01185] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 07/24/2018] [Indexed: 05/10/2023]
Abstract
Subtelomeres of most eukaryotes contain fast-evolving genes usually involved in adaptive processes. In common bean (Phaseolus vulgaris), the Co-2 anthracnose resistance (R) locus corresponds to a cluster of nucleotide-binding-site leucine-rich-repeat (NL) encoding sequences, the prevalent class of plant R genes. To study the recent evolution of this R gene cluster, we used a combination of sequence, genetic and cytogenetic comparative analyses between common bean genotypes from two distinct gene pools (Andean and Mesoamerican) that diverged 0.165 million years ago. Co-2 is a large subtelomeric cluster on chromosome 11 comprising from 32 (Mesoamerican) to 52 (Andean) NL sequences embedded within khipu satellite repeats. Since the recent split between Andean and Mesoamerican gene pools, the Co-2 cluster has experienced numerous gene-pool specific NL losses, leading to distinct NL repertoires. The high proportion of solo-LTR retrotransposons indicates that the Co-2 cluster is located in a hot spot of unequal intra-strand homologous recombination. Furthermore, we observe large segmental duplications involving both Non-Homologous End Joining and Homologous Recombination double-strand break repair pathways. Finally, the identification of a Mesoamerican-specific subtelomeric sequence reveals frequent interchromosomal recombinations between common bean subtelomeres. Altogether, our results highlight that common bean subtelomeres are hot spots of recombination and favor the rapid evolution of R genes. We propose that chromosome ends could act as R gene incubators in many plant genomes.
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Affiliation(s)
- Nicolas W. G. Chen
- Institute of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d’Evry, Université Paris-Diderot Sorbonne Paris Cité, Orsay, France
- IRHS, INRA, AGROCAMPUS OUEST, Université d’Angers, SFR 4207 QUASAV, Beaucouzé, France
| | - Vincent Thareau
- Institute of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d’Evry, Université Paris-Diderot Sorbonne Paris Cité, Orsay, France
| | - Tiago Ribeiro
- Laboratory of Plant Cytogenetics, Federal University of Pernambuco, Recife, Brazil
| | - Ghislaine Magdelenat
- Genoscope/Commissariat à l’Energie Atomique-Centre National de Séquençage, Evry, France
| | - Tom Ashfield
- Department of Biology, Indiana University, Bloomington, IN, United States
| | - Roger W. Innes
- Department of Biology, Indiana University, Bloomington, IN, United States
| | | | - Valérie Geffroy
- Institute of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d’Evry, Université Paris-Diderot Sorbonne Paris Cité, Orsay, France
- *Correspondence: Valérie Geffroy,
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11
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González AM, Godoy L, Santalla M. Dissection of Resistance Genes to Pseudomonas syringae pv. phaseolicola in UI3 Common Bean Cultivar. Int J Mol Sci 2017; 18:E2503. [PMID: 29168746 PMCID: PMC5751106 DOI: 10.3390/ijms18122503] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 11/14/2017] [Accepted: 11/17/2017] [Indexed: 11/25/2022] Open
Abstract
Few quantitative trait loci have been mapped for resistance to Pseudomonas syringae pv. phaseolicola in common bean. Two F₂ populations were developed from the host differential UI3 cultivar. The objective of this study was to further characterize the resistance to races 1, 5, 7 and 9 of Psp included in UI3. Using a QTL mapping approach, 16 and 11 main-effect QTLs for pod and primary leaf resistance were located on LG10, explaining up to 90% and 26% of the phenotypic variation, respectively. The homologous genomic region corresponding to primary leaf resistance QTLs detected tested positive for the presence of resistance-associated gene cluster encoding nucleotide-binding and leucine-rich repeat (NL), Natural Resistance Associated Macrophage (NRAMP) and Pentatricopeptide Repeat family (PPR) proteins. It is worth noting that the main effect QTLs for resistance in pod were located inside a 3.5 Mb genomic region that included the Phvul.010G021200 gene, which encodes a protein that has the highest sequence similarity to the RIN4 gene of Arabidopsis, and can be considered an important candidate gene for the organ-specific QTLs identified here. These results support that resistance to Psp from UI3 might result from the immune response activated by combinations of R proteins, and suggest the guard model as an important mechanism in pod resistance to halo blight. The candidate genes identified here warrant functional studies that will help in characterizing the actual defense gene(s) in UI3 genotype.
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Affiliation(s)
- Ana M González
- Grupo de Biología de Agrosistemas (BAS, www.bas-group.es), Misión Biológica de Galicia-CSIC, P.O. Box 28, 36080 Pontevedra, Spain.
| | - Luís Godoy
- Grupo de Biología de Agrosistemas (BAS, www.bas-group.es), Misión Biológica de Galicia-CSIC, P.O. Box 28, 36080 Pontevedra, Spain.
| | - Marta Santalla
- Grupo de Biología de Agrosistemas (BAS, www.bas-group.es), Misión Biológica de Galicia-CSIC, P.O. Box 28, 36080 Pontevedra, Spain.
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12
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Song H, Wang P, Li C, Han S, Zhao C, Xia H, Bi Y, Guo B, Zhang X, Wang X. Comparative analysis of NBS-LRR genes and their response to Aspergillus flavus in Arachis. PLoS One 2017; 12:e0171181. [PMID: 28158222 PMCID: PMC5291535 DOI: 10.1371/journal.pone.0171181] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 01/17/2017] [Indexed: 12/31/2022] Open
Abstract
Studies have demonstrated that nucleotide-binding site-leucine-rich repeat (NBS-LRR) genes respond to pathogen attack in plants. Characterization of NBS-LRR genes in peanut is not well documented. The newly released whole genome sequences of Arachis duranensis and Arachis ipaënsis have allowed a global analysis of this important gene family in peanut to be conducted. In this study, we identified 393 (AdNBS) and 437 (AiNBS) NBS-LRR genes from A. duranensis and A. ipaënsis, respectively, using bioinformatics approaches. Full-length sequences of 278 AdNBS and 303 AiNBS were identified. Fifty-one orthologous, four AdNBS paralogous, and six AiNBS paralogous gene pairs were predicted. All paralogous gene pairs were located in the same chromosomes, indicating that tandem duplication was the most likely mechanism forming these paralogs. The paralogs mainly underwent purifying selection, but most LRR 8 domains underwent positive selection. More gene clusters were found in A. ipaënsis than in A. duranensis, possibly owing to tandem duplication events occurring more frequently in A. ipaënsis. The expression profile of NBS-LRR genes was different between A. duranensis and A. hypogaea after Aspergillus flavus infection. The up-regulated expression of NBS-LRR in A. duranensis was continuous, while these genes responded to the pathogen temporally in A. hypogaea.
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Affiliation(s)
- Hui Song
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, China
| | - Pengfei Wang
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, China
| | - Changsheng Li
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, China
- College of Life Science, Shandong Normal University, Jinan, China
| | - Suoyi Han
- Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Chuanzhi Zhao
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, China
| | - Han Xia
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, China
| | - Yuping Bi
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, China
| | - Baozhu Guo
- Crop Protection and Management Research Unit, USDA-ARS, Tifton, Georgia, United States of America
| | - Xinyou Zhang
- Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Xingjun Wang
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, China
- College of Life Science, Shandong Normal University, Jinan, China
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13
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Whitham SA, Qi M, Innes RW, Ma W, Lopes-Caitar V, Hewezi T. Molecular Soybean-Pathogen Interactions. ANNUAL REVIEW OF PHYTOPATHOLOGY 2016; 54:443-68. [PMID: 27359370 DOI: 10.1146/annurev-phyto-080615-100156] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Soybean hosts a wide variety of pathogens that cause significant yield losses. The importance of soybean as a major oilseed crop has led to research focused on its interactions with pathogens, such as Soybean mosaic virus, Pseudomonas syringae, Phytophthora sojae, Phakopsora pachyrhizi, and Heterodera glycines. Pioneering work on soybean's interactions with these organisms, which represent the five major pathogen groups (viruses, bacteria, oomycetes, fungi, and nematodes), has contributed to our understanding of the molecular mechanisms underlying virulence and immunity. These mechanisms involve conserved and unique features that validate the need for research in both soybean and homologous model systems. In this review, we discuss identification of effectors and their functions as well as resistance gene-mediated recognition and signaling. We also point out areas in which model systems and recent advances in resources and tools have provided opportunities to gain deeper insights into soybean-pathogen interactions.
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Affiliation(s)
- Steven A Whitham
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa 50011; ,
| | - Mingsheng Qi
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa 50011; ,
| | - Roger W Innes
- Department of Biology, Indiana University, Bloomington, Indiana 47405;
| | - Wenbo Ma
- Department of Plant Pathology and Microbiology, University of California, Riverside, California 92521;
| | - Valéria Lopes-Caitar
- Department of Plant Sciences, University of Tennessee, Knoxville, Tennessee 37996; ,
| | - Tarek Hewezi
- Department of Plant Sciences, University of Tennessee, Knoxville, Tennessee 37996; ,
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14
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Meziadi C, Richard MMS, Derquennes A, Thareau V, Blanchet S, Gratias A, Pflieger S, Geffroy V. Development of molecular markers linked to disease resistance genes in common bean based on whole genome sequence. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2016; 242:351-357. [PMID: 26566851 DOI: 10.1016/j.plantsci.2015.09.006] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2015] [Revised: 09/01/2015] [Accepted: 09/02/2015] [Indexed: 05/03/2023]
Abstract
Common bean (Phaseolus vulgaris) is the most important grain legume for direct human consumption in the world, particularly in developing countries where it constitutes the main source of protein. Unfortunately, common bean yield stability is constrained by a number of pests and diseases. As use of resistant genotypes is the most economic and ecologically safe means for controlling plant diseases, efforts have been made to genetically characterize resistance genes (R genes) in common bean. Despite its agronomic importance, genomic resources available in common bean were limited until the recent sequencing of common bean genome (Andean genotype G19833). Besides allowing the annotation of Nucleotide Binding-Leucine Rich Repeat (NB-LRR) encoding gene family, which is the prevalent class of disease R genes in plants, access to the whole genome sequence of common bean can be of great help for intense selection to increase the overall efficiency of crop improvement programs using marker-assisted selection (MAS). This review presents the state of the art of common bean NB-LRR gene clusters, their peculiar location in subtelomeres and correlation with genetically characterized monogenic R genes, as well as how the availability of the whole genome sequence can boost the development of molecular markers for MAS.
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Affiliation(s)
- Chouaïb Meziadi
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Université Paris-Saclay, Bâtiment 630, 91405 Orsay, France
| | - Manon M S Richard
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Université Paris-Saclay, Bâtiment 630, 91405 Orsay, France
| | - Amandine Derquennes
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Université Paris-Saclay, Bâtiment 630, 91405 Orsay, France
| | - Vincent Thareau
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Université Paris-Saclay, Bâtiment 630, 91405 Orsay, France
| | - Sophie Blanchet
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Université Paris-Saclay, Bâtiment 630, 91405 Orsay, France
| | - Ariane Gratias
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Université Paris-Saclay, Bâtiment 630, 91405 Orsay, France
| | - Stéphanie Pflieger
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Université Paris-Saclay, Bâtiment 630, 91405 Orsay, France
| | - Valérie Geffroy
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Université Paris-Saclay, Bâtiment 630, 91405 Orsay, France.
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15
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Christopoulou M, McHale LK, Kozik A, Reyes-Chin Wo S, Wroblewski T, Michelmore RW. Dissection of Two Complex Clusters of Resistance Genes in Lettuce (Lactuca sativa). MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2015; 28:751-65. [PMID: 25650829 DOI: 10.1094/mpmi-06-14-0175-r] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Of the over 50 phenotypic resistance genes mapped in lettuce, 25 colocalize to three major resistance clusters (MRC) on chromosomes 1, 2, and 4. Similarly, the majority of candidate resistance genes encoding nucleotide binding-leucine rich repeat (NLR) proteins genetically colocalize with phenotypic resistance loci. MRC1 and MRC4 span over 66 and 63 Mb containing 84 and 21 NLR-encoding genes, respectively, as well as 765 and 627 genes that are not related to NLR genes. Forward and reverse genetic approaches were applied to dissect MRC1 and MRC4. Transgenic lines exhibiting silencing were selected using silencing of β-glucuronidase as a reporter. Silencing of two of five NLR-encoding gene families resulted in abrogation of nine of 14 tested resistance phenotypes mapping to these two regions. At MRC1, members of the coiled coil-NLR-encoding RGC1 gene family were implicated in host and nonhost resistance through requirement for Dm5/8- and Dm45-mediated resistance to downy mildew caused by Bremia lactucae as well as the hypersensitive response to effectors AvrB, AvrRpm1, and AvrRpt2 of the nonpathogen Pseudomonas syringae. At MRC4, RGC12 family members, which encode toll interleukin receptor-NLR proteins, were implicated in Dm4-, Dm7-, Dm11-, and Dm44-mediated resistance to B. lactucae. Lesions were identified in the sequence of a candidate gene within dm7 loss-of-resistance mutant lines, confirming that RGC12G confers Dm7.
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Affiliation(s)
- Marilena Christopoulou
- Genome Center and Department of Plant Sciences, University of California-Davis, CA 95616, U.S.A
| | - Leah K McHale
- Genome Center and Department of Plant Sciences, University of California-Davis, CA 95616, U.S.A
| | - Alex Kozik
- Genome Center and Department of Plant Sciences, University of California-Davis, CA 95616, U.S.A
| | - Sebastian Reyes-Chin Wo
- Genome Center and Department of Plant Sciences, University of California-Davis, CA 95616, U.S.A
| | - Tadeusz Wroblewski
- Genome Center and Department of Plant Sciences, University of California-Davis, CA 95616, U.S.A
| | - Richard W Michelmore
- Genome Center and Department of Plant Sciences, University of California-Davis, CA 95616, U.S.A
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16
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Cook DE, Mesarich CH, Thomma BPHJ. Understanding plant immunity as a surveillance system to detect invasion. ANNUAL REVIEW OF PHYTOPATHOLOGY 2015; 53:541-63. [PMID: 26047564 DOI: 10.1146/annurev-phyto-080614-120114] [Citation(s) in RCA: 302] [Impact Index Per Article: 33.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Various conceptual models to describe the plant immune system have been presented. The most recent paradigm to gain wide acceptance in the field is often referred to as the zigzag model, which reconciles the previously formulated gene-for-gene hypothesis with the recognition of general elicitors in a single model. This review focuses on the limitations of the current paradigm of molecular plant-microbe interactions and how it too narrowly defines the plant immune system. As such, we discuss an alternative view of plant innate immunity as a system that evolves to detect invasion. This view accommodates the range from mutualistic to parasitic symbioses that plants form with diverse organisms, as well as the spectrum of ligands that the plant immune system perceives. Finally, how this view can contribute to the current practice of resistance breeding is discussed.
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Affiliation(s)
- David E Cook
- Laboratory of Phytopathology, Wageningen University, 6708 PB Wageningen, The Netherlands; ,
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17
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Kessens R, Ashfield T, Kim SH, Innes RW. Determining the GmRIN4 requirements of the soybean disease resistance proteins Rpg1b and Rpg1r using a nicotiana glutinosa-based agroinfiltration system. PLoS One 2014; 9:e108159. [PMID: 25244054 PMCID: PMC4171518 DOI: 10.1371/journal.pone.0108159] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2014] [Accepted: 08/25/2014] [Indexed: 12/13/2022] Open
Abstract
Rpg1b and Rpg1r are soybean disease resistance (R) genes responsible for conferring resistance to Pseudomonas syringae strains expressing the effectors AvrB and AvrRpm1, respectively. The study of these cloned genes would be greatly facilitated by the availability of a suitable transient expression system. The commonly used Niciotiana benthamiana-based system is not suitable for studying Rpg1b and Rpg1r function, however, because expression of AvrB or AvrRpm1 alone induces a hypersensitive response (HR), indicating that N. benthamiana contains endogenous R genes that recognize these effectors. To identify a suitable alternative host for transient expression assays, we screened 13 species of Nicotiana along with 11 accessions of N. tabacum for lack of response to transient expression of AvrB and AvrRpm1. We found that N. glutinosa did not respond to either effector and was readily transformable as determined by transient expression of β-glucuronidase. Using this system, we determined that Rpg1b-mediated HR in N. glutinosa required co-expression of avrB and a soybean ortholog of the Arabidopsis RIN4 gene. All four soybean RIN4 orthologs tested worked in the assay. In contrast, Rpg1r did not require co-expression of a soybean RIN4 ortholog to recognize AvrRpm1, but recognition was suppressed by co-expression with AvrRpt2. These observations suggest that an endogenous RIN4 gene in N. glutinosa can substitute for the soybean RIN4 ortholog in the recognition of AvrRpm1 by Rpg1r.
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Affiliation(s)
- Ryan Kessens
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
| | - Tom Ashfield
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
| | - Sang Hee Kim
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
| | - Roger W. Innes
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
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18
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Ashfield T, Redditt T, Russell A, Kessens R, Rodibaugh N, Galloway L, Kang Q, Podicheti R, Innes RW. Evolutionary relationship of disease resistance genes in soybean and Arabidopsis specific for the Pseudomonas syringae effectors AvrB and AvrRpm1. PLANT PHYSIOLOGY 2014; 166:235-51. [PMID: 25034017 PMCID: PMC4149710 DOI: 10.1104/pp.114.244715] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2014] [Accepted: 07/13/2014] [Indexed: 05/22/2023]
Abstract
In Arabidopsis (Arabidopsis thaliana), the Pseudomonas syringae effector proteins AvrB and AvrRpm1 are both detected by the RESISTANCE TO PSEUDOMONAS MACULICOLA1 (RPM1) disease resistance (R) protein. By contrast, soybean (Glycine max) can distinguish between these effectors, with AvrB and AvrRpm1 being detected by the Resistance to Pseudomonas glycinea 1b (Rpg1b) and Rpg1r R proteins, respectively. We have been using these genes to investigate the evolution of R gene specificity and have previously identified RPM1 and Rpg1b. Here, we report the cloning of Rpg1r, which, like RPM1 and Rpg1b, encodes a coiled-coil (CC)-nucleotide-binding (NB)-leucine-rich repeat (LRR) protein. As previously found for Rpg1b, we determined that Rpg1r is not orthologous with RPM1, indicating that the ability to detect both AvrB and AvrRpm1 evolved independently in soybean and Arabidopsis. The tightly linked soybean Rpg1b and Rpg1r genes share a close evolutionary relationship, with Rpg1b containing a recombination event that combined a NB domain closely related to Rpg1r with CC and LRR domains from a more distantly related CC-NB-LRR gene. Using structural modeling, we mapped polymorphisms between Rpg1b and Rpg1r onto the predicted tertiary structure of Rpg1b, which revealed highly polymorphic surfaces within both the CC and LRR domains. Assessment of chimeras between Rpg1b and Rpg1r using a transient expression system revealed that AvrB versus AvrRpm1 specificity is determined by the C-terminal portion of the LRR domain. The P. syringae effector AvrRpt2, which targets RPM1 INTERACTOR4 (RIN4) proteins in both Arabidopsis and soybean, partially blocked recognition of both AvrB and AvrRpm1 in soybean, suggesting that both Rpg1b and Rpg1r may detect these effectors via modification of a RIN4 homolog.
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Affiliation(s)
- Tom Ashfield
- Department of Biology, Indiana University, Bloomington, Indiana 47405
| | - Thomas Redditt
- Department of Biology, Indiana University, Bloomington, Indiana 47405
| | - Andrew Russell
- Department of Biology, Indiana University, Bloomington, Indiana 47405
| | - Ryan Kessens
- Department of Biology, Indiana University, Bloomington, Indiana 47405
| | - Natalie Rodibaugh
- Department of Biology, Indiana University, Bloomington, Indiana 47405
| | - Lauren Galloway
- Department of Biology, Indiana University, Bloomington, Indiana 47405
| | - Qing Kang
- Department of Biology, Indiana University, Bloomington, Indiana 47405
| | - Ram Podicheti
- Department of Biology, Indiana University, Bloomington, Indiana 47405
| | - Roger W Innes
- Department of Biology, Indiana University, Bloomington, Indiana 47405
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19
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Richard MMS, Pflieger S, Sévignac M, Thareau V, Blanchet S, Li Y, Jackson SA, Geffroy V. Fine mapping of Co-x, an anthracnose resistance gene to a highly virulent strain of Colletotrichum lindemuthianum in common bean. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2014; 127:1653-66. [PMID: 24859268 DOI: 10.1007/s00122-014-2328-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Accepted: 05/05/2014] [Indexed: 05/03/2023]
Abstract
The Co - x anthracnose R gene of common bean was fine-mapped into a 58 kb region at one end of chromosome 1, where no canonical NB-LRR-encoding genes are present in G19833 genome sequence. Anthracnose, caused by the phytopathogenic fungus Colletotrichum lindemuthianum, is one of the most damaging diseases of common bean, Phaseolus vulgaris. Various resistance (R) genes, named Co-, conferring race-specific resistance to different strains of C. lindemuthianum have been identified. The Andean cultivar JaloEEP558 was reported to carry Co-x on chromosome 1, conferring resistance to the highly virulent strain 100. To fine map Co-x, 181 recombinant inbred lines derived from the cross between JaloEEP558 and BAT93 were genotyped with polymerase chain reaction (PCR)-based markers developed using the genome sequence of the Andean genotype G19833. Analysis of RILs carrying key recombination events positioned Co-x at one end of chromosome 1 to a 58 kb region of the G19833 genome sequence. Annotation of this target region revealed eight genes: three phosphoinositide-specific phospholipases C (PI-PLC), one zinc finger protein and four kinases, suggesting that Co-x is not a classical nucleotide-binding leucine-rich encoding gene. In addition, we identified and characterized the seven members of common bean PI-PLC gene family distributed into two clusters located at the ends of chromosomes 1 and 8. Co-x is not a member of Co-1 allelic series since these two genes are separated by at least 190 kb. Comparative analysis between soybean and common bean revealed that the Co-x syntenic region, located at one end of Glycine max chromosome 18, carries Rhg1, a major QTL contributing to soybean cyst nematode resistance. The PCR-based markers generated in this study should be useful in marker-assisted selection for pyramiding Co-x with other R genes.
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Affiliation(s)
- Manon M S Richard
- CNRS, Institut de Biologie des Plantes, UMR 8618, Université Paris Sud, Saclay Plant Sciences (SPS), Rue Noetzlin, 91405, Orsay, France
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20
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Schmutz J, McClean PE, Mamidi S, Wu GA, Cannon SB, Grimwood J, Jenkins J, Shu S, Song Q, Chavarro C, Torres-Torres M, Geffroy V, Moghaddam SM, Gao D, Abernathy B, Barry K, Blair M, Brick MA, Chovatia M, Gepts P, Goodstein DM, Gonzales M, Hellsten U, Hyten DL, Jia G, Kelly JD, Kudrna D, Lee R, Richard MMS, Miklas PN, Osorno JM, Rodrigues J, Thareau V, Urrea CA, Wang M, Yu Y, Zhang M, Wing RA, Cregan PB, Rokhsar DS, Jackson SA. A reference genome for common bean and genome-wide analysis of dual domestications. Nat Genet 2014; 46:707-13. [PMID: 24908249 PMCID: PMC7048698 DOI: 10.1038/ng.3008] [Citation(s) in RCA: 690] [Impact Index Per Article: 69.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Accepted: 05/15/2014] [Indexed: 01/13/2023]
Abstract
Common bean (Phaseolus vulgaris L.) is the most important grain legume for human consumption and has a role in sustainable agriculture owing to its ability to fix atmospheric nitrogen. We assembled 473 Mb of the 587-Mb genome and genetically anchored 98% of this sequence in 11 chromosome-scale pseudomolecules. We compared the genome for the common bean against the soybean genome to find changes in soybean resulting from polyploidy. Using resequencing of 60 wild individuals and 100 landraces from the genetically differentiated Mesoamerican and Andean gene pools, we confirmed 2 independent domestications from genetic pools that diverged before human colonization. Less than 10% of the 74 Mb of sequence putatively involved in domestication was shared by the two domestication events. We identified a set of genes linked with increased leaf and seed size and combined these results with quantitative trait locus data from Mesoamerican cultivars. Genes affected by domestication may be useful for genomics-enabled crop improvement.
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Affiliation(s)
- Jeremy Schmutz
- US Department of Energy Joint Genome Institute, Walnut Creek, California USA
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama USA
| | - Phillip E McClean
- Department of Plant Sciences, North Dakota State University, Fargo, North Dakota USA
| | - Sujan Mamidi
- Department of Plant Sciences, North Dakota State University, Fargo, North Dakota USA
| | - G Albert Wu
- US Department of Energy Joint Genome Institute, Walnut Creek, California USA
| | - Steven B Cannon
- US Department of Agriculture–Agricultural Research Service, Corn Insects and Crop Genetics Research Unit, Ames, Iowa USA
| | - Jane Grimwood
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama USA
| | - Jerry Jenkins
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama USA
| | - Shengqiang Shu
- US Department of Energy Joint Genome Institute, Walnut Creek, California USA
| | - Qijian Song
- US Department of Agriculture–Agricultural Research Service, Soybean Genomics and Improvement Laboratory, Beltsville, Maryland USA
| | - Carolina Chavarro
- Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia USA
| | | | - Valerie Geffroy
- CNRS, Université Paris–Sud, Institut de Biologie des Plantes, UMR 8618, Saclay Plant Sciences (SPS), Orsay, France
- Institut National de la Recherche Agronomique (INRA), Université Paris–Sud, Unité Mixte de Recherche de Génétique Végétale, Gif-sur-Yvette, France
| | - Samira Mafi Moghaddam
- Department of Plant Sciences, North Dakota State University, Fargo, North Dakota USA
| | - Dongying Gao
- Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia USA
| | - Brian Abernathy
- Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia USA
| | - Kerrie Barry
- US Department of Energy Joint Genome Institute, Walnut Creek, California USA
| | - Matthew Blair
- Department of Agricultural and Natural Sciences, Tennessee State University, Nashville, Tennessee USA
| | - Mark A Brick
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado USA
| | - Mansi Chovatia
- US Department of Energy Joint Genome Institute, Walnut Creek, California USA
| | - Paul Gepts
- Department of Plant Sciences, University of California, Davis, Davis, California USA
| | - David M Goodstein
- US Department of Energy Joint Genome Institute, Walnut Creek, California USA
| | - Michael Gonzales
- Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia USA
| | - Uffe Hellsten
- US Department of Energy Joint Genome Institute, Walnut Creek, California USA
| | - David L Hyten
- US Department of Agriculture–Agricultural Research Service, Soybean Genomics and Improvement Laboratory, Beltsville, Maryland USA
- Present Address: Present addresses: Pioneer Hi-Bred International, Inc., Johnston, Iowa, USA (D.L.H.) and Genética e Melhoramento, Federal University of Viçosa, Viçosa, Brazil (J.R.).,
| | - Gaofeng Jia
- US Department of Agriculture–Agricultural Research Service, Soybean Genomics and Improvement Laboratory, Beltsville, Maryland USA
| | - James D Kelly
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, Michigan USA
| | - Dave Kudrna
- Arizona Genomics Institute, University of Arizona, Tucson, Arizona USA
| | - Rian Lee
- Department of Plant Sciences, North Dakota State University, Fargo, North Dakota USA
| | - Manon M S Richard
- CNRS, Université Paris–Sud, Institut de Biologie des Plantes, UMR 8618, Saclay Plant Sciences (SPS), Orsay, France
| | - Phillip N Miklas
- US Department of Agriculture–Agricultural Research Service, Vegetable and Forage Crop Research Unit, Prosser, Washington USA
| | - Juan M Osorno
- Department of Plant Sciences, North Dakota State University, Fargo, North Dakota USA
| | - Josiane Rodrigues
- US Department of Agriculture–Agricultural Research Service, Soybean Genomics and Improvement Laboratory, Beltsville, Maryland USA
- Present Address: Present addresses: Pioneer Hi-Bred International, Inc., Johnston, Iowa, USA (D.L.H.) and Genética e Melhoramento, Federal University of Viçosa, Viçosa, Brazil (J.R.).,
| | - Vincent Thareau
- CNRS, Université Paris–Sud, Institut de Biologie des Plantes, UMR 8618, Saclay Plant Sciences (SPS), Orsay, France
| | - Carlos A Urrea
- Panhandle Research and Extension Center, University of Nebraska, Scottsbluff, Nebraska USA
| | - Mei Wang
- US Department of Energy Joint Genome Institute, Walnut Creek, California USA
| | - Yeisoo Yu
- Arizona Genomics Institute, University of Arizona, Tucson, Arizona USA
| | - Ming Zhang
- US Department of Energy Joint Genome Institute, Walnut Creek, California USA
| | - Rod A Wing
- Arizona Genomics Institute, University of Arizona, Tucson, Arizona USA
| | - Perry B Cregan
- US Department of Agriculture–Agricultural Research Service, Soybean Genomics and Improvement Laboratory, Beltsville, Maryland USA
| | - Daniel S Rokhsar
- US Department of Energy Joint Genome Institute, Walnut Creek, California USA
| | - Scott A Jackson
- Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia USA
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Campa A, Rodríguez-Suárez C, Giraldez R, Ferreira JJ. Genetic analysis of the response to eleven Colletotrichum lindemuthianum races in a RIL population of common bean (Phaseolus vulgaris L.). BMC PLANT BIOLOGY 2014; 14:115. [PMID: 24779442 PMCID: PMC4021056 DOI: 10.1186/1471-2229-14-115] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2014] [Accepted: 04/17/2014] [Indexed: 05/03/2023]
Abstract
BACKGROUND Bean anthracnose is caused by the fungus Colletotrichum lindemuthianum (Sacc. & Magnus) Lams.- Scrib. Resistance to C. lindemuthianum in common bean (Phaseolus vulgaris L.) generally follows a qualitative mode of inheritance. The pathogen shows extensive pathogenic variation and up to 20 anthracnose resistance loci (named Co-), conferring resistance to specific races, have been described. Anthracnose resistance has generally been investigated by analyzing a limited number of isolates or races in segregating populations. In this work, we analyzed the response against eleven C. lindemuthianum races in a recombinant inbred line (RIL) common bean population derived from the cross Xana × Cornell 49242 in which a saturated linkage map was previously developed. RESULTS A systematic genetic analysis was carried out to dissect the complex resistance segregations observed, which included contingency analyses, subpopulations and genetic mapping. Twenty two resistance genes were identified, some with a complementary mode of action. The Cornell 49242 genotype carries a complex cluster of resistance genes at the end of linkage group (LG) Pv11 corresponding to the previously described anthracnose resistance cluster Co-2. In this position, specific resistance genes to races 3, 6, 7, 19, 38, 39, 65, 357, 449 and 453 were identified, with one of them showing a complementary mode of action. In addition, Cornell 49242 had an independent gene on LG Pv09 showing a complementary mode of action for resistance to race 453. Resistance genes in genotype Xana were located on three regions involving LGs Pv01, Pv02 and Pv04. All resistance genes identified in Xana showed a complementary mode of action, except for two controlling resistance to races 65 and 73 located on LG Pv01, in the position of the previously described anthracnose resistance cluster Co-1. CONCLUSIONS Results shown herein reveal a complex and specific interaction between bean and fungus genotypes leading to anthracnose resistance. Organization of specific resistance genes in clusters including resistance genes with different modes of action (dominant and complementary genes) was also confirmed. Finally, new locations for anthracnose resistance genes were identified in LG Pv09.
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Affiliation(s)
- Ana Campa
- Área de Cultivos Hortofrutícolas y Forestales, SERIDA, Apdo. 13, 33300 Villaviciosa, Asturias, Spain
| | | | - Ramón Giraldez
- Department of Functional Biology, University of Oviedo, 33006 Oviedo, Spain
| | - Juan José Ferreira
- Área de Cultivos Hortofrutícolas y Forestales, SERIDA, Apdo. 13, 33300 Villaviciosa, Asturias, Spain
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22
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Richard MMS, Chen NWG, Thareau V, Pflieger S, Blanchet S, Pedrosa-Harand A, Iwata A, Chavarro C, Jackson SA, Geffroy V. The Subtelomeric khipu Satellite Repeat from Phaseolus vulgaris: Lessons Learned from the Genome Analysis of the Andean Genotype G19833. FRONTIERS IN PLANT SCIENCE 2013; 4:109. [PMID: 24137164 PMCID: PMC3797529 DOI: 10.3389/fpls.2013.00109] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2013] [Accepted: 04/09/2013] [Indexed: 05/10/2023]
Abstract
Subtelomeric regions in eukaryotic organisms are known for harboring species-specific tandemly repeated satellite sequences. However, studies on the molecular organization and evolution of subtelomeric repeats are scarce, especially in plants. Khipu is a satellite DNA of 528-bp repeat unit, specific of the Phaseolus genus, with a subtelomeric distribution in common bean, P. vulgaris. To investigate the genomic organization and the evolution of khipu, we performed genome-wide analysis on the complete genome sequence of the common bean genotype G19833. We identified 2,460 khipu units located at most distal ends of the sequenced regions. Khipu units are arranged in discrete blocks of 2-55 copies and are heterogeneously distributed among the different chromosome ends of G19833 (from 0 to 555 khipus units per chromosome arm). Phylogenetically related khipu units are spread between numerous chromosome ends, suggesting frequent exchanges between non-homologous subtelomeres. However, most subclades contain numerous khipu units from only one or few chromosome ends indicating that local duplication is also driving khipu expansion. Unexpectedly, we also identified 81 khipu units located at centromeres. All the centromeric khipu units belong to a single divergent clade also comprised of a few units from several subtelomeres, suggesting that a few sequence exchanges between centromeres and subtelomeres took place in the common bean genome. The divergence and low copy number of these centromeric units from the subtelomeric units could explain why they were not detected by FISH (Fluorescence in situ Hybridization) although it can not be excluded that these centromeric units may have resulted from errors in the pseudomolecule assembly. Altogether our data highlight extensive sequence exchanges in subtelomeres between non-homologous chromosomes in common bean and confirm that subtelomeres represent one of the most dynamic and rapidly evolving regions in eukaryotic genomes.
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Affiliation(s)
- Manon M. S. Richard
- UMR-CNRS 8618, Saclay Plant Sciences, Institut de Biologie des Plantes, Université Paris SudOrsay Cedex, France
| | - Nicolas W. G. Chen
- UMR-CNRS 8618, Saclay Plant Sciences, Institut de Biologie des Plantes, Université Paris SudOrsay Cedex, France
| | - Vincent Thareau
- UMR-CNRS 8618, Saclay Plant Sciences, Institut de Biologie des Plantes, Université Paris SudOrsay Cedex, France
| | - Stéphanie Pflieger
- UMR-CNRS 8618, Saclay Plant Sciences, Institut de Biologie des Plantes, Université Paris SudOrsay Cedex, France
- Université Paris Diderot, Sorbonne Paris CitéParis, France
| | - Sophie Blanchet
- UMR-CNRS 8618, Saclay Plant Sciences, Institut de Biologie des Plantes, Université Paris SudOrsay Cedex, France
| | - Andrea Pedrosa-Harand
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Universidade Federal de Pernambuco, Rua Nelson Chaves s/nRecife, Pernambuco, Brazil
| | - Aiko Iwata
- Center for Applied Genetic Technologies, Institute for Plant Breeding, Genetics, and Genomics, University of GeorgiaAthens, GA, USA
| | - Carolina Chavarro
- Center for Applied Genetic Technologies, Institute for Plant Breeding, Genetics, and Genomics, University of GeorgiaAthens, GA, USA
| | - Scott A. Jackson
- Center for Applied Genetic Technologies, Institute for Plant Breeding, Genetics, and Genomics, University of GeorgiaAthens, GA, USA
| | - Valérie Geffroy
- UMR-CNRS 8618, Saclay Plant Sciences, Institut de Biologie des Plantes, Université Paris SudOrsay Cedex, France
- Unité Mixte de Recherche de Génétique Végétale, Institut National de la Recherche AgronomiqueGif-sur-Yvette, France
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23
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Pérez-Vega E, Trabanco N, Campa A, Ferreira JJ. Genetic mapping of two genes conferring resistance to powdery mildew in common bean (Phaseolus vulgaris L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2013; 126:1503-1512. [PMID: 23456179 DOI: 10.1007/s00122-013-2068-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Accepted: 02/08/2013] [Indexed: 06/01/2023]
Abstract
Powdery mildew (PM) is a serious disease in many legume species, including the common bean (Phaseolus vulgaris L.). This study investigated the genetic control behind resistance reaction to PM in the bean genotype, Cornell 49242. The results revealed evidence supporting a qualitative mode of inheritance for resistance and the involvement of two independent genes in the resistance reaction. The location of these resistance genes was investigated in a linkage genetic map developed for the XC RIL population. Contingency tests revealed significant associations for 28 loci out of a total of 329 mapped loci. Fifteen were isolated or formed groups with less than two loci. The thirteen remaining loci were located at three regions in linkage groups Pv04, Pv09, and Pv11. The involvement of Pv09 was discarded due to the observed segregation in the subpopulation obtained from the Xana genotype for the loci located in this region. In contrast, the two subpopulations obtained from the Xana genotype for the BM161 locus, linked to the Co-3/9 anthracnose resistance gene (Pv04), and from the Xana genotype for the SCAReoli locus, linked to the Co-2 anthracnose resistance gene (Pv11), exhibited monogenic segregations, suggesting that both regions were involved in the genetic control of resistance. A genetic dissection was carried out to verify the involvement of both regions in the reaction to PM. Two resistant recombinant lines were selected, according to their genotypes, for the block of loci included in the Co-2 and Co-3/9 regions, and they were crossed with the susceptible parent, Xana. Linkage analysis in the respective F2 populations supported the hypothesis that a dominant gene (Pm1) was located in the linkage group Pv11 and another gene (Pm2) was located in the linkage group Pv04. This is the first report showing the localization of resistance genes against powdery mildew in Phaseolus vulgaris and the results offer the opportunity to increase the efficiency of breeding programs by means of marker-assisted selection.
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Affiliation(s)
- Elena Pérez-Vega
- Área de Cultivos Hortofrutícolas y Forestales, Servicio Regional de Investigación y Desarrollo Agroalimentario (SERIDA), 33300 Villaviciosa, Asturias, Spain
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24
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Ashfield T, Egan AN, Pfeil BE, Chen NW, Podicheti R, Ratnaparkhe MB, Ameline-Torregrosa C, Denny R, Cannon S, Doyle JJ, Geffroy V, Roe BA, Saghai Maroof M, Young ND, Innes RW. Evolution of a complex disease resistance gene cluster in diploid Phaseolus and tetraploid Glycine. PLANT PHYSIOLOGY 2012; 159:336-54. [PMID: 22457424 PMCID: PMC3375969 DOI: 10.1104/pp.112.195040] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2012] [Accepted: 03/22/2012] [Indexed: 05/20/2023]
Abstract
We used a comparative genomics approach to investigate the evolution of a complex nucleotide-binding (NB)-leucine-rich repeat (LRR) gene cluster found in soybean (Glycine max) and common bean (Phaseolus vulgaris) that is associated with several disease resistance (R) genes of known function, including Rpg1b (for Resistance to Pseudomonas glycinea1b), an R gene effective against specific races of bacterial blight. Analysis of domains revealed that the amino-terminal coiled-coil (CC) domain, central nucleotide-binding domain (NB-ARC [for APAF1, Resistance genes, and CED4]), and carboxyl-terminal LRR domain have undergone distinct evolutionary paths. Sequence exchanges within the NB-ARC domain were rare. In contrast, interparalogue exchanges involving the CC and LRR domains were common, consistent with both of these regions coevolving with pathogens. Residues under positive selection were overrepresented within the predicted solvent-exposed face of the LRR domain, although several also were detected within the CC and NB-ARC domains. Superimposition of these latter residues onto predicted tertiary structures revealed that the majority are located on the surface, suggestive of a role in interactions with other domains or proteins. Following polyploidy in the Glycine lineage, NB-LRR genes have been preferentially lost from one of the duplicated chromosomes (homeologues found in soybean), and there has been partitioning of NB-LRR clades between the two homeologues. The single orthologous region in common bean contains approximately the same number of paralogues as found in the two soybean homeologues combined. We conclude that while polyploidization in Glycine has not driven a stable increase in family size for NB-LRR genes, it has generated two recombinationally isolated clusters, one of which appears to be in the process of decay.
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Affiliation(s)
| | | | | | - Nicolas W.G. Chen
- Department of Biology, Indiana University, Bloomington, Indiana 47405 (T.A., R.P., R.W.I.); Department of Biology, East Carolina University, Greenville, North Carolina 27858 (A.N.E.); L.H. Bailey Hortorium, Department of Plant Biology, Cornell University, Ithaca, New York 14853 (B.E.P., J.J.D.); Institut de Biotechnologie des Plantes, Université Paris Sud, Saclay Plant Sciences, 91405 Orsay cedex, France (N.W.G.C., V.G.); Department of Crop and Soil Environmental Sciences, Virginia Tech, Blacksburg, Virginia 24061 (M.B.R., M.A.S.M.); Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota 55108 (C.A.-T., R.D., N.D.Y.); United States Department of Agriculture-Agricultural Research Service and Department of Agronomy, Iowa State University, Ames, Iowa 50011 (S.C.); Unité Mixte de Recherche de Génétique Végétale, Institut National de la Recherche Scientifique, 91190 Gif-sur-Yvette, France (V.G.); Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019 (B.A.R.)
| | - Ram Podicheti
- Department of Biology, Indiana University, Bloomington, Indiana 47405 (T.A., R.P., R.W.I.); Department of Biology, East Carolina University, Greenville, North Carolina 27858 (A.N.E.); L.H. Bailey Hortorium, Department of Plant Biology, Cornell University, Ithaca, New York 14853 (B.E.P., J.J.D.); Institut de Biotechnologie des Plantes, Université Paris Sud, Saclay Plant Sciences, 91405 Orsay cedex, France (N.W.G.C., V.G.); Department of Crop and Soil Environmental Sciences, Virginia Tech, Blacksburg, Virginia 24061 (M.B.R., M.A.S.M.); Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota 55108 (C.A.-T., R.D., N.D.Y.); United States Department of Agriculture-Agricultural Research Service and Department of Agronomy, Iowa State University, Ames, Iowa 50011 (S.C.); Unité Mixte de Recherche de Génétique Végétale, Institut National de la Recherche Scientifique, 91190 Gif-sur-Yvette, France (V.G.); Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019 (B.A.R.)
| | | | - Carine Ameline-Torregrosa
- Department of Biology, Indiana University, Bloomington, Indiana 47405 (T.A., R.P., R.W.I.); Department of Biology, East Carolina University, Greenville, North Carolina 27858 (A.N.E.); L.H. Bailey Hortorium, Department of Plant Biology, Cornell University, Ithaca, New York 14853 (B.E.P., J.J.D.); Institut de Biotechnologie des Plantes, Université Paris Sud, Saclay Plant Sciences, 91405 Orsay cedex, France (N.W.G.C., V.G.); Department of Crop and Soil Environmental Sciences, Virginia Tech, Blacksburg, Virginia 24061 (M.B.R., M.A.S.M.); Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota 55108 (C.A.-T., R.D., N.D.Y.); United States Department of Agriculture-Agricultural Research Service and Department of Agronomy, Iowa State University, Ames, Iowa 50011 (S.C.); Unité Mixte de Recherche de Génétique Végétale, Institut National de la Recherche Scientifique, 91190 Gif-sur-Yvette, France (V.G.); Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019 (B.A.R.)
| | - Roxanne Denny
- Department of Biology, Indiana University, Bloomington, Indiana 47405 (T.A., R.P., R.W.I.); Department of Biology, East Carolina University, Greenville, North Carolina 27858 (A.N.E.); L.H. Bailey Hortorium, Department of Plant Biology, Cornell University, Ithaca, New York 14853 (B.E.P., J.J.D.); Institut de Biotechnologie des Plantes, Université Paris Sud, Saclay Plant Sciences, 91405 Orsay cedex, France (N.W.G.C., V.G.); Department of Crop and Soil Environmental Sciences, Virginia Tech, Blacksburg, Virginia 24061 (M.B.R., M.A.S.M.); Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota 55108 (C.A.-T., R.D., N.D.Y.); United States Department of Agriculture-Agricultural Research Service and Department of Agronomy, Iowa State University, Ames, Iowa 50011 (S.C.); Unité Mixte de Recherche de Génétique Végétale, Institut National de la Recherche Scientifique, 91190 Gif-sur-Yvette, France (V.G.); Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019 (B.A.R.)
| | - Steven Cannon
- Department of Biology, Indiana University, Bloomington, Indiana 47405 (T.A., R.P., R.W.I.); Department of Biology, East Carolina University, Greenville, North Carolina 27858 (A.N.E.); L.H. Bailey Hortorium, Department of Plant Biology, Cornell University, Ithaca, New York 14853 (B.E.P., J.J.D.); Institut de Biotechnologie des Plantes, Université Paris Sud, Saclay Plant Sciences, 91405 Orsay cedex, France (N.W.G.C., V.G.); Department of Crop and Soil Environmental Sciences, Virginia Tech, Blacksburg, Virginia 24061 (M.B.R., M.A.S.M.); Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota 55108 (C.A.-T., R.D., N.D.Y.); United States Department of Agriculture-Agricultural Research Service and Department of Agronomy, Iowa State University, Ames, Iowa 50011 (S.C.); Unité Mixte de Recherche de Génétique Végétale, Institut National de la Recherche Scientifique, 91190 Gif-sur-Yvette, France (V.G.); Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019 (B.A.R.)
| | - Jeff J. Doyle
- Department of Biology, Indiana University, Bloomington, Indiana 47405 (T.A., R.P., R.W.I.); Department of Biology, East Carolina University, Greenville, North Carolina 27858 (A.N.E.); L.H. Bailey Hortorium, Department of Plant Biology, Cornell University, Ithaca, New York 14853 (B.E.P., J.J.D.); Institut de Biotechnologie des Plantes, Université Paris Sud, Saclay Plant Sciences, 91405 Orsay cedex, France (N.W.G.C., V.G.); Department of Crop and Soil Environmental Sciences, Virginia Tech, Blacksburg, Virginia 24061 (M.B.R., M.A.S.M.); Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota 55108 (C.A.-T., R.D., N.D.Y.); United States Department of Agriculture-Agricultural Research Service and Department of Agronomy, Iowa State University, Ames, Iowa 50011 (S.C.); Unité Mixte de Recherche de Génétique Végétale, Institut National de la Recherche Scientifique, 91190 Gif-sur-Yvette, France (V.G.); Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019 (B.A.R.)
| | - Valérie Geffroy
- Department of Biology, Indiana University, Bloomington, Indiana 47405 (T.A., R.P., R.W.I.); Department of Biology, East Carolina University, Greenville, North Carolina 27858 (A.N.E.); L.H. Bailey Hortorium, Department of Plant Biology, Cornell University, Ithaca, New York 14853 (B.E.P., J.J.D.); Institut de Biotechnologie des Plantes, Université Paris Sud, Saclay Plant Sciences, 91405 Orsay cedex, France (N.W.G.C., V.G.); Department of Crop and Soil Environmental Sciences, Virginia Tech, Blacksburg, Virginia 24061 (M.B.R., M.A.S.M.); Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota 55108 (C.A.-T., R.D., N.D.Y.); United States Department of Agriculture-Agricultural Research Service and Department of Agronomy, Iowa State University, Ames, Iowa 50011 (S.C.); Unité Mixte de Recherche de Génétique Végétale, Institut National de la Recherche Scientifique, 91190 Gif-sur-Yvette, France (V.G.); Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019 (B.A.R.)
| | - Bruce A. Roe
- Department of Biology, Indiana University, Bloomington, Indiana 47405 (T.A., R.P., R.W.I.); Department of Biology, East Carolina University, Greenville, North Carolina 27858 (A.N.E.); L.H. Bailey Hortorium, Department of Plant Biology, Cornell University, Ithaca, New York 14853 (B.E.P., J.J.D.); Institut de Biotechnologie des Plantes, Université Paris Sud, Saclay Plant Sciences, 91405 Orsay cedex, France (N.W.G.C., V.G.); Department of Crop and Soil Environmental Sciences, Virginia Tech, Blacksburg, Virginia 24061 (M.B.R., M.A.S.M.); Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota 55108 (C.A.-T., R.D., N.D.Y.); United States Department of Agriculture-Agricultural Research Service and Department of Agronomy, Iowa State University, Ames, Iowa 50011 (S.C.); Unité Mixte de Recherche de Génétique Végétale, Institut National de la Recherche Scientifique, 91190 Gif-sur-Yvette, France (V.G.); Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019 (B.A.R.)
| | - M.A. Saghai Maroof
- Department of Biology, Indiana University, Bloomington, Indiana 47405 (T.A., R.P., R.W.I.); Department of Biology, East Carolina University, Greenville, North Carolina 27858 (A.N.E.); L.H. Bailey Hortorium, Department of Plant Biology, Cornell University, Ithaca, New York 14853 (B.E.P., J.J.D.); Institut de Biotechnologie des Plantes, Université Paris Sud, Saclay Plant Sciences, 91405 Orsay cedex, France (N.W.G.C., V.G.); Department of Crop and Soil Environmental Sciences, Virginia Tech, Blacksburg, Virginia 24061 (M.B.R., M.A.S.M.); Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota 55108 (C.A.-T., R.D., N.D.Y.); United States Department of Agriculture-Agricultural Research Service and Department of Agronomy, Iowa State University, Ames, Iowa 50011 (S.C.); Unité Mixte de Recherche de Génétique Végétale, Institut National de la Recherche Scientifique, 91190 Gif-sur-Yvette, France (V.G.); Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019 (B.A.R.)
| | - Nevin D. Young
- Department of Biology, Indiana University, Bloomington, Indiana 47405 (T.A., R.P., R.W.I.); Department of Biology, East Carolina University, Greenville, North Carolina 27858 (A.N.E.); L.H. Bailey Hortorium, Department of Plant Biology, Cornell University, Ithaca, New York 14853 (B.E.P., J.J.D.); Institut de Biotechnologie des Plantes, Université Paris Sud, Saclay Plant Sciences, 91405 Orsay cedex, France (N.W.G.C., V.G.); Department of Crop and Soil Environmental Sciences, Virginia Tech, Blacksburg, Virginia 24061 (M.B.R., M.A.S.M.); Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota 55108 (C.A.-T., R.D., N.D.Y.); United States Department of Agriculture-Agricultural Research Service and Department of Agronomy, Iowa State University, Ames, Iowa 50011 (S.C.); Unité Mixte de Recherche de Génétique Végétale, Institut National de la Recherche Scientifique, 91190 Gif-sur-Yvette, France (V.G.); Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019 (B.A.R.)
| | - Roger W. Innes
- Department of Biology, Indiana University, Bloomington, Indiana 47405 (T.A., R.P., R.W.I.); Department of Biology, East Carolina University, Greenville, North Carolina 27858 (A.N.E.); L.H. Bailey Hortorium, Department of Plant Biology, Cornell University, Ithaca, New York 14853 (B.E.P., J.J.D.); Institut de Biotechnologie des Plantes, Université Paris Sud, Saclay Plant Sciences, 91405 Orsay cedex, France (N.W.G.C., V.G.); Department of Crop and Soil Environmental Sciences, Virginia Tech, Blacksburg, Virginia 24061 (M.B.R., M.A.S.M.); Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota 55108 (C.A.-T., R.D., N.D.Y.); United States Department of Agriculture-Agricultural Research Service and Department of Agronomy, Iowa State University, Ames, Iowa 50011 (S.C.); Unité Mixte de Recherche de Génétique Végétale, Institut National de la Recherche Scientifique, 91190 Gif-sur-Yvette, France (V.G.); Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019 (B.A.R.)
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Hou S, Mu R, Ma G, Xu X, Zhang C, Yang Y, Wu D. Pseudomonas syringae pv. phaseolicola effector HopF1 inhibits pathogen-associated molecular pattern-triggered immunity in a RIN4-independent manner in common bean (Phaseolus vulgaris). FEMS Microbiol Lett 2011; 323:35-43. [PMID: 22092678 DOI: 10.1111/j.1574-6968.2011.02356.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2011] [Revised: 05/09/2011] [Accepted: 06/30/2011] [Indexed: 01/14/2023] Open
Abstract
Plant pathogens usually promote pathogenesis by secreting effector proteins into host plant cells. One of the secreted effectors of Pseudomonas syringae pv. phaseolicola, the causative agent of halo-blight disease in common bean (Phaseolus vulgaris), HopF1, activates effector-triggered immunity (ETI) in a bean cultivar containing R1 resistance gene, but displays virulence function in a bean cultivar without the R1 gene. The virulence mechanism of the effector remained unknown, although it was identified more than a decade ago. Here we demonstrated that HopF1 can inhibit pathogen-associated molecular pattern-triggered immunity (PTI) in a susceptible bean cultivar Tendergreen. HopF1 directly interacted with two RPM1-interacting protein 4 (RIN4) orthologs of bean, PvRIN4a and PvRIN4b. Like RIN4 in Arabidopsis, both PvRIN4 orthologs negatively regulated the PTI responses in bean. However, the virulence function of HopF1 was enhanced in Tendergreen silencing PvRIN4. Furthermore, silencing PvRIN4a compromised the avrβ1-induced hypersensitive response (HR), which previously was reported to be suppressed by HopF1. Together, these results demonstrated that PvRIN4 orthologs were not the virulence target of HopF1 for inhibiting PTI, but probably for interfering with ETI.
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Affiliation(s)
- Shuguo Hou
- School of Municipal and Environmental Engineering, Shandong jianzhu University, Jinan, China.
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