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A Comprehensive Transcriptional Profiling of Pepper Responses to Root-Knot Nematode. Genes (Basel) 2020; 11:genes11121507. [PMID: 33333784 PMCID: PMC7765216 DOI: 10.3390/genes11121507] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 12/09/2020] [Accepted: 12/10/2020] [Indexed: 02/06/2023] Open
Abstract
Genetic resistance remains a key component in integrated pest management systems. The cosmopolitan root-knot nematode (RKN; Meloidogyne spp.) proves a significant management challenge as virulence and pathogenicity vary among and within species. RKN greatly reduces commercial bell pepper yield, and breeding programs continuously develop cultivars to emerging nematode threats. However, there is a lack of knowledge concerning the nature and forms of nematode resistance. Defining how resistant and susceptible pepper cultivars mount defenses against RKN attacks can help inform breeding programs. Here, we characterized the transcriptional responses of the highly related resistant (Charleston Belle) and susceptible (Keystone Resistance Giant) pepper cultivars throughout early nematode infection stages. Comprehensive transcriptomic sequencing of resistant and susceptible cultivar roots with or without Meloidogyneincognita infection over three-time points; covering early penetration (1-day), through feeding site maintenance (7-days post-inoculation), produced > 300 million high quality reads. Close examination of chromosome P9, on which nematode resistance hotspots are located, showed more differentially expressed genes were upregulated in resistant cultivar at day 1 when compared to the susceptible cultivar. Our comprehensive approach to transcriptomic profiling of pepper resistance revealed novel insights into how RKN causes disease and the plant responses mounted to counter nematode attack. This work broadens the definition of resistance from a single loci concept to a more complex array of interrelated pathways. Focus on these pathways in breeding programs may provide more sustainable and enduring forms of resistance.
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Correlation Between Volatile Compounds and Spiciness in Domesticated and Wild Fresh Chili Peppers. FOOD BIOPROCESS TECH 2019. [DOI: 10.1007/s11947-019-02297-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Slootweg EJ, Spiridon LN, Martin EC, Tameling WIL, Townsend PD, Pomp R, Roosien J, Drawska O, Sukarta OCA, Schots A, Borst JW, Joosten MHAJ, Bakker J, Smant G, Cann MJ, Petrescu AJ, Goverse A. Distinct Roles of Non-Overlapping Surface Regions of the Coiled-Coil Domain in the Potato Immune Receptor Rx1. PLANT PHYSIOLOGY 2018; 178:1310-1331. [PMID: 30194238 PMCID: PMC6236623 DOI: 10.1104/pp.18.00603] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 08/28/2018] [Indexed: 05/20/2023]
Abstract
The intracellular immune receptor Rx1 of potato (Solanum tuberosum), which confers effector-triggered immunity to Potato virus X, consists of a central nucleotide-binding domain (NB-ARC) flanked by a carboxyl-terminal leucine-rich repeat (LRR) domain and an amino-terminal coiled-coil (CC) domain. Rx1 activity is strictly regulated by interdomain interactions between the NB-ARC and LRR, but the contribution of the CC domain in regulating Rx1 activity or immune signaling is not fully understood. Therefore, we used a structure-informed approach to investigate the role of the CC domain in Rx1 functionality. Targeted mutagenesis of CC surface residues revealed separate regions required for the intramolecular and intermolecular interaction of the CC with the NB-ARC-LRR and the cofactor Ran GTPase-activating protein2 (RanGAP2), respectively. None of the mutant Rx1 proteins was constitutively active, indicating that the CC does not contribute to the autoinhibition of Rx1 activity. Instead, the CC domain acted as a modulator of downstream responses involved in effector-triggered immunity. Systematic disruption of the hydrophobic interface between the four helices of the CC enabled the uncoupling of cell death and disease resistance responses. Moreover, a strong dominant negative effect on Rx1-mediated resistance and cell death was observed upon coexpression of the CC alone with full-length Rx1 protein, which depended on the RanGAP2-binding surface of the CC. Surprisingly, coexpression of the N-terminal half of the CC enhanced Rx1-mediated resistance, which further indicated that the CC functions as a scaffold for downstream components involved in the modulation of disease resistance or cell death signaling.
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Affiliation(s)
- Erik J Slootweg
- Laboratory of Nematology, Department of Plant Sciences, Wageningen University, 6708 PB Wageningen, The Netherlands
| | | | - Eliza C Martin
- Institute of Biochemistry of the Romanian Academy, 060031 Bucharest, Romania
| | - Wladimir I L Tameling
- Laboratory of Phytopathology, Department of Plant Sciences, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Philip D Townsend
- Department of Biosciences and Biophysical Sciences Institute, Durham University, Durham DH1 3LE, United Kingdom
| | - Rikus Pomp
- Laboratory of Nematology, Department of Plant Sciences, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Jan Roosien
- Laboratory of Nematology, Department of Plant Sciences, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Olga Drawska
- Laboratory of Nematology, Department of Plant Sciences, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Octavina C A Sukarta
- Laboratory of Nematology, Department of Plant Sciences, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Arjen Schots
- Laboratory of Nematology, Department of Plant Sciences, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Jan Willem Borst
- Laboratory of Biochemistry/Microspectroscopy Centre, Department of Agrotechnology and Food Sciences, Wageningen University, 6708 WE Wageningen, The Netherlands
| | - Matthieu H A J Joosten
- Laboratory of Phytopathology, Department of Plant Sciences, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Jaap Bakker
- Laboratory of Nematology, Department of Plant Sciences, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Geert Smant
- Laboratory of Nematology, Department of Plant Sciences, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Martin J Cann
- Department of Biosciences and Biophysical Sciences Institute, Durham University, Durham DH1 3LE, United Kingdom
| | | | - Aska Goverse
- Laboratory of Nematology, Department of Plant Sciences, Wageningen University, 6708 PB Wageningen, The Netherlands
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Sukarta OCA, Slootweg EJ, Goverse A. Structure-informed insights for NLR functioning in plant immunity. Semin Cell Dev Biol 2016; 56:134-149. [PMID: 27208725 DOI: 10.1016/j.semcdb.2016.05.012] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2016] [Revised: 05/11/2016] [Accepted: 05/17/2016] [Indexed: 01/07/2023]
Abstract
To respond to foreign invaders, plants have evolved a cell autonomous multilayered immune system consisting of extra- and intracellular immune receptors. Nucleotide binding and oligomerization domain (NOD)-like receptors (NLRs) mediate recognition of pathogen effectors inside the cell and trigger a host specific defense response, often involving controlled cell death. NLRs consist of a central nucleotide-binding domain, which is flanked by an N-terminal CC or TIR domain and a C-terminal leucine-rich repeat domain (LRR). These multidomain proteins function as a molecular switch and their activity is tightly controlled by intra and inter-molecular interactions. In contrast to metazoan NLRs, the structural basis underlying NLR functioning as a pathogen sensor and activator of immune responses in plants is largely unknown. However, the first crystal structures of a number of plant NLR domains were recently obtained. In addition, biochemical and structure-informed analyses revealed novel insights in the cooperation between NLR domains and the formation of pre- and post activation complexes, including the coordinated activity of NLR pairs as pathogen sensor and executor of immune responses. Moreover, the discovery of novel integrated domains underscores the structural diversity of NLRs and provides alternative models for how these immune receptors function in plants. In this review, we will highlight these recent advances to provide novel insights in the structural, biochemical and molecular aspects involved in plant NLR functioning.
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Affiliation(s)
- Octavina C A Sukarta
- Dept. of Plant Sciences, Laboratory of Nematology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands.
| | - Erik J Slootweg
- Dept. of Plant Sciences, Laboratory of Nematology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands.
| | - Aska Goverse
- Dept. of Plant Sciences, Laboratory of Nematology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands.
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Barbary A, Djian-Caporalino C, Marteu N, Fazari A, Caromel B, Castagnone-Sereno P, Palloix A. Plant Genetic Background Increasing the Efficiency and Durability of Major Resistance Genes to Root-knot Nematodes Can Be Resolved into a Few Resistance QTLs. FRONTIERS IN PLANT SCIENCE 2016; 7:632. [PMID: 27242835 PMCID: PMC4861812 DOI: 10.3389/fpls.2016.00632] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Accepted: 04/25/2016] [Indexed: 05/24/2023]
Abstract
With the banning of most chemical nematicides, the control of root-knot nematodes (RKNs) in vegetable crops is now based essentially on the deployment of single, major resistance genes (R-genes). However, these genes are rare and their efficacy is threatened by the capacity of RKNs to adapt. In pepper, several dominant R-genes are effective against RKNs, and their efficacy and durability have been shown to be greater in a partially resistant genetic background. However, the genetic determinants of this partial resistance were unknown. Here, a quantitative trait loci (QTL) analysis was performed on the F2:3 population from the cross between Yolo Wonder, an accession considered partially resistant or resistant, depending on the RKN species, and Doux Long des Landes, a susceptible cultivar. A genetic linkage map was constructed from 130 F2 individuals, and the 130 F3 families were tested for resistance to the three main RKN species, Meloidogyne incognita, M. arenaria, and M. javanica. For the first time in the pepper-RKN pathosystem, four major QTLs were identified and mapped to two clusters. The cluster on chromosome P1 includes three tightly linked QTLs with specific effects against individual RKN species. The fourth QTL, providing specific resistance to M. javanica, mapped to pepper chromosome P9, which is known to carry multiple NBS-LRR repeats, together with major R-genes for resistance to nematodes and other pathogens. The newly discovered cluster on chromosome P1 has a broad spectrum of action with major additive effects on resistance. These data highlight the role of host QTLs involved in plant-RKN interactions and provide innovative potential for the breeding of new pepper cultivars or rootstocks combining quantitative resistance and major R-genes, to increase both the efficacy and durability of RKN control by resistance genes.
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Affiliation(s)
- Arnaud Barbary
- INRA, University of Nice Sophia Antipolis, CNRS, UMR 1355-7254, Institut Sophia AgrobiotechSophia Antipolis, France
| | - Caroline Djian-Caporalino
- INRA, University of Nice Sophia Antipolis, CNRS, UMR 1355-7254, Institut Sophia AgrobiotechSophia Antipolis, France
| | - Nathalie Marteu
- INRA, University of Nice Sophia Antipolis, CNRS, UMR 1355-7254, Institut Sophia AgrobiotechSophia Antipolis, France
| | - Ariane Fazari
- INRA, University of Nice Sophia Antipolis, CNRS, UMR 1355-7254, Institut Sophia AgrobiotechSophia Antipolis, France
| | - Bernard Caromel
- INRA, UR1052, Génétique et Amélioration des Fruits et LégumesMontfavet, France
| | - Philippe Castagnone-Sereno
- INRA, University of Nice Sophia Antipolis, CNRS, UMR 1355-7254, Institut Sophia AgrobiotechSophia Antipolis, France
| | - Alain Palloix
- INRA, UR1052, Génétique et Amélioration des Fruits et LégumesMontfavet, France
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Barbary A, Djian-Caporalino C, Palloix A, Castagnone-Sereno P. Host genetic resistance to root-knot nematodes, Meloidogyne spp., in Solanaceae: from genes to the field. PEST MANAGEMENT SCIENCE 2015; 71:1591-1598. [PMID: 26248710 DOI: 10.1002/ps.4091] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Revised: 08/04/2015] [Accepted: 08/05/2015] [Indexed: 06/04/2023]
Abstract
Root-knot nematodes (RKNs) heavily damage most solanaceous crops worldwide. Fortunately, major resistance genes are available in a number of plant species, and their use provides a safe and economically relevant strategy for RKN control. From a structural point of view, these genes often harbour NBS-LRR motifs (i.e. a nucleotide binding site and a leucine rich repeat region near the carboxy terminus) and are organised in syntenic clusters in solanaceous genomes. Their introgression from wild to cultivated plants remains a challenge for breeders, although facilitated by marker-assisted selection. As shown with other pathosystems, the genetic background into which the resistance genes are introgressed is of prime importance to both the expression of the resistance and its durability, as exemplified by the recent discovery of quantitative trait loci conferring quantitative resistance to RKNs in pepper. The deployment of resistance genes at a large scale may result in the emergence and spread of virulent nematode populations able to overcome them, as already reported in tomato and pepper. Therefore, careful management of the resistance genes available in solanaceous crops is crucial to avoid significant reduction in the duration of RKN genetic control in the field. From that perspective, only rational management combining breeding and cultivation practices will allow the design and implementation of innovative, sustainable crop production systems that protect the resistance genes and maintain their durability.
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Affiliation(s)
- Arnaud Barbary
- INRA, Institut Sophia Agrobiotech, Sophia Antipolis, France
- Université de Nice Sophia Antipolis, Institut Sophia Agrobiotech, Sophia Antipolis, France
- CNRS, Institut Sophia Agrobiotech, Sophia Antipolis, France
| | - Caroline Djian-Caporalino
- INRA, Institut Sophia Agrobiotech, Sophia Antipolis, France
- Université de Nice Sophia Antipolis, Institut Sophia Agrobiotech, Sophia Antipolis, France
- CNRS, Institut Sophia Agrobiotech, Sophia Antipolis, France
| | - Alain Palloix
- INRA, Génétique et Amélioration des Fruits et Légumes, Montfavet Cedex, France
| | - Philippe Castagnone-Sereno
- INRA, Institut Sophia Agrobiotech, Sophia Antipolis, France
- Université de Nice Sophia Antipolis, Institut Sophia Agrobiotech, Sophia Antipolis, France
- CNRS, Institut Sophia Agrobiotech, Sophia Antipolis, France
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Destefanis M, Nagy I, Rigney B, Bryan GJ, McLean K, Hein I, Griffin D, Milbourne D. A disease resistance locus on potato and tomato chromosome 4 exhibits a conserved multipartite structure displaying different rates of evolution in different lineages. BMC PLANT BIOLOGY 2015; 15:255. [PMID: 26496718 PMCID: PMC4619397 DOI: 10.1186/s12870-015-0645-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Accepted: 10/14/2015] [Indexed: 06/05/2023]
Abstract
BACKGROUND In plant genomes, NB-LRR based resistance (R) genes tend to occur in clusters of variable size in a relatively small number of genomic regions. R-gene sequences mostly differentiate by accumulating point mutations and gene conversion events. Potato and tomato chromosome 4 harbours a syntenic R-gene locus (known as the R2 locus in potato) that has mainly been examined in central American/Mexican wild potato species on the basis of its contribution to resistance to late blight, caused by the oomycete pathogen Phytophthora infestans. Evidence to date indicates the occurrence of a fast evolutionary mode characterized by gene conversion events at the locus in these genotypes. RESULTS A physical map of the R2 locus was developed for three Solanum tuberosum genotypes and used to identify the tomato syntenic sequence. Functional annotation of the locus revealed the presence of numerous resistance gene homologs (RGHs) belonging to the R2 gene family (R2GHs) organized into a total of 4 discrete physical clusters, three of which were conserved across S. tuberosum and tomato. Phylogenetic analysis showed clear orthology/paralogy relationships between S. tuberosum R2GHs but not in R2GHs cloned from Solanum wild species. This study confirmed that, in contrast to the wild species R2GHs, which have evolved through extensive sequence exchanges between paralogs, gene conversion was not a major force for differentiation in S. tuberosum R2GHs, and orthology/paralogy relationships have been maintained via a slow accumulation of point mutations in these genotypes. CONCLUSIONS S. tuberosum and Solanum lycopersicum R2GHs evolved mostly through duplication and deletion events, followed by gradual accumulation of mutations. Conversely, widespread gene conversion is the major evolutionary force that has shaped the locus in Mexican wild potato species. We conclude that different selective forces shaped the evolution of the R2 locus in these lineages and that co-evolution with a pathogen steered selection on different evolutionary paths.
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Affiliation(s)
- Marialaura Destefanis
- Crops, Environment and Land Use Programme, Teagasc, Oak Park, Carlow, Ireland.
- Pesticides, Plant Health & Seed Testing Laboratories, Department of Agriculture, Food and the Marine, Backweston Campus, Celbridge, Co. Kildare, Ireland.
| | - Istvan Nagy
- Crops, Environment and Land Use Programme, Teagasc, Oak Park, Carlow, Ireland.
- Department of Molecular Biology and Genetics, Aarhus University, Forsøgsvej 1, 4200, Slagelse, Denmark.
| | - Brian Rigney
- Crops, Environment and Land Use Programme, Teagasc, Oak Park, Carlow, Ireland.
| | - Glenn J Bryan
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, DD2 5DA, UK.
| | - Karen McLean
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, DD2 5DA, UK.
| | - Ingo Hein
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, DD2 5DA, UK.
| | - Denis Griffin
- Crops, Environment and Land Use Programme, Teagasc, Oak Park, Carlow, Ireland.
| | - Dan Milbourne
- Crops, Environment and Land Use Programme, Teagasc, Oak Park, Carlow, Ireland.
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Vega-Arreguín JC, Jalloh A, Bos JI, Moffett P. Recognition of an Avr3a homologue plays a major role in mediating nonhost resistance to Phytophthora capsici in Nicotiana species. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2014; 27:770-80. [PMID: 24725207 DOI: 10.1094/mpmi-01-14-0014-r] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Nonhost resistance is a commonly occurring phenomenon wherein all accessions or cultivars of a plant species are resistant to all strains of a pathogen species and is likely the manifestation of multiple molecular mechanisms. Phytophthora capsici is a soil-borne oomycete that causes Phytophthora blight disease in many solanaceous and cucurbitaceous plants worldwide. Interest in P. capsici has increased considerably with the sequencing of its genome and its increasing occurrence in multiple crops. However, molecular interactions between P. capsici and both its hosts and its nonhosts are poorly defined. We show here that tobacco (Nicotiana tabacum) acts like a nonhost for P. capsici and responds to P. capsici infection with a hypersensitive response (HR). Furthermore, we have found that a P. capsici Avr3a-like gene (PcAvr3a1) encoding a putative RXLR effector protein produces a HR upon transient expression in tobacco and several other Nicotiana species. This HR response correlated with resistance in 19 of 23 Nicotiana species and accessions tested, and knock-down of PcAvr3a1 expression by host-induced gene silencing allowed infection of resistant tobacco. Our results suggest that many Nicotiana species have the capacity to recognize PcAvr3a1 via the products of endogenous disease resistance (R) genes and that this R gene-mediated response is a major component of nonhost resistance to P. capsici.
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Slootweg EJ, Spiridon LN, Roosien J, Butterbach P, Pomp R, Westerhof L, Wilbers R, Bakker E, Bakker J, Petrescu AJ, Smant G, Goverse A. Structural determinants at the interface of the ARC2 and leucine-rich repeat domains control the activation of the plant immune receptors Rx1 and Gpa2. PLANT PHYSIOLOGY 2013; 162:1510-28. [PMID: 23660837 PMCID: PMC3707565 DOI: 10.1104/pp.113.218842] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Accepted: 05/07/2013] [Indexed: 05/19/2023]
Abstract
Many plant and animal immune receptors have a modular nucleotide-binding-leucine-rich repeat (NB-LRR) architecture in which a nucleotide-binding switch domain, NB-ARC, is tethered to a LRR sensor domain. The cooperation between the switch and sensor domains, which regulates the activation of these proteins, is poorly understood. Here, we report structural determinants governing the interaction between the NB-ARC and LRR in the highly homologous plant immune receptors Gpa2 and Rx1, which recognize the potato cyst nematode Globodera pallida and Potato virus X, respectively. Systematic shuffling of polymorphic sites between Gpa2 and Rx1 showed that a minimal region in the ARC2 and N-terminal repeats of the LRR domain coordinate the activation state of the protein. We identified two closely spaced amino acid residues in this region of the ARC2 (positions 401 and 403) that distinguish between autoactivation and effector-triggered activation. Furthermore, a highly acidic loop region in the ARC2 domain and basic patches in the N-terminal end of the LRR domain were demonstrated to be required for the physical interaction between the ARC2 and LRR. The NB-ARC and LRR domains dissociate upon effector-dependent activation, and the complementary-charged regions are predicted to mediate a fast reassociation, enabling multiple rounds of activation. Finally, we present a mechanistic model showing how the ARC2, NB, and N-terminal half of the LRR form a clamp, which regulates the dissociation and reassociation of the switch and sensor domains in NB-LRR proteins.
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Affiliation(s)
- Erik J Slootweg
- Laboratory of Nematology, Department of Plant Sciences, Wageningen University, 6708 PB Wageningen, The Netherlands.
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Abstract
Plant pararetroviruses integrate serendipitously into their host genomes. The banana genome harbors integrated copies of banana streak virus (BSV) named endogenous BSV (eBSV) that are able to release infectious pararetrovirus. In this investigation, we characterized integrants of three BSV species-Goldfinger (eBSGFV), Imove (eBSImV), and Obino l'Ewai (eBSOLV)-in the seedy Musa balbisiana Pisang klutuk wulung (PKW) by studying their molecular structure, genomic organization, genomic landscape, and infectious capacity. All eBSVs exhibit extensive viral genome duplications and rearrangements. eBSV segregation analysis on an F1 population of PKW combined with fluorescent in situ hybridization analysis showed that eBSImV, eBSOLV, and eBSGFV are each present at a single locus. eBSOLV and eBSGFV contain two distinct alleles, whereas eBSImV has two structurally identical alleles. Genotyping of both eBSV and viral particles expressed in the progeny demonstrated that only one allele for each species is infectious. The infectious allele of eBSImV could not be identified since the two alleles are identical. Finally, we demonstrate that eBSGFV and eBSOLV are located on chromosome 1 and eBSImV is located on chromosome 2 of the reference Musa genome published recently. The structure and evolution of eBSVs suggest sequential integration into the plant genome, and haplotype divergence analysis confirms that the three loci display differential evolution. Based on our data, we propose a model for BSV integration and eBSV evolution in the Musa balbisiana genome. The mutual benefits of this unique host-pathogen association are also discussed.
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Yang L, Li D, Li Y, Gu X, Huang S, Garcia-Mas J, Weng Y. A 1,681-locus consensus genetic map of cultivated cucumber including 67 NB-LRR resistance gene homolog and ten gene loci. BMC PLANT BIOLOGY 2013; 13:53. [PMID: 23531125 PMCID: PMC3626583 DOI: 10.1186/1471-2229-13-53] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2012] [Accepted: 03/11/2013] [Indexed: 05/18/2023]
Abstract
BACKGROUND Cucumber is an important vegetable crop that is susceptible to many pathogens, but no disease resistance (R) genes have been cloned. The availability of whole genome sequences provides an excellent opportunity for systematic identification and characterization of the nucleotide binding and leucine-rich repeat (NB-LRR) type R gene homolog (RGH) sequences in the genome. Cucumber has a very narrow genetic base making it difficult to construct high-density genetic maps. Development of a consensus map by synthesizing information from multiple segregating populations is a method of choice to increase marker density. As such, the objectives of the present study were to identify and characterize NB-LRR type RGHs, and to develop a high-density, integrated cucumber genetic-physical map anchored with RGH loci. RESULTS From the Gy14 draft genome, 70 NB-containing RGHs were identified and characterized. Most RGHs were in clusters with uneven distribution across seven chromosomes. In silico analysis indicated that all 70 RGHs had EST support for gene expression. Phylogenetic analysis classified 58 RGHs into two clades: CNL and TNL. Comparative analysis revealed high-degree sequence homology and synteny in chromosomal locations of these RGH members between the cucumber and melon genomes. Fifty-four molecular markers were developed to delimit 67 of the 70 RGHs, which were integrated into a genetic map through linkage analysis. A 1,681-locus cucumber consensus map including 10 gene loci and spanning 730.0 cM in seven linkage groups was developed by integrating three component maps with a bin-mapping strategy. Physically, 308 scaffolds with 193.2 Mbp total DNA sequences were anchored onto this consensus map that covered 52.6% of the 367 Mbp cucumber genome. CONCLUSIONS Cucumber contains relatively few NB-LRR RGHs that are clustered and unevenly distributed in the genome. All RGHs seem to be transcribed and shared significant sequence homology and synteny with the melon genome suggesting conservation of these RGHs in the Cucumis lineage. The 1,681-locus consensus genetic-physical map developed and the RGHs identified and characterized herein are valuable genomics resources that may have many applications such as quantitative trait loci identification, map-based gene cloning, association mapping, marker-assisted selection, as well as assembly of a more complete cucumber genome.
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Affiliation(s)
- Luming Yang
- Horticulture Department, University of Wisconsin, Madison, WI 53706, USA
| | - Dawei Li
- Horticulture Department, University of Wisconsin, Madison, WI 53706, USA
- Horticulture College, Northwest A&F University, Yangling, 712100, China
| | - Yuhong Li
- Horticulture Department, University of Wisconsin, Madison, WI 53706, USA
- Horticulture College, Northwest A&F University, Yangling, 712100, China
| | - Xingfang Gu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100018, China
| | - Sanwen Huang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100018, China
| | - Jordi Garcia-Mas
- IRTA, Center for Research in Agricultural Genomics CSIC-IRTA-UAB-UB, Bellaterra, Barcelona, 08193, Spain
| | - Yiqun Weng
- Horticulture Department, University of Wisconsin, Madison, WI 53706, USA
- USDA-ARS Vegetable Crops Research Unit, Horticulture Department, University of Wisconsin, Madison, WI, 53706, USA
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Johnson EB, Haggard JE, St.Clair DA. Fractionation, stability, and isolate-specificity of QTL for resistance to Phytophthora infestans in cultivated tomato (Solanum lycopersicum). G3 (BETHESDA, MD.) 2012; 2:1145-59. [PMID: 23050225 PMCID: PMC3464107 DOI: 10.1534/g3.112.003459] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Accepted: 07/16/2012] [Indexed: 11/18/2022]
Abstract
Cultivated tomato (Solanum lycopersicum) is susceptible to late blight, a major disease caused by Phytophthora infestans, but quantitative resistance exists in the wild tomato species S. habrochaites. Previously, we mapped several quantitative trait loci (QTL) from S. habrochaites and then introgressed each individually into S. lycopersicum. Near-isogenic lines (NILs) were developed, each containing a single introgressed QTL on chromosome 5 or 11. NILs were used to create two recombinant sub-NIL populations, one for each target chromosome region, for higher-resolution mapping. The sub-NIL populations were evaluated for foliar and stem resistance to P. infestans in replicated field experiments over two years, and in replicated growth chamber experiments for resistance to three California isolates. Each of the original single QTL on chromosomes 5 and 11 fractionated into between two and six QTL for both foliar and stem resistance, indicating a complex genetic architecture. The majority of QTL from the field experiments were detected in multiple locations or years, and two of the seven QTL detected in growth chambers were co-located with QTL detected in field experiments, indicating stability of some QTL across environments. QTL that confer foliar and stem resistance frequently co-localized, suggesting that pleiotropy and/or tightly linked genes control the trait phenotypes. Other QTL exhibited isolate-specificity and QTL × environment interactions. Map-based comparisons between QTL mapped in this study and Solanaceae resistance genes/QTL detected in other published studies revealed multiple cases of co-location, suggesting conservation of gene function.
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Affiliation(s)
- Emily B. Johnson
- Department of Plant Sciences, University of California, Davis, California 95616
| | - J. Erron Haggard
- Department of Plant Sciences, University of California, Davis, California 95616
| | - Dina A. St.Clair
- Department of Plant Sciences, University of California, Davis, California 95616
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Lukasik-Shreepaathy E, Slootweg E, Richter H, Goverse A, Cornelissen BJC, Takken FLW. Dual regulatory roles of the extended N terminus for activation of the tomato MI-1.2 resistance protein. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2012; 25:1045-57. [PMID: 22512381 DOI: 10.1094/mpmi-11-11-0302] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Plant resistance (R) proteins mediate race-specific immunity and initiate host defenses that are often accompanied by a localized cell-death response. Most R proteins belong to the nucleotide binding-leucine-rich repeat (NB-LRR) protein family, as they carry a central NB-ARC domain fused to an LRR domain. The coiled-coil (CC) domain at the N terminus of some solanaceous NB-LRR proteins is extended with a solanaceae domain (SD). Tomato Mi-1.2, which confers resistance against nematodes, white flies, psyllids, and aphids, encodes a typical SD-CNL protein. Here, we analyzed the role of the extended N terminus for Mi-1.2 activation. Removal of the first part of the N terminus (Nt1) induced Mi-1.2-mediated cell death that could be suppressed by overexpression of the second half of the N-terminal region. Yet, autoactivating NB-ARC-LRR mutants require in trans coexpression of the N-terminal region to induce cell death, indicating that the N terminus functions both as a negative and as a positive regulator. Based on secondary structure predictions, we could link both activities to three distinct subdomains, a typical CC domain and two novel, structurally-conserved helical subdomains called SD1 and SD2. A negative regulatory function could be assigned to the SD1, whereas SD2 and the CC together function as positive regulators of Mi-1.2-mediated cell death.
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Quirin EA, Mann H, Meyer RS, Traini A, Chiusano ML, Litt A, Bradeen JM. Evolutionary meta-analysis of solanaceous resistance gene and solanum resistance gene analog sequences and a practical framework for cross-species comparisons. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2012; 25:603-612. [PMID: 22352721 DOI: 10.1094/mpmi-12-11-0318-r] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Cross-species comparative genomics approaches have been employed to map and clone many important disease resistance (R) genes from Solanum species-especially wild relatives of potato and tomato. These efforts will increase with the recent release of potato genome sequence and the impending release of tomato genome sequence. Most R genes belong to the prominent nucleotide binding site-leucine rich repeat (NBS-LRR) class and conserved NBS-LRR protein motifs enable survey of the R gene space of a plant genome by generation of resistance gene analogs (RGA), polymerase chain reaction fragments derived from R genes. We generated a collection of 97 RGA from the disease-resistant wild potato S. bulbocastanum, complementing smaller collections from other Solanum species. To further comparative genomics approaches, we combined all known Solanum RGA and cloned solanaceous NBS-LRR gene sequences, nearly 800 sequences in total, into a single meta-analysis. We defined R gene diversity bins that reflect both evolutionary relationships and DNA cross-hybridization results. The resulting framework is amendable and expandable, providing the research community with a common vocabulary for present and future study of R gene lineages. Through a series of sequence and hybridization experiments, we demonstrate that all tested R gene lineages are of ancient origin, are shared between Solanum species, and can be successfully accessed via comparative genomics approaches.
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Affiliation(s)
- Edmund A Quirin
- University of Minnesota, Department of Plant Pathology, 495 Borlaug Hall/1991 Upper Buford Circle, St. Paul, MN 55108,USA
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15
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Abstract
In plants and animals, the NLR family of receptors perceives non-self and modified-self molecules inside host cells and mediates innate immune responses to microbial pathogens. Despite their similar biological functions and protein architecture, animal NLRs are normally activated by conserved microbe- or damage-associated molecular patterns, whereas plant NLRs typically detect strain-specific pathogen effectors. Plant NLRs recognize either the effector structure or effector-mediated modifications of host proteins. The latter indirect mechanism for the perception of non-self, as well as the within-species diversification of plant NLRs, maximize the capacity to recognize non-self through the use of a finite number of innate immunoreceptors. We discuss recent insights into NLR activation, signal initiation through the homotypic association of N-terminal domains and subcellular receptor dynamics in plants and compare those with NLR functions in animals.
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16
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Bakker E, Borm T, Prins P, van der Vossen E, Uenk G, Arens M, de Boer J, van Eck H, Muskens M, Vossen J, van der Linden G, van Ham R, Klein-Lankhorst R, Visser R, Smant G, Bakker J, Goverse A. A genome-wide genetic map of NB-LRR disease resistance loci in potato. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2011; 123:493-508. [PMID: 21590328 PMCID: PMC3135832 DOI: 10.1007/s00122-011-1602-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2010] [Accepted: 04/26/2011] [Indexed: 05/14/2023]
Abstract
Like all plants, potato has evolved a surveillance system consisting of a large array of genes encoding for immune receptors that confer resistance to pathogens and pests. The majority of these so-called resistance or R proteins belong to the super-family that harbour a nucleotide binding and a leucine-rich-repeat domain (NB-LRR). Here, sequence information of the conserved NB domain was used to investigate the genome-wide genetic distribution of the NB-LRR resistance gene loci in potato. We analysed the sequences of 288 unique BAC clones selected using filter hybridisation screening of a BAC library of the diploid potato clone RH89-039-16 (S. tuberosum ssp. tuberosum) and a physical map of this BAC library. This resulted in the identification of 738 partial and full-length NB-LRR sequences. Based on homology of these sequences with known resistance genes, 280 and 448 sequences were classified as TIR-NB-LRR (TNL) and CC-NB-LRR (CNL) sequences, respectively. Genetic mapping revealed the presence of 15 TNL and 32 CNL loci. Thirty-six are novel, while three TNL loci and eight CNL loci are syntenic with previously identified functional resistance genes. The genetic map was complemented with 68 universal CAPS markers and 82 disease resistance trait loci described in literature, providing an excellent template for genetic studies and applied research in potato.
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Affiliation(s)
- Erin Bakker
- Laboratory of Nematology, Wageningen University and Research Centre, Droevendaalsesteeg 1, Wageningen, The Netherlands.
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Finkers-Tomczak A, Bakker E, de Boer J, van der Vossen E, Achenbach U, Golas T, Suryaningrat S, Smant G, Bakker J, Goverse A. Comparative sequence analysis of the potato cyst nematode resistance locus H1 reveals a major lack of co-linearity between three haplotypes in potato (Solanum tuberosum ssp.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2011; 122:595-608. [PMID: 21049265 PMCID: PMC3026667 DOI: 10.1007/s00122-010-1472-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2010] [Accepted: 09/30/2010] [Indexed: 05/04/2023]
Abstract
The H1 locus confers resistance to the potato cyst nematode Globodera rostochiensis pathotypes 1 and 4. It is positioned at the distal end of chromosome V of the diploid Solanum tuberosum genotype SH83-92-488 (SH) on an introgression segment derived from S. tuberosum ssp. andigena. Markers from a high-resolution genetic map of the H1 locus (Bakker et al. in Theor Appl Genet 109:146-152, 2004) were used to screen a BAC library to construct a physical map covering a 341-kb region of the resistant haplotype coming from SH. For comparison, physical maps were also generated of the two haplotypes from the diploid susceptible genotype RH89-039-16 (S. tuberosum ssp. tuberosum/S. phureja), spanning syntenic regions of 700 and 319 kb. Gene predictions on the genomic segments resulted in the identification of a large cluster consisting of variable numbers of the CC-NB-LRR type of R genes for each haplotype. Furthermore, the regions were interspersed with numerous transposable elements and genes coding for an extensin-like protein and an amino acid transporter. Comparative analysis revealed a major lack of gene order conservation in the sequences of the three closely related haplotypes. Our data provide insight in the evolutionary mechanisms shaping the H1 locus and will facilitate the map-based cloning of the H1 resistance gene.
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Baurens FC, Bocs S, Rouard M, Matsumoto T, Miller RNG, Rodier-Goud M, MBéguié-A-MBéguié D, Yahiaoui N. Mechanisms of haplotype divergence at the RGA08 nucleotide-binding leucine-rich repeat gene locus in wild banana (Musa balbisiana). BMC PLANT BIOLOGY 2010; 10:149. [PMID: 20637079 PMCID: PMC3017797 DOI: 10.1186/1471-2229-10-149] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2009] [Accepted: 07/16/2010] [Indexed: 05/09/2023]
Abstract
BACKGROUND Comparative sequence analysis of complex loci such as resistance gene analog clusters allows estimating the degree of sequence conservation and mechanisms of divergence at the intraspecies level. In banana (Musa sp.), two diploid wild species Musa acuminata (A genome) and Musa balbisiana (B genome) contribute to the polyploid genome of many cultivars. The M. balbisiana species is associated with vigour and tolerance to pests and disease and little is known on the genome structure and haplotype diversity within this species. Here, we compare two genomic sequences of 253 and 223 kb corresponding to two haplotypes of the RGA08 resistance gene analog locus in M. balbisiana "Pisang Klutuk Wulung" (PKW). RESULTS Sequence comparison revealed two regions of contrasting features. The first is a highly colinear gene-rich region where the two haplotypes diverge only by single nucleotide polymorphisms and two repetitive element insertions. The second corresponds to a large cluster of RGA08 genes, with 13 and 18 predicted RGA genes and pseudogenes spread over 131 and 152 kb respectively on each haplotype. The RGA08 cluster is enriched in repetitive element insertions, in duplicated non-coding intergenic sequences including low complexity regions and shows structural variations between haplotypes. Although some allelic relationships are retained, a large diversity of RGA08 genes occurs in this single M. balbisiana genotype, with several RGA08 paralogs specific to each haplotype. The RGA08 gene family has evolved by mechanisms of unequal recombination, intragenic sequence exchange and diversifying selection. An unequal recombination event taking place between duplicated non-coding intergenic sequences resulted in a different RGA08 gene content between haplotypes pointing out the role of such duplicated regions in the evolution of RGA clusters. Based on the synonymous substitution rate in coding sequences, we estimated a 1 million year divergence time for these M. balbisiana haplotypes. CONCLUSIONS A large RGA08 gene cluster identified in wild banana corresponds to a highly variable genomic region between haplotypes surrounded by conserved flanking regions. High level of sequence identity (70 to 99%) of the genic and intergenic regions suggests a recent and rapid evolution of this cluster in M. balbisiana.
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Affiliation(s)
| | - Stéphanie Bocs
- CIRAD, UMR DAP, TA A-96/03, Avenue Agropolis, F-34398 Montpellier Cedex 5, France
| | - Mathieu Rouard
- Bioversity International, Parc Scientifique Agropolis II, F-34397 Montpellier Cedex 5, France
| | - Takashi Matsumoto
- Rice Genome Research Program (RGP), National Institute of Agrobiological Sciences (NIAS)/Institute of the Society for Techno-innovation of Agriculture, Forestry and Fisheries, Tsukuba, Ibaraki 305-8602, Japan
| | - Robert NG Miller
- Postgraduate program in Genomic Science and Biotechnology, Universidade Católica de Brasília, SGAN 916, Módulo B, CEP 70.790-160, Brasília, DF, Brazil
- Universidade de Brasília, Campus Universitário Darcy Ribeiro, Instituto de Ciências Biológicas, Departamento de Biologia Celular, Asa Norte, Brasília, Brazil
| | | | | | - Nabila Yahiaoui
- CIRAD, UMR DAP, TA A-96/03, Avenue Agropolis, F-34398 Montpellier Cedex 5, France
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Abstract
One branch of plant innate immunity is mediated through what is traditionally known as race-specific or gene-for-gene resistance wherein the outcome of an attempted infection is determined by the genotypes of both the host and the pathogen. Dominant plant disease resistance (R) genes confer resistance to a variety of biotrophic pathogens, including viruses, encoding corresponding dominant avirulence (Avr) genes. R genes are among the most highly variable plant genes known, both within and between populations. Plant genomes encode hundreds of R genes that code for NB-LRR proteins, so named because they posses nucleotide-binding (NB) and leucine-rich repeat (LRR) domains. Many matching pairs of NB-LRR and Avr proteins have been identified as well as cellular proteins that mediate R/Avr interactions, and the molecular analysis of these interactions have led to the formulation of models of how products of R genes recognize pathogens. Data from multiple NB-LRR systems indicate that the LRR domains of NB-LRR proteins determine recognition specificity. However, recent evidence suggests that NB-LRR proteins have co-opted cellular recognition co-factors that mediate interactions between Avr proteins and the N-terminal domains of NB-LRR proteins.
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