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Moury B, Michon T, Simon V, Palloix A. A Single Nonsynonymous Substitution in the RNA-Dependent RNA Polymerase of Potato virus Y Allows the Simultaneous Breakdown of Two Different Forms of Antiviral Resistance in Capsicum annuum. Viruses 2023; 15:v15051081. [PMID: 37243167 DOI: 10.3390/v15051081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 04/24/2023] [Accepted: 04/25/2023] [Indexed: 05/28/2023] Open
Abstract
The dominant Pvr4 gene in pepper (Capsicum annuum) confers resistance to members of six potyvirus species, all of which belong to the Potato virus Y (PVY) phylogenetic group. The corresponding avirulence factor in the PVY genome is the NIb cistron (i.e., RNA-dependent RNA polymerase). Here, we describe a new source of potyvirus resistance in the Guatemalan accession C. annuum cv. PM949. PM949 is resistant to members of at least three potyvirus species, a subset of those controlled by Pvr4. The F1 progeny between PM949 and the susceptible cultivar Yolo Wonder was susceptible to PVY, indicating that the resistance is recessive. The segregation ratio between resistant and susceptible plants observed in the F2 progeny matched preferably with resistance being determined by two unlinked recessive genes independently conferring resistance to PVY. Inoculations by grafting resulted in the selection of PVY mutants breaking PM949 resistance and, less efficiently, Pvr4-mediated resistance. The codon substitution E472K in the NIb cistron of PVY, which was shown previously to be sufficient to break Pvr4 resistance, was also sufficient to break PM949 resistance, a rare example of cross-pathogenicity effect. In contrast, the other selected NIb mutants showed specific infectivity in PM949 or Pvr4 plants. Comparison of Pvr4 and PM949 resistance, which share the same target in PVY, provides interesting insights into the determinants of resistance durability.
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Affiliation(s)
- Benoît Moury
- INRAE, Pathologie Végétale, 84140 Montfavet, France
| | - Thierry Michon
- UMR Biologie du Fruit et Pathologie, INRAE, Université de Bordeaux, CS 20032, 33882 Villenave d'Ornon, France
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2
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Tamisier L, Szadkowski M, Girardot G, Djian‐Caporalino C, Palloix A, Hirsch J, Moury B. Concurrent evolution of resistance and tolerance to potato virus Y in Capsicum annuum revealed by genome-wide association. Mol Plant Pathol 2022; 23:254-264. [PMID: 34729890 PMCID: PMC8743019 DOI: 10.1111/mpp.13157] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 10/19/2021] [Accepted: 10/20/2021] [Indexed: 05/21/2023]
Abstract
We performed a genome-wide association study of pepper (Capsicum annuum) tolerance to potato virus Y (PVY). For 254 pepper accessions, we estimated the tolerance to PVY as the coefficient of regression of the fresh weight (or height) of PVY-infected and mock-inoculated plants against within-plant virus load. Small (strongly negative) coefficients of regression indicate low tolerance because plant biomass or growth decreases sharply as virus load increases. The tolerance level varied largely, with some pepper accessions showing no symptoms or fairly mild mosaics, whereas about half (48%) of the accessions showed necrotic symptoms. We found two adjacent single-nucleotide polymorphisms (SNPs) at one extremity of chromosome 9 that were significantly associated with tolerance to PVY. Similarly, in three biparental pepper progenies, we showed that the induction of necrosis on PVY systemic infection segregated as a monogenic trait determined by a locus on chromosome 9. Our results also demonstrate the existence of a negative correlation between resistance and tolerance among the cultivated pepper accessions at both the phenotypic and genetic levels. By comparing the distributions of the tolerance-associated SNP alleles and previously identified PVY resistance-associated SNP alleles, we showed that cultivated pepper accessions possess favourable alleles for both resistance and tolerance less frequently than expected under random associations, while the minority of wild pepper accessions frequently combined resistance and tolerance alleles. This divergent evolution of PVY resistance and tolerance could be related to pepper domestication or farmer's selection.
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Affiliation(s)
- Lucie Tamisier
- Pathologie VégétaleINRAEMontfavetFrance
- GAFLINRAEMontfavetFrance
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3
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Tamisier L, Szadkowski M, Nemouchi G, Lefebvre V, Szadkowski E, Duboscq R, Santoni S, Sarah G, Sauvage C, Palloix A, Moury B. Genome-wide association mapping of QTLs implied in potato virus Y population sizes in pepper: evidence for widespread resistance QTL pyramiding. Mol Plant Pathol 2020; 21:3-16. [PMID: 31605444 PMCID: PMC6913244 DOI: 10.1111/mpp.12874] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
In this study, we looked for genetic factors in the pepper (Capsicum annuum) germplasm that control the number of potato virus Y (PVY) particles entering the plant (i.e. effective population size at inoculation) and the PVY accumulation at the systemic level (i.e. census population size). Using genotyping-by-sequencing (GBS) in a core collection of 256 pepper accessions, we obtained 10 307 single nucleotide polymorphisms (SNPs) covering the whole genome. Genome-wide association studies (GWAS) detected seven SNPs significantly associated with the virus population size at inoculation and/or systemic level on chromosomes 4, 6, 9 and 12. Two SNPs on chromosome 4 associated with both PVY population sizes map closely to the major resistance gene pvr2 encoding the eukaryotic initiation factor 4E. No obvious candidates for resistance were identified in the confidence intervals for the other chromosomes. SNPs detected on chromosomes 6 and 12 colocalized with resistance quantitative trait loci (QTLs) previously identified with a biparental population. These results show the efficiency of GBS and GWAS in C. annuum, indicate highly consistent results between GWAS and classical QTL mapping, and suggest that resistance QTLs identified with a biparental population are representative of a much larger collection of pepper accessions. Moreover, the resistance alleles at these different loci were more frequently combined than expected by chance in the core collection, indicating widespread pyramiding of resistance QTLs and widespread combination of resistance QTLs and major effect genes. Such pyramiding may increase resistance efficiency and/or durability.
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Affiliation(s)
- Lucie Tamisier
- GAFLINRA84140MontfavetFrance
- Pathologie VégétaleINRA84140MontfavetFrance
- Present address:
Plant Pathology LaboratoryTERRA‐Gembloux Agro‐Bio TechUniversity of LiègePassage des Déportés, 25030GemblouxBelgium
| | - Marion Szadkowski
- GAFLINRA84140MontfavetFrance
- Pathologie VégétaleINRA84140MontfavetFrance
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Rousseau E, Tamisier L, Fabre F, Simon V, Szadkowski M, Bouchez O, Zanchetta C, Girardot G, Mailleret L, Grognard F, Palloix A, Moury B. Impact of genetic drift, selection and accumulation level on virus adaptation to its host plants. Mol Plant Pathol 2018; 19:2575-2589. [PMID: 30074299 PMCID: PMC6638063 DOI: 10.1111/mpp.12730] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The efficiency of plant major resistance genes is limited by the emergence and spread of resistance-breaking mutants. Modulation of the evolutionary forces acting on pathogen populations constitutes a promising way to increase the durability of these genes. We studied the effect of four plant traits affecting these evolutionary forces on the rate of resistance breakdown (RB) by a virus. Two of these traits correspond to virus effective population sizes (Ne ) at either plant inoculation or during infection. The third trait corresponds to differential selection exerted by the plant on the virus population. Finally, the fourth trait corresponds to within-plant virus accumulation (VA). These traits were measured experimentally on Potato virus Y (PVY) inoculated to a set of 84 pepper doubled-haploid lines, all carrying the same pvr23 resistance gene, but having contrasting genetic backgrounds. The lines showed extensive variation for the rate of pvr23 RB by PVY and for the four other traits of interest. A generalized linear model showed that three of these four traits, with the exception of Ne at inoculation, and several pairwise interactions between them had significant effects on RB. RB increased with increasing values of Ne during plant infection or VA. The effect of differential selection was more complex because of a strong interaction with VA. When VA was high, RB increased as the differential selection increased. An opposite relationship between RB and differential selection was observed when VA was low. This study provides a framework to select plants with appropriate virus evolution-related traits to avoid or delay RB.
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Affiliation(s)
- Elsa Rousseau
- Pathologie VégétaleINRA84140MontfavetFrance
- Université Côte d'Azur, Inria, INRA, CNRS, Sorbonne UniversitéBiocore TeamSophia AntipolisFrance
- Université Côte d'Azur, INRA, CNRS, ISAFrance
- Present address:
IBM Almaden Research CenterSan Jose, CA 95120–6099USA
| | - Lucie Tamisier
- Pathologie VégétaleINRA84140MontfavetFrance
- GAFL, INRA84140MontfavetFrance
- Present address:
Université de Liège, Terra‐Gembloux Agro-Bio Tech, PlantPathology Laboratory, Passage des Déportés2, GemblouxBelgium, 5030
| | | | - Vincent Simon
- Pathologie VégétaleINRA84140MontfavetFrance
- UMR BFPINRA33882Villenave d'OrnonFrance
| | | | - Olivier Bouchez
- INRAGeT‐PlaGe, US 1426, Genotoul, 31326 Castanet‐TolosanFrance
| | | | | | - Ludovic Mailleret
- Université Côte d'Azur, Inria, INRA, CNRS, Sorbonne UniversitéBiocore TeamSophia AntipolisFrance
- Université Côte d'Azur, INRA, CNRS, ISAFrance
| | - Frederic Grognard
- Université Côte d'Azur, Inria, INRA, CNRS, Sorbonne UniversitéBiocore TeamSophia AntipolisFrance
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Rousseau E, Moury B, Mailleret L, Senoussi R, Palloix A, Simon V, Valière S, Grognard F, Fabre F. Estimating virus effective population size and selection without neutral markers. PLoS Pathog 2017; 13:e1006702. [PMID: 29155894 PMCID: PMC5720836 DOI: 10.1371/journal.ppat.1006702] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Revised: 12/07/2017] [Accepted: 10/19/2017] [Indexed: 12/04/2022] Open
Abstract
By combining high-throughput sequencing (HTS) with experimental evolution, we can observe the within-host dynamics of pathogen variants of biomedical or ecological interest. We studied the evolutionary dynamics of five variants of Potato virus Y (PVY) in 15 doubled-haploid lines of pepper. All plants were inoculated with the same mixture of virus variants and variant frequencies were determined by HTS in eight plants of each pepper line at each of six sampling dates. We developed a method for estimating the intensities of selection and genetic drift in a multi-allelic Wright-Fisher model, applicable whether these forces are strong or weak, and in the absence of neutral markers. This method requires variant frequency determination at several time points, in independent hosts. The parameters are the selection coefficients for each PVY variant and four effective population sizes Ne at different time-points of the experiment. Numerical simulations of asexual haploid Wright-Fisher populations subjected to contrasting genetic drift (Ne ∈ [10, 2000]) and selection (|s| ∈ [0, 0.15]) regimes were used to validate the method proposed. The experiment in closely related pepper host genotypes revealed that viruses experienced a considerable diversity of selection and genetic drift regimes. The resulting variant dynamics were accurately described by Wright-Fisher models. The fitness ranks of the variants were almost identical between host genotypes. By contrast, the dynamics of Ne were highly variable, although a bottleneck was often identified during the systemic movement of the virus. We demonstrated that, for a fixed initial PVY population, virus effective population size is a heritable trait in plants. These findings pave the way for the breeding of plant varieties exposing viruses to stronger genetic drift, thereby slowing virus adaptation. A growing number of experimental evolution studies are using an “evolve-and-resequence” approach to observe the within-host dynamics of pathogen variants of biomedical or ecological interest. The resulting data are particularly appropriate for studying the effects of evolutionary forces, such as selection and genetic drift, on the emergence of new pathogen variants. However, it remains challenging to unravel the effects of selection and genetic drift in the absence of neutral markers, a situation frequently encountered for microbes, such as viruses, due to their small constrained genomes. Using such an approach on a plant virus, we observed that the same set of virus variants displayed highly diverse dynamics in closely related plant genotypes. We developed and validated a method that does not require neutral markers, for estimating selection coefficients and effective population sizes from these experimental evolution data. We found that the viruses experienced considerable diversity in genetic drift regimes, depending on host genotype. Importantly, genetic drift experienced by virus populations was shown to be a heritable plant trait. These findings pave the way for the breeding of plant varieties exposing viruses to strong genetic drift, thereby slowing virus adaptation.
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Affiliation(s)
- Elsa Rousseau
- Université Côte d’Azur, Inria, INRA, CNRS, UPMC Univ Paris 06, Biocore team, Sophia Antipolis, France
- Université Côte d’Azur, INRA, CNRS, ISA, Sophia Antipolis, France
- Pathologie Végétale, INRA, 84140 Montfavet, France
- * E-mail: (ER); (FF)
| | - Benoît Moury
- Pathologie Végétale, INRA, 84140 Montfavet, France
| | - Ludovic Mailleret
- Université Côte d’Azur, Inria, INRA, CNRS, UPMC Univ Paris 06, Biocore team, Sophia Antipolis, France
- Université Côte d’Azur, INRA, CNRS, ISA, Sophia Antipolis, France
| | | | | | - Vincent Simon
- Pathologie Végétale, INRA, 84140 Montfavet, France
- UMR BFP, INRA, Villenave d’Ornon, France
| | - Sophie Valière
- GeT-PlaGe, INRA, Genotoul, Castanet-tolosan, France
- UAR DEPT GA, INRA, Castanet-Tolosan, France
| | - Frédéric Grognard
- Université Côte d’Azur, Inria, INRA, CNRS, UPMC Univ Paris 06, Biocore team, Sophia Antipolis, France
| | - Frédéric Fabre
- UMR SAVE, INRA, Villenave d’Ornon, France
- * E-mail: (ER); (FF)
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Tamisier L, Rousseau E, Barraillé S, Nemouchi G, Szadkowski M, Mailleret L, Grognard F, Fabre F, Moury B, Palloix A. Quantitative trait loci in pepper control the effective population size of two RNA viruses at inoculation. J Gen Virol 2017; 98:1923-1931. [PMID: 28691663 DOI: 10.1099/jgv.0.000835] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Infection of plants by viruses is a complex process involving several steps: inoculation into plant cells, replication in inoculated cells and plant colonization. The success of the different steps depends, in part, on the viral effective population size (Ne), defined as the number of individuals passing their genes to the next generation. During infection, the virus population will undergo bottlenecks, leading to drastic reductions in Ne and, potentially, to the loss of the fittest variants. Therefore, it is crucial to better understand how plants affect Ne. We aimed to (i) identify the plant genetic factors controlling Ne during inoculation, (ii) understand the mechanisms used by the plant to control Ne and (iii) compare these genetic factors with the genes controlling plant resistance to viruses. Ne was measured in a doubled-haploid population of Capsicum annuum. Plants were inoculated with either a Potato virus Y (PVY) construct expressing the green fluorescent protein or a necrotic variant of Cucumber mosaic virus (CMV). Newas assessed by counting the number of primary infection foci on cotyledons for PVY or the number of necrotic local lesions on leaves for CMV. The number of foci and lesions was correlated (r=0.57) and showed a high heritability (h2=0.93 for PVY and h2=0.98 for CMV). The Ne of the two viruses was controlled by both common quantitative trait loci (QTLs) and virus-specific QTLs, indicating the contribution of general and specific mechanisms. The PVY-specific QTL colocalizes with a QTL that reduces PVY accumulation and the capacity to break down a major-effect resistance gene.
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Affiliation(s)
- Lucie Tamisier
- INRA, UR1052 GAFL, Unité de Génétique et Amélioration des Fruits et Légumes, Domaine St Maurice - 67 Allée des Chênes, CS 60094, F-84143 Montfavet Cedex, France.,INRA, UR407 PV, Unité de Pathologie Végétale, Domaine St Maurice - 67 Allée des Chênes, CS 60094, F-84143 Montfavet Cedex, France
| | - Elsa Rousseau
- INRIA, Biocore Team, F-06902 Sophia Antipolis, France.,INRA, Université Nice Sophia Antipolis, CNRS, UMR 1355-7254 Institut Sophia Agrobiotech, Sophia Antipolis, France.,INRA, UR407 PV, Unité de Pathologie Végétale, Domaine St Maurice - 67 Allée des Chênes, CS 60094, F-84143 Montfavet Cedex, France
| | - Sebastien Barraillé
- INRA, UR407 PV, Unité de Pathologie Végétale, Domaine St Maurice - 67 Allée des Chênes, CS 60094, F-84143 Montfavet Cedex, France
| | - Ghislaine Nemouchi
- INRA, UR1052 GAFL, Unité de Génétique et Amélioration des Fruits et Légumes, Domaine St Maurice - 67 Allée des Chênes, CS 60094, F-84143 Montfavet Cedex, France
| | - Marion Szadkowski
- INRA, UR1052 GAFL, Unité de Génétique et Amélioration des Fruits et Légumes, Domaine St Maurice - 67 Allée des Chênes, CS 60094, F-84143 Montfavet Cedex, France
| | - Ludovic Mailleret
- INRIA, Biocore Team, F-06902 Sophia Antipolis, France.,INRA, Université Nice Sophia Antipolis, CNRS, UMR 1355-7254 Institut Sophia Agrobiotech, Sophia Antipolis, France
| | | | - Frederic Fabre
- INRA, UMR 1065 Santé et Agroécologie du Vignoble, BP 81, 33883 Villenave d'Ornon cedex, France
| | - Benoit Moury
- INRA, UR407 PV, Unité de Pathologie Végétale, Domaine St Maurice - 67 Allée des Chênes, CS 60094, F-84143 Montfavet Cedex, France
| | - Alain Palloix
- INRA, UR1052 GAFL, Unité de Génétique et Amélioration des Fruits et Légumes, Domaine St Maurice - 67 Allée des Chênes, CS 60094, F-84143 Montfavet Cedex, France
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7
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Caranta C, Coleno F, Durel CE, Jeuffroy MH, Lannou C, Moury B, Palloix A. Special issue for the plant resistance sustainability international conference, la colle sur loup, france, 16-19 october 2012. Infect Genet Evol 2016; 27:445. [PMID: 25267145 DOI: 10.1016/j.meegid.2014.09.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Carole Caranta
- INRA Département Biologie et Amélioration des Plantes (BAP), Versailles, France.
| | - François Coleno
- UMR1048 SADAPT, INRA-AgroParisTech, Thiverval-Grignon, France.
| | - Charles-Eric Durel
- INRA Centre d'Angers-Nantes, UMR1345 Institut de Recherche en Horticulture et Semences - IRHS, Beaucouzé, France.
| | | | - Christian Lannou
- INRA Département Santé des Plantes et Environnement (SPE), Sophia-Antipolis, France.
| | - Benoît Moury
- INRA Centre PACA, UR407 Pathologie Végétale, Domaine St Maurice, Montfavet, France.
| | - Alain Palloix
- INRA Centre PACA, UR1052 Génétique et Amélioration des Fruits et Légumes, Montfavet, France.
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8
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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. Front Plant Sci 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] [What about the content of this article? (0)] [Affiliation(s)] [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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Quenouille J, Saint-Felix L, Moury B, Palloix A. Diversity of genetic backgrounds modulating the durability of a major resistance gene. Analysis of a core collection of pepper landraces resistant to Potato virus Y. Mol Plant Pathol 2016; 17:296-302. [PMID: 25967744 PMCID: PMC6638519 DOI: 10.1111/mpp.12277] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The evolution of resistance-breaking capacity in pathogen populations has been shown to depend on the plant genetic background surrounding the resistance genes. We evaluated a core collection of pepper (Capsicum annuum) landraces, representing the worldwide genetic diversity, for its ability to modulate the breakdown frequency by Potato virus Y of major resistance alleles at the pvr2 locus encoding the eukaryotic initiation factor 4E (eIF4E). Depending on the pepper landrace, the breakdown frequency of a given resistance allele varied from 0% to 52.5%, attesting to their diversity and the availability of genetic backgrounds favourable to resistance durability in the plant germplasm. The mutations in the virus genome involved in resistance breakdown also differed between plant genotypes, indicating differential selection effects exerted on the virus population by the different genetic backgrounds. The breakdown frequency was positively correlated with the level of virus accumulation, confirming the impact of quantitative resistance loci on resistance durability. Among these loci, pvr6, encoding an isoform of eIF4E, was associated with a major effect on virus accumulation and on the breakdown frequency of the pvr2-mediated resistance. This exploration of plant genetic diversity delivered new resources for the control of pathogen evolution and the increase in resistance durability.
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Affiliation(s)
- Julie Quenouille
- INRA, UR407 Pathologie Végétale, CS 60094, F-84143, Montfavet Cedex, France
- INRA, UR1052 GAFL, CS 60094, F-84143, Montfavet Cedex, France
| | - Ludovic Saint-Felix
- INRA, UR407 Pathologie Végétale, CS 60094, F-84143, Montfavet Cedex, France
- INRA, UR1052 GAFL, CS 60094, F-84143, Montfavet Cedex, France
| | - Benoit Moury
- INRA, UR407 Pathologie Végétale, CS 60094, F-84143, Montfavet Cedex, France
| | - Alain Palloix
- INRA, UR1052 GAFL, CS 60094, F-84143, Montfavet Cedex, France
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10
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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 Manag Sci 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] [What about the content of this article? (0)] [Affiliation(s)] [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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11
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Qin C, Yu C, Shen Y, Fang X, Chen L, Min J, Cheng J, Zhao S, Xu M, Luo Y, Yang Y, Wu Z, Mao L, Wu H, Ling-Hu C, Zhou H, Lin H, González-Morales S, Trejo-Saavedra DL, Tian H, Tang X, Zhao M, Huang Z, Zhou A, Yao X, Cui J, Li W, Chen Z, Feng Y, Niu Y, Bi S, Yang X, Li W, Cai H, Luo X, Montes-Hernández S, Leyva-González MA, Xiong Z, He X, Bai L, Tan S, Tang X, Liu D, Liu J, Zhang S, Chen M, Zhang L, Zhang L, Zhang Y, Liao W, Zhang Y, Wang M, Lv X, Wen B, Liu H, Luan H, Zhang Y, Yang S, Wang X, Xu J, Li X, Li S, Wang J, Palloix A, Bosland PW, Li Y, Krogh A, Rivera-Bustamante RF, Herrera-Estrella L, Yin Y, Yu J, Hu K, Zhang Z. Whole-genome sequencing of cultivated and wild peppers provides insights into Capsicum domestication and specialization. Proc Natl Acad Sci U S A 2014; 111:5135-5140. [PMID: 24591624 DOI: 10.4172/2168-9881.s1.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2023] Open
Abstract
As an economic crop, pepper satisfies people's spicy taste and has medicinal uses worldwide. To gain a better understanding of Capsicum evolution, domestication, and specialization, we present here the genome sequence of the cultivated pepper Zunla-1 (C. annuum L.) and its wild progenitor Chiltepin (C. annuum var. glabriusculum). We estimate that the pepper genome expanded ∼0.3 Mya (with respect to the genome of other Solanaceae) by a rapid amplification of retrotransposons elements, resulting in a genome comprised of ∼81% repetitive sequences. Approximately 79% of 3.48-Gb scaffolds containing 34,476 protein-coding genes were anchored to chromosomes by a high-density genetic map. Comparison of cultivated and wild pepper genomes with 20 resequencing accessions revealed molecular footprints of artificial selection, providing us with a list of candidate domestication genes. We also found that dosage compensation effect of tandem duplication genes probably contributed to the pungent diversification in pepper. The Capsicum reference genome provides crucial information for the study of not only the evolution of the pepper genome but also, the Solanaceae family, and it will facilitate the establishment of more effective pepper breeding programs.
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Affiliation(s)
- Cheng Qin
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Maize Research Institute of Sichuan Agricultural University, Wenjiang 611130, China
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12
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Quenouille J, Paulhiac E, Moury B, Palloix A. Quantitative trait loci from the host genetic background modulate the durability of a resistance gene: a rational basis for sustainable resistance breeding in plants. Heredity (Edinb) 2014; 112:579-87. [PMID: 24569635 DOI: 10.1038/hdy.2013.138] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Revised: 11/06/2013] [Accepted: 11/08/2013] [Indexed: 11/09/2022] Open
Abstract
The combination of major resistance genes with quantitative resistance factors is hypothesized as a promising breeding strategy to preserve the durability of resistant cultivar, as recently observed in different pathosystems. Using the pepper (Capsicum annuum)/Potato virus Y (PVY, genus Potyvirus) pathosystem, we aimed at identifying plant genetic factors directly affecting the frequency of virus adaptation to the major resistance gene pvr2(3) and at comparing them with genetic factors affecting quantitative resistance. The resistance breakdown frequency was a highly heritable trait (h(2)=0.87). Four loci including additive quantitative trait loci (QTLs) and epistatic interactions explained together 70% of the variance of pvr2(3) breakdown frequency. Three of the four QTLs controlling pvr2(3) breakdown frequency were also involved in quantitative resistance, strongly suggesting that QTLs controlling quantitative resistance have a pleiotropic effect on the durability of the major resistance gene. With the first mapping of QTLs directly affecting resistance durability, this study provides a rationale for sustainable resistance breeding. Surprisingly, a genetic trade-off was observed between the durability of PVY resistance controlled by pvr2(3) and the spectrum of the resistance against different potyviruses. This trade-off seemed to have been resolved by the combination of minor-effect durability QTLs under long-term farmer selection.
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Affiliation(s)
- J Quenouille
- 1] INRA, UR1052 GAFL, Montfavet Cedex, France [2] INRA, UR407 Pathologie Végétale, Montfavet Cedex, France
| | - E Paulhiac
- INRA, UR1052 GAFL, Montfavet Cedex, France
| | - B Moury
- INRA, UR407 Pathologie Végétale, Montfavet Cedex, France
| | - A Palloix
- INRA, UR1052 GAFL, Montfavet Cedex, France
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13
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Djian-Caporalino C, Palloix A, Fazari A, Marteu N, Barbary A, Abad P, Sage-Palloix AM, Mateille T, Risso S, Lanza R, Taussig C, Castagnone-Sereno P. Pyramiding, alternating or mixing: comparative performances of deployment strategies of nematode resistance genes to promote plant resistance efficiency and durability. BMC Plant Biol 2014; 14:53. [PMID: 24559060 PMCID: PMC3944934 DOI: 10.1186/1471-2229-14-53] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Accepted: 02/14/2014] [Indexed: 05/18/2023]
Abstract
BACKGROUND Resistant cultivars are key elements for pathogen control and pesticide reduction, but their repeated use may lead to the emergence of virulent pathogen populations, able to overcome the resistance. Increased research efforts, mainly based on theoretical studies, explore spatio-temporal deployment strategies of resistance genes in order to maximize their durability. We evaluated experimentally three of these strategies to control root-knot nematodes: cultivar mixtures, alternating and pyramiding resistance genes, under controlled and field conditions over a 3-years period, assessing the efficiency and the durability of resistance in a protected crop rotation system with pepper as summer crop and lettuce as winter crop. RESULTS The choice of the resistance gene and the genetic background in which it is introgressed, affected the frequency of resistance breakdown. The pyramiding of two different resistance genes in one genotype suppressed the emergence of virulent isolates. Alternating different resistance genes in rotation was also efficient to decrease virulent populations in fields due to the specificity of the virulence and the trapping effect of resistant plants. Mixing resistant cultivars together appeared as a less efficient strategy to control nematodes. CONCLUSIONS This work provides experimental evidence that, in a cropping system with seasonal sequences of vegetable species, pyramiding or alternating resistance genes benefit yields in the long-term by increasing the durability of resistant cultivars and improving the long-term control of a soil-borne pest. To our knowledge, this result is the first one obtained for a plant-nematode interaction, which helps demonstrate the general applicability of such strategies for breeding and sustainable management of resistant cultivars against pathogens.
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Affiliation(s)
| | - Alain Palloix
- INRA, UR1052, Génétique et Amélioration des Fruits et Légumes, CS 60094, Montfavet, Cedex F-84143, France
| | - Ariane Fazari
- INRA, UMR1355 INRA/UNSA/CNRS, Institut Sophia Agrobiotech, BP167, Sophia Antipolis F-06903, France
| | - Nathalie Marteu
- INRA, UMR1355 INRA/UNSA/CNRS, Institut Sophia Agrobiotech, BP167, Sophia Antipolis F-06903, France
| | - Arnaud Barbary
- INRA, UMR1355 INRA/UNSA/CNRS, Institut Sophia Agrobiotech, BP167, Sophia Antipolis F-06903, France
| | - Pierre Abad
- INRA, UMR1355 INRA/UNSA/CNRS, Institut Sophia Agrobiotech, BP167, Sophia Antipolis F-06903, France
| | - Anne-Marie Sage-Palloix
- INRA, UR1052, Génétique et Amélioration des Fruits et Légumes, CS 60094, Montfavet, Cedex F-84143, France
| | - Thierry Mateille
- IRD, UMR CBGP, Campus de Baillarguet, CS30016, Montferrier-sur-Lez, Cedex F-34988, France
| | - Sabine Risso
- Chambre d’Agriculture des Alpes Maritimes, MIN Fleurs 17 - Box 85, Nice, Cedex 06286, France
| | - Roger Lanza
- Chambre d’Agriculture des Alpes Maritimes, MIN Fleurs 17 - Box 85, Nice, Cedex 06286, France
| | - Catherine Taussig
- APREL, Association Provençale de Recherche et d’Expérimentation Légumière, Route de Mollégès, Saint-Rémy de Provence F-13210, France
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Barbary A, Palloix A, Fazari A, Marteu N, Castagnone-Sereno P, Djian-Caporalino C. The plant genetic background affects the efficiency of the pepper major nematode resistance genes Me1 and Me3. Theor Appl Genet 2014; 127:499-507. [PMID: 24258389 DOI: 10.1007/s00122-013-2235-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2013] [Accepted: 11/05/2013] [Indexed: 06/02/2023]
Abstract
The plant genetic background influences the efficiency of major resistance genes to root-knot nematodes in pepper and has to be considered in breeding strategies. Root-knot nematodes (RKNs), Meloidogyne spp., are extremely polyphagous plant parasites worldwide. Since the use of most chemical nematicides is being prohibited, genetic resistance is an efficient alternative way to protect crops against these pests. However, nematode populations proved able to breakdown plant resistance, and genetic resources in terms of resistance genes (R-genes) are limited. Sustainable management of these valuable resources is thus a key point of R-gene durability. In pepper, Me1 and Me3 are two dominant major R-genes, currently used in breeding programs to control M. arenaria, M. incognita and M. javanica, the three main RKN species. These two genes differ in the hypersensitive response induced by nematode infection. In this study, they were introgressed in either a susceptible or a partially resistant genetic background, in either homozygous or heterozygous allelic status. Challenging these genotypes with an avirulent M. incognita isolate demonstrated that (1) the efficiency of the R-genes in reducing the reproductive potential of RKNs is strongly affected by the plant genetic background, (2) the allelic status of the R-genes has no effect on nematode reproduction. These results highlight the primary importance of the choice of both the R-gene and the genetic background into which it is introgressed during the selection of new elite cultivars by plant breeders.
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Affiliation(s)
- A Barbary
- INRA, UMR1355 Institut Sophia Agrobiotech, 06903, Sophia Antipolis, France,
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15
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Moury B, Charron C, Janzac B, Simon V, Gallois JL, Palloix A, Caranta C. Evolution of plant eukaryotic initiation factor 4E (eIF4E) and potyvirus genome-linked protein (VPg): a game of mirrors impacting resistance spectrum and durability. Infect Genet Evol 2013; 27:472-80. [PMID: 24309680 DOI: 10.1016/j.meegid.2013.11.024] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Revised: 11/18/2013] [Accepted: 11/25/2013] [Indexed: 11/29/2022]
Abstract
Polymorphism in the plant eukaryotic translation initiation factor 4E (eIF4E) and potyvirus genome-linked protein (VPg) determine, in many cases, the outcome of the confrontation between these two organisms: compatibility (i.e. infection of the plant by the virus) or incompatibility (i.e. resistance of the plant to the virus). The two interacting proteins eIF4E and VPg show strikingly similar evolution patterns. Most codon positions in their coding sequences are highly constrained for nonsynonymous substitutions but a small number shows evidence for positive selection. Several of these latter positions were shown to be functionally important, conferring resistance to the host or pathogenicity to the virus. Determining the mutational pathways involved in pepper eIF4E diversification revealed a link between an increase of the pepper resistance spectrum towards a panel of potyvirus species and an increase of durability of the resistance towards Potato virus Y. This relationship questions the interest of using more generally the spectrum of action of a plant resistance gene as a predictor of its durability potential.
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Affiliation(s)
- B Moury
- INRA, UR407 Pathologie Végétale, Domaine Saint Maurice, CS 60094, F-84143 Montfavet Cedex, France.
| | - C Charron
- INRA, UR1052, Génétique et Amélioration des Fruits et Légumes, Domaine Saint Maurice, CS 60094, F-84143 Montfavet Cedex, France
| | - B Janzac
- INRA, UR407 Pathologie Végétale, Domaine Saint Maurice, CS 60094, F-84143 Montfavet Cedex, France; INRA, UR1052, Génétique et Amélioration des Fruits et Légumes, Domaine Saint Maurice, CS 60094, F-84143 Montfavet Cedex, France
| | - V Simon
- INRA, UR407 Pathologie Végétale, Domaine Saint Maurice, CS 60094, F-84143 Montfavet Cedex, France
| | - J L Gallois
- INRA, UR1052, Génétique et Amélioration des Fruits et Légumes, Domaine Saint Maurice, CS 60094, F-84143 Montfavet Cedex, France
| | - A Palloix
- INRA, UR1052, Génétique et Amélioration des Fruits et Légumes, Domaine Saint Maurice, CS 60094, F-84143 Montfavet Cedex, France
| | - C Caranta
- INRA, UR1052, Génétique et Amélioration des Fruits et Légumes, Domaine Saint Maurice, CS 60094, F-84143 Montfavet Cedex, France
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16
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Alimi NA, Bink MCAM, Dieleman JA, Magán JJ, Wubs AM, Palloix A, van Eeuwijk FA. Multi-trait and multi-environment QTL analyses of yield and a set of physiological traits in pepper. Theor Appl Genet 2013; 126:2597-625. [PMID: 23903631 DOI: 10.1007/s00122-013-2160-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Accepted: 07/12/2013] [Indexed: 05/24/2023]
Abstract
A mixed model framework was defined for QTL analysis of multiple traits across multiple environments for a RIL population in pepper. Detection power for QTLs increased considerably and detailed study of QTL by environment interactions and pleiotropy was facilitated. For many agronomic crops, yield is measured simultaneously with other traits across multiple environments. The study of yield can benefit from joint analysis with other traits and relations between yield and other traits can be exploited to develop indirect selection strategies. We compare the performance of three multi-response QTL approaches based on mixed models: a multi-trait approach (MT), a multi-environment approach (ME), and a multi-trait multi-environment approach (MTME). The data come from a multi-environment experiment in pepper, for which 15 traits were measured in four environments. The approaches were compared in terms of number of QTLs detected for each trait, the explained variance, and the accuracy of prediction for the final QTL model. For the four environments together, the superior MTME approach delivered a total of 47 regions containing putative QTLs. Many of these QTLs were pleiotropic and showed quantitative QTL by environment interaction. MTME was superior to ME and MT in the number of QTLs, the explained variance and accuracy of predictions. The large number of model parameters in the MTME approach was challenging and we propose several guidelines to help obtain a stable final QTL model. The results confirmed the feasibility and strengths of novel mixed model QTL methodology to study the architecture of complex traits.
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Affiliation(s)
- N A Alimi
- Biometris-Wageningen University & Research Centre, P. O. Box 100, 6700 AC, Wageningen, The Netherlands
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17
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Alimi NA, Bink MCAM, Dieleman JA, Magán JJ, Wubs AM, Palloix A, van Eeuwijk FA. Multi-trait and multi-environment QTL analyses of yield and a set of physiological traits in pepper. Theor Appl Genet 2013. [PMID: 23903631 DOI: 10.1007/s00122-013-2160-2163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
A mixed model framework was defined for QTL analysis of multiple traits across multiple environments for a RIL population in pepper. Detection power for QTLs increased considerably and detailed study of QTL by environment interactions and pleiotropy was facilitated. For many agronomic crops, yield is measured simultaneously with other traits across multiple environments. The study of yield can benefit from joint analysis with other traits and relations between yield and other traits can be exploited to develop indirect selection strategies. We compare the performance of three multi-response QTL approaches based on mixed models: a multi-trait approach (MT), a multi-environment approach (ME), and a multi-trait multi-environment approach (MTME). The data come from a multi-environment experiment in pepper, for which 15 traits were measured in four environments. The approaches were compared in terms of number of QTLs detected for each trait, the explained variance, and the accuracy of prediction for the final QTL model. For the four environments together, the superior MTME approach delivered a total of 47 regions containing putative QTLs. Many of these QTLs were pleiotropic and showed quantitative QTL by environment interaction. MTME was superior to ME and MT in the number of QTLs, the explained variance and accuracy of predictions. The large number of model parameters in the MTME approach was challenging and we propose several guidelines to help obtain a stable final QTL model. The results confirmed the feasibility and strengths of novel mixed model QTL methodology to study the architecture of complex traits.
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Affiliation(s)
- N A Alimi
- Biometris-Wageningen University & Research Centre, P. O. Box 100, 6700 AC, Wageningen, The Netherlands
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18
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Quenouille J, Montarry J, Palloix A, Moury B. Farther, slower, stronger: how the plant genetic background protects a major resistance gene from breakdown. Mol Plant Pathol 2013; 14:109-18. [PMID: 23046402 PMCID: PMC6638760 DOI: 10.1111/j.1364-3703.2012.00834.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Genetic resistance provides efficient control of crop diseases, but is limited by pathogen evolution capacities which often result in resistance breakdown. It has been demonstrated recently, in three different pathosystems, that polygenic resistances combining a major-effect gene and quantitative resistance controlled by the genetic background are more durable than monogenic resistances (with the same major gene in a susceptible genetic background), but the underlying mechanisms are unknown. Using the pepper-Potato virus Y system, we examined three mechanisms that could account for the greater durability of the polygenic resistances: (i) the additional quantitative resistance conferred by the genetic background; (ii) the increase in the number of mutations required for resistance breakdown; and (iii) the slower selection of adapted resistance-breaking mutants within the viral population. The three mechanisms were experimentally validated. The first explained a large part of the variation in resistance breakdown frequency and is therefore expected to be a major determinant of resistance durability. Quantitative resistance factors also had an influence on the second mechanism by modifying the virus mutational pathways towards resistance breakdown and could also have an influence on the third mechanism by increasing genetic drift effects on the viral population. The relevance of these results for other plant-pathogen systems and their importance in plant breeding are discussed.
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19
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van der Heijden G, Song Y, Horgan G, Polder G, Dieleman A, Bink M, Palloix A, van Eeuwijk F, Glasbey C. SPICY: towards automated phenotyping of large pepper plants in the greenhouse. Funct Plant Biol 2012; 39:870-877. [PMID: 32480837 DOI: 10.1071/fp12019] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2012] [Accepted: 04/02/2012] [Indexed: 05/26/2023]
Abstract
Most high-throughput systems for automated plant phenotyping involve a fixed recording cabinet to which plants are transported. However, important greenhouse plants like pepper are too tall to be transported. In this research we developed a system to automatically measure plant characteristics of tall pepper plants in the greenhouse. With a device equipped with multiple cameras, images of plants are recorded at a 5cm interval over a height of 3m. Two types of features are extracted: (1) features from a 3D reconstruction of the plant canopy; and (2) statistical features derived directly from RGB images. The experiment comprised 151 genotypes of a recombinant inbred population of pepper, to examine the heritability and quantitative trait loci (QTL) of the features. Features extracted from the 3D reconstruction of the canopy were leaf size and leaf angle, with heritabilities of 0.70 and 0.56 respectively. Three QTL were found for leaf size, and one for leaf angle. From the statistical features, plant height showed a good correlation (0.93) with manual measurements, and QTL were in accordance with QTL of manual measurements. For total leaf area, the heritability was 0.55, and two of the three QTL found by manual measurement were found by image analysis.
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Affiliation(s)
| | - Yu Song
- BioSS, King's Buildings, Edinburgh EH9 3JZ, UK
| | | | - Gerrit Polder
- Wageningen UR, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Anja Dieleman
- Wageningen UR, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Marco Bink
- Wageningen UR, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Alain Palloix
- INRA, UR1052 GAFL, BP 94, F-84143 Montfavet cedex, France
| | - Fred van Eeuwijk
- Wageningen UR, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
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20
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Lefebvre V, Palloix A, Caranta C, Pochard E. Construction of an intraspecific integrated linkage map of pepper using molecular markers and doubled-haploid progenies. Genome 2012; 38:112-21. [PMID: 18470157 DOI: 10.1139/g95-014] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
An integrated molecular linkage map of pepper (Capsicum annuum L.), including mainly RFLP and RAPD markers, has been constructed by alignment of three intraspecific linkage maps generated by segregating doubled-haploid progenies. A total of 85 markers covered approximately 820 cM in 14 linkage groups. Four linkage groups were assigned to 4 chromosomes. Two new genes of agronomic interest were located: L controlling hypersensitive resistance to TMV and up controlling the erect habit of the fruits. The C gene controlling the fruit pungency was more precisely located. This map is estimated to represent from 36 to 59% of the total pepper genome. An examination of segregation data has revealed several genomic regions with aberrant segregation ratios often favouring the agronomic big-fruited parents, particularly in crosses involving the exotic parent CM334, suggesting that these genome regions are subjected to selection during the process of doubled-haploid production. The suitability of doubled-haploid progenies for mapping projects and the differences observed between this intraspecific integrated map with earlier published interspecific pepper maps are discussed.
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21
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Montarry J, Cartier E, Jacquemond M, Palloix A, Moury B. Virus adaptation to quantitative plant resistance: erosion or breakdown? J Evol Biol 2012; 25:2242-52. [DOI: 10.1111/j.1420-9101.2012.02600.x] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2012] [Revised: 07/19/2012] [Accepted: 07/21/2012] [Indexed: 11/30/2022]
Affiliation(s)
| | - E. Cartier
- INRA; UR407 Pathologie Végétale; Montfavet; France
| | | | - A. Palloix
- INRA; UR1052 Génétique et Amélioration des Fruits et Légumes (GAFL); Montfavet; France
| | - B. Moury
- INRA; UR407 Pathologie Végétale; Montfavet; France
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22
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Nicolaï M, Pisani C, Bouchet JP, Vuylsteke M, Palloix A. Short Communication Discovery of a large set of SNP and SSR genetic markers by high-throughput sequencing of pepper (Capsicum annuum). Genet Mol Res 2012; 11:2295-300. [DOI: 10.4238/2012.august.13.3] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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23
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Lebeau A, Daunay MC, Frary A, Palloix A, Wang JF, Dintinger J, Chiroleu F, Wicker E, Prior P. Bacterial wilt resistance in tomato, pepper, and eggplant: genetic resources respond to diverse strains in the Ralstonia solanacearum species complex. Phytopathology 2011; 101:154-65. [PMID: 20795852 DOI: 10.1094/phyto-02-10-0048] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Bacterial wilt, caused by strains belonging to the Ralstonia solanacearum species complex, inflicts severe economic losses in many crops worldwide. Host resistance remains the most effective control strategy against this disease. However, wilt resistance is often overcome due to the considerable variation among pathogen strains. To help breeders circumvent this problem, we assembled a worldwide collection of 30 accessions of tomato, eggplant and pepper (Core-TEP), most of which are commonly used as sources of resistance to R. solanacearum or for mapping quantitative trait loci. The Core-TEP lines were challenged with a core collection of 12 pathogen strains (Core-Rs2) representing the phylogenetic diversity of R. solanacearum. We observed six interaction phenotypes, from highly susceptible to highly resistant. Intermediate phenotypes resulted from the plants' ability to tolerate latent infections (i.e., bacterial colonization of vascular elements with limited or no wilting). The Core-Rs2 strains partitioned into three pathotypes on pepper accessions, five on tomato, and six on eggplant. A "pathoprofile" concept was developed to characterize the strain clusters, which displayed six virulence patterns on the whole set of Core-TEP host accessions. Neither pathotypes nor pathoprofiles were phylotype specific. Pathoprofiles with high aggressiveness were mainly found in strains from phylotypes I, IIB, and III. One pathoprofile included a strain that overcame almost all resistance sources.
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Affiliation(s)
- A Lebeau
- CIRAD, UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropicale, 7 Chemin de l'IRAT, 97410, Saint-Pierre Cedex, La Réunion, France
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24
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Janzac B, Montarry J, Palloix A, Navaud O, Moury B. A point mutation in the polymerase of Potato virus Y confers virulence toward the Pvr4 resistance of pepper and a high competitiveness cost in susceptible cultivar. Mol Plant Microbe Interact 2010; 23:823-830. [PMID: 20459321 DOI: 10.1094/mpmi-23-6-0823] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
To understand why the Pvr4 resistance of pepper against Potyvirus spp. remained durable in field conditions while virulent Potato virus Y (PVY) variants could be selected in the laboratory, we studied the molecular mechanisms which generated these variants and the consequences on viral fitness. Using a reverse genetics approach with an infectious cDNA clone of PVY, we found that the region coding for the NIb protein (RNA-dependent RNA polymerase) of PVY was the avirulence factor corresponding to Pvr4 and that a single nonsynonymous nucleotide substitution in that region, an adenosine to guanosine substitution at position 8,424 of the PVY genome (A(8424)G), was sufficient for virulence. This substitution imposed a high competitiveness cost to the virus against an avirulent PVY variant in plants devoid of Pvr4. In addition, during serial passages in susceptible pepper plants, the only observed possibility of the virulent mutant to increase its fitness was through the G(8424)A reversion, strengthening the high durability potential of the Pvr4 resistance. This is in accordance with the fact that the NIb protein is one of the most constrained proteins expressed by the PVY genome and, more generally, by Potyvirus spp., and with a previously developed model predicting the durability of virus resistances as a function of the evolutionary constraint applied on corresponding avirulence factors.
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Rubio M, Nicolaï M, Caranta C, Palloix A. Allele mining in the pepper gene pool provided new complementation effects between pvr2-eIF4E and pvr6-eIF(iso)4E alleles for resistance to pepper veinal mottle virus. J Gen Virol 2009; 90:2808-2814. [DOI: 10.1099/vir.0.013151-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Molecular cloning of recessive resistance genes to potyviruses in a large range of host species identified the eukaryotic translation initiation factor 4E (eIF4E) as an essential determinant in the outcome of potyvirus infection. Resistance results from a few amino acid changes in the eIF4E protein encoded by the recessive resistance allele that disrupt the direct interaction with the potyviral protein VPg. In plants, several loci encode two protein subfamilies, eIF4E and eIF(iso)4E. While most eIF4E-mediated resistance to potyviruses depends on mutations in a single eIF4E protein, simultaneous mutations in eIF4E (corresponding to the pvr2 locus) and eIF(iso)4E (corresponding to the pvr6 locus) are required to prevent pepper veinal mottle virus (PVMV) infection in pepper. We used this model to look for additional alleles at the pvr2-eIF4E locus that result in resistance when combined with the pvr6-eIF(iso)4E resistant allele. Among the 12 pvr2-eIF4E resistance alleles sequenced in the pepper gene pool, three were shown to have a complementary effect with pvr6-eIF(iso)4E for resistance. Two amino acid changes were exclusively shared by these three alleles and were systematically associated with a second amino acid change, suggesting that these substitutions are associated with resistance expression. The availability of new resistant allele combinations increases the possibility for the durable deployment of resistance against this pepper virus which is prevalent in Africa.
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Affiliation(s)
- Manuel Rubio
- INRA, Centre d'Avignon, UR1052, Unité de Génétique et Amélioration des Fruits et Légumes, BP 94, 84143 Montfavet cedex, France
| | - Maryse Nicolaï
- INRA, Centre d'Avignon, UR1052, Unité de Génétique et Amélioration des Fruits et Légumes, BP 94, 84143 Montfavet cedex, France
| | - Carole Caranta
- INRA, Centre d'Avignon, UR1052, Unité de Génétique et Amélioration des Fruits et Légumes, BP 94, 84143 Montfavet cedex, France
| | - Alain Palloix
- INRA, Centre d'Avignon, UR1052, Unité de Génétique et Amélioration des Fruits et Légumes, BP 94, 84143 Montfavet cedex, France
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Tam SM, Lefebvre V, Palloix A, Sage-Palloix AM, Mhiri C, Grandbastien MA. LTR-retrotransposons Tnt1 and T135 markers reveal genetic diversity and evolutionary relationships of domesticated peppers. Theor Appl Genet 2009; 119:973-89. [PMID: 19618162 DOI: 10.1007/s00122-009-1102-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2009] [Accepted: 06/25/2009] [Indexed: 05/03/2023]
Abstract
Plant genetic resources often constitute the foundation of successful breeding programs. Pepper (Capsicum annuum L.) is one of the most economically important and diversely utilized Solanaceous crop species worldwide, but less studied compared to tomato and potato. We developed and used molecular markers based on two copia-type retrotransposons, Tnt1 and T135, in a set of Capsicum species and wild relatives from diverse geographical origins. Results showed that Tnt1 and T135 insertion polymorphisms are very useful for studying genetic diversity and relationships within and among pepper species. Clusters of accessions correspond to cultivar types based on fruit shape, pungency, geographic origin and pedigree. Genetic diversity values, normally reflective of past transposition activity and population dynamics, showed positive correlation with the average number of insertions per accession. Similar evolutionary relationships are observed to that inferred by previous karyosystematics studies. These observations support the possibility that retrotransposons have contributed to genome inflation during Capsicum evolution.
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Affiliation(s)
- Sheh May Tam
- Laboratoire de Biologie Cellulaire, UR501, Institut Jean-Pierre Bourgin, INRA, 78026, Versailles Cedex, France
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Janzac B, Fabre F, Palloix A, Moury B. Constraints on evolution of virus avirulence factors predict the durability of corresponding plant resistances. Mol Plant Pathol 2009; 10:599-610. [PMID: 19694951 PMCID: PMC6640373 DOI: 10.1111/j.1364-3703.2009.00554.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
SUMMARY Understanding the factors driving pathogen emergence and re-emergence is a major challenge, particularly in agriculture, where the use of resistant plant cultivars imposes strong selective pressures on plant pathogen populations and leads frequently to 'resistance breakdown'. Presently, durable resistances are only identified after a long period of large-scale cultivation of resistant cultivars. We propose a new predictor of the durability of plant resistance. Because resistance breakdown involves modifications in the avirulence factors of pathogens, we tested for correlations between the evolutionary constraints acting on avirulence factors or their diversity and the durability of the corresponding resistance genes in the case of plant-virus interactions. An analysis performed on 20 virus species-resistance gene combinations revealed that the selective constraints applied on amino acid substitutions in virus avirulence factors correlate with the observed durability of the corresponding resistance genes. On the basis of this result, a model predicting the potential durability of resistance genes as a function of the selective constraints applied on the corresponding avirulence factors is proposed to help breeders to select the most durable resistance genes.
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Affiliation(s)
- Berenger Janzac
- INRA, UR407 Pathologie Végétale, Domaine Saint Maurice, BP94, F-84140 Montfavet, France.
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Barchi L, Lefebvre V, Sage-Palloix AM, Lanteri S, Palloix A. QTL analysis of plant development and fruit traits in pepper and performance of selective phenotyping. Theor Appl Genet 2009; 118:1157-71. [PMID: 19219599 DOI: 10.1007/s00122-009-0970-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2008] [Accepted: 01/15/2009] [Indexed: 05/03/2023]
Abstract
A QTL analysis was performed to determine the genetic basis of 13 horticultural traits conditioning yield in pepper (Capsicum annuum). The mapping population was a large population of 297 recombinant inbred lines (RIL) originating from a cross between the large-fruited bell pepper cultivar 'Yolo Wonder' and the small-fruited chilli pepper 'Criollo de Morelos 334'. A total of 76 QTLs were detected for 13 fruit and plant traits, grouped in 28 chromosome regions. These QTLs explained together between 7% (internode growth time) and 91% (fruit diameter) of the phenotypic variation. The QTL analysis was also performed on two subsets of 141 and 93 RILs sampled using the MapPop software. The smaller populations allowed for the detection of a reduced set of QTLs and reduced the overall percentage of trait variation explained by QTLs. The frequency of false positives as well as the individual effect of QTLs increased in reduced population sets as a result of reduced sampling. The results from the QTL analysis permitted an overall glance over the genetic architecture of traits considered by breeders for selection. Colinearities between clusters of QTLs controlling fruit traits and/or plant development in distinct pepper species and in related solanaceous crop species (tomato and eggplant) suggests that shared mechanisms control the shape and growth of different organs throughout these species.
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Affiliation(s)
- Lorenzo Barchi
- INRA-Avignon, UR 1052, Génétique et Amélioration des Fruits et Légumes, BP 94, 84143, Montfavet Cedex, France
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Fabre F, Bruchou C, Palloix A, Moury B. Key determinants of resistance durability to plant viruses: insights from a model linking within- and between-host dynamics. Virus Res 2009; 141:140-9. [PMID: 19159653 DOI: 10.1016/j.virusres.2008.11.021] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/18/2008] [Indexed: 10/21/2022]
Abstract
The emergence of new genotypes of parasites involves several evolutionary, epidemiological and ecological processes whose individual effects and interactions are difficult to disentangle using experimental approaches. Here, a model is proposed to investigate how these processes lead to the emergence of plant viral genotypes breaking down qualitative resistance genes. At the individual plant scale, selection, drift and mutation processes shape the evolution of viral populations from a set of differential equations. The spatial segregation of virus genotypes in their hosts is also considered. At the host population scale, the epidemiological dynamics is given by an individual-based algorithm. Global sensitivity analyses allowed ranking the ten demo-genetic and epidemiological parameters of the model according to their impact on the mean and variance of the risk of breakdown of a plant resistance. Demo-genetic parameters (number and nature of mutations involved in breakdown, fitness of mutant genotypes) had the largest impact on the mean breakdown risk, whereas epidemiological parameters had more influence on its standard deviation. It is discussed how these results can be used to choose the potentially most durable resistance genes among a pool of candidates. Finally, our analyses point out the parameters which should be estimated more precisely to improve durability predictions.
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Affiliation(s)
- Frédéric Fabre
- INRA, UR 407 Unité Pathologie Végétale, Montfavet, France.
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Palloix A, Ayme V, Moury B. Durability of plant major resistance genes to pathogens depends on the genetic background, experimental evidence and consequences for breeding strategies. New Phytol 2009; 183:190-199. [PMID: 19344475 DOI: 10.1111/j.1469-8137.2009.02827.x] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
* The breakdown of plant resistance by pathogen populations is a limit to the genetic control of crop disease. Polygenic resistance is postulated as a durable alternative to defeated major resistance genes. Here, we tested this postulate in the pepper-Potato virus Y interaction. * The virus was selected for virulence towards monogenic and polygenic host resistance, using serial inoculations in laboratory and in natural epidemic conditions. The frequency of resistance breakdown and the genetic changes in the virus avirulence gene were analysed. * The monogenic resistance provided by the pvr2(3) gene was defeated at high frequency when introgressed in a susceptible genetic background whereas it was not when combined to partial resistance quantitative trait loci. The suppression of emergence of virulent mutants because of the genetic background resulted both from a differential selection effect and the necessity for the virus to generate multiple mutations. The virus adaptation to the polygenic resistance required a step-by-step selection with a primary selection for virulence towards the major gene, followed by selection for adaptation to the genetic background. * Polygenic resistance proved more durable than monogenic resistance, but breeding strategies giving priority to major resistance factors may jeopardize the progress in durability expected from polygenic resistance.
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Affiliation(s)
- A Palloix
- INRA Avignon, GAFL, UR1052, BP194, F-84143 Montfavet cedex, France
| | - V Ayme
- INRA Avignon, GAFL, UR1052, BP194, F-84143 Montfavet cedex, France
- INRA Avignon, Unité de pathologie Végétale, UR 407, BP94, F-84143 Montfavet cedex, France
| | - B Moury
- INRA Avignon, Unité de pathologie Végétale, UR 407, BP94, F-84143 Montfavet cedex, France
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Rubio M, Caranta C, Palloix A. Functional markers for selection of potyvirus resistance alleles at the pvr2-eIF4E locus in pepper using tetra-primer ARMS-PCR. Genome 2008; 51:767-71. [PMID: 18772955 DOI: 10.1139/g08-056] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Functional markers targeted on single nucleotide polymorphisms (SNPs) responsible for phenotypic variation constitute optimal tools for marker-assisted selection (MAS) of resistance alleles with different specificities. Here, we used the tetra-primer ARMS-PCR procedure to assay SNP signatures of four distinct alleles at the pvr2-eIF4E locus, which controls pepper resistance to several potyviruses. These simple, economical, and codominant markers open the way for MAS of pepper genotypes resistant to the potyviral strains and species that are prevalent in distinct cultivation areas across the world.
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Affiliation(s)
- Manuel Rubio
- INRA, Centre d'Avignon, UR1052, Unité de Génétique et Amélioration des Fruits et Légumes, BP 94, 84143 Montfavet CEDEX, France
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Janzac B, Fabre MF, Palloix A, Moury B. Characterization of a new potyvirus infecting pepper crops in Ecuador. Arch Virol 2008; 153:1543-8. [PMID: 18553171 DOI: 10.1007/s00705-008-0132-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2008] [Accepted: 04/30/2008] [Indexed: 11/28/2022]
Abstract
Sequencing 2,951 nucleotides of the 3' proximal region of the genome of a potyvirus isolate collected from Capsicum pubescens (rocoto) pepper in Ecuador revealed that this was the first representative of a new species tentatively named Ecuadorian rocoto virus (ERV). Phylogeny reconstruction showed that this isolate clustered with potato virus V (PVV), Peru tomato virus and wild potato mosaic virus into a monophyletic group, and was closest to PVV. The isolate was shown to be infectious in tobacco, tomato and, contrary to PVV, in pepper. The pvr2(1), pvr2(2), and Pvr4 genes present in many pepper cultivars conferred resistance toward this isolate and could help control ERV.
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Affiliation(s)
- Bérenger Janzac
- Institut National de la Recherche Agronomique, UR 407 Pathologie Végétale, Domaine St Maurice BP 94, Montfavet, France.
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Charron C, Nicolaï M, Gallois JL, Robaglia C, Moury B, Palloix A, Caranta C. Natural variation and functional analyses provide evidence for co-evolution between plant eIF4E and potyviral VPg. Plant J 2008; 54:56-68. [PMID: 18182024 DOI: 10.1111/j.1365-313x.2008.03407.x] [Citation(s) in RCA: 147] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Amino acid substitutions in the eukaryotic translation initiation factor 4E (eIF4E) result in recessive resistance to potyviruses in a range of plant species, including Capsicum spp. Correspondingly, amino acid changes in the central part of the viral genome-linked protein (VPg) are responsible for the potyvirus's ability to overcome eIF4E-mediated resistance. A key observation was that physical interaction between eIF4E and the VPg is required for viral infection, and eIF4E mutations that cause resistance prevent VPg binding and inhibit the viral cycle. In this study, polymorphism analysis of the pvr2-eIF4E coding sequence in a worldwide sample of 25 C. annuum accessions identified 10 allelic variants with exclusively non-synonymous variations clustered in two surface loops of eIF4E. Resistance and genetic complementation assays demonstrated that pvr2 variants, each with signature amino acid changes, corresponded to potyvirus resistance alleles. Systematic analysis of the interactions between eIF4E proteins encoded by the 10 pvr2 alleles and VPgs of virulent and avirulent potato virus Y (PVY) and tobacco etch virus (TEV) strains demonstrated that resistance phenotypes arose from disruption of the interaction between eIF4E and VPg, and that viral adaptation to eIF4E-mediated resistance resulted from restored interaction with the resistance protein. Complementation of an eIF4E knockout yeast strain by C. annuum eIF4E proteins further shows that amino acid changes did not impede essential eIF4E functions. Altogether, these results argue in favour of a co-evolutionary 'arms race' between Capsicum eIF4E and potyviral VPg.
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Affiliation(s)
- Carine Charron
- INRA-UR1052, Genetics and Breeding of Fruits and Vegetables, Domaine St Maurice, BP94, F-84143 Montfavet, France
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Barchi L, Bonnet J, Boudet C, Signoret P, Nagy I, Lanteri S, Palloix A, Lefebvre V. A high-resolution, intraspecific linkage map of pepper (Capsicum annuum L.) and selection of reduced recombinant inbred line subsets for fast mapping. Genome 2007; 50:51-60. [PMID: 17546071 DOI: 10.1139/g06-140] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A high-resolution, intraspecific linkage map of pepper (Capsicum annuum L.) was constructed from a population of 297 recombinant inbred lines. The parents were the large-fruited inbred cultivar 'Yolo Wonder' and the hot pepper line 'Criollo de Morelos 334', which is heavily used as a source of resistance to a number of diseases. A set of 587 markers (507 amplified fragment length polymorphisms, 40 simple sequence repeats, 19 restriction fragment length polymorphisms, 17 sequence-specific amplified polymorphisms, and 4 sequence tagged sites) were used to generate the map; of these, 489 were assembled into 49 linkage groups (LGs), including 14 LGs with 10 to 60 markers per LG and 35 with 2 to 9 markers per LG. The framework map covered 1857 cM with an average intermarker distance of 5.71 cM. Twenty-three LGs, composed of 69% of the markers and covering 1553 cM, were assigned to 1 of the 12 haploid pepper chromosomes, leaving 26 LGs (304 cM) unassigned. The chromosome framework map built with 250 markers led to a high level of mapping confidence and an average intermarker distance of 6.54 cM. By applying MapPop software, it was possible to select smaller subsets of 141 or 93 most informative individuals with a view to reducing the time and cost of further mapping and phenotyping. To define the smallest number of individuals sufficient for assigning any new marker to a chromosome, subsets from 12 to 45 individuals and a set of 13 markers distributed over all 12 chromosomes were screened. In most cases, the markers were correctly assigned to their expected chromosome, but the accuracy of the map position decreased as the number of individuals was reduced.
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Affiliation(s)
- Lorenzo Barchi
- INRA, UR1052 Génétique et Amélioration des Fruits et Légumes, BP94, Montfavet F-84140, France
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Ayme V, Petit-Pierre J, Souche S, Palloix A, Moury B. Molecular dissection of the potato virus Y VPg virulence factor reveals complex adaptations to the pvr2 resistance allelic series in pepper. J Gen Virol 2007; 88:1594-1601. [PMID: 17412992 DOI: 10.1099/vir.0.82702-0] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The virulence properties of potato virus Y (PVY) towards an allelic series at the pvr2 locus in pepper genotypes are related to variations in the genome-linked viral protein (VPg). Eleven amino acid substitutions in the central part of the VPg were identified in strains differing by their virulence properties and were introduced, either singly or in combination, in an infectious PVY clone to get an in-depth genetic analysis of the virulence determinant. The virulence spectrum of these mutants was evaluated by inoculation of four pepper genotypes carrying different alleles at the pvr2 locus. The mutations introduced had complex effects on virulence, including antagonistic epistasis and trade-offs for virulence towards different pvr2 alleles. In addition, several mutants showed new virulence properties that were unknown in the natural environment. Such complex effects of mutations on plant virus virulence are unprecedented. They provide a better understanding of the variable levels of durability of the resistance conferred by the different pvr2 alleles, and have important consequences for a durable management of the resistances.
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Affiliation(s)
- Valérie Ayme
- INRA, UR1052 Génétique et Amélioration des Fruits et Légumes, F-84143 Montfavet, France
- INRA, UR407 Pathologie Végétale, F-84143 Montfavet, France
| | | | - Sylvie Souche
- INRA, UR407 Pathologie Végétale, F-84143 Montfavet, France
| | - Alain Palloix
- INRA, UR1052 Génétique et Amélioration des Fruits et Légumes, F-84143 Montfavet, France
| | - Benoît Moury
- INRA, UR407 Pathologie Végétale, F-84143 Montfavet, France
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Bonnet J, Danan S, Boudet C, Barchi L, Sage-Palloix AM, Caromel B, Palloix A, Lefebvre V. Are the polygenic architectures of resistance to Phytophthora capsici and P. parasitica independent in pepper? Theor Appl Genet 2007; 115:253-64. [PMID: 17497121 DOI: 10.1007/s00122-007-0561-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2007] [Accepted: 04/11/2007] [Indexed: 05/15/2023]
Abstract
The pepper accession Criollo de Morelos 334 is the most efficient source of resistance currently known to Phytophthora capsici and P. parasitica. To investigate whether genetic controls of resistance to two Phytophthora species are independent, we compared the genetic architecture of resistance of CM334 to both Phytophthora species. The RIL population F5YC used to construct the high-resolution genetic linkage map of pepper was assessed for resistance to one isolate of each Phytophthora species. Inheritance of the P. capsici and P. parasitica resistance was polygenic. Twelve additive QTLs involved in the P. capsici resistance and 14 additive QTLs involved in the P. parasitica resistance were detected. The QTLs identified in this progeny were specific to these Phytophthora species. Comparative mapping analysis with literature data identified three colocations between resistance QTLs to P. parasitica and P. capsici in pepper. Whereas this result suggests presence of common resistance factors to the two Phytophthora species in pepper, which possibly derive from common ancestral genes, calculation of the colocation probability indicates that these colocations could occur by chance.
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Affiliation(s)
- Julien Bonnet
- INRA, UR1052 GAFL Génétique et Amélioration des Fruits et Légumes, BP94, 84140, Montfavet, France
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Djian-Caporalino C, Fazari A, Arguel MJ, Vernie T, VandeCasteele C, Faure I, Brunoud G, Pijarowski L, Palloix A, Lefebvre V, Abad P. Root-knot nematode (Meloidogyne spp.) Me resistance genes in pepper (Capsicum annuum L.) are clustered on the P9 chromosome. Theor Appl Genet 2007; 114:473-86. [PMID: 17136373 DOI: 10.1007/s00122-006-0447-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2006] [Accepted: 10/25/2006] [Indexed: 05/12/2023]
Abstract
The root-knot nematode (Meloidogyne spp.) is a major plant pathogen, affecting several solanaceous crops worldwide. In Capsicum annuum, resistance to this pathogen is controlled by several independent dominant genes--the Me genes. Six Me genes have previously been shown to be stable at high temperature in three highly resistant and genetically distant accessions: PI 322719, PI 201234, and CM334 (Criollo de Morelos 334). Some genes (Me4, Mech1, and Mech2) are specific to certain Meloidogyne species or populations, whereas others (Me1, Me3, and Me7) are effective against a wide range of Meloidogyne species, including M. arenaria, M. javanica, and M. incognita, the most common species in Mediterranean and tropical areas. These genes direct different response patterns in root cells depending on the pepper line and nematode species. Allelism tests and fine mapping using the BSA-AFLP approach showed these genes to be different but linked, with a recombination frequency of 0.02-0.18. Three of the PCR-based markers identified in several genetic backgrounds were common to the six Me genes. Comparative mapping with CarthaGene software indicated that these six genes clustered in a single genomic region within a 28 cM interval. Four markers were used to anchor this cluster on the P9 chromosome on an intraspecific reference map for peppers. Other disease resistance factors have earlier been mapped in the vicinity of this cluster. This genomic area is colinear to chromosome T12 of tomato and chromosome XII of potato. Four other nematode resistance genes have earlier been identified in this area, suggesting that these nematode resistance genes are located in orthologous genomic regions in Solanaceae.
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Affiliation(s)
- C Djian-Caporalino
- INRA, UMR 1064 Interactions Plantes Microorganismes et Santé Végétale, BP167, F-06903, Sophia Antipolis, France.
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Djian-Caporalino C, Lefebvre V, Sage-Daubèze AM, Palloix A. Capsicum. Genetic Resources, Chromosome Engineering, and Crop Improvement 2006. [DOI: 10.1201/9781420009569.ch6] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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Ruffel S, Gallois JL, Moury B, Robaglia C, Palloix A, Caranta C. Simultaneous mutations in translation initiation factors eIF4E and eIF(iso)4E are required to prevent pepper veinal mottle virus infection of pepper. J Gen Virol 2006; 87:2089-2098. [PMID: 16760413 DOI: 10.1099/vir.0.81817-0] [Citation(s) in RCA: 121] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Capsicum resistance to Pepper veinal mottle virus (PVMV) results from complementation between the pvr2 and pvr6 resistance genes: recessive alleles at these two loci are necessary for resistance, whereas any dominant allele confers susceptibility. In line with previous results showing that pvr2 resistance alleles encode mutated versions of the eukaryotic translation initiation factor 4E (eIF4E), the involvement of other members of the eIF4E multigenic family in PVMV resistance was investigated. It was demonstrated that pvr6 corresponds to an eIF(iso)4E gene, predicted to encode the second cap-binding isoform identified in plants. Comparative genetic mapping in pepper and tomato indicated that eIF(iso)4E maps in the same genomic region as pvr6. Sequence analysis revealed an 82 nt deletion in eIF(iso)4E cDNAs from genotypes with the pvr6 resistance allele, leading to a truncated protein. This deletion was shown to co-segregate with pvr6 in doubled haploid and F(2) progeny. Transient expression in a PVMV-resistant genotype of eIF(iso)4E derived from a genotype with the pvr6(+) susceptibility allele resulted in loss of resistance to subsequent PVMV inoculation, confirming that pvr6 encodes the translation factor eIF(iso)4E. Similarly, transient expression of eIF4E from a genotype with the pvr2(+)-eIF4E susceptibility allele also resulted in loss of resistance, demonstrating that wild-type eIF4E and eIF(iso)4E are susceptibility factors for PVMV and that resistance results from the combined effect of mutations in the two cap-binding isoforms. Thus, whilst most potyviruses specifically require one eIF4E isoform to perform their replication cycle, PVMV uses either eIF4E or eIF(iso)4E for infection of pepper.
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Affiliation(s)
- Sandrine Ruffel
- INRA, Genetics and Breeding of Fruits and Vegetables, Domaine St Maurice, BP 94, F-84143 Montfavet, France
| | - Jean-Luc Gallois
- INRA, Genetics and Breeding of Fruits and Vegetables, Domaine St Maurice, BP 94, F-84143 Montfavet, France
| | - Benoît Moury
- Plant Pathology, Domaine St Maurice, BP 94, F-84143 Montfavet, France
| | - Christophe Robaglia
- Laboratoire de Génétique et Biophysique des Plantes, CEA-CNRS-Université Aix-Marseille II, Faculté des Sciences de Luminy, F-13009 Marseille, France
| | - Alain Palloix
- INRA, Genetics and Breeding of Fruits and Vegetables, Domaine St Maurice, BP 94, F-84143 Montfavet, France
| | - Carole Caranta
- INRA, Genetics and Breeding of Fruits and Vegetables, Domaine St Maurice, BP 94, F-84143 Montfavet, France
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Ayme V, Souche S, Caranta C, Jacquemond M, Chadoeuf J, Palloix A, Moury B. Different mutations in the genome-linked protein VPg of potato virus Y confer virulence on the pvr2(3) resistance in pepper. Mol Plant Microbe Interact 2006; 19:557-63. [PMID: 16673943 DOI: 10.1094/mpmi-19-0557] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Five different amino acid substitutions in the VPg of Potato virus Y were shown to be independently responsible for virulence toward pvr2(3) resistance gene of pepper. A consequence of these multiple mutations toward virulence involving single nucleotide substitutions is a particularly high frequency of resistance breaking (37% of inoculated plants from the first inoculation) and suggests a potentially low durability of pvr2(3) resistance. These five mutants were observed with significantly different frequencies, one of them being overrepresented. Genetic drift alone could not explain the observed distribution of virulent mutants. More plausible scenarios were obtained by taking into account either the relative substitution rates, the relative fitness of the mutants in pvr2(3) pepper plants, or both.
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Affiliation(s)
- Valérie Ayme
- I.N.R.A., Unité de Pathologie Végétale, BP94, F-84143 Montfavet, France
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Caromel B, Mugniéry D, Kerlan MC, Andrzejewski S, Palloix A, Ellissèche D, Rousselle-Bourgeois F, Lefebvre V. Resistance quantitative trait loci originating from Solanum sparsipilum act independently on the sex ratio of Globodera pallida and together for developing a necrotic reaction. Mol Plant Microbe Interact 2005; 18:1186-94. [PMID: 16353553 DOI: 10.1094/mpmi-18-1186] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Plant resistance to nematodes is related to the ability of the host to reduce the development of nematode juveniles into females. Resistance to the potato cyst nematode (PCN) Globodera pallida, originating from the wild species Solanum sparsipilum, was dissected by a quantitative trait loci (QTL) approach. Two QTL explained 89% of the phenotypic variation. The QTL GpaV(s)spl on chromosome V displayed the major effect on the cyst number (coefficient of determination [R2] = 76.6%). It restricted G. pallida development to 16.2% of juveniles, 81.5% of males, and 2.3% of females. The QTL GpaXI(s)spl on chromosome XI displayed a lower effect on the cyst number (R2 = 12.7%). It restricted G. pallida development to 13.8% of juveniles, 35.4% of males, and 50.8% of females. Clones carrying both QTL restricted the nematode development to 58.1% juveniles, 41.1% of males, and 0.8% of females. We demonstrated that potato clones carrying both QTL showed a strong necrotic reaction in roots infected by nematodes, while no such reaction was observed in clones carrying a single QTL. This result underlines the importance to introgress together GpaV(s)spl and GpaXI(s)spl into potato cultivars, in order to reduce the density of this quarantine pest in soil and to decrease the risk of selecting overcoming G. pallida subpopulations.
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Affiliation(s)
- Bernard Caromel
- Institut National de la Recherche Agronomique, UGAFL, Unité de Génétique et d'Amélioration des Fruits et Légumes, Domaine Saint Maurice, Montfavet, France.
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Lafortune D, Béramis M, Daubèze AM, Boissot N, Palloix A. Partial Resistance of Pepper to Bacterial Wilt Is Oligogenic and Stable Under Tropical Conditions. Plant Dis 2005; 89:501-506. [PMID: 30795429 DOI: 10.1094/pd-89-0501] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Genetic analysis of resistance of pepper to bacterial wilt was performed in the doubled haploid progeny from a cross between a resistant parental line PM 687 and a susceptible cultivar Yolo Wonder. After artificial inoculation with a local isolate of Ralstonia solanacearum, the progeny consisting of 90 lines was transplanted into a naturally infested field in Guadeloupe, Lesser Antilles. The 2 years of experimentation resulted in repeatable results, with a high heritability of the resistance, attesting the reliability of the evaluation procedure and the stability of the resistance over years. Two to five genes with additive effects were estimated to control the resistance, indicating an oligogenic control as observed in tomato sources of resistance. Relationships with resistance to other soilborne or tropical diseases were examined. Susceptibility to Tobacco mosaic virus (TMV) and to nematodes (Meloidogyne spp.) were significantly linked with resistance to bacterial wilt, whereas neither resistance to Phytophthora capsici nor to Leveillula taurica were linked. The similarity of the genetics of resistance to bacterial wilt in pepper and tomato and linkage with TMV resistance locus warrant the comparative mapping of the resistance quantitative trait loci in the genomes of the two species.
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Affiliation(s)
- Denis Lafortune
- INRA-URPV, Domaine Duclos, Prise d'eau, 97170 Petit Bourg, France
| | - Michel Béramis
- INRA-URPV, Domaine Duclos, Prise d'eau, 97170 Petit Bourg, France
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Moury B, Palloix A, Caranta C, Gognalons P, Souche S, Selassie KG, Marchoux G. Serological, Molecular, and Pathotype Diversity of Pepper veinal mottle virus and Chili veinal mottle virus. Phytopathology 2005; 95:227-232. [PMID: 18943114 DOI: 10.1094/phyto-95-0227] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
ABSTRACT Variability within the pepper-infecting potyviruses Pepper veinal mottle virus (PVMV) and Chili veinal mottle virus (ChiVMV) in Africa and Asia was investigated. Coat protein (CP) gene sequence diversity revealed three clades that corresponded to three geographic locations and there was no evidence of presence of the ChiVMV/Asian group in western or central Africa. These clades included closely related isolates that potentially belong to two viral species, which is consistent with current nomenclature. These clades could not be unambiguously identified with polyclonal antisera; however, reverse transcription-polymerase chain reactions allowed differentiation of the isolates into two species based on a large indel in the CP gene. PVMV and ChiVMV isolates were classified into three and two pathotypes, respectively, in relation to pepper genotypes carrying different resistance factors. Specificity of resistance only partially corresponded to molecular diversity of the isolates. Only one isolate of PVMV could infect pepper genotypes carrying the two recessive genes pvr6 and pvr2 (2); however, these genotypes were not infected by PVMV in field trials in Senegal, despite a high prevalence of PVMV in the surrounding pepper plants.
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Ruffel S, Caranta C, Palloix A, Lefebvre V, Caboche M, Bendahmane A. Structural analysis of the eukaryotic initiation factor 4E gene controlling potyvirus resistance in pepper: exploitation of a BAC library. Gene 2004; 338:209-16. [PMID: 15315824 DOI: 10.1016/j.gene.2004.05.010] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2003] [Revised: 04/21/2004] [Accepted: 05/17/2004] [Indexed: 11/28/2022]
Abstract
The pvr2 locus in pepper codes for a eukaryotic translation initiation factor 4E (eIF4E) gene that confers resistance to viruses belonging to the potyvirus genus. In this work, we describe the isolation and characterisation of the genomic sequence carrying the pvr2 locus. A Bacterial Artificial Chromosome (BAC) library that consisted of 239,232 clones with an average insert size of 123 kilobases (kb) was constructed from a Capsicum annuum line with the pvr2(+) allele for susceptibility to potato virus Y (PVY) and tobacco etch virus (TEV). Based on a polymerase chain reaction (PCR) screen with single-copy markers, three to seven positive BAC clones per markers were identified, indicating that the BAC library is suitable for pepper genome analysis. To determine the genomic organization of the pepper eIF4E gene, the library was screened with primers designed from the cDNA sequence and four positive BAC clones carrying the pvr2 locus were identified. A 7-kb DNA fragment containing the complete eIF4E gene was sub-cloned from the positive BAC clones and analysed. The eIF4E gene is organised into five exons and four introns and showed a strictly conserved exon/intron structure with eIF4E genes from Arabidopsis thaliana and rice. Moreover, the splice sites between plant exons 1/2 and 2/3 are conserved among eukaryotes including human, Drosophila and yeast. Several potential binding sites for MADS box transcription factors within the 5' flanking region of eIF4E genes from the three plant species were also predicted.
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Affiliation(s)
- Sandrine Ruffel
- INRA, Plant Genomics Research Unit, 2 rue G. Cremieux, CP 5708, F-91057 Evry Cedex, France
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Wang LH, Zhang BX, Lefebvre V, Huang SW, Daubèze AM, Palloix A. QTL analysis of fertility restoration in cytoplasmic male sterile pepper. Theor Appl Genet 2004; 109:1058-63. [PMID: 15173931 DOI: 10.1007/s00122-004-1715-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2003] [Accepted: 04/27/2004] [Indexed: 05/24/2023]
Abstract
Fertility restoration of Peterson's cytoplasmic male-sterility in pepper (Capsicum annuum L.) is quantitative and environment-dependent. QTL analysis of fertility restoration was performed based on the test-cross progeny of 77013A (a strict cytoplasmic-genetic male sterile line) and a doubled haploid population of 114 lines obtained from an F1 hybrid between Yolo wonder (a sterility maintainer line) and Perennial (a fertility-restorer line). The fertility of the test-crossed lines was assessed under greenhouse and open field conditions using three criteria related to pollen or seed production. One major QTL for fertility restoration was mapped to chromosome P6. It was significant in all the environments and for all the traits, accounting for 20-69% of the phenotypic variation, depending on the trait. Four additional minor QTLs were also detected on chromosomes P5, P2, and linkage groups PY3 and PY1, accounting for 7-17% of the phenotypic variation. Most of the alleles increasing fertility originated from the restorer parent, except for two alleles at minor QTLs. Phenotypic analysis and genetic dissection indicated that breeding pepper for complete sterility of female lines and high hybrid fertility requires complex combinations of alleles from both parents and a strict control of the environment.
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Affiliation(s)
- L H Wang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 12 Zhongguancun Nandajie, Beijing, 100081, China
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Abstract
Breeding for virus resistance is often considered the most efficient and simplest way to avoid the losses due to plant virus diseases. Resistance mechanisms are very diverse and interact with various stages of the virus cycle in the host plant. Resistances may also differ in their specificity, stability and durability. Breeding for resistance is a long and costly process, therefore to be cost effective it should provide durable protection. Three pathosystems are discussed to illustrate some of the field and laboratory approaches that can be used to assess resistance durability: Cucumber mosaic virus-specific resistance in melon, Zucchini yellow mosaic virus tolerance in zucchini squash, and extreme resistance to Potato virus X in potato. The possibility of predicting resistance durability is discussed in relation to the nature of the resistance, the genetic changes required for a virus to overcome the resistance and the effects of such changes on virus fitness.
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Affiliation(s)
- H Lecoq
- INRA, Station de Pathologie Végétale, Domaine Saint Maurice, BP 94, 84143 Montfavet cedex, France.
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Thabuis A, Lefebvre V, Bernard G, Daubèze AM, Phaly T, Pochard E, Palloix A. Phenotypic and molecular evaluation of a recurrent selection program for a polygenic resistance to Phytophthora capsici in pepper. Theor Appl Genet 2004; 109:342-351. [PMID: 15014880 DOI: 10.1007/s00122-004-1633-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2003] [Accepted: 02/09/2004] [Indexed: 05/24/2023]
Abstract
'Criollo de Morelos 334' (CM334) is one of the most promising sources of resistance to Phytophthora capsici in pepper. This Mexican accession is distantly related to bell pepper and its resistance displays a complex inheritance. The QTLs involved in resistance to P. capsici were previously mapped. In order to transfer the resistance factors from CM334 into a bell pepper genetic background, a modified, recurrent breeding scheme was initiated. The breeding population was divided into three sub-populations which were screened by distinct phenotypic tests of increasing severity. The plants from the first sub-population were screened with low-severity tests and backcrossed to the susceptible bell pepper; the plants from the second and third sub-populations were screened by more severe resistance tests and crossed with the plants from the first and second sub-populations, respectively. In this study, the phenotypic data for the three sub-populations during five screening/intermating cycles were analysed. In parallel, the changes in allelic frequencies at molecular markers linked to the resistance QTLs were reported. The resistance phenotype and allelic frequencies strongly depended on the sub-population and screening severity. Regarding allelic frequency changes across the selection cycles, a loss of resistant QTL alleles was observed in the first sub-population, particularly for the low-effect QTLs, whereas a better conservation of the resistant QTL alleles was observed in the two other sub-populations. The same trend was observed in the phenotypic data with an increasing resistance level from the first to the third sub-populations. The changes in the allelic frequencies of loci not linked to resistance QTLs and for horticultural traits across the breeding process indicated that the recovery of the recipient parent genome was not significantly affected by the selection for resistance.
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Affiliation(s)
- A Thabuis
- Genetics and Breeding of Fruits and Vegetables, Institut National de la Recherche Agronomique, BP94, 84143 Montfavet Cedex, France
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Moury B, Morel C, Johansen E, Guilbaud L, Souche S, Ayme V, Caranta C, Palloix A, Jacquemond M. Mutations in potato virus Y genome-linked protein determine virulence toward recessive resistances in Capsicum annuum and Lycopersicon hirsutum. Mol Plant Microbe Interact 2004; 17:322-329. [PMID: 15000399 DOI: 10.1094/mpmi.2004.17.3.322] [Citation(s) in RCA: 115] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The recessive resistance genes pot-1 and pvr2 in Lycopersicon hirsutum and Capsicum annuum, respectively, control Potato virus Y (PVY) accumulation in the inoculated leaves. Infectious cDNA molecules from two PVY isolates differing in their virulence toward these resistances were obtained using two different strategies. Chimeras constructed with these cDNA clones showed that a single nucleotide change corresponding to an amino acid substitution (Arg119His) in the central part of the viral protein genome-linked (VPg) was involved in virulence toward the pot-1 resistance. On the other hand, 15 nucleotide changes corresponding to five putative amino acid differences in the same region of the VPg affected virulence toward the pvr2(1) and pvr2(2) resistances. Substitution models identified six and five codons within the central and C terminal parts of the VPg for PVY and for the related potyvirus Potato virus A, respectively, which undergo positive selection. This suggests that the role of the VPg-encoding region is determined by the protein and not by the viral RNA apart from its protein-encoding capacity.
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Affiliation(s)
- Benoît Moury
- Station de Pathologie Végétale, Institut National de la Recherche Agronomique, F-84143 Montfavet cedex, France.
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Lefebvre V, Daubèze AM, Rouppe van der Voort J, Peleman J, Bardin M, Palloix A. QTLs for resistance to powdery mildew in pepper under natural and artificial infections. Theor Appl Genet 2003; 107:661-6. [PMID: 12819909 DOI: 10.1007/s00122-003-1307-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2003] [Accepted: 02/02/2003] [Indexed: 05/20/2023]
Abstract
Epidemics of powdery mildew due to Leveillula taurica is an increasing problem in pepper production areas, particularly in coastal regions or greenhouse cultivation. The highly resistant genitor 'H3' was submitted to genetic analysis and QTL mapping in order to promote the introgression of its oligogenic resistance into large and sweet-fruited cultivars. The doubled-haploid progeny from the cross 'H3' (resistant) by 'Vania' (susceptible) was tested for resistance under both natural field infection and artificial inoculation tests, and QTL detection was compared for those two methods. Seven genomic regions including additive QTLs and epistatic interactions were detected, explaining altogether the major part of genotypic variance. Two genomic regions were common to both the evaluation methods, whereas other QTLs were method-specific, reflecting the environment dependence of powdery mildew epidemics. Orthologies with tomato genomic regions carrying resistance genes to L. taurica and Oidium lycopersicum were revealed by comparative mapping with pepper. Tight linkages between the detected QTLs and virus resistance or fruit color traits in pepper were also shown, which adds to the agronomic importance of these regions in pepper breeding programs.
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Affiliation(s)
- V Lefebvre
- Institut National de la Recherche Agronomique, Genetics and Breeding of Fruits and Vegetables, BP94, 84143 Montfavet cedex, France.
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Thabuis A, Palloix A, Pflieger S, Daubèze AM, Caranta C, Lefebvre V. Comparative mapping of Phytophthora resistance loci in pepper germplasm: evidence for conserved resistance loci across Solanaceae and for a large genetic diversity. Theor Appl Genet 2003; 106:1473-85. [PMID: 12750791 DOI: 10.1007/s00122-003-1206-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2002] [Accepted: 09/25/2002] [Indexed: 05/20/2023]
Abstract
Phytophthora capsici Leonian, known as the causal agent of the stem, collar and root rot, is one of the most serious problems limiting the pepper crop in many areas in the world. Genetic resistance to the parasite displays complex inheritance. Quantitative trait locus (QTL) analysis was performed in three intraspecific pepper populations, each involving an unrelated resistant accession. Resistance was evaluated by artificial inoculations of roots and stems, allowing the measurement of four components involved in different steps of the plant-pathogen interaction. The three genetic maps were aligned using common markers, which enabled the detection of QTLs involved in each resistance component and the comparison of resistance factors existing among the three resistant accessions. The major resistance factor was found to be common to the three populations. Another resistance factor was found conserved between two populations, the others being specific to a single cross. This comparison across intraspecific germplasm revealed a large variability for quantitative resistance loci to P. capsici. It also provided insights both into the allelic relationships between QTLs across pepper germplasm and for the comparative mapping of resistance factors across the Solanaceae.
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Affiliation(s)
- A Thabuis
- INRA, Genetics and Breeding of Fruits and Vegetables, BP 94, 84143 Montfavet cedex, France
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