The French Departments of Guadeloupe and Martinique are particularly sensitive to the problem of invasive species. This problem is the responsibility of the Services and other organizations in charge of animal and plant health. These agencies have established concerted information activities and regional co-operation aimed at preventing the introduction and the control of invasive species, which could have important economic impacts on agricultural production and the ecosystems of these Departments. We report the strategy of regional co-operation and progress pertaining to some potential invasive species or species undergoing mutation, and the prospects for controlling them in the event of their introduction.

Molecular breeding, a powerful technique to increase crop yield, tries to predict yield by crop growth models with genotype specific, environment-independent yield components and environmental indices as inputs. A fluorescence-trait-based approach is presented to approximate some costly and time-consuming measurements of yield components. Temporal monitoring of chlorophyll a fluorescence resulted in fluorescence traits with high heritability (0.60-0.82) that could act as proxies for model inputs. Medium-sized Pearson's correlations were calculated between fluorescence traits, light-use efficiency (LUE), and fruit related parameters up to 0.53. Multi-trait quantitative trait locus (QTL) analyses identified genomic regions of pepper (Capsicum annuum L.) involved in the phenotypic variation of the fluorescence traits. Fluorescence QTLs found on linkage groups P6, P7, and P11 corresponded to QTLs for number of fruits, partitioning into fruits, and LUE. Fluorescence parameters within 1 min of the fluorescence response curve can thus be useful to approximate yield component traits.

Description du sujet. Une approche système basée sur la co-conception et l’évaluation expérimentale in situ de prototypes de systèmes de culture (SDC) a été mise en œuvre dans le projet INRA « GeDuNem » pour une gestion durable des nématodes à galles (NG) dans les systèmes maraîchers sous abris. Objectifs. Il s’agissait (i) d’évaluer pendant quatre ans diverses stratégies de culture combinant résistances génétiques et pratiques culturales (rotations culturales incluant des plantes sensibles, résistantes et non-hôtes, gestion de l’interculture avec couvert végétal nématicide ou solarisation) pour réduire les populations de NG dans le sol et augmenter la durabilité des résistances variétales à ces bioagresseurs, (ii) d’étudier leur impact sur les communautés de nématodes rencontrées et (iii) d’évaluer l’acceptabilité des nouveaux SDC par les agriculteurs. Méthode. Trois prototypes de SDC, co-conçus entre acteurs de la recherche et ceux du développement, ont été comparés à des SDC appliqués classiquement en région méditerranéenne et évalués grâce à des dispositifs complémentaires : (i) expérimentations-système sur trois sites de producteurs du Sud de la France ; (ii) expérimentations analytiques pour approfondir les mécanismes d’action des leviers mobilisés ; (iii) enquêtes pour évaluer l’acceptabilité des prototypes par les agriculteurs. Résultats. Les trois SDC se sont révélés efficaces (90 % de réduction des NG, protection des Solanaceae à résistance partielle, pas d’effet négatif sur les nématodes non phytoparasites) et durables lorsque les conditions d’application et les équilibres biologiques du sol étaient favorables (nématofaune totale diversifiée et abondante). Leur degré d’acceptabilité dépendait du type d’exploitation et de la sensibilité des agriculteurs face à l’innovation. Conclusions. Ces nouveaux SDC doivent encore être améliorés, en interaction avec les producteurs, tant en termes d’efficacité, par l’introduction de nouveaux leviers agroécologiques, que de cout. Les recherches futures devront aussi s’ouvrir à la gestion plus globale de la santé des sols.

Root‐knot nematodes (RKNs), Meloidogyne spp., are a major disease problem in solanaceous crops worldwide, including pepper (Capsicum spp.). Genetic control provides an economically and environmentally sustainable protection alternative to soil fumigants. In pepper, resistance to the main RKN species (M. incognita, M. javanica and M. arenaria) is conferred by the major genes (R genes) Me1, Me3 and N. However, RKNs are able to develop virulence, thus endangering the efficiency of R genes. Quantitative resistance (QR) against Meloidogyne spp. is expected to provide an alternative to R genes, or to be combined with R genes, to increase the resistance efficiency and durability in pepper. In order to explore the ability of QR to protect pepper against RKNs, five pepper inbred lines, differing in their QR level, were tested directly, or after combination with the Me1 and Me3 genes, for their resistance to a panel of M. arenaria, M. javanica and M. incognita isolates. The M. arenaria and M. javanica isolates showed low pathogenicity to pepper, unlike the M. incognita isolates. The QR, controlled by the pepper genetic background, displayed a high resistance level with a broad spectrum of action, protecting pepper against Me3‐virulent as well as avirulent M. incognita isolates. The QR was also expressed when combined with the Me1 and Me3 genes, but presented additive genetic effects so that heterozygous F1 hybrids proved less resistant than homozygous inbred lines. The discovery of this QR is expected to provide promising applications for preserving the efficiency and durability of nematode resistance.

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 pvr23 and at comparing them with genetic factors affecting quantitative resistance. The resistance breakdown frequency was a highly heritable trait (h2=0.87). Four loci including additive quantitative trait loci (QTLs) and epistatic interactions explained together 70% of the variance of pvr23 breakdown frequency. Three of the four QTLs controlling pvr23 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 pvr23 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.

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.

KEY MESSAGE: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.

An interesting strategy for improvement of a complex trait dissects the complex trait in a number of physiological component traits, with the latter having hopefully a simple genetic basis. The complex trait is then improved via improvement of its component traits. As first part of such a strategy to improve yield in pepper, we present genetic and QTL analyses for four pepper experiments. Sixteen traits were analysed for a population of 149 recombinant inbred lines, obtained from a cross between the large-fruited pepper cultivar 'Yolo Wonder' (YW) and the small fruited pepper 'Criollo de Morelos 334' (CM334). The marker data consisted of 493 markers assembled into 17 linkage groups covering 1,775 cM. The trait distributions were unimodal, although sometimes skewed. Many traits displayed heterosis and transgression. Heritabilities were high (mean 0.86, with a range between 0.43 and 0.96). A multiple QTL mapping approach per trait and environment yielded 24 QTLs. The average numbers of QTLs per trait was two, ranging between zero and six. The total explained trait variance by QTLs varied between 9 and 61 %. QTL effects differed quantitatively between environments, but not qualitatively. For stem-related traits, the trait-increasing QTL alleles came from parent CM334, while for leaf and fruit related traits the increasing QTL alleles came from parent YW. The QTLs on linkage groups 1b, 2, 3a, 4, 6 and 12 showed pleiotropic effects with patterns that were consistent with the genetic correlations. These results contribute to a better understanding of the genetics of yield-related physiological traits in pepper and represent a first step in the improvement of the target trait yield.

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.

In breeding the best genotypes for diverse conditions, ideally the breeder should test all his crossings under all these conditions. Especially with complex physiological traits like yield, which exhibit large variation, this would require many expensive and large field trials. The EU project “Smart tools for Prediction Improvement of Crop Yield” (SPICY) aims at the development of a suite of tools to help breeders in predicting phenotypic response of genotypes for complex traits under a range of environmental conditions. Pepper is used as a model crop. The primary tool to be developed is an integrated gene-to-phenotype model, which integrates the approaches of QTL and crop growth modelling. To generate data to develop and validate these models, a recombinant inbred line (RIL) population of Capsicum annuum ‘Yolo Wonder’ × ‘Criollo de Morelos 334’ was phenotyped at two sites (Netherlands and Spain) and in two seasons (spring and autumn). Phenotyping was done both manually by measuring characteristics like fruit set and development rate, and by newly developed image analysis and fluorescence tools permitting high throughput phenotyping of dynamic trait expression. In the analysis of the data, the complex trait yield was analysed in the components contributing to the total fresh fruit yield. The results of the phenotyping experiments will be used as input in the crop growth models. The genotype-to-phenotype model, combination of crop growth models and QTL analysis tools which will be developed in the EU-SPICY project will be able to predict phenotypic response based on genetic information.

Genetic markers based on single nucleotide polymorphisms (SNPs) are in increasing demand for genome mapping and fingerprinting of breeding populations in crop plants. Recent advances in high-throughput sequencing provide the opportunity for whole-genome resequencing and identification of allelic variants by mapping the reads to a reference genome. However, for many species, such as pepper (Capsicum annuum), a reference genome sequence is not yet available. To this end, we sequenced the C. annuum cv. "Yolo Wonder" transcriptome using Roche 454 pyrosequencing and assembled de novo 23,748 isotigs and 60,370 singletons. Mapping of 10,886,425 reads obtained by the Illumina GA II sequencing of C. annuum cv. "Criollo de Morelos 334" to the "Yolo Wonder" transcriptome allowed for SNP identification. By setting a threshold value that allows selecting reliable SNPs with minimal loss of information, 11,849 reliable SNPs spread across 5919 isotigs were identified. In addition, 853 single sequence repeats were obtained. This information has been made available online.

Adaptation of populations to new environments is frequently costly due to trade-offs between life history traits, and consequently, parasites are expected to be locally adapted to sympatric hosts. Also, during adaptation to the host, an increase in parasite fitness could have direct consequences on its aggressiveness (i.e. the quantity of damages caused to the host by the virus). These two phenomena have been observed in the context of pathogen adaptation to host's qualitative and monogenic resistances. However, the ability of pathogens to adapt to quantitative polygenic plant resistances and the consequences of these potential adaptations on other pathogen life history traits remain to be evaluated. Potato virus Y and two pepper genotypes (one susceptible and one with quantitative resistance) were used, and experimental evolutions showed that adaptation to a quantitative resistance was possible and resulted in resistance breakdown. This adaptation was associated to a fitness cost on the susceptible cultivar, but had no consequence either in terms of aggressiveness, which could be explained by a high tolerance level, or in terms of aphid transmission efficiency. We concluded that quantitative resistances are not necessarily durable but management strategies mixing susceptible and resistant cultivars in space and/or in time should be useful to preserve their efficiency.

QTL for a complex trait like yield tend to be unstable across environments and show QTL by environment interaction. Direct improvement of complex traits by selecting on QTL is therefore difficult. For improvement of complex traits, crop growth models can be useful, as such models can dissect a target trait into a number of component traits. QTL for the component traits are assumed to be more stable across environments. The target trait can be reconstructed from its component traits together with environmental inputs. Instead of observed component traits, QTL fits for component traits may be used when QTL explain a reasonable proportion of the variation in the components. We applied this dissection approach to the target trait total shoot biomass for a population of 149 recombinant inbred lines from the intraspecific cross of Capsicum annuum 'Yolo Wonder' and 'Criollo de Morelos 334'. A simple LINTUL-type simulation model was used, with rate of change of leaf area index and light use efficiency as genotype specific component traits. These two component traits were determined in four phenotyping experiments (spring and autumn cultivations in the Netherlands and Spain), and subjected to QTL analysis. Seven QTL were found for both component traits. For leaf area index development rate 40 to 50% of the observed variance was explained by the QTL, while this was slightly lower for light use efficiency (23-39%). Using the QTL fitted values of the component traits following QTL analysis, the crop simulation model explained 27-43% of the observed variation in total shoot biomass, which was higher than the variation explained by the QTL for total shoot biomass itself for most experiments. The approach of dissecting a complex trait into its component traits is therefore a promising one. Next step is to extend the model with biomass partitioning.

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.

* 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.

The dominant Pvr4 gene identified in Capsicum annuum cv. Criollo de Morelos 334 (CM334) is frequently used in pepper cultivars because it possesses one of the largest spectra of action among plant virus resistance genes. This gene was previously shown to confer efficient resistance to all known Potato virus Y isolates, to Pepper mottle virus, to Pepper yellow mosaic virus and to Ecuadorian rocoto virus. This study showed that the W4 line, derived from CM334 and carrying Pvr4, was also resistant to Peru tomato mosaic virus and Pepper severe mosaic virus, but not to Pepper veinal mottle virus, Chilli veinal mottle virus or Tobacco etch virus. It was noticed that the phenotype of the resistance was atypical since, in the W4 line, hypersensitive reaction or extreme resistance could be observed, depending on virus isolates and inoculated organs. Despite the large deployment of Pvr4 in hybrid cultivars, the numerous tests performed in controlled conditions and the use of W4 serial back‐inoculations with potyvirus isolates controlled by this line, no virulent variant isolates were obtained. However, it was shown that the use of graft inoculation experiments allow PVY virulent variants to be selected.

Markers assisted selection is still seldom used in pepper breeding in China,though many markers are reported recently.In order to obtain genotypes for researching of relationship of QTLs resistant to PVY,AFLP,CAPS and SCAR markers were used to assist selection of QTLs for resistance to PVY in BC_2 and BC_1S_1 segregating progenies from pepper‘Perennial’and‘Yolo Wonder’.With the markers,47 plants with resistant allele in major QTL locus,then from which 25 plants with resistant allele in LG9 PY2,at last 11 plants with resistant allele in LG11 P10 were selected from the BC2 population.And 55 plants with homozy- gous resistant allele in LG9 PY2,and 12 plants with homozygous resistant allele in major QTL were selected from the BC_1S_1 population.X~2 analysis showed that the segregating ratio in fact is not significantly different with that in theory.