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International audience; Many recessive resistances against potyviruses are mediated by eukaryotic translation initiation factor 4E (eIF4E). In tobacco, the va resistance gene commonly used to control Potato virus Y (PVY) corresponds to a large deletion affecting the eIF4E-1 gene on chromosome 21. Here, we compared the resistance durability conferred by various types of mutations affecting eIF4E-1 (deletions of various sizes, frameshift or nonsense mutations). The 'large deletion' genotypes displayed the broadest and most durable resistance, whereas frameshift and nonsense mutants displayed a less durable resistance, with rapid and frequent apparition of resistance-breaking variants. In addition, genetic and transcriptomic analyses revealed that resistance durability is strongly impacted by a complex genetic locus on chromosome 14, which contains three other eIF4E genes. One of these, eIF4E-3, is rearranged as a hybrid gene between eIF4E-2 and eIF4E-3 (eIF4E-2-3 ) in the genotypes showing the most durable resistance, while eIF4E-2 is differentially expressed between the tested varieties. RNA-seq and quantitative reverse transcriptase-polymerase chain reaction experiments demonstrated that eIF4E-2 expression level is positively correlated with resistance durability. These results suggest that besides the nature of the mutation affecting eIF4E-1, three factors linked with a complex locus may potentially impact va durability: loss of an integral eIF4E-3, presence of eIF4E-2-3 and overexpression of eIF4E-2. This latter gene might act as a decoy in a non-productive virus-plant interaction, limiting the ability of PVY to evolve towards resistance breaking. Taken together, these results show that va resistance durability can in large part be explained by complex redundancy effects in the eIF4E gene family.

International audience; Intragenesis is an important alternative to transgenesis to produce modified plants 27 containing native DNA only. A key point to develop such a strategy is the availability of 28 regulatory sequences controlling the expression of the gene of interest. With the aim of 29 finding apple gene promoters either inducible by the fire blight pathogen Erwinia amylovora 30 (Ea) or moderately constitutive, we focused on polyphenoloxidase genes (PPO). These genes 31 encode oxidative enzymes involved in many physiological processes and have been 32 previously shown to be up-regulated during the Ea infection process. We found ten PPO and 33 two PPO-like sequences in the apple genome and characterized the promoters of MdPPO16 34 (pPPO16) and MdKFDV02 PPO-like (pKFDV02) for their potential as Ea-inducible and low-35 constitutive regulatory sequences respectively. Expression levels of reporter genes fused to 36 these promoters and transiently or stably expressed in apple were quantified after various 37 treatments. Unlike pKFDV02 which displayed a variable activity, pPPO16 allowed a fast and 38 strong expression of transgenes in apple following Ea infection in a Type 3 Secretion System 39 dependent manner. Altogether our results indicate that pKFDV02 did not keep its promises as 40 a constitutive and weak promoter whereas pPPO16, the first Ea-inducible promoter cloned 41 from apple, can be a useful component of intragenic strategies to create fire blight resistant 42 apple genotypes.

The objective was to further the understanding of the complex interaction between the soil microbiota, a plant pathogen and the host plant. The effect of different soil microbial diversities on the level of disease and on the transcriptomes of the interacting pathogen and host plant was studied., Summary The contribution of surrounding plant microbiota to disease development has led to the ‘pathobiome’ concept, which represents the interaction between the pathogen, the host plant and the associated biotic microbial community, resulting or not in plant disease. The aim herein is to understand how the soil microbial environment may influence the functions of a pathogen and its pathogenesis, and the molecular response of the plant to the infection, with a dual‐RNAseq transcriptomics approach. We address this question using Brassica napus and Plasmodiophora brassicae, the pathogen responsible for clubroot. A time‐course experiment was conducted to study interactions between P. brassicae, two B. napus genotypes and three soils harbouring high, medium or low microbiota diversities and levels of richness. The soil microbial diversity levels had an impact on disease development (symptom levels and pathogen quantity). The P. brassicae and B. napus transcriptional patterns were modulated by these microbial diversities, these modulations being dependent on the host genotype plant and the kinetic time. The functional analysis of gene expressions allowed the identification of pathogen and plant host functions potentially involved in the change of plant disease level, such as pathogenicity‐related genes (NUDIX effector) in P. brassicae and plant defence‐related genes (glucosinolate metabolism) in B. napus.

Members of the genus Clavibacter are economically important bacterial plant pathogens infecting a set of diverse agricultural crops (e.g., alfalfa, corn, potato, tomato, and wheat). Tomato-associated Clavibacter sp. strains account for a great portion of the genetic diversity of the genus, and C. michiganensissensu stricto (formerly C. michiganensis subsp. michiganensis), causing bacterial canker disease, is considered one of the most destructive seed-borne agents for the crop worldwide. However, current taxonomic descriptions of the genus do not reflect the existing diversity of the strains, resulting in unsatisfactory results in quarantine surveys for the pathogens. In this study, we used all the available genome sequences of Clavibacter sp. strains, including the type strains of newly described subspecies, to provide precise insight into the diversity of tomato-associated members of the genus and further clarify the taxonomic status of the strains using genotypic and phenotypic features. The results of phylogenetic analyses revealed the existence of nine hypothetical new species among the investigated strains. None of the three new subspecies (i.e., C. michiganensis subsp. californiensis, C. michiganensis subsp. chilensis, and C. michiganensis subsp. phaseoli) is included within the tomato-pathogenic C. michiganensissensu stricto lineage. Although comparative genomics revealed the lack of chp and tomA pathogenicity determinant gene clusters in the nonpathogenic strains, a number of pathogenicity-related genes were noted to be present in all the strains regardless of their pathogenicity characteristics. Altogether, our results indicate a need for a formal taxonomic reconsideration of tomato-associated Clavibacter sp. strains to facilitate differentiation of the lineages in quarantine inspections. IMPORTANCEClavibacter spp. are economically important bacterial plant pathogens infecting a set of diverse agricultural crops, such as alfalfa, corn, pepper, potato, tomato, and wheat. A number of plant-pathogenic members of the genus (e.g., C. michiganensissensu stricto and C. sepedonicus, infecting tomato and potato plants, respectively) are included in the A2 (high-risk) list of quarantine pathogens by the European and Mediterranean Plant Protection Organization (EPPO). Although tomato-associated members of Clavibacter spp. account for a significant portion of the genetic diversity in the genus, only the strains belonging to C. michiganensissensu stricto (formerly C. michiganensis subsp. michiganensis) cause bacterial canker disease of tomato and are subjected to the quarantine inspections. Hence, discrimination between the pathogenic and nonpathogenic Clavibacter sp. strains associated with tomato seeds and transplants plays a pivotal role in the accurate detection and cost-efficient management of the disease. On the other hand, detailed information on the genetic contents of different lineages of the genus would lead to the development of genome-informed specific detection techniques. In this study, we have provided an overview of the phylogenetic and genomic differences between the pathogenic and nonpathogenic tomato-associated Clavibacter sp. strains. We also noted that the taxonomic status of newly introduced subspecies of C. michiganensis (i.e., C. michiganensis subsp. californiensis, C. michiganensis subsp. chilensis, and C. michiganensis subsp. phaseoli) should be reconsidered.

International audience

International audience; 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.

Oilseed rape residues are a crucial determinant of stem canker epidemiology, as they support the sexual reproduction of the fungal pathogen Leptosphaeria maculans. The aim of this study was to characterise the impact of a resistance gene against L. maculans infection on residue microbial communities and to identify micro-organisms interacting with this pathogen during residue degradation. We used near-isogenic lines to obtain healthy and infected host plants. The microbiome associated with the two types of plant residues was characterised by metabarcoding. A combination of linear discriminant analysis and ecological network analysis was used to compare the microbial communities and to identify micro-organisms interacting with L. maculans. Fungal community structure differed between the two lines at harvest, but not subsequently, suggesting that the presence/absence of the resistance gene influences the microbiome at the base of the stem whilst the plant is alive, but that this does not necessarily lead to differential colonisation of the residues by fungi. Direct interactions with other members of the community involved many fungal and bacterial ASVs (amplicon sequence variants). L. maculans appeared to play a minor role in networks, whereas one ASV affiliated to Plenodomus biglobosus (synonym Leptosphaeria biglobosa) from the Leptosphaeria species complex was considered a keystone taxon in the networks at harvest. This approach could be used to identify and promote micro-organisms with beneficial effects against residue-borne pathogens, and more broadly, to decipher the complex interactions between multi-species pathosystems and other microbial components in crop residues.

Les bactériophages tiennent une place prépondérante dans le monde vivant. Du point de vue épistémologique, ils participent à la compréhension du vivant via trois aspects fondamentaux : (i) les mécanismes moléculaires les plus intimes du fonctionnement des infections virales et de celui des cellules elles-mêmes (biologie moléculaire) ; (ii) le fonctionnement des écosystèmes (écologie) ; et (iii) la dynamique adaptative des populations virales et bactériennes (évolution). À travers une présentation historique de la découverte des bactériophages et de leurs fascinantes propriétés, cette revue relate la genèse des découvertes fondamentales associées à l’étude des bactériophages et présente une vision synthétique des champs de recherche actuels., Bacteriophages have a prominent place in the living world. They participate to our understanding of the living world through three main aspects : (i) the dissection of the most intimist aspects of viral infection molecular mechanisms (molecular biology), (ii) the description and functioning mechanisms of ecosystems (ecology), and (iii) the adaptive dynamics of integrated viral and host-cell populations (evolution). This review looks back at the genesis of these fundamental findings and draws a picture of the most active fields of current research.

Flavescence dor&eacute, e (FD) is a severe epidemic disease of grapevines caused by FD phytoplasma (FDP) transmitted by the leafhopper vector Scaphoideus titanus. The recent sequencing of the 647-kbp FDP genome highlighted an unusual number of genes encoding ATP-dependent zinc proteases FtsH, which have been linked to variations in the virulence of &ldquo, Candidatus Phytoplasma mali&rdquo, strains. The aims of the present study were to predict the FtsH repertoire of FDP, to predict the functional domains and topologies of the encoded proteins in the phytoplasma membrane and to measure the expression profiles in different hosts. Eight complete ftsH genes have been identified in the FDP genome. In addition to ftsH6, which appeared to be the original bacterial ortholog, the other seven gene copies were clustered on a common distinct phylogenetic branch, suggesting intra-genome duplication of ftsH. The expression of these proteins, quantified in plants and insect vectors in natural and experimental pathosystems, appeared to be modulated in a host-dependent manner. Two of the eight FtsH C-tails were predicted by Phobius software to be extracellular and, therefore, in direct contact with the host cellular content. As phytoplasmas cannot synthesize amino acids, our data raised questions regarding the involvement of FtsH in the adaptation to hosts via potentially enhanced recycling of phytoplasma cellular proteins and host protein degradation.

Dès 1917, dans l’article où il décrit ses premières observations et propose le nom de bactériophage, Félix d’Hérelle rapporte une première utilisation de ces virus pour traiter des infections bactériennes, donnant ainsi naissance à la phagothérapie. Le développement de cette application a montré qu’il était possible de mettre en place des traitements ciblant spécifiquement les bactéries, tels que ceux basés sur l’utilisation d’antibiotiques. Ces derniers, de par leur très grande efficacité et simplicité d’utilisation, ont provoqué le quasi-abandon de la phagothérapie. Aujourd’hui, un nombre croissant de bactéries pathogènes pour l’homme présente des phénotypes de résistance à plusieurs familles d’antibiotiques. Les infections causées par ces bactéries imposent l’utilisation de molécules au spectre d’activité toujours plus large et placent certains patients en situation d’impasse thérapeutique. Cet état de fait a relancé les recherches pour permettre le déploiement de la phagothérapie afin de traiter des patients mais aussi des animaux et des plantes. En fait, les domaines d’applications thérapeutiques des bactériophages s’élargissent au fur et à mesure que les agents antibactériens de nature chimique sont remis en cause, voire interdits. Cette revue revient sur les principes fondamentaux des applications thérapeutiques des bactériophages et expose les données récentes dans les domaines pour lesquels une exploitation commerciale est en cours ou sur le point d’émerger., In the 1917 article in which Félix d'Hérelle describes his first observations and proposes the name of bacteriophage, he also reports the first use of these viruses to treat bacterial infections, thus giving birth to phage therapy. Soon after antibiotics supplanted bacteriophages. Today, bacteria resistant to multiple antibiotics become a growing public health issue worldwide. This situation has revived research aiming at developing the antibacterial activity of bacteriophages to treat patients as well as diseases in animals and plants. In fact, the areas of applications of bacteriophages as antibacterial are widening as current solutions of chemical nature are questioned. This review summarizes the basic principles of therapeutic applications of bacteriophages and presents recent data in areas where commercial exploitation is occurring or about to emerge.

Durant 6 ans, le programme Verger Cidricole de Demain a expérimenté 9 vergers de pommiers à cidre bas-intrants « ECO », implantés chez 9 cidriculteurs du Nord-Ouest de la France. En comparaison à 9 vergers témoin « PROD », le projet visait à évaluer la faisabilité technique et les performances économiques, environnementales, sociales et agronomiques de ces vergers prototypes, où des pratiques culturales ont été combinées dans une approche dite « système ». Grâce à l’enregistrement de près de 40 000 données, des références technico-économiques ont été acquises sur les moyens permettant de réduire les intrants en jeune verger, notamment l’emploi des produits phytosanitaires. Les 9 systèmes « ECO » ont atteint une réduction moyenne des IFT hors biocontrôle de 48%. Combinées aux changements de pratiques de fertilisation et de couverture sur l’inter-rang (implantation de bandes fleuries), les méthodes alternatives au désherbage chimique du rang testées semblent davantage pénaliser l’entrée en production des systèmes « ECO » que la réduction des fongicides et des insecticides. En revanche, les stratégies alternatives testées contre la tavelure ont permis de réduire significativement les IFT fongicides sans conséquence pour la production des vergers « ECO ». Des itinéraires techniques viables à plus bas intrants restent donc possibles en verger cidricole à conditions d’optimiser certains leviers et leur combinaison, parmi lesquels : la génétique (résistance variétale et porte-greffes adaptés), la prophylaxie, le biocontrôle, l’efficience (outils d’aide à la décision et seuils d’intervention), la protection physique (bâche tissée ou mulch de copeaux de bois sur le rang associé à une fertilisation optimale), la lutte biologique (par conservation via l’implantation de bandes fleuries)., The “Verger Cidricole de Demain” (literally: Cider Apple Orchards of the Future) research project had experimented for 6 years with 9 low-input cider apple orchards named “ECO”. These were established under field conditions in 9 cider growers spread out in the north-west of France. With regard to 9 cider apple orchard references named “PROD”, the project aimed at assessing the technical feasibility and the economic, environmental, social and agronomic performances of these orchard prototypes, where cultural practices had been combined in a systemic approach. Thanks to the record of about 40,000 data points, technical and economic references had been acquired to reduce inputs in young cider apple orchards, such as the use of pesticides. The 9 ECO systems reached an average reduction of the chemical treatment frequency index (in French: IFT) of 48 % with regard to the PROD reference. When combined with changes in fertilization and plantation of flower strips in the orchard inter-rows, the alternatives to herbicide use in weed management seem to be more penalizing on the first fruiting than the reduction of fungicides and insecticides. However, thanks to the tested alternative strategies to fight apple scab, fungicide treatment frequency index was significantly reduced without impacting the yields of the ECO orchards. Viable low-input farming practices remain possible in cider apple orchards if some technics and their combinations are optimised. Among these are: genetics (varietal resistance and adapted rootstocks), prophylaxis, biocontrol products, efficiency (models and decision thresholds), physical protections (inert mulches on the tree rows for weed management, such as wood chip mulch or weed fabric, associated with an optimal fertilization), beneficial insects (by preservation with plantation of flower strips).

Three phages targeting Pseudomonas syringae GAW0113 have been isolated from organic waste samples: Pseudomonas phage Bertil, Misse and Strit. The phages have double-stranded DNA genomes ranging from 41342 to 41374 bp in size comprising 50 to 51 open reading frames. The three phages genomes are highly similar and genomic comparison analyses shows that they all belong to the Autographivirinae subfamily of the family Podoviridae. The phages are however only distantly related to other members of this family, and have limited gene synteny with type-phages of other genera within Autographivirinae, suggesting that the newly isolated phages could represent a new genus.

Zucchini (Cucurbita pepo) is worldwide affected by Pseudomonas syringae, inducing vein clearing, stunting, and necroses during plantlet development. A collection of 58 P. syringae strains isolated from diseased zucchini plantlets was characterized by multilocus sequence analysis (MLSA). A subset of 23 strains responsible for vein clearing of zucchini (VCZ) was evaluated for pathogenicity on zucchini, and their genomes were sequenced. The host range of six VCZ strains was evaluated on 11 cucurbit species. Most VCZ strains belong to clades 2a and 2b-a within phylogroup 2 of P. syringae species complex and are closely related to other strains previously isolated from cucurbits. Genome analyses revealed diversity among VCZ strains within each clade. One main cluster, once referred to by the invalid pathovar name (peponis), gathers VCZ strains presenting a narrow host range including zucchini and squashes. Other VCZ strains present a large host range including zucchini, squashes, cucumber, melons, and in some cases watermelon. The VCZ strain pathogenic features are strongly associated with type III effector repertoires. The presence of avrRpt2 and absence of hopZ5 are associated with a narrow host range, whereas the presence of hopZ5 and absence of avrRpt2 are most generally associated with a large host range. To better detect the different clusters identified with whole genome sequence and pathogenicity analyses, we used a specific-k-mers approach to refine the MLSA scheme. Using this novel MLSA scheme to type P. syringae isolates from diseased cucurbits would give insight into distribution of worldwide strains and origin of epidemics.

International audience; Banana (Musa spp.) is one of the most widely cultivated subtropical fruits around the globe. Banana cultivation has been extensively increased in southeastern Iran over the last two decades. Recently, banana fruits possessing rotten and blackened fingertip symptoms were observed in Sistan‐Baluchestan, Iran. Isolation and characterization of the causal agent showed that the pathogen belongs to the multifaceted bacterial species Burkholderia cenocepacia. Pathogenicity tests and host range assays showed that the strains were pathogenic on banana, as well as carrot, onion and potato. All the strains were resistant to 50 mg L−1 rifampicin and 200 mg L−1 copper sulphate. Phylogenetic analysis of 16S rRNA and recA gene sequences showed that the strains belong to two different genomovars of B. cenocepacia (III‐A and III‐B), which also include environmental and cystic fibrosis associated strains of the species. The results obtained from recA phylogeny were confirmed using multilocus sequence analysis (MLSA), although MLSA showed that the banana strains were clustered as a novel phylogroup among the members of both genomovars. Banana‐pathogenic B. cenocepacia strains isolated in Iran were different from the strains isolated in Taiwan, as the ‘B. cepacia epidemic strain marker’ reported in the Taiwanese strains was absent from Iranian strains. To the authors’ knowledge, this is the first MLSA‐based study on the banana‐pathogenic strains of B. cenocepacia. However, further in‐depth molecular studies are needed to decipher the relationships between the banana fingertip rot pathogen and the clinical strains of B. cenocepacia.

Genetic resistance is a useful strategy to control plant disease, but its effectiveness may be reduced over time due to the emergence of pathogens able to circumvent the defences of the plant. However, the pyramiding of different resistance factors in the same plant can improve the effectiveness and durability of the resistance. To investigate the potential for this approach in apple to control scab disease we surveyed scab incidence in two experimental orchards located more than 300 km apart planted with apple genotypes carrying quantitative resistance and major gene resistance alone or in combination. Our results showed that the effectiveness of pyramiding in controlling scab was dependent on the site and could not be completely explained by the effectiveness level of the resistances alone.

The formation of the haustorium in holoparasitic plants as demonstrated in Phelipanche ramosa is initiated through perception of a host-exudated cytokinin and a cytokinin signaling response., The heterotrophic lifestyle of parasitic plants relies on the development of the haustorium, a specific infectious organ required for attachment to host roots. While haustorium development is initiated upon chemodetection of host-derived molecules in hemiparasitic plants, the induction of haustorium formation remains largely unknown in holoparasitic species such as Phelipanche ramosa. This work demonstrates that the root exudates of the host plant Brassica napus contain allelochemicals displaying haustorium-inducing activity on P. ramosa germinating seeds, which increases the parasite aggressiveness. A de novo assembled transcriptome and microarray approach with P. ramosa during early haustorium formation upon treatment with B. napus root exudates allowed the identification of differentially expressed genes involved in hormone signaling. Bioassays using exogenous cytokinins and the specific cytokinin receptor inhibitor PI-55 showed that cytokinins induced haustorium formation and increased parasite aggressiveness. Root exudates triggered the expression of cytokinin-responsive genes during early haustorium development in germinated seeds, and bio-guided UPLC-ESI(+)-/MS/MS analysis showed that these exudates contain a cytokinin with dihydrozeatin characteristics. These results suggest that cytokinins constitutively exudated from host roots play a major role in haustorium formation and aggressiveness in P. ramosa.

UMR BFP - Equipe Virologie; International audience; We developed an innovative RNAi concept based on two gene constructs built from the capsid gene (CP) cistron of the Plum pox virus (PPV) genome. First, designated as amiCPRNA, a potential molecule interfering with PPV genome translation and the second one is the ami-siCPRNA to target viral genome translation and PPV RNA replication. Following the previous engineering of these constructs in an experimental herbaceous host, they were introduced into Prunus domestica (plum tree) genome. Previously propagated onto a susceptible rootstock, these clones were graft-inoculated with PPV. After four dormancy cycles, and consistent with our experience of PPV infection, some clones showed a common phenomenon of silencing that can differ between the detailed plant phenotypes. Three different phenotypes were developed by the amisiCPRNA clones. First, the high resistance character shown by the amisiCPRNA plum-7 that was similar to the resistance expressed by HoneySweet plum. Secondly, a recovery reaction was developed by the two other amisiCPRNA plum-3 and plum-4 that differed from the rest, characterized as susceptible clones, among these were the amiCPRNA plums. Having assessed the behavior of these plums versus the herbaceous host accumulating the similar form of RNAi: ami-, si-, and ami-siRNA, challenging assays in perennials consistently reflect the natural context of viral genome targeting

We thank the staff of the INRAE Experimental facilities of the Plant Pathology research unit (IEPV) who ensured the production and maintenance of the plants and plant-growth facilities that allowed us to do this work. https://doi.org/10.15454/8DGF-QF70; International audience; Thirty-one melon accessions were screened for resistance to the begomoviruses melon Melon chlorotic mosaic virus (MeCMV) and tomato Tomato leaf curl New Delhi virus (ToLCNDV). Five accessions presented nearly complete resistance to both viruses. Accession IC-274014, showing the highest level of resistance to both viruses, was crossed with the susceptible cultivar ‘Védrantais’. The F1, F2, F3/F4 and both back-cross progenies were mechanically inoculated with MeCMV. Plants without symptoms nor virus detection by ELISA and/or PCR were considered as resistant. The segregations were compatible with two recessive and one dominant independent genes simultaneously required for resistance. Inheritance of resistance to ToLCNDV in the F2 was best explained by one recessive gene and two independent dominant genes simultaneously required. Some F3 and F4 families selected for resistance to MeCMV were also resistant to ToLCNDV, suggesting that common or tightly linked genes were involved in resistance to both viruses. We propose the names begomovirus resistance-1 and Begomovirus resistance-2 for these genes (symbols bgm-1 and Bgm-2). Resistance to MeCMV in IC-274014 was controlled by bgm-1, Bgm-2 and the recessive gene melon chlorotic mosaic virus resistance (mecmv); resistance to ToLCNDV was controlled by bgm-1, Bgm-2 and the dominant gene Tomato leaf curl New Delhi virus resistance (Tolcndv).

National audience

Published in Rimbaud, L., Dallot, S., Bruchou, C., Thoyer, S., Jacquot, E., Soubeyrand, S., Thébaud, G. (2019). Improving management strategies of plant diseases using sequential sensitivity analyses. Phytopathology, 109, 1184-1197. DOI:10.1094/PHYTO-06-18-0196-R; Improvement of management strategies of epidemics is often hampered by constraints on experiments at large spatiotemporal scales. A promising approach consists of modelling the biological epidemic process and human interventions, which both impact disease spread. However, few methods enable the simultaneous optimisation of the numerous parameters of sophisticated control strategies. To do so, we propose a heuristic approach (i.e., a practical improvement method approximating an optimal solution) based on sequential sensitivity analyses. In addition, we use an economic improvement criterion, based on the net present value, accounting for both the cost of the different control measures and the benefit generated by disease suppression. This work is motivated by sharka (caused by Plum pox virus ), a vector-borne disease of prunus trees (especially apricot, peach and plum) whose management in orchards is mainly based on surveillance and tree removal. We identified the key parameters of a spatiotemporal model simulating sharka spread and control, and approximated optimal values for these parameters. The results indicate that the current French management of sharka efficiently controls the disease, but can be economically improved using alternative strategies that are identified and discussed. The general approach should help policymakers to design sustainable and cost-effective strategies for disease management.

International audience; Apples are a nutritious food source with significant amounts of polyphenols that contribute to human health and wellbeing, primarily as dietary antioxidants. Although numerous pre- and post-harvest factors can affect the composition of polyphenols in apples, genetics is presumed to play a major role because polyphenol concentration varies dramatically among apple cultivars. Here we investigated the genetic architecture of apple polyphenols by combining high performance liquid chromatography (HPLC) data with similar to 100,000 single nucleotide polymorphisms (SNPs) from two diverse apple populations. We found that polyphenols can vary in concentration by up to two orders of magnitude across cultivars, and that this dramatic variation was often predictable using genetic markers and frequently controlled by a small number of large effect genetic loci. Using GWAS, we identified candidate genes for the production of quercitrin, epicatechin, catechin, chlorogenic acid, 4-O-caffeoylquinic acid and procyanidins B1, B2, and C1. Our observation that a relatively simple genetic architecture underlies the dramatic variation of key polyphenols in apples suggests that breeders may be able to improve the nutritional value of apples through marker-assisted breeding or gene editing.

International audience; Potato and tomato are important crops in Algerian agriculture, and both are threatened by abiotic and biotic stresses, and early blight is a major disease affecting both crops. Surveys carried out from 2012 to 2015 in 12 major growing regions for these crops yielded a total of 247 Alternaria isolates having morphological and cultural characteristics of sections Alternaria and Porri. Since early blight symptoms and morphological characteristics of the isolates did not allow sharp distinction between the different large-spored species of Alternaria, the isolates in section Porri, often considered primary causes of the diseases, were selected for molecular characterization by diagnostic PCR using specific primers. This allowed species identification of 147 Alternaria isolates as A. solani, A. protenta, A. grandis or A. linariae. These species were present on potato and tomato crops at varying frequencies, depending on the hosts and on bioclimatic locations. Pathogenicity tests for the four species, on detached leaflets and whole seedlings, showed that all were pathogenic to potato and tomato, with varying virulence. These results suggest that parasitic specialization of these Alternaria species on solanaceous plants should be reconsidered

Integration of unusual domains in plant immune receptors is a widespread mechanism of NLR diversification enabling specific pathogen detection.

In autumn 2001, severe yellowing symptoms were observed on greenhouse-grown cucumbers near Perpignan (southern France). Leaf samples were collected from two sites where plants displayed symptoms ranging from limited yellowing of the older leaves to severe, complete yellowing of the whole plant. Cucurbit aphid-borne yellows virus, a polerovirus that causes similar symptoms was not detected in doubleantibody sandwich enzyme-linked immunosorbent assay (DAS-ELISA) using a specific antiserum. Total RNA was extracted from fresh leaf tissues and used in reverse transcription-polymerase chain reaction (1) with primers specific for two whitefly-borne viruses also inducing yellows and occurring in the Mediterranean basin (1): Beet pseudo yellows virus (BPYV, genus Closterovirus) transmitted by Trialeurodes vaporariorum (West.) and Cucurbit yellow stunting disorder virus (CYSDV, genus Crinivirus) transmitted by Bemisia tabaci (Genn.). No BPYV was detected in this survey, but CYSDV was present in all samples. In subsequent surveys conducted in the spring and summer of 2002, BPYV and CYSDV were detected, sometimes in mixed infections, in samples collected from the same region. The complete CYSDV coat protein gene was amplified by PCR using specific primers (2), yielding the expected-size fragment of 756 bp. The French isolate (GenBank Accession No. AY204220) shared 99.6 to 100% nucleotide sequence identity in the sequenced CP fragments (700 nt) with isolates of the most common, highly homogenous subgroup of CYSDV that has emerged recently in the Middle East, southwestern Europe (Spain and Portugal), United States, and Morocco (2). To our knowledge, this is the first report of CYSDV in France and it shows the threat represented by the current emergence of B. tabaci-transmitted viruses. References: (1) I. C. Livieratos et al. Plant Pathol. 47:362, 1998. (2) L. Rubio et al. J. Gen. Virol. 82:929, 2001.

Sequiviruses are isometric aphidborne plant viruses. Dandelion yellow mosaic virus (DaYMV), genus Sequivirus, was isolated from dandelion and lettuce in Europe. Lettuce mottle virus (LeMoV), a putative sequivirus, is often found in mixed infections with Lettuce mosaic virus (LMV) in Brazil (3). DaYMV, LeMoV and LMV cause similar mosaics in field-grown lettuce. Differences in biology and sequence suggest that DaYMV and LeMoV are distinct species (2). Forty-two and 101 lettuce samples with mosaic symptoms collected from two locations near Santiago during a survey of lettuce viruses in Chile in 2002 and 2003, respectively, were analyzed for the presence of LeMoV using reverse transcription polymerase chain reaction (RT-PCR). Total RNA was extracted (1) and used for RT-PCR with the specific LeMoV primers pairs Lmo3 (5′ ACATGAGCACTAGTGAGG 3′) and Lmo4 (5′ AGATAGAGCCGTCT GGCG 3′) (2). One of the 42 and three of the 101 samples produced the expected 300-bp fragment. Isometric particles of 30 nm diameter, typical of a sequivirus, were visualized by transmission electron microscopy. These samples were tested using RT-PCR for the presence of LMV and Cucumber mosaic virus (CMV), but no mixed infections were observed. One isolate, Ch36, was reamplified with the degenerate primer pairs DALE 1 (5′ GARTTCAACATGCACGCCAG 3′) and DALE 2 (5′ TTTTTCTCCCCATYCGTCAT 3′) which amplify part of the putative replicase gene (2) and produced a 563-bp fragment that was cloned on pGEM-T Easy (Promega, Madison, WI) and sequenced. The Ch36 product (EMBL Accession No. AM039965) showed 97% amino acid identity with LeMoV from Brazil, 79% with DaYMV, 72% with the sequivirus Parsnip yellow fleck virus, and 34% with the waikavirus Maize chlorotic dwarf virus. To our knowledge, this is the first report of a sequivirus in field lettuce in Chile, and although the virus was found at low incidence, this report extends the range of LeMoV to the western side of the Cordillera de Los Andes. The impact of LeMoV needs to be further analyzed in Chile, Brazil, and possibly other South American countries. References: (1) Y. D. Bertheau et al. DNA amplification by polymerase chain reaction (PCR) 1998. In: Methods for the Detection and Quantification of Erwinia carotovora subsp. atroseptica on potatoes. M. C. N. Perombelon and J. M. van der Wolff, eds. Scott. Crop Res. Inst. Occasional Publ., Dundee, 1998. (2) A. S. Jadão. Caracterização parcial e desenvolvimento de oligonucleotídeos específicos para detecção de sequivirus infectando alface. Ph.D. thesis. FCA-UNESP-Botucatu, Brazil, 2004. (3) O. Stangarlin et al. Plant Dis. 84:490, 2000.

The potyvirus Lettuce mosaic virus (LMV) is a common pathogen of lettuce crops worldwide, but it also infects other Asteraceae spp. including ornamentals (2,3,4). Cape daisies (Osteospermum sp.) are widely grown perennial ornamentals reported to be natural hosts of LMV (2,4), which causes faint leaf mosaic and sometimes mild flower breaking. A preliminary observation of mosaic symptoms prompted a large-scale survey during the spring of 2005 in Cape daisies grown in the Tunis metropolitan area and the south of Tunisia (Djerba, Medenine). Two hundred seventy-one samples (Tunis: 14 sites, 219 samples; South: 9 sites, 52 samples) were randomly collected from nurseries, roadway plantings, and home gardens and analyzed. Ninety-three samples (Tunis: 40%, South: 12%; overall: 34%) showed distinct mosaic symptoms. LMV infection was verified by immuno-tissue printing on all collected samples (1), providing evidence for even higher infection levels (Tunis: 60%; South: 25%; overall: 56%). This technique, therefore, allowed the detection of symptomless infection in a significant proportion of samples. It should however, be stressed that symptoms can be very difficult to observe in water-stressed plants, a situation frequently observed in Tunisia. Subsequent PCR analysis with LMV-specific primers (1) of a subset of 24 symptomatic and tissue-print-positive samples confirmed LMV infection in all cases. This is to our knowledge, the first report of LMV infection in Cape daisies in Tunisia. The very high rate of infection observed suggests that these popular ornamentals might constitute a reservoir of LMV as previously reported in the United States (4). References: (1) H. Fakhfakh et al. J. Plant Pathol. 83:3, 2001. (2) R. Jordan and M. Guaragna. (Abstr.) Phytopathology 96(suppl.):S56, 2006. (3) O. Le Gall. No. 399 in: Description of Plant Viruses. A. T. Jones et al., eds. CMI/AAB, Kew, Surrey, UK, 2003. (4) D. C. Opgenorth et al. Plant Dis. 75:751, 1991.

During the fall of 2003, mild mosaic symptoms were observed in melon (Cucumis melo L.) plants grown in glasshouses near Eyragues (southeastern France) resembling those caused by the Bemisia tabaci transmitted Cucumber vein yellowing virus (CVYV, genus Ipomovirus, family Potyviridae). In addition, large numbers of B. tabaci were observed to be colonizing these crops. The identification of CVYV was established through differential host range reaction, immunosorbent electron microscopy (IEM), and reverse transcription (RT)-PCR experiments. Crude sap from symptomatic leaves was used to inoculate differential host plants. Mild mosaic symptoms were observed on melon, and cucumber developed vein-clearing symptoms typical of CVYV. No symptoms were observed in Chenopodium quinoa, C. amaranticolor, Nicotiana benthamiana, N. tabacum, and Vigna sinensis. Numerous, slightly flexuous, elongated virus particles were observed in infected plant extracts; these particles were decorated by a polyclonal antiserum raised against a Sudanese CVYV isolate. To confirm CVYV identification, total RNA extracts (TRI-Reagent, Sigma Chemical, St. Louis, MO) were obtained from the original symptomatic melon tissues. RT-PCR was carried out using CVYV-specific primers CVYV-CP-5′: 5′-GCTTCTGGTTCTCAAGTGGA-3′ and CVYV-CP- 3′: 5′-GATGCATCAGTTGTCAGATG-3′ designed according to the partial sequence of the coat protein gene of CVYV-Isr (GenBank Accession No. AF233429) (2). A 540-bp fragment corresponding to the central region of CVYV coat protein was amplified from total RNA extracted from symptomatic but not from asymptomatic melon tissue. Direct sequencing was done on RT-PCR products (GenBank Accession No. EF441272). The sequence was 95 and 99% identical to that reported for CVYV isolates from Israel and Spain, respectively. CVYV was first described in Israel and has recently emerged as the cause of important diseases in Spain and Portugal (1,3). Shortly after detecting CVYV during 2003, efforts were made to eradicate the virus in susceptible crops. CVYV was not detected again during intensive surveys conducted in southeastern France during 2004, 2005, and 2006, suggesting that the CVYV detected during 2003 resulted from an accidental introduction and that the virus has not become established in France. References: (1) I. M. Cuadrado et al. Plant Dis. 85:336, 2001. (2) H. Lecoq et al. J. Gen. Virol. 81:2289, 2000. (3) D. Louro et al. Plant Pathol. 53:241, 2004.

International audience; The specificities of the plant environment and its effects on fungal growth are not yet fully explored. Both pH and Eh play a key role during this interaction, but are often studied independently or at different scales. We aimed at investigating whether the methods developed for the joint characterization of the pH and Eh in soil could be transposed to fungi. On artificial media, the growth of all 16 species tested significantly altered either Eh, pH or both. Measuring Eh reveals that even the species not modifying pH can have an impact on the surrounding environment. Reciprocally, fungi responded to pH and Eh parameters, both quantitatively with a decrease in colony diameter and qualitatively with colony aspect repeatedly and thoroughly modified. In infected oilseed rape plant stems, pH and Eh were significantly altered. The observed alcalinisation or acidification correlates with canker length. The joint characterization of both parameters will allow understanding the impact of fungi on their environment, and conversely of the environment on fungal growth. The availability of methods for measurement opens the prospect to study combinations of stresses, and get an understanding of the involvement of pH and Eh modifications in these interactions.

National audience

Background Diseases caused by Pseudomonas syringae (Ps) are recognized as the most damaging factors in fruit trees with a significant economic and sanitary impact on crops. Among them, bacterial canker of apricot is exceedingly difficult to control due to a lack of efficient prophylactic measures. Several sources of partial resistance have been identified among genetic resources but the underlying genetic pattern has not been elucidated thus far. In this study, we phenotyped bacterial canker susceptibility in an apricot core-collection of 73 accessions over 4 years by measuring canker and superficial browning lengths issued from artificial inoculations in the orchard. In order to investigate the genetic architecture of partial resistance, we performed a genome-wide association study using best linear unbiased predictors on genetic (G) and genetic x year (G × Y) interaction effects extracted from linear mixed models. Using a set of 63,236 single-nucleotide polymorphism markers genotyped in the germplasm over the whole genome, multi-locus and multi-variate mixed models aimed at mapping the resistance while controlling for relatedness between individuals. Results We detected 11 significant associations over 7 candidate loci linked to disease resistance under the two most severe years. Colocalizations between G and G × Y terms indicated a modulation on allelic effect depending on environmental conditions. Among the candidate loci, two loci on chromosomes 5 and 6 had a high impact on both canker length and superficial browning, explaining 41 and 26% of the total phenotypic variance, respectively. We found unexpected long-range linkage disequilibrium (LD) between these two markers revealing an inter-chromosomal LD block linking the two underlying genes. This result supports the hypothesis of a co-adaptation effect due to selection through population demography. Candidate genes annotations suggest a functional pathway involving abscisic acid, a hormone mainly known for mediating abiotic stress responses but also reported as a potential factor in plant-pathogen interactions. Conclusions Our study contributed to the first detailed characterization of the genetic determinants of partial resistance to bacterial canker in a Rosaceae species. It provided tools for fruit tree breeding by identifying progenitors with favorable haplotypes and by providing major-effect markers for a marker-assisted selection strategy. Electronic supplementary material The online version of this article (10.1186/s12870-019-1631-3) contains supplementary material, which is available to authorized users.

International audience; Pseudomonas syringae is the most frequently emerging group of plant pathogenic bacteria. Because this bacterium is ubiquitous as an epiphyte and on various substrates in non-agricultural settings, there are many questions about how to assess the risk for plant disease posed by strains in the environment. Although P. syringae is considered to have discrete host ranges in defined pathovars, there have been few reports of comprehensive comparisons of host range potential. Here we present results of host range tests for 134 strains, representing eight phylogroups, from epidemics and environmental reservoirs on 15 to 22 plant species per test conducted in four separate tests to determine the patterns and extent of host range. We sought to identify trends that are indicative of distinct pathotypes and to assess if strains in the P. syringae complex are indeed restricted in their host range. We show that for each test, strains display a diversity of host ranges from very restricted to very broad regardless of the gamut of phylogroups used in the test. Overall, strains form an overlapping continuum of host range potential with equal representation of narrow, moderate and broad host ranges. Groups of distinct pathotypes, including strains with currently the same pathovar name, could not be identified. The absence of groupings was validated with statistical tests for pattern recognition. The extent of host range was positively correlated with the capacity of strains to swarm on semi-solid agar medium and with the abundance of genes in biosynthetic clusters and was inversely correlated with the abundance of genes for proteins with transmembrane domains in their genomes. Our results are consistent with the current paradigm that disease symptoms are the result of multiple molecular interactions between P. syringae and its plant host that are modulated by abiotic and biotic conditions. This leads us to propose that pathovar denominations do not correspond to the underlying biology of P. syringae. A new concept of pathogenicity that accounts for the continuum of pathogenic potential in P. syringae would open new perspectives to understand the evolution of pathogenicity in this bacterium and new insights to anticipate disease and to manage plant health.

Environmental exposure to radiofrequency electromagnetic fields (RF-EMFs) from mobile telephony has rapidly increased in the last two decades and this trend is expected to continue. The effects of this exposure at plant community level are unknown and difficult to assess in a scientifically appropriate manner. Such an assessment can be scientifically adequate if a studied plant community is completely new and control-impact radiation treatment is used. In this review we aimed to predict ecological effects and identify indicators of the impact of bioactive RF-EMFs at the mobile telephony frequency range on plant communities. We considered the scenario where a plant community was exposed to radiation generated by a base transmitting station antenna mounted on a nearby mast. This plant community can be represented by mesic meadow, ruderal or arable weed community, or other herbaceous, moderately productive vegetation type. We concentrated primarily on radiation effects that can be recorded for a year since the exposure started. To predict them we used physical theories of radiowave propagation in vegetation and the knowledge on plants physiological responses to RF-EMF. Our indicators can be used for the detection of the impact of RF-EMFs on vegetation in a control-impact experiment. The identified indicators can be classified into the following groups: (1) canopy parameters; (2) plant characteristics to be measured in the field or laboratory in a number of individuals that represent the populations of selected species; (3) community weighted means/medians (CWMs) of plant traits and strategies; (4) the abundance of other organisms that interact with plants and can influence their fitness or population size. The group of canopy parameters includes mean height, vertical vegetation structure and dry weight of above-ground standing phytomass. Plant characteristics requiring biometric sampling in the field are plant height, the number of fruits and seeds, as well as seed viability. The group of plant traits that are calculated as CWMs covers seed releasing height, seed dispersal mode, SLA, leaf orientation, month of germination and flowering, Ellenberg’s light indicator value, and the proportion of individuals in the classes of competitors and stress tolerators according to Grime's CSR strategy scheme. The group of “non-plant” indicators includes primarily the frequency of flower visits by beetles, wasps, hoverflies, and bees that have their nests over ground. To detect ecological responses that occur for the first year since a herbaceous community has been exposed to potentially bioactive RF-EMF, the first two indicators groups should be used., Amparo Lázaro was supported by a Ramón y Cajal contract (RYC-2015-19034) from the Spanish Ministry of Economy and Competitiveness.

Cucumber vein yellowing virus (CVYV) is emerging throughout the Mediterranean Basin, where it causes important damages on cucumber and melon crops. It has been suggested that CVYV originated from the Middle East and has spread only recently to other areas. In this work, an isolate from Sudan was characterized and surveys performed in that country between 1992 and 2012 revealed a long‐term presence of CVYV with a high molecular variability, showing that the virus has long been endemic in Sub‐Saharan Africa. Comparison of the full‐length sequences of 11 CVYV isolates from different geographic origins revealed recombination events in CVYV populations from the Mediterranean Basin and the Middle East, and evidence for different selection pressures along the genome. These results shed a new light on the evolution of CVYV.

Texture plays a major role in the determination of fruit quality in apple. Due to its physiological and economic relevance, this trait has been largely investigated, leading to the fixation of the major gene PG1 controlling firmness in elite cultivars. To further improve fruit texture, the targeting of an undisclosed reservoir of loci with minor effects is compelling. In this work, we aimed to unlock this potential with a genomic selection approach by predicting fruit acoustic and mechanical features as obtained with a TA.XTplus texture analyzer in 537 individuals genotyped with 8,294 SNP markers. The best prediction accuracies following cross-validations within the training set (TRS) of 259 individuals were obtained for the acoustic linear distance (0.64). Prediction accuracy was further improved through the optimization of TRS size and composition according to the test set. With this strategy, a maximal accuracy of 0.81 was obtained when predicting the synthetic trait PC1 in the family ‘Gala × Pink Lady’. We discuss the impact of genetic relatedness and clustering on trait variability and predictability. Moreover, we demonstrated the need for a comprehensive dissection of the complex texture phenotype and the potentiality of using genomic selection to improve fruit quality in apple.HighlightA genomic selection study, together with the optimization of the training set, demonstrated the possibility to accurately predict texture sub-traits valuable for the amelioration of fruit quality in apple.

Background: Yearly, France produces more than 20000 tons of garlic representing 3500 producers and 3000 ha. Since the mid-2000s and in spite of high demanding production specifications, a phytopathogenic fungus belonging to genus Fusarium, causes damage during storage leading to root and bulb rots. The annual losses have a major impact on the viability of the French industry.[br/] Objectives: Two major objectives were to : • Elucidate the etiology of the disease on garlic • Develop a test to evaluate the aggressiveness of strains[br/] Methods: Strains were isolated from the two major French production areas (South West and South East) during the 2017 and 2018 production campaigns. Eleven garlic varieties on more than 90 plots were used. All tested cloves were surface-sterilized with NaOCl and fungi were allowed to develop on PDA. To evaluate aggressiveness of each strain, twelve surface-sterilized cloves soaked in 1.0*106 spores/mL were used. All cloves were placed separately at 23°C at saturated humidity for 18 days. Symptoms were noted with rating scale from 0 (absence of symptoms) to 5 (clove entirely brown). Every 2 days, Area Under the Disease Progress Curve was calculated for each clove.[br/] Results: In total, 1580 strains were successfully isolated, 262 identified (98% F. proliferatum and 2% F. oxysporum) and 48 tested for their aggressiveness. All varieties seemed to be infected equally, some plots more than the others. All tested strains shows aggressiveness on garlic, from 60 to 140% as compared to a reference strain.

To sustain epidemiological studies on coconut lethal yellowing disease (CLYD), a devastating disease in Africa caused by a phytoplasma, we developed a multilocus sequence typing (MLST) scheme for 'Candidatus Phytoplasma palmicola' based on 8 housekeeping genes. At the continental level, eight different sequence types were identified among 132 'Ca. Phytoplasma palmicola-' infected coconuts collected in Ghana, Nigeria and Mozambique where CLYD epidemics are still very active. 'Ca. Phytoplasma palmicola' appeared to be a bacterium submitted to strong bottlenecks, reducing the fixation of positively selected beneficial mutations into the bacterial population. This phenomenon, as well as a limited plant host range, could explain the observed country-specific distribution of the eight haplotypes. As an alternative means to increase fitness, bacteria can also undergo genetic exchange; however, no evidence for such recombination events were found for 'Ca. Phytoplasma palmicola'. The implications for CLYD epidemiology and prophylactic control are discussed. The usefulness of seven housekeeping genes to investigate the genetic diversity in the genus 'Candidatus Phytoplasma' is underlined. IMPORTANCE: Coconut is an important crop for both industry and small stakeholders in many intertropical countries. Phytoplasma-associated lethal yellowing-like diseases have become one of the major pests that limit coconut cultivation as they have emerged in different parts of the world. We developed a multilocus sequence typing scheme for tracking epidemics of 'Ca. Phytoplasma palmicola', which is responsible for coconut lethal yellowing disease (CLYD) on the African continent. MLST analysis applied to diseased coconut samples collected in western and eastern African countries also showed the existence of three distinct populations of 'Ca. Phytoplasma palmicola' with low intrapopulation diversity. The reasons for the observed genetic bottlenecks resulting in strong geographic patterns remain to be established but could result from the lethality of CLYD and dominance of short distance insect-mediated transmission in its spread.

Cydia pomonella granulovirus, in particular CpGV-M isolate, is used as a biological control against the codling moth (CM), Cydia pomonella. As a result of intensive control over the years, codling moth populations have developed resistance against this isolate. This resistance is now called type I resistance. Isolates, among them, CpGV-R5, have been found that are able to overcome type I resistance. Both CpGV-M and CpGV-R5 are used in orchards to control the codling moth. High resolution melting (HRM) has been adapted to differentiate between CpGV-M and CpGV-R5 isolates. Specific PCR primers have been designed for the CpGV p38 gene, encompassing the variable region responsible for the ability to overcome resistance. Because each amplicon has a specific melting point, it is possible to identify the CpGV-M and CpGV-R5 genotypes and to quantify their relative proportion. This method has been validated using mixtures of occlusion bodies of each isolate at various proportions. Then, the HRM has been used to estimate the proportion of each genotype in infected larvae or in occlusion bodies (OBs) extracted from dead larvae. This method allows a rapid detection of genotype replication and enables the assessment of either success or failure of the infection in field conditions.

We thank the staff of the INRAE Experimental facilities of the Plant Pathology research unit (IEPV) for their involvement in field experiments. https://doi.org/10.15454/8DGF-QF70; International audience; Flower strips appear to be a promising lever for promoting pest control but a careful selection of the plant species used is needed prior to implementation to avoid possible negative side effects. In the case of open field melon crops, the main pitfall would be to generate aphid and aphid-borne virus reservoirs near the crops. Combining biotests under controlled conditions and data from the literature, we assessed 18 candidate plant species, and ruled-out those posing a potential risk of hosting Aphis gossypii (melon pest and virus vector), Myzus persicae (virus vector) and/or viruses (Cucurbit aphid-borne yellows virus (CABYV), Cucumber mosaic virus (CMV), Watermelon mosaic virus (WMV) and Zucchini yellow mosaic virus (ZYMV)). Five plant species made it through the selection process: cornflower, grass pea, sainfoin, salad burnet and sweet marjoram. Flower strips sown with a mix of these five plant species were evaluated in a five-year field experiment. They displayed a flowering continuum likely to provide a food resource to natural enemies throughout the growing season. Their potential to host natural enemies was compared to those of grass strips and bare soil by monitoring generalist and specialist predators within the different field margins and melon crop. Flower margins supported significantly more of these natural enemies than grass margins and bare soil. All predator taxa analyzed responded positively to the floral resources displayed. Spiders were 3.2 times more abundant in pitfall traps placed in flower margins than in bare soil. Generalist predators and aphid specialist predators collected using a vacuum sampler were 5.5 and 9.1 times more abundant in flower margins than in bare soil, respectively. Interception traps set for weekly periods showed that coccinellid and syrphid fluxes were significantly enhanced near flower margins.

National audience

La lutte chimique préventive est encore aujourd’hui le principal moyen de lutte contre les bioagresseurs en culture de laitue d’hiver sous abri. Des stratégies alternatives ont été explorées dans le projet LILLA, visant soit à fournir des références expérimentales manquantes sur des techniques non chimiques de protection des plantes, soit à tester des conduites de cultures basées sur des stratégies intégrées de protection, limitant le recours aux pesticides. Des leviers innovants, comme une résistance génétique accrue aux agents de la pourriture du collet, ou la conduite de l’irrigation en goutte à goutte au lieu de l’aspersion, ont pu être identifiés. En considérant un ensemble de 23 essais comparatifs de conduite des cultures, une diminution de moitié du nombre de traitements fongicides en association avec des techniques alternatives ne montre pas une augmentation statistique du risque de perte de récolte. Contre les pucerons, les stratégies de contrôle biologique testées restent à améliorer. Le coût de mise en oeuvre des techniques alternatives est significatif mais, pour la plupart d’entre elles, reste modéré. Les plus efficaces de ces techniques pourraient plus facilement être mises en oeuvre dans les exploitations si les incertitudes sur les revenus de la récolte étaient moins grandes., Preventive chemical control is still today the main mean of managing pests in winter lettuce under shelter. Alternative strategies have been explored in the LILLA project, either to provide needed experimental results on non-chemical plant protection techniques, or to test cropping systems based on integrated protection strategies that reduce the use of pesticides. Innovative pest management levers, including increased genetic resistance to basal rots, or the use of drip instead of sprinkler-irrigation. Considering a set of 23 comparative crop management trials, halving the number of fungicide treatments in combination with alternative techniques does not show a statistical increase in the risk of crop failure. The biological control strategies tested against aphids remain to be improved. The cost of implementing alternative techniques is significant but remains moderate in most cases. The most effective of these techniques could be more easily implemented by farmers if uncertainties about crop income were lower.

To test the importance of the host genotype in maintaining virus genetic diversity, five experimental populations were constructed by mixing two Cydia pomonella granulovirus isolates, the Mexican isolate CpGV-M and the CpGV-R5, in ratios of 99% M + 1% R, 95% M + 5% R, 90% M + 10% R, 50% M + 50% R, and 10% M + 90% R. CpGV-M and CpGV-R5 differ in their ability to replicate in codling moth larvae carrying the type I resistance. This ability is associated with a genetic marker located in the virus pe38 gene. Six successive cycles of replication were carried out with each virus population on a fully-permissive codling moth colony (CpNPP), as well as on a host colony (RGV) that carries the type I resistance, and thus blocks CpGV-M replication. The infectivity of offspring viruses was tested on both hosts. Replication on the CpNPP leads to virus lineages preserving the pe38 markers characteristic of both isolates, while replication on the RGV colony drastically reduces the frequency of the CpGV-M pe38 marker. Virus progeny obtained after replication on CpNPP show consistently higher pathogenicity than that of progeny viruses obtained by replication on RGV, independently of the host used for testing.

Botrytis cinerea est un champignon pathogène de plus de 200 espèces végétales. Parmi elles, beaucoup sont des espèces cultivées; la tomate en fait partie. La lutte chimique contre ce pathogène est compliquée puisque des résistances à la plupart des fongicides utilisés sont apparues. Néanmoins il existe de nombreuses méthodes de lutte alternatives. Les agents de biocontrôle en font partie. Le greffage est très répandu en culture de tomate sous serre, notamment pour son effet protecteur contre certains pathogènes telluriques. Cependant, aucune information n’existe sur un effet bénéfique potentiel du greffage de la tomate contre des parasites aériens tels que B. cinerea, utilisé seul ou en combinaison avec l’application d’agents de biocontrôle. [br/] Ces effets ont été étudiés dans le cadre du projet européen « EUCLID », pour une variété de tomate (Clodano), greffée sur elle-même ou sur une variété porte-greffe classique (Emperador), en combinaison avec quatre agents de biocontrôle (Regalia, Prestop, Serenade et un produit issu du projet EUCLID). Le greffage n’a montré aucun effet protecteur direct contre B. cinerea chez la tomate et il n’a pas affecté l’efficacité protectrice des produits Serenade et Regalia. Par contre une réduction de protection, faible (, The fungus Botrytis cinerea is pathogenic on more than 200 plant species. Many of which are cultivated; tomato is one of them. Chemical control of B. cinerea is complicated by the appearance of resistances against the majority of registered fungicides. However a lot of alternative methods already exist, including the use of biocontrol agents. Grafting is a commonly used in greenhouse tomato production, as it provides a good level of protection against certain soil-borne pathogens. However, there is no information on its potential protective effect against air-borne pathogens such as B. cinerea or on possible interference with the protective effect of treatments with biocontrol agents. [br/] These effects were investigated in the context of the « EUCLID » European project, for a commercial tomato variety (Clodano) grafted on itself or on a commonly used rootstock variety (Emperador), in combination with the application of four biocontrol agent efficiencies (Regalia, Prestop, Serenade and a product developed within the EUCLID project). Grafting provided no direct protective effect against B. cinerea and it did not alter the efficiency of Serenade and Regalia. However, a small (