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Orobanche cumana (sunflower broomrape) is an obligate parasitic plant that specifically infects sunflower roots, causing yield losses. By combining genomics and genetics in a map-based cloning strategy, we located the HaOr7 resistance gene to O. cumana in a 55 kb genomic region on chromosome 7 containing a single gene. The HaOr7 gene encodes a receptor-like LRR kinase protein sharing similarity with Xa21 in rice, conferring resistance to the bacteria Xanthomonas oryzae pv. oryzae. The complete HAOR7 protein was found in all resistant lines, while susceptible lines all encoded a truncated protein lacking the transmembrane and the kinase domains. We showed that HaOr7 confers resistance by preventing the connection of O. cumana to the vascular system of the sunflower roots in a gene-for-gene relationship. Our results illustrate how plants can use similar mechanisms for the resistance to parasitic plants as the ones for resistance to microorganisms. HaOr7 is the first resistance gene to O. cumana to be cloned in sunflower, opening new avenues for a more sustainable resistance to sunflower broomrape and to parasitic plants in crops.; Orobanche cumana est une plante parasite obligatoire qui infecte spécifiquement le tournesol, entrainant des pertes de rendement. En combinant des études génétiques et génomiques dans une approche de clonage positionnel, le gène de résistance à l'orobanche du tournesol HaOr7 a été cartographié dans une région de 55 kb du chromosome 7, contenant un gène unique. Le gène HaOr7 code pour un récepteur membranaire de type LRR kinase, montrant de l'homologie avec le gène Xa21 qui confère la résistance à la bactérie Xanthomonas oryzae pv. Oryzae chez le riz. Toutes les lignées résistantes comportaient un allèle du gène codant pour la protéine HAOR7 complète tandis que les allèles du gène de toutes les lignées sensibles codaient pour une protéine tronquée, sans le domaine kinase, ni le domaine transmembranaire. Nous avons montré que HaOr7 confère une résistance en empêchant O. cumana de se connecter au système vasculaire des racines de tournesol, dans une relation gène-pour-gène. Nos résultats illustrent que les plantes utilisent des mécanismes de résistance contre les plantes parasites similaires à ceux qu'elles utilisent pour lutter contre les microorganismes pathogènes. HaOr7 est le premier gène de résistance à O. cumana à avoir été caractérisé chez le tournesol, ouvrant de nouvelles voies pour une résistance plus durable à O. cumana et aux plantes parasites.

Advances in biotechnology have rendered tracking of quantitative trait loci (QTLs) a much easier task, making phenotyping, and not genotyping, the main bottleneck to integrating quantitative host plant resistance into breeding programs. The relevance of phenotyping methods is conditioned by their ability to predict the performance of a genotype at the field scale. Components of resistance represent the keystone hierarchy level between resistance expression in the field (the breeder's scale) and QTLs (the geneticist's scale). We describe approaches for upscaling processes to identify components of resistance that best predict field resistance, and for decision making for selection in breeding programs. We further highlight avenues for future research considering specific processes: disease transmission, defoliation, disease escape, polyetic processes, and interactions between components of resistance.

Screening a priori durable resistance in tomato to Phytophthora infestans using its pathogenicity effectors. Effectome meeting 2016

Journées jeunes chercheurs du département BAP sont organisés par Eric Jenczewski et Christopher Sauvage Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech; A priori durable resistance in tomato to Phytophthora infestans using its pathogenicity effectors. Journées Jeunes Chercheurs du DBAP

Quantitative plant resistance affects the aggressiveness of pathogens and is usually considered more durable than qualitative resistance. However, the efficiency of a quantitative resistance based on an isolate-specific Quantitative Trait Locus (QTL) is expected to decrease over time due to the selection of isolates with a high level of aggressiveness on resistant plants. To test this hypothesis, we surveyed scab incidence over an eight-year period in an orchard planted with susceptible and quantitatively resistant apple genotypes. We sampled 79 Venturia inaequalis isolates from this orchard at three dates and we tested their level of aggressiveness under controlled conditions. Isolates sampled on resistant genotypes triggered higher lesion density and exhibited a higher sporulation rate on apple carrying the resistance allele of the QTL T1 compared to isolates sampled on susceptible genotypes. Due to this ability to select aggressive isolates, we expected the QTL T1 to be non-durable. However, our results showed that the quantitative resistance based on the QTL T1 remained efficient in orchard over an eight-year period, with only a slow decrease in efficiency and no detectable increase of the aggressiveness of fungal isolates over time. We conclude that knowledge on the specificity of a QTL is not sufficient to evaluate its durability. Deciphering molecular mechanisms associated with resistance QTLs, genetic determinants of aggressiveness and putative trade-offs within pathogen populations is needed to help in understanding the erosion processes.

National audience; Stone fruit crops Prunus spp. grown under Mediterranean climates are severely damaged by root-knot nematodes (RKN) Me/oidogyne spp. and breeding for RKN-resistant rootstocks is a promising control alternative to nematicide ban. Resistance (R) genes that confer different spectra have been identified and mapped in plums (Ma and Rjap), peach (RMia) and almond (RMja). Thus sustainable resistance in Prunus is based on pyramiding of R genes in interspecific rootstock mate rial to take into account the risk of resistance breaking in the durable plant-nematode interaction for perennials. The Ma gene from Myrabalan plum has been shown to confer a complete-spectrum, high-Ievel and heat-stable resistance to both mitotic (M. arenaria, M. incognito, M. javanico and M. entera/obii) and meiotic (M. f/oridensis) RKN. Ma triggers a hypersensitive-like reaction (HLR) in raot apices and severe nematode attacks induce _ the development of subterminal lateral rootlets replacing primary terminal apices and providing an acive, resist,ance response to HLR damage (1). Sustainability of resistance conferred by Ma has been challenged in multi-year experiments applying a high and continuous nematode inoculum pressure by co-cultivation of RKN-infested susceptible tomato plants together with Prunus plants carrying Ma or, for comparison, with R tomato plants carrying the Mi-l reference gene. Galling and virulent nematode individuals have been observed in Mi-l resistant tomatoes but not in Ma-carrying Prunus plants. The positional cloning of the Ma locus in accession P.2175 has been performed using high resolution mapping developed in two successive steps totalling over 3000 segregants. The Ma locus interval has been reduced to a 32-kb cluster of three TIR-NB-LRR genes (TNLl to TNL3) including a pseudogene (TNL2) and a truncated gene (TNL3). Using A. rhizogenes transformed hairy raots and composite plants (2), the best candidate gene, TNLl, comprising the genomic sequence and the native promoter region (15.3 kb), has been validated as Ma as it conferred the same complete-spectrum and high-Ievel resistance as in the donor accession P.2175. The full-Iength cDNA (2048 aa) of Ma is the longest of ail R genes cloned tc-date. Its TNL structure is extended by a huge Cvterminal post-LRR (PL) region (1088 aa) comprising five repeated PL exons (3).

Stone fruit crops Prunus spp. grown under Mediterranean climates are severely damaged by root-knot nematodes (RKN) Me/oidogyne spp. and breeding for RKN-resistant rootstocks is a promising control alternative to nematicide ban. Resistance (R) genes that confer different spectra have been identified and mapped in plums (Ma and Rjap), peach (RMia) and almond (RMja). Thus sustainable resistance in Prunus is based on pyramiding of R genes in interspecific rootstock mate rial to take into account the risk of resistance breaking in the durable plant-nematode interaction for perennials. The Ma gene from Myrabalan plum has been shown to confer a complete-spectrum, high-Ievel and heat-stable resistance to both mitotic (M. arenaria, M. incognito, M. javanico and M. entera/obii) and meiotic (M. f/oridensis) RKN. Ma triggers a hypersensitive-like reaction (HLR) in raot apices and severe nematode attacks induce _ the development of subterminal lateral rootlets replacing primary terminal apices and providing an acive, resist,ance response to HLR damage (1). Sustainability of resistance conferred by Ma has been challenged in multi-year experiments applying a high and continuous nematode inoculum pressure by co-cultivation of RKN-infested susceptible tomato plants together with Prunus plants carrying Ma or, for comparison, with R tomato plants carrying the Mi-l reference gene. Galling and virulent nematode individuals have been observed in Mi-l resistant tomatoes but not in Ma-carrying Prunus plants. The positional cloning of the Ma locus in accession P.2175 has been performed using high resolution mapping developed in two successive steps totalling over 3000 segregants. The Ma locus interval has been reduced to a 32-kb cluster of three TIR-NB-LRR genes (TNLl to TNL3) including a pseudogene (TNL2) and a truncated gene (TNL3). Using A. rhizogenes transformed hairy raots and composite plants (2), the best candidate gene, TNLl, comprising the genomic sequence and the native promoter region (15.3 kb), has been validated as Ma as it conferred the same complete-spectrum and high-Ievel resistance as in the donor accession P.2175. The full-Iength cDNA (2048 aa) of Ma is the longest of ail R genes cloned tc-date. Its TNL structure is extended by a huge Cvterminal post-LRR (PL) region (1088 aa) comprising five repeated PL exons (3).

Recherche des déterminants génétiques de l'aptitude au contournement du gène de résistance Rus chez la rouille du peuplier Melampsora larici-populina

National audience; The melon aphid, Aphis gossypii, is a major pest of many crops. Molecular markers have revealed a host race organization of the species and 8 microsatellite markers have allowed the identification of 21 multilocus genotypes (MLGs) among clones collected into colonies on Cucurbits. Aphid resistance have been identified in several melon accessions; it is controlled by a major gene, Vat, and some quantitative trait loci (QTLs). We built melon populations combining different loci of resistance, in a homogenous genetic background. They were cultivated in melon producing areas with contrasted aphid populations. Then, we showed a significant effect of the Vat gene on aphid density but non effect of the QTLs. One hundred and two MLGs were attributed to 2596 collected in trials, 54 MLGs were observed only once, five MLGs were only observed in the French West Indies, 19 MLGs were observed both in South eastern and South western France. Nevertheless, we did not observe a significant effect of the resistance loci on the diversity index of Shanon. Among clones collected into 125 colonies, we only identified 10 MLGs, five out of them were identified in clones collected on Vat-melon. The resistance loci might have an effect on the diversity of the South-eastern populations.; Aphis gossypii, puceron ravageur majeur des cultures, est structuré en race d’hôtes. Huit marqueurs microsatellite ont permis d’identifier 21 génotypes multilocus (MLG)parmi les individus développant des colonies sur les Cucurbitacées. De nombreuses sources de résistance ont été identifiées chez le melon, la résistance est contrôlée par un gène majeur, Vat, et des loci à effet quantitatif (QTL). Nous avons construit des populations de melon combinant différemment ces loci dans un fond génétique homogène. Elles ont été cultivées en plein champ dans trois zones de production du melon présentant des populations de pucerons très contrastées. Sur la densité des populations, nous avons observé un effet significatif du gène Vat mais aucun effet des QTL. Parmi les 2596 pucerons collectés dans les essais, 102 MLG ont été identifiées, dont 54 une seule fois. Dix-neuf MLG ont été observés dans le Sud-est et le Sud-ouest ; seulement cinq MLG ont été observés aux Antilles (non identifiées en métropole). On n'observe pas d’effet significatif du gène Vat et des QTL sur l’indice de diversité de Shanon. Parmi 125 clones échantillonnés dans des colonies, nous avons identifié seulement 10 MLG dont 5 dans des clones échantillonnées sur des melons porteurs du gène Vat. L’effet du gène Vat et des QTL sur la diversité des populations serait restreint à la région Sud-est.

National audience; The melon aphid, Aphis gossypii, is a major pest of many crops. Molecular markers have revealed a host race organization of the species and 8 microsatellite markers have allowed the identification of 21 multilocus genotypes (MLGs) among clones collected into colonies on Cucurbits. Aphid resistance have been identified in several melon accessions; it is controlled by a major gene, Vat, and some quantitative trait loci (QTLs). We built melon populations combining different loci of resistance, in a homogenous genetic background. They were cultivated in melon producing areas with contrasted aphid populations. Then, we showed a significant effect of the Vat gene on aphid density but non effect of the QTLs. One hundred and two MLGs were attributed to 2596 collected in trials, 54 MLGs were observed only once, five MLGs were only observed in the French West Indies, 19 MLGs were observed both in South eastern and South western France. Nevertheless, we did not observe a significant effect of the resistance loci on the diversity index of Shanon. Among clones collected into 125 colonies, we only identified 10 MLGs, five out of them were identified in clones collected on Vat-melon. The resistance loci might have an effect on the diversity of the South-eastern populations.; Aphis gossypii, puceron ravageur majeur des cultures, est structuré en race d’hôtes. Huit marqueurs microsatellite ont permis d’identifier 21 génotypes multilocus (MLG)parmi les individus développant des colonies sur les Cucurbitacées. De nombreuses sources de résistance ont été identifiées chez le melon, la résistance est contrôlée par un gène majeur, Vat, et des loci à effet quantitatif (QTL). Nous avons construit des populations de melon combinant différemment ces loci dans un fond génétique homogène. Elles ont été cultivées en plein champ dans trois zones de production du melon présentant des populations de pucerons très contrastées. Sur la densité des populations, nous avons observé un effet significatif du gène Vat mais aucun effet des QTL. Parmi les 2596 pucerons collectés dans les essais, 102 MLG ont été identifiées, dont 54 une seule fois. Dix-neuf MLG ont été observés dans le Sud-est et le Sud-ouest ; seulement cinq MLG ont été observés aux Antilles (non identifiées en métropole). On n'observe pas d’effet significatif du gène Vat et des QTL sur l’indice de diversité de Shanon. Parmi 125 clones échantillonnés dans des colonies, nous avons identifié seulement 10 MLG dont 5 dans des clones échantillonnées sur des melons porteurs du gène Vat. L’effet du gène Vat et des QTL sur la diversité des populations serait restreint à la région Sud-est.

Viruses that infect plants are responsible for reduction in both yield and quality of crops around the world, and are thus of great economic importance. This has provided the impetus for the extensive research into the molecular and cellular biology of these pathogens and into their interaction with their plant hosts and their vectors. However interest in plant viruses extends beyond their ability to damage crops. Many plant viruses, for example tobacco mosaic virus, have been used as model systems to provide basic understanding of how viruses express genes and replicate. Others permitted the elucidation of the processes underlying RNA silencing, now recognised as a core epigenetic mechanism underpinning numerous areas of biology. This book attests to the huge diversity of research in plant molecular virology. Written by world authorities in the field, the book opens with two chapters on the translation and replication of viral RNA. Following chapters cover topics such as viral movement within and between plants, plant responses to viral infection, antiviral control measures, virus evolution, and newly emerging plant viruses. To close there are two chapters on biotechnological applications of plant viruses. Throughout the book the focus is on the most recent, cutting-edge research, making this book essential reading for everyone, from researchers and scholars to students, working with plant viruses.

Breeding for virus resistance was successful in the past years using conventional breeding methods since many virus resistant cultivars have been delivered for a wide range of crops. Genome mapping provided molecular markers for many resistance loci (i.e., major genes or Quantitative Trait Loci) that were introgressed into cultivars e.g., through backcross breeding schemes. Molecular mapping also delivered much information on the genomic architecture of polygenic and quantitative resistances. However, marker assisted selection for such complex traits is difficult so that the combination of quantitative resistance factors from multiallelic origins commonly relies on sophisticated phenotyping procedures. The cloning of resistance genes and the rapid development of high throughput molecular technologies increased the access to functional markers and multiallelic markers, promoting the applicability of marker assisted selection for complex traits at the whole genome scale in the near future. In parallel, the advances in the identification of molecular determinants of plant/virus interactions and in genetics and evolution of virus populations provide new selection criteria for breeders to choose the most durable resistance genes and gene combinations, so that breeding for durable virus resistance becomes an accessible quest

Aphis gossypii, puceron ravageur majeur des cultures, est structuré en race d’hôtes. Huit marqueurs microsatellite ont permis d’identifier 21 génotypes multilocus (MLG)parmi les individus développant des colonies sur les Cucurbitacées. De nombreuses sources de résistance ont été identifiées chez le melon, la résistance est contrôlée par un gène majeur, Vat, et des loci à effet quantitatif (QTL). Nous avons construit des populations de melon combinant différemment ces loci dans un fond génétique homogène. Elles ont été cultivées en plein champ dans trois zones de production du melon présentant des populations de pucerons très contrastées. Sur la densité des populations, nous avons observé un effet significatif du gène Vat mais aucun effet des QTL. Parmi les 2596 pucerons collectés dans les essais, 102 MLG ont été identifiées, dont 54 une seule fois. Dix-neuf MLG ont été observés dans le Sud-est et le Sud-ouest ; seulement cinq MLG ont été observés aux Antilles (non identifiées en métropole). On n'observe pas d’effet significatif du gène Vat et des QTL sur l’indice de diversité de Shanon. Parmi 125 clones échantillonnés dans des colonies, nous avons identifié seulement 10 MLG dont 5 dans des clones échantillonnées sur des melons porteurs du gène Vat. L’effet du gène Vat et des QTL sur la diversité des populations serait restreint à la région Sud-est., The melon aphid, Aphis gossypii, is a major pest of many crops. Molecular markers have revealed a host race organization of the species and 8 microsatellite markers have allowed the identification of 21 multilocus genotypes (MLGs) among clones collected into colonies on Cucurbits. Aphid resistance have been identified in several melon accessions; it is controlled by a major gene, Vat, and some quantitative trait loci (QTLs). We built melon populations combining different loci of resistance, in a homogenous genetic background. They were cultivated in melon producing areas with contrasted aphid populations. Then, we showed a significant effect of the Vat gene on aphid density but non effect of the QTLs. One hundred and two MLGs were attributed to 2596 collected in trials, 54 MLGs were observed only once, five MLGs were only observed in the French West Indies, 19 MLGs were observed both in South eastern and South western France. Nevertheless, we did not observe a significant effect of the resistance loci on the diversity index of Shanon. Among clones collected into 125 colonies, we only identified 10 MLGs, five out of them were identified in clones collected on Vat-melon. The resistance loci might have an effect on the diversity of the South-eastern populations.

International audience; Evolutionary processes responsible for parasite adaptation to their hosts determine our capacity to manage sustainably resistant plant crops. Most plant–parasite interactions studied so far correspond to gene-for-gene models in which the nature of the alleles present at a plant resistance locus and at a pathogen pathogenicity locus determine entirely the outcome of their confrontation. The interaction between the pepper pvr2 resistance locus and Potato virus Y (PVY) genome-linked protein VPg locus obeys this kind of model. Using synthetic chimeras between two parental PVY cDNA clones, we showed that the viral genetic background surrounding the VPg pathogenicity locus had a strong impact on the resistance breakdown capacity of the virus. Indeed, recombination of the cylindrical inclusion (CI) coding region between two PVY cDNA clones multiplied by six the virus capacity to break down the pvr23-mediated resistance. High-throughput sequencing allowed the exploration of the diversity of PVY populations in response to the selection pressure of the pvr23 resistance. The CI chimera, which possessed an increased resistance breakdown capacity, did not show an increased mutation accumulation rate. Instead, selection of the most frequent resistance-breaking mutation seemed to be more efficient for the CI chimera than for the parental virus clone. These results echoed previous observations, which showed that the plant genetic background in which the pvr23 resistance gene was introduced modified strongly the efficiency of selection of resistance-breaking mutations by PVY. In a broader context, the PVY CI coding region is one of the first identified genetic factors to determine the evolvability of a plant virus.

International audience; Stone fruit crops Prunus spp. grown under Mediterranean climates are severely damaged by root-knot nematodes (RKN) Meloidogyne spp. and breeding for RKN-resistant rootstocks is a promising control alternative to nematicide ban. Resistance (R) genes that confer different spectra have been identified and mapped in plums (Ma and Rjap), peach (RMia) and almond (RMja). Thus sustainable resistance in Prunus is based on pyramiding of R genes in interspecific rootstock mate rial to take into account the risk of resistance breaking in the durable plant-nematode interaction for perennials. The Ma gene from Myrabalan plum has been shown to confer a complete-spectrum, high-Ievel and heat-stable resistance to both mitotic (M. arenaria, M. incognito, M. javanico and M. enterolobii) and meiotic (M. f/oridensis) RKN. Ma triggers a hypersensitive-like reaction (HLR) in raot apices and severe nematode attacks induce the development of subterminal lateral rootlets replacing primary terminal apices and providing an acive, resist,ance response to HLR damage (1). Sustainability of resistance conferred by Ma has been challenged in multi-year experiments applying a high and continuous nematode inoculum pressure by co-cultivation of RKN-infested susceptible tomato plants together with Prunus plants carrying Ma or, for comparison, with R tomato plants carrying the Mi-l reference gene. Galling and virulent nematode individuals have been observed in Mi-l resistant tomatoes but not in Ma-carrying Prunus plants. The positional cloning of the Ma locus in accession P.2175 has been performed using high resolution mapping developed in two successive steps totalling over 3000 segregants. The Ma locus interval has been reduced to a 32-kb cluster of three TIR-NB-LRR genes (TNLl to TNL3) including a pseudogene (TNL2) and a truncated gene (TNL3). Using A. rhizogenes transformed hairy raots and composite plants (2), the best candidate gene, TNLl, comprising the genomic sequence and the native promoter region (15.3 kb), has been validated as Ma as it conferred the same complete-spectrum and high-Ievel resistance as in the donor accession P.2175. The full-Iength cDNA (2048 aa) of Ma is the longest of ail R genes cloned tc-date. Its TNL structure is extended by a huge Cvterminal post-LRR (PL) region (1088 aa) comprising five repeated PL exons (3)