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Trabajo presentado en el 14th World Congress on Parasitic Plants (From genome to field), celebrado en Asilomar (California) el 24 y 25 de junio de 2017., Orobanche cumana (sunflower broomrape) is an obligate parasitic plant that specifically infects sunflower (Helianthus annuus). It is one of the main limiting factors of sunflower crop in Eastern Europe, Spain and Asia. In 2007, the first infested fields have been reported in France. Breeding for resistance in sunflower was successful but new more virulent races of O. cumana often overcame the resistance genes. The first developmental stages of O. cumana occur underground. The germination of the seeds is first stimulated by sunflower root exudates before entering the host root through a haustorium. Without roots nor chlorophyll, O. cumana depends on sunflower for water and nutrients supply. It connects to the vascular system of the sunflower root and store metabolites in a tubercle before emerging a flowering shoot. The inactivation of these developmental stages is a key resistance mechanism in sunflower. A better understanding of the biology of O. cumana will help to identify new resistance processes and resistance genes in sunflower. In the frame of a collaborative project between French and Spanish research institutes, we have produced a first version of the 1.42 Gb genome sequence of O. cumana by combining PacBio sequencing, optical mapping and genetic map. More than twenty transcriptomic RNA-seq experiments from O. cumana were used for annotating the genome sequence. This first sequence assembly (622 scaffolds, 1.38Gb, N50=5.9Mb) and its annotation will be provided through a Web Genome Browser to the public research community. Our strategy to obtain and finalize the genome assembly as well as results on population diversity will be presented. The genome sequence of O. cumana will enable the characterization of its physiology and development. Avirulence genes should be identified more efficiently and, as putative interactor with sunflower proteins, should help in identifying new resistance genes in sunflower. This resource will help in understanding parasitic plants’ biology and evolution, like parasitism capacity acquisition.

International audience; Prediction of hybrid performance using incomplete factorial mating designs is widely used in breeding programs including different heterotic groups. Based on the general combining ability (GCA) of the parents, predictions are accurate only if the genetic variance resulting from the specific combining ability is small and both parents have phenotyped descendants. Genomic selection (GS) can predict performance using a model trained on both phenotyped and genotyped hybrids that do not necessarily include all hybrid parents. Therefore. GS could overcome the issue of unknown parent GCA. Here, we compared the accuracy of classical GCA-based and genomic predictions for oil content of sunflower seeds using several GS models. Our study involved 452 sunflower hybrids from an incomplete factorial design of 36 female and 36 male lines. Re-sequencing of parental lines allowed to identify 468,194 non-redundant SNPs and to infer the hybrid genotypes. Oil content was observed in a multi-environment trial (MET) over 3 years, leading to nine different environments. We compared GCA-based model to different GS models including female and male genomic kinships with the addition of the female-by-male interaction genomic kinship, the use of functional knowledge as SNPs in genes of oil metabolic pathways, and with epistasis modeling. When both parents have descendants in the training set, the predictive ability was high even for GCA-based prediction, with an average MET value of 0.782. GS performed slightly better (+0.2%). Neither the inclusion of the female-by-male interaction, nor functional knowledge of oil metabolism, nor epistasis modeling improved the GS accuracy. GS greatly improved predictive ability when one or both parents were untested in the training set, increasing GCA-based predictive ability by 10.4% from 0.575 to 0.635 in the MET. In this scenario, performing GS only considering SNPs in oil metabolic pathways did not improve whole genome GS prediction but increased GCA-based prediction ability by 6.4%. Our results show that GS is a major improvement to breeding efficiency compared to the classical GCA modeling when either one or both parents are not well-characterized. This finding could therefore accelerate breeding through reducing phenotyping efforts and more effectively targeting for the most promising crosses.

Understanding the genetic basis of phenotypic plasticity is crucial for predicting and managing climate change effects on wild plants and crops. Here, we combined crop modeling and quantitative genetics to study the genetic control of oil yield plasticity for multiple abiotic stresses in sunflower. First we developed stress indicators to characterize 14 environments for three abiotic stresses (cold, drought and nitrogen) using the SUNFLO crop model and phenotypic variations of three commercial varieties. The computed plant stress indicators better explain yield variation than descriptors at the climatic or crop levels. In those environments, we observed oil yield of 317 sunflower hybrids and regressed it with three selected stress indicators. The slopes of cold stress norm reaction were used as plasticity phenotypes in the following genome-wide association study. Among the 65,534 tested SNP, we identified nine QTL controlling oil yield plasticity to cold stress. Associated SNP are localized in genes previously shown to be involved in cold stress responses: oligopeptide transporters, LTP, cystatin, alternative oxidase, or root development. This novel approach opens new perspectives to identify genomic regions involved in genotype-by-environment interaction of a complex traits to multiple stresses in realistic natural or agronomical conditions.

The domesticated sunflower, Helianthus annuus L., is a global oil crop that has promise for climate change adaptation, because it can maintain stable yields across a wide variety of environmental conditions, including drought. Even greater resilience is achievable through the mining of resistance alleles from compatible wild sunflower relatives, including numerous extremophile species. Here we report a high-quality reference for the sunflower genome (3.6 gigabases), together with extensive transcriptomic data from vegetative and floral organs. The genome mostly consists of highly similar, related sequences and required single-molecule real-time sequencing technologies for successful assembly. Genome analyses enabled the reconstruction of the evolutionary history of the Asterids, further establishing the existence of a whole-genome triplication at the base of the Asterids II clade and a sunflower-specific whole-genome duplication around 29 million years ago. An integrative approach combining quantitative genetics, expression and diversity data permitted development of comprehensive gene networks for two major breeding traits, flowering time and oil metabolism, and revealed new candidate genes in these networks. We found that the genomic architecture of flowering time has been shaped by the most recent whole-genome duplication, which suggests that ancient paralogues can remain in the same regulatory networks for dozens of millions of years. This genome represents a cornerstone for future research programs aiming to exploit genetic diversity to improve biotic and abiotic stress resistance and oil production, while also considering agricultural constraints and human nutritional needs.

Characterization of plant morphological and physiological responses is a limiting step to breed crops adapted to drought-limiting conditions. Automation of plant management on a phenotyping platform overcomes it by allowing large scale experimentation with yet accurate and individual plant monitoring. In response to both genetic and eco-physiological experimentation requirements, we developed the HELIAPHEN platform. This unique outdoor platform can host 1300 plants, such as sunflower, in 15L pots. It allows plant growth in climatic conditions similar to field, as well as a precise and automated monitoring of plant water consumption thanks to a prototype robot. Its primary functions are to move autonomously on the 600m2 platform, and to treat each pot at its location (including weighing and watering up to a targeted weight). Beyond these functions, the robot takes at each handling, plant images from multiple angles with four cameras, to follow the evolution of morphological traits along with the description of the water status. In addition, a ultrasound radar measures automatically plant height and a laser measures stem diameter at the plant basis. These secondary functions are currently improved with new captors such as a light curtain and a 3D laser in order to reconstitute a 3D representation of the plant. To validate the meaning of the HELIAPHEN outputs, we confirmed the impact of drought stress managed with the robot on seed weight, number and thousand kemel weight (TKW). Furthermore, we observed a correlation between field and HELIAPHEN data for TKW and seed number observed on 45 sunflower hybrids.

La résistance quantitative du tournesol (Helianthus annuus) au mildiou (Plasmopara halstedii), mise en évidence récemment, est difficile à évaluer. Un réseau de onze expérimentations associant la GEVESSNES, deux laboratoires de l’INRA et Terres Inovia a été construit afin de proposer une méthodologie permettant de mieux caractériser et quantifier cette résistance. En plus de lignées témoins, 17 lignées recombinantes obtenues par l’INRA et portant entre 0 et 3 QTL (quantitative trait loci) impliqués dans la résistance quantitative du tournesol au mildiou ont été testées face à 5 pathotypes de mildiou : 710, 704, 714, 304 et 334. Bien que des différences aient été observées entre laboratoires, les résultats ont permis de poser les bases d’un futur protocole utilisable en routine pour valoriser ce type de résistance dès la création variétale jusqu’à l’inscription puis la post-inscription des variétés., A quantitative resistance of sunflower (Helianthus annuus) to downy mildew (Plasmopara halstedii) has been identified a few years ago. An experimental network involving several labs (GEVES-SNES, INRA and Terres Inovia) over several years aimed at describing and quantifying such a quantitative response. It was hoped to propose a methodology useable to improve sustainable resistance. In addition to check varieties and breeding lines, 17 recombinant inbred lines carrying 0 to 3 quantitative trait loci alleles for quantitative resistance were tested with five downy mildew pathotypes (710, 704, 714, 304, 334). While the experimental results revealed some discrepancies between experiments, this study provided a first experimental protocol to evaluate quantitative resistance both for breeding and for variety registration and development

Trabajo presentado en el 13th World Congress on Parasitic Plants (Parasitic plants: the good, the bad, and the mysterious), celebrado en Kunming (China) del 5 al 10 de julio de 2015., Sunflower is an important crop and is mainly used for oil production. Orobanche cumana is a major disease in cultivated areas around the black sea and in Spain. The pathogen spread more recently to several other countries (France, China ...). During the last ten years, several new O. cumana races have emerged but very few efficient methods were available to control their development. Genetic resistance was the more efficient and introgression of major resistance loci was successfully used to produce new resistant sunflower varieties (from races A to E). With the recent emergence of new virulent races (called F and F+), novel resistance loci need to be mapped and characterized. A recombinant inbred line population, derived from the cross between the lines HA89 and LR1, has been developed by INRA. It has been previously characterized for the resistance to the race E of O. cumana. We used this population to map QTLs controlling quantitative resistance to race F. The phenotyping has been conducted on the 107 lines of the population at different stages of the interaction. We evaluated each line for (i) the capacity of their root exudate to induce germination of O. cumana seeds, (ii) their ability to induce incompatible attachment, (iii) the number of broomrape tubercles in growth chamber, and (iv) the number of broomrape emergences in the field. Different response profiles were observed at these 4 stages of development, indicating several resistance mechanisms in sunflower. Interestingly, even if the two parental lines showed a close resistant phenotype, we observed a large diversity of the resistance level in the population. Combined with this detailed phenotyping analysis, we performed the genotyping of the sunflower recombinant inbred lines using an AXIOM array of 586 985 SNPs. QTLs will be mapped for the different traits.

Downy mildew of sunflower is caused by Plasmopara halstedii (Farlow) Berlese & de Toni. Plasmopara halstedii is an obligate biotrophic oomycete pathogen that attacks annual Helianthus species and cultivated sunflower, Helianthus annuus. Depending on the sunflower developmental stage at which infection occurs, the characteristic symptoms range from young seedling death, plant dwarfing, leaf bleaching and sporulation to the production of infertile flowers. Downy mildew attacks can have a great economic impact on sunflower crops, and several Pl resistance genes are present in cultivars to protect them against the disease. Nevertheless, some of these resistances have been overcome by the occurrence of novel isolates of the pathogen showing increased virulence. A better characterization of P. halstedii infection and dissemination mechanisms, and the identification of the molecular basis of the interaction with sunflower, is a prerequisite to efficiently fight this pathogen. This review summarizes what is currently known about P. halstedii, provides new insights into its infection cycle on resistant and susceptible sunflower lines using scanning electron and light microscopy imaging, and sheds light on the pathogenicity factors of P. halstedii obtained from recent molecular data. TAXONOMY: Kingdom Stramenopila; Phylum Oomycota; Class Oomycetes; Order Peronosporales; Family Peronosporaceae; Genus Plasmopara; Species Plasmopara halstedii. DISEASE SYMPTOMS: Sunflower seedling damping off, dwarfing of the plant, bleaching of leaves, starting from veins, and visible white sporulation, initially on the lower side of cotyledons and leaves. Plasmopara halstedii infection may severely impact sunflower seed yield. INFECTION PROCESS: In spring, germination of overwintered sexual oospores leads to sunflower root infection. Intercellular hyphae are responsible for systemic plant colonization and the induction of disease symptoms. Under humid and fresh conditions, dissemination structures are produced by the pathogen on all plant organs to release asexual zoosporangia. These zoosporangia play an important role in pathogen dissemination, as they release motile zoospores that are responsible for leaf infections on neighbouring plants. DISEASE CONTROL: Disease control is obtained by both chemical seed treatment (mefenoxam) and the deployment of dominant major resistance genes, denoted Pl. However, the pathogen has developed fungicide resistance and has overcome some plant resistance genes. Research for more sustainable strategies based on the identification of the molecular basis of the interaction are in progress. USEFUL WEBSITES: http://www.heliagene.org/HP, http://lipm‐helianthus.toulouse.inra.fr/dokuwiki/doku.php?id=start, https://www.heliagene.org/PlasmoparaSpecies (soon available).

Trabajo presentado en el Third Internacional Symposium on broomrape (Orobanche spp.) in Sunflower, celebrado en Córdoba (España) del 3 al 6 de junio de 2014., The plant parasite Orobanche cumana is a major threat for the sunflower crop. The emergence of new, virulent “races” during the ten past years reinforced the need to develop new approaches, knowledge and tools in order to control this pest efficiently. Breeding is the most sustainable approach to control broomrape in the field. A RIL population derived from a cross between HA89 and LR1, an inbred line bred from an interspecific cross with Helianthus debilis had been previously characterized for resistance to O. cumana race E, but no data is available for new races. The aim of this study was to characterize the HA89xLR1 RIL population for resistance to race F and to identify QTLs associated with this resistance. The population was phenotyped by counting the number of healthy broomrape tubercles and the rate of tubercle necrosis on young sunflower plants raised in a growth chamber with four biological replications. Differences in l resistance were observed among the RIL population, with some resistant genotypes and some highly susceptible genotypes. The polymorphism of 111 SNP markers previously mapped on a consensus genetic map was used for the QTL detection. Four QTLs were detected on four linkage groups (LG01, LG07, LG15 and LG17), with two QTLs controlling the number of tubercles per plant and two others controlling necrosis. This study suggests that the resistance to O. cumana race F is controlled by several QTLs affecting differently the number of tubercle and the induction of tubercle necrosis., This research was supported by the French Association for the Promotion of Oilseed Crops Breeding (PROMOSOL).