Genetic control of plasticity of oil yield for combined abiotic stresses using a joint approach of crop modeling and genome-wide association

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.Comment: 12 pages, 5 figures, Plant, Cell and Environmen

Study of the predictive potential of molecular biomarkers of endocrine disruption in the estuarine copepod Eurytemora affinis and characterization of endocrine disruption mode of action by using in vitro assays : example of two model pesticide : chlordecone and pyriproxyfen, alone and in mixture

Les écosystèmes aquatiques constituent la destination finale des contaminants. Les organismes aquatiques sont ainsi impactés par un cocktail de molécules, dont les produits phytosanitaires. Le caractère perturbateur endocrinien (PE) de certains d’entre eux est particulièrement préoccupant. La présente étude explore les effets de pesticides modèles à potentiel PE – la chlordécone (CLD) et le pyriproxyfène (PXF), seuls et en mélange – chez le copépode estuarien Eurytemora affinis par des approches écotoxicogénomiques innovantes. En réponse aux PE, l’accent a été porté sur les effets de ces composés sur la reproduction, la croissance ou le développement. En parallèle, l’affinité des pesticides aux récepteurs aux oestrogènes et aux androgènes humains d’une part, et aux ecdystéroïdes d’autre part, a été étudiée grâce à des outils bio analytiques afin d’évaluer la pertinence de l’utilisation du potentiel PE défini par les tests cellulaires comme critère d’exclusion dans la réglementation européenne des pesticides. Ces travaux de thèse présentent, pour la première fois, les transcriptomes et protéomes d’E. affinis après exposition aux PE. Un effet sexe-dépendant a été observé par les deux approches « omics » révélant un plus fort impact des composés sur les copépodes mâles. Des gènes et protéines, impliqués dans le processus de mue et dans la gamétogénèse ont été identifiés comme candidats pour le développement de biomarqueurs moléculaires de PE chez les crustacés. Les tests cellulaires ont permis de mettre en évidence des interactions entre les contaminants et les récepteurs hormonaux. Toutefois, le screening de molécules par les tests YES/YAS/anti-YES/anti-YAS s’est heurté à quelques limites d’interprétations. Enfin, les résultats du test S2 EcR, souligne la pertinence de l'utilisation couplée de tests spécifiques d’un système endocrinien de vertébrés et d’invertébrés dans l’évaluation du risque des composés PE.Aquatic ecosystems constitute the chemicals’ final destination. Among the xenobiotics, endocrine disruptors (ED) are compounds of major concern. In this context, ED pesticides effects were investigated in the widespread copepod Eurytemora Affinis using ecotoxicogenomics technics. In response to PE pesticides, focus was made on reproduction, growth and development. In order to evaluate the endocrine activity, in vitro tests (YES/YAS/anti-YES/anti-YAS and S2 EcR) were used to screen the compounds alone and in mixtures. These results were discussed to evaluate the “cut off criterion” used in European assessment. This work presents for the first time, transcriptomes and proteomes of E. affinis after PXF and CLD –alone and in binary mixture- exposure. A sex dependent effect was observed by the two “omics” approaches. Male copepods were more impacted by contaminants than female copepods. Genes and proteins (e.g. chitin deacetylase, kelch protein) were identified as candidates for the development of ED molecular biomarkers. In vitro tests highlighted binding of pesticides with both vertebrate and invertebrate receptors. However, a toxicity for the highest concentrations tested and some limits for the interpretation of mixtures results were limiting in YES/YAS/anti-YES/anti-YAS assays. The last observation represents particularly a major concern for interpretation of the ED mode of action of environmental matrix. S2 EcR highlighted some complementary results about the mode of action of chemicals alone and in binary mixtures. These results accentuate the need to combine vertebrate specific test and invertebrate specific test in ED risk assessment

Couplage d’approches écotoxicogénomiques chez le copépode estuarien Eurytemora affinis et d’outils bio-analytiques pour l’évaluation du caractère perturbateur endocrinien des contaminants aquatiques : exemple de deux pesticides modèles : le pyriproxyfène et la chlordécone, seuls et en mélange

Aquatic ecosystems constitute the chemicals’ final destination. Among the xenobiotics, endocrine disruptors (ED) are compounds of major concern. In this context, ED pesticides effects were investigated in the widespread copepod Eurytemora Affinis using ecotoxicogenomics technics. In response to PE pesticides, focus was made on reproduction, growth and development. In order to evaluate the endocrine activity, in vitro tests (YES/YAS/anti-YES/anti-YAS and S2 EcR) were used to screen the compounds alone and in mixtures. These results were discussed to evaluate the “cut off criterion” used in European assessment. This work presents for the first time, transcriptomes and proteomes of E. affinis after PXF and CLD –alone and in binary mixture- exposure. A sex dependent effect was observed by the two “omics” approaches. Male copepods were more impacted by contaminants than female copepods. Genes and proteins (e.g. chitin deacetylase, kelch protein) were identified as candidates for the development of ED molecular biomarkers. In vitro tests highlighted binding of pesticides with both vertebrate and invertebrate receptors. However, a toxicity for the highest concentrations tested and some limits for the interpretation of mixtures results were limiting in YES/YAS/anti-YES/anti-YAS assays. The last observation represents particularly a major concern for interpretation of the ED mode of action of environmental matrix. S2 EcR highlighted some complementary results about the mode of action of chemicals alone and in binary mixtures. These results accentuate the need to combine vertebrate specific test and invertebrate specific test in ED risk assessment.Les écosystèmes aquatiques constituent la destination finale des contaminants. Les organismes aquatiques sont ainsi impactés par un cocktail de molécules, dont les produits phytosanitaires. Le caractère perturbateur endocrinien (PE) de certains d’entre eux est particulièrement préoccupant. La présente étude explore les effets de pesticides modèles à potentiel PE – la chlordécone (CLD) et le pyriproxyfène (PXF), seuls et en mélange – chez le copépode estuarien Eurytemora affinis par des approches écotoxicogénomiques innovantes. En réponse aux PE, l’accent a été porté sur les effets de ces composés sur la reproduction, la croissance ou le développement. En parallèle, l’affinité des pesticides aux récepteurs aux oestrogènes et aux androgènes humains d’une part, et aux ecdystéroïdes d’autre part, a été étudiée grâce à des outils bio analytiques afin d’évaluer la pertinence de l’utilisation du potentiel PE défini par les tests cellulaires comme critère d’exclusion dans la réglementation européenne des pesticides. Ces travaux de thèse présentent, pour la première fois, les transcriptomes et protéomes d’E. affinis après exposition aux PE. Un effet sexe-dépendant a été observé par les deux approches « omics » révélant un plus fort impact des composés sur les copépodes mâles. Des gènes et protéines, impliqués dans le processus de mue et dans la gamétogénèse ont été identifiés comme candidats pour le développement de biomarqueurs moléculaires de PE chez les crustacés. Les tests cellulaires ont permis de mettre en évidence des interactions entre les contaminants et les récepteurs hormonaux. Toutefois, le screening de molécules par les tests YES/YAS/anti-YES/anti-YAS s’est heurté à quelques limites d’interprétations. Enfin, les résultats du test S2 EcR, souligne la pertinence de l'utilisation couplée de tests spécifiques d’un système endocrinien de vertébrés et d’invertébrés dans l’évaluation du risque des composés PE

Characterization of a vitellogenin-like and an ecdysone receptor cDNAs in the estuarine copepod Eurytemora affinis

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Controversial use of vitellogenin as a biomarker of endocrine disruption in crustaceans: New adverse pieces of evidence in the copepod Eurytemora affinis

International audienceIn recent years, the interest in the use of vitellogenin (VTG) as a biomarker of endocrine disruption in fish has led to VTG being considered as a potential tool in invertebrates. Among aquatic invertebrate models in ecotoxicology, the copepods are considered as reference species in marine, estuarine and freshwater ecosystems. In this context, we identified a VTG cDNA in Eurytemora affinis. The Ea-VTG2 cDNA is 5416bp in length with an open reading frame (ORF) of 5310bp that encodes a putative protein of 1769 amino acids residues. Phylogenetic analysis confirmed the hypothesis of a VTG duplication event before the emergence of the copepod species. The analysis of the Ea-VTG2 expression by qPCR in males and females according to their reproductive stages allowed transcript basal levels to be determined. The expression pattern revealed a gradual increase of transcript levels during maturation in females. Important inter-sex differences were observed with a VTG level in males ranging from about 1900- to 6800-fold lower than in females depending on their stage. Moreover, the protein was only detected in ovigerous females. The inducibility of Ea-VTG2 by chemicals was studied in males exposed to either a model of endocrine disruptor in vertebrates i.e. 4-nonylphenol (4-NP) or a crustacean hormone i.e. Methyl Farnesoate (MF), and in males sampled from a multi-contaminated estuary. No induction was highlighted. The VTG should not be considered as an appropriate biomarker in E. affinis as previously suggested for other crustaceans

Transcriptome analysis of the copepod Eurytemora affinis upon exposure to endocrine disruptor pesticides: Focus on reproduction and development

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