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La consommation de cannabis durant l'adolescence est associée à des risques accrus de problèmes de santé mentale, y compris la toxicomanie et la psychose. Tout en considérant qu'une partie de l'étiologie de ces troubles est héréditaire, nous avons étudié le risque génétique de psychose et de troubles liés à l'usage de substances et leurs relations avec le cannabis et le système endocannabinoïde. Dans notre premier travail, nous avons étudié la relation entre les marqueurs génétiques endocannabinoïdes et les troubles d’usage d'alcool (TUA) pour deux cohortes d'adolescents. À l’aide d’approches de gènes candidats, nous avons démontré une relation significative entre ces gènes endocannabinoïdes et les TUA, mais ces résultats n'ont pas été répliqués chez une deuxième cohorte indépendante. Lors d’une seconde étude, nous avons examiné si la relation entre le score de risque polygénique pour la schizophrénie (PRS-Sz) et les expériences prépsychotiques (PLE) est médiée et/ou modérée par la consommation de cannabis, pour deux cohortes indépendantes. Des modèles de régression de médiation et de modération ont été utilisés pour examiner dans quelle mesure la relation prospective entre PRS-Sz et PLE est expliquée par la consommation de cannabis. Les résultats des analyses de médiation et de modération n'étaient pas significatifs, bien que le PRS-Sz et la consommation de cannabis aient tous deux prédit indépendamment les PLE. Ces résultats suggèrent que la consommation de cannabis reste un facteur de risque de psychose, au-delà de la vulnérabilité génétique connue pour la schizophrénie et qu’il n'y a pas de preuve que les individus génétiquement vulnérables étaient plus sensibles aux conséquences psychotiques de la consommation de cannabis. Le travail décrit démontre que les risques posés par la consommation de cannabis chez les adolescents pourraient ne pas être associés à une prédisposition génétique aux maladies psychiatriques, nonobstant l’implication du système endocannabinoïde dans la pathogenèse de ces mêmes maladies., Cannabis consumption during adolescence, increases the likelihood of adverse mental health outcomes, including substance abuse and psychosis. Considering that part of the etiology of these disorders are heritable, we aimed to elucidate the genetic risk for psychosis and substance use disorders and their relationships to cannabis and the endocannabinoid system. In our first work, we investigated the relationship between endocannabinoid genetic markers and alcohol use disorder in two adolescent cohorts. Through candidate gene approaches we demonstrated a significant relationship between these endocannabinoid genes and AUD, but the results were not replicated in the second cohort. In a second work, we examined if the relationship between polygenic risk score for schizophrenia (PRS-Sz) and psychotic like experiences (PLE) is mediated and/or moderated by cannabis use, in two cohorts. Mediation and moderation regression models were used to examine the extent to which the prospective relationship between PRS-Sz and PLE is accounted for by cannabis use. The results of both the mediation and moderation analyses were not significant, although PRS-Sz and cannabis use both independently predicted PLE. These results suggest that cannabis use remains a risk factor for psychotic-like experiences, over and above known genetic vulnerability for schizophrenia and there was no evidence that genetically vulnerable individuals were more susceptible to the psychosis-related outcomes of adolescent onset cannabis use. The work described demonstrates that the risks posed by adolescent cannabis consumption may be unrelated to one’s genetic predisposition to psychiatric disease, notwithstanding the involvement of the endocannabinoid system in the pathogenesis of these same diseases.

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.

International audience; Effector proteins play crucial roles in determining the outcome of various plant-parasite interactions. Aphids inject salivary effector proteins into plants to facilitate phloem feeding, but some proteins might trigger defense responses in certain plants. The pea aphid, Acyrthosiphon pisum, forms multiple biotypes, and each biotype is specialized to feed on a small number of closely related legume species. Interestingly, all the previously identified biotypes can feed on Vicia faba; hence, it serves as a universal host plant of A. pisum. We hypothesized that the salivary effector proteins have a key role in determining the compatibility between specific host species and A. pisum biotypes and that each biotype produces saliva containing a specific mixture of effector proteins due to differential expression of encoding genes. As the first step to address these hypotheses, we conducted two sets of RNA-seq experiments. RNA-seq analysis of dissected salivary glands (SGs) from reference alfalfa- and pea-specialized A. pisum lines revealed common and line-specific repertoires of candidate salivary effector genes. Based on the results, we created an extended catalogue of A. pisum salivary effector candidates. Next, we used aphid head samples, which contain SGs, to examine biotype-specific expression patterns of candidate salivary genes. RNA-seq analysis of head samples of alfalfa- and pea-specialized biotypes, each represented by three genetically distinct aphid lines reared on either a universal or specific host plant, showed that a majority of the candidate salivary effector genes was expressed in both biotypes at a similar level. Nonetheless, we identified small sets of genes that were differentially regulated in a biotype-specific manner. Little host plant effect (universal vs. specific) was observed on the expression of candidate salivary genes. Analysis of previously obtained genome re-sequenced data of the two biotypes revealed the copy number variations that might explain the differential expression of some candidate salivary genes. In addition, at least four candidate effector genes that were present in the alfalfa biotype but might not be encoded in the pea biotype were identified. This work sets the stage for future functional characterization of candidate genes potentially involved in the determination of plant specificity of pea aphid biotypes

Epub ahead of print; International audience; Roses have high cultural and economic importance as ornamental plants and in the perfume industry. We report the rose whole-genome sequencing and assembly and resequencing of major genotypes that contributed to rose domestication. We generated a homozygous genotype from a heterozygous diploid modern rose progenitor, Rosa chinensis ‘Old Blush’. Using single-molecule real-time sequencing and a meta-assembly approach, we obtained one of the most comprehensive plant genomes to date. Diversity analyses highlighted the mosaic origin of ‘La France’, one of the first hybrids combining the growth vigor of European species and the recurrent blooming of Chinese species. Genomic segments of Chinese ancestry identified new candidate genes for recurrent blooming. Reconstructing regulatory and secondary metabolism pathways allowed us to propose a model of interconnected regulation of scent and flower color. This genome provides a foundation for understanding the mechanisms governing rose traits and should accelerate improvement in roses, Rosaceae and ornamentals.

Very few causal genes have been identified by quantitative trait loci (QTL) mapping because of the large size of QTL, and most of them were identified thanks to functional links already known with the targeted phenotype. Here, we propose to combine selection signature detection, coding SNP annotation, and cis-expression QTL analyses to identify potential causal genes underlying QTL identified in divergent line designs. As a model, we chose experimental chicken lines divergently selected for only one trait, the abdominal fat weight, in which several QTL were previously mapped. Using new haplotype-based statistics exploiting the very high SNP density generated through whole-genome resequencing, we found 129 significant selective sweeps. Most of the QTL colocalized with at least one sweep, which markedly narrowed candidate region size. Some of those sweeps contained only one gene, therefore making them strong positional causal candidates with no presupposed function. We then focused on two of these QTL/sweeps. The absence of nonsynonymous SNPs in their coding regions strongly suggests the existence of causal mutations acting in cis on their expression, confirmed by cis-eQTL identification using either allele-specific expression or genetic mapping analyses. Additional expression analyses of those two genes in the chicken and mice contrasted for adiposity reinforces their link with this phenotype. This study shows for the first time the interest of combining selective sweeps mapping, coding SNP annotation and cis-eQTL analyses for identifying causative genes for a complex trait, in the context of divergent lines selected for this specific trait. Moreover, it highlights two genes, JAG2 and PARK2, as new potential negative and positive key regulators of adiposity in chicken and mice.

International audience; The incorporation of DNA into plant genomes followed by regeneration of non-chimeric stable plants (transformation) remains a major challenge for most plant species. Forest trees are particularly difficult as a result of their biochemistry, aging, desire for clonal fidelity, delayed reproduction, and high diversity. We review two complementary approaches to transformation that appear to hold promise for forest trees.

Plant uridine diphosphate (UDP)-glucosyltransferases (UGT) catalyze the glucosylation of xenobiotic, endogenous substrates and phytotoxic agents produced by pathogens such as mycotoxins. The Bradi5g03300 UGT-encoding gene from the model plant Brachypodium distachyon was previously shown to confer tolerance to the mycotoxin deoxynivalenol (DON) through glucosylation into DON 3-O-glucose (D3G). This gene was shown to be involved in early establishment of quantitative resistance to Fusarium Head Blight, a major disease of small-grain cereals. In the present work, using a translational biology approach, we identified and characterized a wheat candidate gene, Traes_2BS_14CA35D5D, orthologous to Bradi5g03300 on the short arm of chromosome 2B of bread wheat (Triticum aestivum L.). We showed that this UGT-encoding gene was highly inducible upon infection by a DON-producing Fusarium graminearum strain while not induced upon infection by a strain unable to produce DON. Transformation of this wheat UGT-encoding gene into B. distachyon revealed its ability to confer FHB resistance and root tolerance to DON as well as to potentially conjugate DON into D3G in planta and its impact on total DON reduction. In conclusion, we provide a UGT-encoding candidate gene to include in selection process for FHB resistance.

Abscission is the mechanism by which plants disconnect unfertilized flowers, ripe fruits, senescent or diseased organs from the plant. In tomato, pedicel abscission is an important agronomic factor that controls yield and post-harvest fruit quality. Two non-allelic mutations, jointless (j) and jointless-2 (j-2), controlling pedicel abscission zone formation have been documented but only j-2 has been extensively used in breeding. J was shown to encode a MADS-box protein. Using a combination of physical mapping and gene expression analysis we identified a positional candidate, Solyc12g038510, associated with j-2 phenotype. Targeted knockout of Solyc12g038510, using CRISPR/Cas9 system, validated our hypothesis. Solyc12g038510 encodes the MADS-box protein SlMBP21. Molecular analysis of j-2 natural variation revealed two independent loss-of-function mutants. The first results of an insertion of a Rider retrotransposable element. The second results of a stop codon mutation that leads to a truncated protein form. To bring new insights into the role of J and J-2 in abscission zone formation, we phenotyped the single and the double mutants and the engineered alleles. We showed that J is epistatic to J-2 and that the branched inflorescences and the leafy sepals observed in accessions harboring j-2 alleles are likely the consequences of linkage drags.

Les vents violents, tels qu’observés lors de tempêtes, représentent un risque majeurpour la stabilité mécanique des arbres et peuvent avoir un effet dévastateur sur les forêts. Les recherches des dernières décennies ont montré que les sollicitations récurrentes par les vents courants constitueraient un facteur d’acclimatation à des évènements extrêmes. Or, les scenarii envisagés dans le cadre des changements climatiques globaux prévoient une augmentation de la fréquence des tempêtes en Europe occidentale, tandis que la vitesse des vents courants diminuerait. Afin d’aider les propriétaires forestiers dans leurs choix de gestion, il apparaît pertinent de mieux évaluer la capacité future des arbres à acclimater leurs structures en réponse aux flexions répétées lesquelles constituent la composante majeur du vent. Cette acclimatation pourrait impliquer des modifications quantitatives et qualitatives de la production du bois. Il apparaît alors nécessaire d'acquérir une meilleure compréhension de l’effet des sollicitations mécaniques sur l'activité du tissu à l’origine du bois - le cambium - et sur la différenciation des cellules du bois.Ici, nous présentons une analyse des conséquences morphologiques et anatomiques de flexions unidirectionnelles, répétées et d’intensité contrôlée (mimant l’effet du vent) sur de jeunes tiges de peuplier. L’une des originalités de ce travail réside dans la prise en compte de la répartition spatiale inégale des variables physiques sur la section transversale de la tige.Tandis que la croissance secondaire semble ne pas dépendre pas du type de contrainte appliqué (tension ou compression des tissus), la différenciation du bois semble être modulée différentiellement selon les contraintes mécaniques. Le bois produit sous contraintes transitoires de tension semble présenter des similitudes avec le bois de tension produit chez les feuillus sous l’effet du stimulus gravité. L’acclimatation au vent du peuplier pourrait donc impliquer la mise en place d’un bois modifié (ou bois de réaction) permettant un ajustement de ses propriétés mécaniques. L’identification d’acteurs moléculaires impliqués dans ces réponses est en cours et pourrait à plus long terme aider à l’établissement de stratégies de sélection.

The high resolution integration of bread wheat genetic and genomic resources accumulated during the last decades offers the opportunity to unveil candidate genes driving major agronomical traits to an unprecedented scale. We combined 27 public quantitative genetic studies and four genetic maps to deliver an exhaustive consensus map consisting of 140,315 molecular markers hosting 221, 73, and 82 Quantitative Trait Loci (QTL) for respectively yield, baking quality, and grain protein content (GPC) related traits. Projection of the consensus genetic map and associated QTLs onto the wheat syntenome made of 99,386 genes ordered on the 21 chromosomes delivered a complete and non-redundant repertoire of 18, 8, 6 metaQTLs for respectively yield, baking quality and GPC, altogether associated to 15,772 genes (delivering 28,630 SNP-based makers) including 37 major candidates. Overall, this study illustrates a translational research approach in transferring information gained from grass relatives to dissect the genomic regions hosting major loci governing key agronomical traits in bread wheat, their flanking markers and associated candidate genes to be now considered as a key resource for breeding programs.

The genetic basis of quantitative disease resistance has been studied in crops for several decades as an alternative to R gene mediated resistance. The most important disease in the potato crop is late blight, caused by the oomycete Phytophthora infestans. Quantitative disease resistance (QDR), as any other quantitative trait in plants, can be genetically mapped to understand the genetic architecture. Association mapping using DNA-based markers has been implemented in many crops to dissect quantitative traits. We used an association mapping approach with candidate genes to identify the first genes associated with quantitative resistance to late blight in Solanum tuberosum Group Phureja. Twenty-nine candidate genes were selected from a set of genes that were differentially expressed during the resistance response to late blight in tetraploid European potato cultivars. The 29 genes were amplified and sequenced in 104 accessions of S. tuberosum Group Phureja from Latin America. We identified 238 SNPs in the selected genes and tested them for association with resistance to late blight. The phenotypic data were obtained under field conditions by determining the area under disease progress curve (AUDPC) in two seasons and in two locations. Two genes were associated with QDR to late blight, a potato homolog of thylakoid lumen 15 kDa protein (StTL15A) and a stem 28 kDa glycoprotein (StGP28). Key message: A first association mapping experiment was conducted in Solanum tuberosum Group Phureja germplasm, which identified among 29 candidates two genes associated with quantitative resistance to late blight.

Bacterial wilt (BW) is a major disease of solanaceous crops caused by the Ralstonia solanacearum species complex (RSSC). Strains are grouped into five phylotypes (I, IIA, IIB, III, and IV). Varietal resistance is the most sustainable strategy for managing BW. Nevertheless, breeding to improve cultivar resistance has been limited by the pathogen's extensive genetic diversity. Identifying the genetic bases of specific and non-specific resistance is a prerequisite to breed improvement. A major gene (ERs1) was previously mapped in eggplant (Solanum melongena L.) using an intraspecific population of recombinant inbred lines derived from the cross of susceptible MM738 (S) x resistant AG91-25 (R). ERs1 was originally found to control three strains from phylotype I, while being totally ineffective against a virulent strain from the same phylotype. We tested this population against four additional RSSC strains, representing phylotypes I, IIA, IIB, and III in order to clarify the action spectrum of ERs1. We recorded wilting symptoms and bacterial stem colonization under controlled artificial inoculation. We constructed a high-density genetic map of the population using single nucleotide polymorphisms (SNPs) developed from genotyping-by-sequencing and added 168 molecular markers [amplified fragment length polymorphisms (AFLPs), simple sequence repeats (SSRs), and sequence-related amplified polymorphisms (SRAPs)] developed previously. The new linkage map based on a total of 1,035 markers was anchored on eggplant, tomato, and potato genomes. Quantitative trait locus (QTL) mapping for resistance against a total of eight RSSC strains resulted in the detection of one major phylotype-specific QTL and two broad-spectrum QTLs. The major QTL, which specifically controls three phylotype I strains, was located at the bottom of chromosome 9 and corresponded to the previously identified major gene ERs1. Five candidate R-genes were underlying this QTL, with different alleles between the parents. The two other QTLs detected on chromosomes 2 and 5 were found to be associated with partial resistance to strains of phylotypes I, IIA, III and strains of phylotypes IIA and III, respectively. Markers closely linked to these three QTLs will be crucial for breeding eggplant with broad-spectrum resistance to BW. Furthermore, our study provides an important contribution to the molecular characterization of ERs1, which was initially considered to be a major resistance gene.

International audience; Soil acidity poses a major threat to productivity of several crops; mainly due to the prevalence of toxic levels of Al3+ and Mn2+. Crop productivity could be harnessed on acid soils via the development of plant varieties tolerant to phytotoxic levels of these cations. In this study, we investigated the extent of natural variation for Mn2+ tolerance among ten parental lines of the Australian and International canola mapping populations. Response to Mn2+ toxicity was measured on the bases of cotyledon chlorosis, shoot biomass, and leaf area in nutrient solution under control (9 mu M of MnCl2 center dot 4H(2)O) and Mn treatment (125 mu M of MnCl2 center dot 4H(2)O). Among parental lines, we selected Darmor-bzh and Yudal that showed significant and contrasting variation in Mn2+ tolerance to understand genetic control and identify the quantitative trait loci (QTL) underlying Mn2+ tolerance. We evaluated parental lines and their doubled haploid (DH) progenies (196 lines) derived from an F-1 cross, Darmor-bzh/ Yudal for Mn2+ tolerance. Mn2+-tolerant genotypes had significantly higher shoot biomass and leaf area compared to Mn2+-sensitive genotypes. A genetic linkage map based on 7,805 DArTseq markers corresponding to 2,094 unique loci was constructed and further utilized for QTL identification. A major locus, BnMn2+.A09 was further mapped with a SNP marker, Bn-A09-p29012402 (LOD score of 34.6) accounting for most of the variation in Mn2+ tolerance on chromosome A09. This is the first report on the genomic localization of a Mn2+ tolerance locus in B. napus. Additionally, an ortholog of A. thaliana encoding for cation efflux facilitator transporter was located within 3,991 bp from significant SNP marker associated with BnMn2+.A09. A suite of genome sequence based markers (DArTseq and Illumina Infinium SNPs) flanking the BnMn2+.A09 locus would provide an invaluable tool for various molecular breeding applications to improve canola production and profitability on Mn2+ toxic soils.

Abscission is the mechanism by which plants disconnect unfertilized flowers, ripe fruits, senescent or diseased organs from the plant. In tomato, pedicel abscission is an important agronomic factor that controls yield and post-harvest fruit quality. Two non-allelic mutations, jointless (j) and jointless-2 (j-2), controlling pedicel abscission zone formation have been documented but only j-2 has been extensively used in breeding. J was shown to encode a MADS-box protein. Using a combination of physical mapping and gene expression analysis we identified a positional candidate, Solyc12g038510, associated with j-2 phenotype. Targeted knockout of Solyc12g038510, using CRISPR/Cas9 system, validated our hypothesis. Solyc12g038510 encodes the MADS-box protein SlMBP21. Molecular analysis of j-2 natural variation revealed two independent loss-of-function mutants. The first results of an insertion of a Rider retrotransposable element. The second results of a stop codon mutation that leads to a truncated protein form. To bring new insights into the role of J and J-2 in abscission zone formation, we phenotyped the single and the double mutants and the engineered alleles. We showed that J is epistatic to J-2 and that the branched inflorescences and the leafy sepals observed in accessions harboring j-2 alleles are likely the consequences of linkage drags.

International audience; Vitamin E (VE) is the generic term for four tocopherols and four tocotrienols that exhibit the biological activity of alpha-tocopherol. VE status, which is usually estimated by measuring fasting blood VE concentration, is affected by numerous factors, such as dietary VE intake, VE absorption efficiency, and VE catabolism. Several of these factors are in turn modulated by genetic variations in genes encoding proteins involved in these factors. To identify these genetic variations, two strategies have been used: genome-wide association studies and candidate gene association studies. Each of these strategies has its advantages and its drawbacks, nevertheless they have allowed us to identify a list of single nucleotide polymorphisms associated with fasting blood VE concentration and alpha-tocopherol bioavailability. However, much work remains to be done to identify, and to replicate in different populations, all the single nucleotide polymorphisms involved, to assess the possible involvement of other kind of genetic variations, e.g., copy number variants and epigenetic modifications, in order to establish a reliable list of genetic variations that will allow us to predict the VE status of an individual by knowing their genotype in these genetic variations. Yet, the potential usefulness of this area of research is exciting with regard to personalized nutrition and for future clinical trials dedicated to assessing the biological effects of the various isoforms of VE.

L’hypertension essentielle étant un facteur majeur de morbidité, la compréhension de son l’étiologie est prépondérante. Ainsi, la découverte de nouvelles composantes ou mécanismes de régulation de la PA par l’identification de QTL et l’étude de leurs interactions s’avère une approche prometteuse. L’utilisation de souches congéniques de rats pour l’étude de l’hypertension est une stratégie payante puisqu’elle permet de masquer les effets de l’environnement, tout en gardant le caractère polygénique de la PA. Longtemps conçu comme un trait issu de l’accumulation des effets minimes des QTL, la PA est régulée par une architecture basée sur l’existence d’interactions épistatiques. L’analyse par paires de QTL individuels a permis d’établir une modularité dans l’organisation des QTL chez le rat Dahl Salt-sensitive en fonction de la présence ou de l’absence d’une interaction épistatique entre eux. Ainsi, deux modules épistatiques ont été établis; EM1 et EM2 où tous les QTL appartenant à EM1 sont épistatiques entre eux et agissent de façon additive avec les membres de EM2. Des hiérarchies dans la régulation peuvent alors être révélées si les QTL d’un même EM ont des effets opposés. L’identification de la nature moléculaire des candidats C18QTL4/Hdhd2 et C18QTL3/Tcof1, membres du EM1, et de l’interaction épistatique entre ces deux QTL, a permis, en plus, d’élucider une régulation séquentielle au sein du module. Hdhd2 pourrait agir en amont de Tcof1 et réguler ce dernier par une modification post-traductionnelle. Cette interaction est la première évidence expérimentale de la prédiction des relations entre QTL, phénomène établi par leur modularisation. Le dévoilement du fonctionnement de l’architecture génétique à la base du contrôle de la PA et la découverte des gènes responsables des QTL permettrait d’élargir les cibles thérapeutiques et donc de développer des traitements antihypertenseurs plus efficaces., Essential hypertension is a major risk factor for cardiovascular diseases. Understanding the etiology of this pathology is of the outmost importance. Thus, unraveling novel genetic components and mechanisms regulating blood pressure (BP) via QTL identification and QTL-QTL interaction analysis is a promising strategy. Congenic strains establishment is a common and fruitful means for achieving such goal. A quantitative trait, such as BP, has long been thought to result from the accumulation of infinitesimal effects exerted by multiple QTL. Nevertheless, BP is controlled by an epistasis-based architecture. Pair-wise comparisons of individual QTL based on the existence or lack-of epistatic interaction between them allowed us to establish a modularized organization of BP QTL in the Dahl Salt-sensitive model. Hence, two epistatic modules, namely EM1 and EM2 were constituted. In this fashion, any member of the EM1 is epistatic to all the other members of the same module and is additive to those of EM2. Regulatory hierarchies among BP with paradoxical effects can be revealed within each EM. The molecular identification of EM1 members, C18QTL4/Hdhd2 and C18QTL3/Tcof1, as well as the revelation of the molecular basis for their epistatic interaction enabled us to suggest a sequential regulation within this EM. Hdhd2 could act upstream of Tcof1 and regulate it by post-transcriptional modification. This interaction is the first experimental evidence derived from the predictive model of QTL modularization. The elucidation of the molecular mechanisms underlying the genetic architecture of BP, as well as the identification of the causal genes for QTL will lay the grounds for expanding therapeutic targets and for developing more efficient antihypertensive treatments.

The present study investigates the genetic determinism of flowering and maturity dates, two traits highly affected by global climate change. Flowering and maturity dates were evaluated on five progenies from three Prunus species, peach, apricot and sweet cherry, during 3–8 years. Quantitative trait locus (QTL) detection was performed separately for each year and also by integrating data from all years together. High heritability estimates were obtained for flowering and maturity dates. Several QTLs for flowering and maturity dates were highly stable, detected each year of evaluation, suggesting that they were not affected by climatic variations. For flowering date, major QTLs were detected on linkage groups (LG) 4 for apricot and sweet cherry and on LG6 for peach. QTLs were identified on LG2, LG3, LG4 and LG7 for the three species. For maturity date, a major QTL was detected on LG4 in the three species. Using the peach genome sequence data, candidate genes underlying the major QTLs on LG4 and LG6 were investigated and key genes were identified. Our results provide a basis for the identification of genes involved in flowering and maturity dates that could be used to develop cultivar ideotypes adapted to future climatic conditions., This work was partially supported by the ISAFRUIT Project funded by the European Commission—Food Quality and Safety of the 6th Framework Program of RTD (No. FP6-FOOD-CT-2006-016279).

Contact: fax: +91 40 30713074/30713075. E-mail address: r.k.varshney@cgiar.org; International audience; The transcription factor, DREB2A, is one of the promising candidate genes involved in dehydration tolerance in crop plants. In order to isolate DREB2A homologues across cereals (rice, barley and sorghum) and legumes (common bean and chickpea), specific or degenerate primers were used. Gene/phylogenetic trees were constructed using a non-redundant set of 19 DREB1A and 27 DREB2A amino acid sequences and were combined with taxonomic/species tree to prepare reconciled phylogenetic trees. In total, 86 degenerate primers were designed for different clades and 295 degenerate primer combinations were used to amplify DREB homologues in targeted crop species. Successful amplification of DREB2A was obtained in case of sorghum. In parallel, gene-specific primers were used to amplify DREB2A homologues in rice, barley, common bean and chickpea. Seven to eight diverse genotypes from targeted species were used for sequence analysis at DREB2A locus identified/isolated. A maximum of eight SNPs were found in the common bean DREB2A, indicating two distinct haplotypes, three SNPs with five haplotypes were observed in barley whereas a single SNP was observed in rice, sorghum and chickpea. Parsimony based phylogenetic tree revealed distinct clustering of cereals and legumes. Furthermore, alignment of corresponding amino acid sequences showed conservation of AP2 domain across the targeted species.

Testing how populations are locally adapted and predicting their response to their future environment is of key importance in view of climate change. Landscape genomics is a powerful approach to investigate genes and environmental factors involved in local adaptation. In a pooled amplicon sequencing approach of 94 genes in 71 populations, we tested if >3'500 single nucleotide polymorphisms (SNPs) in the three most common oak species in Switzerland (Quercus petraea, Q. pubescens, Q. robur) show an association with abiotic factors related to local topography, historical climate, and soil characteristics. In the analysis including all species, the most frequently associated environmental factors were those best describing the habitats of the species. In the species-specific analyses, the most important environmental factors and associated SNPs greatly differed among species. However, we identified one SNP and seven genes that were associated to the same environmental factor across all species. We finally used regressions of allele frequencies of the most strongly associated SNPs along environmental gradients to predict the risk of non-adaptedness (RONA), which represents the average change in allele frequency at climate-associated loci theoretically required to match future climatic conditions. RONA is considerable for some populations and species (up to 48% in single populations) and strongly differs among species. Given the long generation time of oaks, some of the required allele frequency changes might not be realistic to achieve based on standing genetic variation. Hence, future adaptedness requires gene flow or planting of individuals carrying beneficial alleles from habitats currently matching future climatic conditions. This article is protected by copyright. All rights reserved.

Rphq2 , a minor gene for partial resistance to Puccinia hordei , was physically mapped in a 188 kbp introgression with suppressed recombination between haplotypes of rphq2 and Rphq2 barley cultivars. Partial and non-host resistances to rust fungi in barley (Hordeum vulgare) may be based on pathogen-associated molecular pattern (PAMP)-triggered immunity. Understanding partial resistance may help to understand non-host resistance, and vice versa. We constructed two non-gridded BAC libraries from cultivar Vada and line SusPtrit. Vada is immune to non-adapted Puccinia rust fungi, and partially resistant to P. hordei. SusPtrit is susceptible to several non-adapted rust fungi, and has been used for mapping QTLs for non-host and partial resistance. The BAC libraries help to identify genes determining the natural variation for partial and non-host resistances of barley to rust fungi. A major-effect QTL, Rphq2, for partial resistance to P. hordei was mapped in a complete Vada and an incomplete SusPtrit contig. The physical distance between the markers flanking Rphq2 was 195 Kbp in Vada and at least 226 Kbp in SusPtrit. This marker interval was predicted to contain 12 genes in either accession, of which only five genes were in common. The haplotypes represented by Vada and SusPtrit were found in 57 and 43 %, respectively, of a 194 barley accessions panel. The lack of homology between the two haplotypes probably explains the suppression of recombination in the Rphq2 area and limit further genetic resolution in fine mapping. The possible candidate genes for Rphq2 encode peroxidases, kinases and a member of seven-in-absentia protein family. This result suggests that Rphq2 does not belong to the NB-LRR gene family and does not resemble any of the partial resistance genes cloned previously.

Lignocellulosic biomass is a renewable resource of interest for biorefinery. However, current poplar varieties have not been selected for this specific purpose. The factors affecting biomass yield and chemical properties need thus to be studied. With this objective, we have initiated a systems biology approach, integrating genomic, transcriptomic and phenotypic data in natural populations of black poplar (Populus nigra). Up to now, we have focused on a subset of 12 genotypes from 6 populations and trialled in a randomized complete block design located at INRA Orléans, France. The transcriptome of 2 biological replicates of each genotype has been explored through RNA sequencing (RNAseq) of pools of young differentiating xylem and cambium. Additionally, biomass yield was evaluated through measurements of height and diameter on 6 replicates of each genotype across several years and rotations, while biomass propertieswere assessed through chemical analyses of lignin, cellulose and hemicellulose concentrations as well as saccharification potential on 3 replicates of each genotype. The resulting data were used to build a weighted gene co-expression network and identify gene modules whose expression was correlated with biomass yield and/or quality at the genotypic level. Remarkably, the largest module (1,460 transcripts) was significantly associated with klason lignin content and displayed an enrichment in genes involved in secondary cell wall formation. Four candidate genes from this module were further selected to validate the detected quantitative trait transcripts (QTTs) on 2 new replicates of the 12 genotypes using RT-qPCR. The resulting expression levels were significantly correlated to those previously quantified by RNAseq and to the klason lignin content in the wood samples. These results demonstrate the interest of our approach, and thus open some prospects towards the identification of new candidate genes whose functions remain to be elucidated.

Background Genome-wide association (GWA) mapping has recently emerged as a valuable approach for refining the genetic basis of polygenic resistance to plant diseases, which are increasingly used in integrated strategies for durable crop protection. Aphanomyces euteiches is a soil-borne pathogen of pea and other legumes worldwide, which causes yield-damaging root rot. Linkage mapping studies reported quantitative trait loci (QTL) controlling resistance to A. euteiches in pea. However the confidence intervals (CIs) of these QTL remained large and were often linked to undesirable alleles, which limited their application in breeding. The aim of this study was to use a GWA approach to validate and refine CIs of the previously reported Aphanomyces resistance QTL, as well as identify new resistance loci. Methods A pea-Aphanomyces collection of 175 pea lines, enriched in germplasm derived from previously studied resistant sources, was evaluated for resistance to A. euteiches in field infested nurseries in nine environments and with two strains in climatic chambers. The collection was genotyped using 13,204 SNPs from the recently developed GenoPea Infinium® BeadChip. Results GWA analysis detected a total of 52 QTL of small size-intervals associated with resistance to A. euteiches, using the recently developed Multi-Locus Mixed Model. The analysis validated six of the seven previously reported main Aphanomyces resistance QTL and detected novel resistance loci. It also provided marker haplotypes at 14 consistent QTL regions associated with increased resistance and highlighted accumulation of favourable haplotypes in the most resistant lines. Previous linkages between resistance alleles and undesired late-flowering alleles for dry pea breeding were mostly confirmed, but the linkage between loci controlling resistance and coloured flowers was broken due to the high resolution of the analysis. A high proportion of the putative candidate genes underlying resistance loci encoded stress-related proteins and others suggested that the QTL are involved in diverse functions. Conclusion This study provides valuable markers, marker haplotypes and germplasm lines to increase levels of partial resistance to A. euteiches in pea breeding. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2429-4) contains supplementary material, which is available to authorized users.

Highlight Tomato quality could be improved under deficit irrigation while maintaining yield. The underlying genetic architecture is polygenic and varies with water availability. Candidate genes related to primary metabolism were identified., Water scarcity constitutes a crucial constraint for agriculture productivity. High-throughput approaches in model plant species identified hundreds of genes potentially involved in survival under drought, but few having beneficial effects on quality and yield. Nonetheless, controlled water deficit may improve fruit quality through higher concentration of flavor compounds. The underlying genetic determinants are still poorly known. In this study, we phenotyped 141 highly diverse small fruit tomato accessions for 27 traits under two contrasting watering conditions. A subset of 55 accessions exhibited increased metabolite contents and maintained yield under water deficit. Using 6100 single nucleotide polymorphisms (SNPs), association mapping revealed 31, 41, and 44 quantitative trait loci (QTLs) under drought, control, and both conditions, respectively. Twenty-five additional QTLs were interactive between conditions, emphasizing the interest in accounting for QTLs by watering regime interactions in fruit quality improvement. Combining our results with the loci previously identified in a biparental progeny resulted in 11 common QTLs and contributed to a first detailed characterization of the genetic determinants of response to water deficit in tomato. Major QTLs for fruit quality traits were dissected and candidate genes were proposed using expression and polymorphism data. The outcomes provide a basis for fruit quality improvement under deficit irrigation while limiting yield losses.

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Plum pox virus (PPV), the causal agent of sharka disease, is one of the most studied plant viruses, and major advances in detection techniques, genome characterization and organization, gene expression, transmission, and the description of candidate genes involved in PPV resistance have been described. However, information concerning the plant response to PPV infection is very scarce. In this review, we provide an updated summary of the research carried out to date in order to elucidate how plants cope with PPV infection and their response at different levels, including the physiological, biochemical, proteomic, and genetic levels. Knowledge about how plants respond to PPV infection can contribute to the development of new strategies to cope with this disease. Due to the fact that PPV induces an oxidative stress in plants, the bio-fortification of the antioxidative defences, by classical or biotechnological approaches, would be a useful tool to cope with PPV infection. Nevertheless, there are still some gaps in knowledge related to PPV–plant interaction that remain to be filled, such as the effect of PPV on the hormonal profile of the plant or on the plant metabolome., PDV thanks CSIC and the Spanish Ministry of the Economy and Competitiveness for his Ramon &Cajal research contract, co-financed with FEDER funds.

GenFam est un système intégratif d'analyse de familles de gènes. Ce système permet (i) de créer des familles de gènes de génomes complets, (ii) d'exécuter une analyse phylogénétique de cette famille à travers le gestionnaire de workflows Galaxy afin de définir l es relations d'homologie, (iii) d'étudier des événements évolutifs à partir de blocs de synténie précalculées avec le workflow SynMap de la plateforme de génomique comparative (CoGe) et (iv) d'intégrer ces résultats dans l'interface de visualisation synthé tique. La première application de GenFam est d'identifier des gènes candidats pour la tolérance aux stress environnementaux. Il nécessite de mettre en évidence la présence de séquences régulatrices cis spécifiques de la réponse aux stress (de type ABRE, DR E). Dans ce contexte, nous avons besoin d'intégrer de nouveaux outils afin de découvrir et chercher des sites de fixation de facteurs de transcription (Transcription Factor Binding Sites, TFBS) dans les séquences promotrices des gènes membre de la famille étudiée. Ce workflow Galaxy va, d'une part, sélectionner les régions flanquantes en 5' ou en 3' des gènes d'intérêts selon le choix de l'utilisateur. D'autre part, les régions flanquantes sont analysées afin de découvrir et rechercher les motifs de séquenc es régulatrices cis spécifiques de la réponse aux stress avec des méthodes complémentaires comme MEME, STIF, PHYME. Ces résultats ainsi que l'annotation fonctionnelle des gènes étiquetés comme étant impliqués dans la réponse au stress seront intégrés dans l'interface de visualisation. Ce travail doit permettre une réflexion sur la notion d'orthologie fonctionnelle et effectuer une recherche translationnelle depuis les espèces modèles jusqu'aux espèces d'intérêt agronomique (i.e identifier des gènes candidat s pour la réponse au stress du caféier à partir d'informations fonctionnelles connues chez Arabidopsis).

EFPP 2002 : disease resistance in plant pathology; International audience

In fruit species, the flowering is a major event which strongly influences fructification. This process tiny controlled by many genetic and environmental factors is still little known. In sweet cherry (Prunus avium), flowers open out only after having satisfied chill and heat requirements. The effects of climate change on the flowering are already notable and could induce important economic losses. Identification of genetic and molecular determinants involved in the flowering will allow the improvement of varietal selection programs to obtain trees adapted to future climate conditions. Objective of this thesis is to increase the knowledge of these determinants and identify genes involved in flowering in sweet cherry. By studying two intraspecific progenies ‘Regina’ × ‘Lapins’ and ‘Regina’ × ‘Garnet’, detection of many quantitative trait loci (QTL) on all linkage groups (LG) has enabled us to confirm the strong involvement of chill requirements in the flowering as well as the complexity of these traits. QTL with major effect was localized on the LG4. In regions covered by all the QTLs controlling flowering date, a hundred candidate genes (CG) for this trait was identified. A subset of these GC was then studied for their expression during development of buds by quantitative PCR (qPCR). In the long term, this work will serve as a basis for the identification and selection of genes that allow obtaining genotypes adapted to future climate conditions.; Chez les espèces fruitières, la floraison est un évènement majeur qui influencera fortement la fructification. Ce processus, finement régulé par de nombreux facteurs génétiques et environnementaux, est encore peu connu. Chez le cerisier doux (Prunus avium), les fleurs ne s’épanouissent qu’après avoir satisfait des besoins en froid et en chaud. Les effets du changement climatique sur la floraison sont déjà notables et pourraient induire d’importantes pertes économiques. La compréhension des déterminants génétiques et moléculaires impliqués dans la floraison permettra l’amélioration des programmes de sélection variétale visant l’obtention d’arbres adaptés aux futures conditions climatiques. L’objectif de cette thèse est d’accroître les connaissances sur ces déterminants et d’identifier les gènes contrôlant la floraison chez le cerisier. En étudiant les deux familles intra spécifiques ‘Regina’ × ‘Lapins’ et ‘Regina’ × ‘Garnet’, la détection de nombreux quantitative trait loci (QTL) sur l’ensemble des groupes de liaisons (GL) a permis de confirmer la forte implication des besoins en froid dans la floraison ainsi que la complexité de ces caractères. Un QTL à effet majeur a été localisé sur le GL4. Dans les régions couvertes par les QTL contrôlant la date de floraison, une centaine de gènes candidats (GC) pour ce caractère a été identifiée. Un sous ensemble de ces GC a ensuite été étudié pour leur expression au cours du développement des bourgeons par PCR quantitative (qPCR). A terme, ces travaux serviront de bases pour l’identification et la sélection de gènes qui permettront l’obtention de génotypes adaptés aux futures conditions climatiques.

Improving the traits that underlie meat quality is a major challenge in the beef industry. The objective of this paper was to detect QTL linked to sensory meat quality traits in 3 French beef cattle breeds. We genotyped 1,059, 1,219, and 947 young bulls and their sires belonging to the Charolais, Limousin, and Blonde d'Aquitaine breeds, respectively, using the Illumina BovineSNP50 BeadChip (Illumina Inc., San Diego, CA). After estimating relevant genetic parameters using VCE software, we performed a linkage disequilibrium and linkage analysis on 4 meat traits: intramuscular fat content, muscle lightness, shear force, and tenderness score. Heritability coefficients largely ranged between 0.10 and 0.24; however, they reached a maximum of 0.44 and 0.50 for intramuscular fat content and tenderness score, respectively, in the Charolais breed. The 2 meat texture traits, shear force and tenderness score, were strongly genetically correlated (-0.91 in the Charolais and Limousin breed and -0.86 in the Blonde d'Aquitaine breed), indicating that they are 2 different measures of approximately the same trait. The genetic correlation between tenderness and intramuscular fat content differed across breeds. Using a significance threshold of 5 × 10(-4) for QTL detection, we found more than 200 significant positions across the 29 autosomal chromosomes for the 4 traits in the Charolais and Blonde d'Aquitaine breeds; in contrast, there were only 78 significant positions in the Limousin breed. Few QTL were common across breeds. We detected QTL for intramuscular fat content located near the myostatin gene in the Charolais and Blonde d'Aquitaine breeds. No mutation in this gene has been reported for the Blonde d'Aquitaine breed; therefore, it suggests that an unknown mutation could be segregating in this breed. We confirmed that, in certain breeds, markers in the calpastatin and calpain 1 gene regions affect tenderness. We also found new QTL as several QTL on chromosome 3 that are significantly associated with meat tenderness in the Blonde d'Aquitaine breed. Overall, these results greatly contribute to the goal of building a panel of markers that can be used to select animals of high meat quality.

The possibility of using lignocellulosic biomass produced from forest crops in order to obtain second generation biofuels is a key issue in the current context of climate change and the promotion of renewable energy sources. It is therefore important to make progress in the functional characterization of the candidate genes (CGs) associated with wood property traits relevant to this use as well as to determine the effect of different environmental factors (saline stress among others) on the expression of those genes. Populus spp. are among the forest species which rouse the most interest in the short term. Our objective is to carry out a dasometric, physiological and candidate gene expression characterization in hybrid genotypes of Populus which are suitable for use in short rotation growing under saline stress conditions. The trials were conducted under controlled greenhouse conditions. P. x canadensis ‘Oudenberg’, P. tremula x P. alba `717-1B4 ’and two autochthonous P. alba clones were tested from cuttings in individual pots. Two stress levels were applied: NaCl 68 and 137 mM, The parameters evaluated were, i) survival and expression of leaf necrosis symptoms, ii) relative height and diameter growth rate, iii) dry aerial and root biomass iiii) functional variables: net photosynthesis rate (A), stomatal conductance (gs) to infer intrinsecal water use efficiency (IWUE), and chlorophyll content. Significant interspecific differences were revealed with regard to salt stress responses, both in terms of damage symptomology and growth, production and functional variables. P. alba genotypes displayed the greatest tolerance. Transcript levels were analyzed in stem samples by Fluidigm technology for 80 selected genes related to secondary cell wall deposition (MYB and NAC transcription factors, hormone signaling, lignification, etc.). All genotypes showed changes in transcript profiles in response to salt, although the magnitude of the response was different among genotypes. About 77 % of the selected genes showed lower transcript level in plants under salt stress when compared to the salt-free treatment. The impact of salt stress on the expression of selected genes was lower in both P. alba genotypes, in agreement with the greatest tolerance.

Cette recherche a été focalisée sur l’étude de la variabilité génétique et des mécanismes associés à une adaptation d’A. bisporus à la culture dans des conditions subtropicales. Elle a été subdivisée en trois parties : [br/] 1- identification de la diversité de l’aptitude à fructifier à haute température (FHT+) dans un échantillon de souches sauvages collectées dans plusieurs localités de pays d’Amérique du Nord et d’Europe. Dans cet ensemble nous avons inclus des représentants des trois variétés d’Agaricus à savoir : les variétés bisporus, burnettii et eurotetrasporus ; [br/] 2- la caractérisation d’un gène candidat de thermo-tolérance dans des souches FHT+ et FHT- et l’identification de son implication dans le caractère FHT+ ; [br/] 3- l’étude du déterminisme génétique du caractère FHT+.[br/] Toutes les souches de la variété burnettii sont capables de produire des champignons avec de forts rendements à haute température. Cette aptitude est un élément de leur adaptation aux conditions climatiques rencontrée par la population originale. Seulement quelques souches d’A. bisporus var. bisporus ont révélés un bon potentiel pour fructifier à 25°C, mais sans relation avec les conditions climatiques de leur zone d’origine. Le gène étudié n’était que légèrement impliqué dans la réaction au stress thermique. Nous l’avons renommé aap1 car nous avons montré qu’il appartient à une nouvelle sous-famille des homologues du gène YAP1 de levure. Il n’est pas un contributeur dominant pour la thermo-tolérance d’A. bisporus, mais la protéine qu’il code peut être impliquée comme facteur de transcription de résistance générale au stress. En fait le caractère FHT+ est un caractère quantitatif sous contrôle polygénique. Il peut être hérité d’un parent de la variété burnetti dans une descendance intervariétale. Au cours de ce travail, des souches d’A. bisporus possédant des potentiels intéressants pour la culture en conditions subtropicales ont été identifiées et les bases génétiques pour un programme de création variétale pour introduire ces caractères dans des souches déjà cultivées ont été identifiées.

International audience; The end-use value of bread wheat (Triticum aestivum L.) grain is mainly determined by grain storage protein (GSP) content and composition. Glutenins and gliadins are the two main classes of GSPs in wheat. They are produced by genes mainly controlled at the transcriptional level by a network involving at least eight transcription factors (TFs). This network could lead to the stable allometric scaling relationships observed between the quantity of GSPs, gliadins or glutenins and the total quantity of nitrogen (N) per grain. Chromosomic regions involved in GSP accumulation, composition and allometric grain N allocation were identified using linkage mapping in 196 accessions of a bread wheat worldwide core collection grown in three environments. We used 873 markers for genome-wide association and 167 single nucleotide polymorphism markers in 51 candidate genes, including 35 TFs expressed in the grain, for candidate association. We identified 95 associated loci, 29 (31%) of which were inside or in strong linkage disequilibrium with candidate genes. As expected, structural GSP genes were associated with studied traits. In addition, several loci putatively trans-regulating GSP accumulation were uncovered. Seven candidate TFs were associated or in strong linkage disequilibrium with markers associated with the composition or quantity of glutenin or gliadin, or allometric grain N allocation parameters, confirming the importance of the transcriptional control of GSP accumulation. Our results suggest that the genetic determinants of glutenin and gliadin compositions are mostly distinct from each other.

National audience

Chickpea is an important food legume crop for the semi-arid regions, however, its productivity is adversely affected by various biotic and abiotic stresses. Identification of candidate genes associated with abiotic stress response will help breeding efforts aiming to enhance its productivity. With this objective, 10 abiotic stress responsive candidate genes were selected on the basis of prior knowledge of this complex trait. These 10 genes were subjected to allele specific sequencing across a chickpea reference set comprising 300 genotypes including 211 genotypes of chickpea mini core collection. A total of 1.3 Mbp sequence data were generated. Multiple sequence alignment (MSA) revealed 79 SNPs and 41 indels in nine genes while the CAP2 gene was found to be conserved across all the genotypes. Among 10 candidate genes, the maximum number of SNPs (34) was observed in abscisic acid stress and ripening (ASR) gene including 22 transitions, 11 transversions and one tri-allelic SNP. Nucleotide diversity varied from 0.0004 to 0.0029 while polymorphism information content (PIC) values ranged from 0.01 (AKIN gene) to 0.43 (CAP2 promoter). Haplotype analysis revealed that alleles were represented by more than two haplotype blocks, except alleles of the CAP2 and sucrose synthase (SuSy) gene, where only one haplotype was identified. These genes can be used for association analysis and if validated, may be useful for enhancing abiotic stress, including drought tolerance, through molecular breeding.

Chez les espèces fruitières, la floraison est un évènement majeur qui influencera fortement la fructification. Ce processus, finement régulé par de nombreux facteurs génétiques et environnementaux, est encore peu connu. Chez le cerisier doux (Prunus avium), les fleurs ne s’épanouissent qu’après avoir satisfait des besoins en froid et en chaud. Les effets du changement climatique sur la floraison sont déjà notables et pourraient induire d’importantes pertes économiques. La compréhension des déterminants génétiques et moléculaires impliqués dans la floraison permettra l’amélioration des programmes de sélection variétale visant l’obtention d’arbres adaptés aux futures conditions climatiques. L’objectif de cette thèse est d’accroître les connaissances sur ces déterminants et d’identifier les gènes contrôlant la floraison chez le cerisier. En étudiant les deux familles intra spécifiques ‘Regina’ × ‘Lapins’ et ‘Regina’ × ‘Garnet’, la détection de nombreux quantitative trait loci (QTL) sur l’ensemble des groupes de liaisons (GL) a permis de confirmer la forte implication des besoins en froid dans la floraison ainsi que la complexité de ces caractères. Un QTL à effet majeur a été localisé sur le GL4. Dans les régions couvertes par les QTL contrôlant la date de floraison, une centaine de gènes candidats (GC) pour ce caractère a été identifiée. Un sous ensemble de ces GC a ensuite été étudié pour leur expression au cours du développement des bourgeons par PCR quantitative (qPCR). A terme, ces travaux serviront de bases pour l’identification et la sélection de gènes qui permettront l’obtention de génotypes adaptés aux futures conditions climatiques., In fruit species, the flowering is a major event which strongly influences fructification. This process tiny controlled by many genetic and environmental factors is still little known. In sweet cherry (Prunus avium), flowers open out only after having satisfied chill and heat requirements. The effects of climate change on the flowering are already notable and could induce important economic losses. Identification of genetic and molecular determinants involved in the flowering will allow the improvement of varietal selection programs to obtain trees adapted to future climate conditions. Objective of this thesis is to increase the knowledge of these determinants and identify genes involved in flowering in sweet cherry. By studying two intraspecific progenies ‘Regina’ × ‘Lapins’ and ‘Regina’ × ‘Garnet’, detection of many quantitative trait loci (QTL) on all linkage groups (LG) has enabled us to confirm the strong involvement of chill requirements in the flowering as well as the complexity of these traits. QTL with major effect was localized on the LG4. In regions covered by all the QTLs controlling flowering date, a hundred candidate genes (CG) for this trait was identified. A subset of these GC was then studied for their expression during development of buds by quantitative PCR (qPCR). In the long term, this work will serve as a basis for the identification and selection of genes that allow obtaining genotypes adapted to future climate conditions.

Anthocyanin-rich peaches, because of their antioxidant properties and their strong attractiveness to consumers, are increasingly considered in French peach varietal innovation programs that integrate plant genomics and classical breeding. In this study, we describe a new blood-flesh trait identified in the ‘Wu Yue Xian’ peach accession from China. ‘Wu Yue Xian’ exhibits a fully red mesocarp during the later stages of fruit development, both with green midrib leaf and normal growth of the tree. This blood-flesh phenotype clearly differs from that determined by a single recessive locus (bf) in ‘Harrow Blood’, a clone showing blood-flesh in both immature and mature fruit associated with red midrib leaf and reduced tree height. We have then provided genetic evidence that blood-flesh phenotype of ‘Wu Yue Xian’ was controlled by a single dominant locus, designated DBF (Dominant Blood-Flesh), in four successive families derived from this accession. A genetic linkage map of the blood-flesh parent (‘D6090’) of the fourth population was constructed, including 102 SSRs spanning a total distance of 562.3 cM in eight linkage groups. Whereas the bf locus is located to linkage group 4, we mapped DBF to the top of linkage group 5, thus proving that DBF and bf loci are not alleles. Among 64 predicted genes in the DBF region (505 kbp), three genes of the dihydroflavonol-4-reductase family were identified as good candidates for the control of the DBF trait. Furthermore, SSR markers flanking DBF, such as AMPP157 and AMPPG178, supply a good basis to implement marker-assisted selection for this trait.

International audience; Phenol is a major pollutant in aquatic ecosystems due to its chemical stability, water solubility and environmental mobility. To date, little is known about the molecular modifications of invertebrates under phenol stress. In the present study, we used Solexa sequencing technology to investigate the transcriptome and differentially expressed genes (DEGs) of midges (Chironomus kiinensis) in response to phenol stress. A total of 51,518,972 and 51,150,832 clean reads in the phenol-treated and control libraries, respectively, were obtained and assembled into 51,014 non-redundant (Nr) consensus sequences. A total of 6,032 unigenes were classified by Gene Ontology (GO), and 18,366 unigenes were categorized into 238 Kyoto Encyclopedia of Genes and Genomes (KEGG) categories. These genes included representatives from almost all functional categories. A total of 10,724 differentially expressed genes (P value

After the rediscovery of the Mendel’s laws, the domesticated European rabbit (Orycolagus cuniculus) has been the objective of pioneering studies on coat colour genetics. However, despite the early role of this species in defining genetic mechanisms determining this phenotypic trait, only recently a few loci have been characterized at the molecular level analysing also in rabbits genes already shown to affect coat colour in mice. We herein investigated the rabbit premelanosome protein (PMEL) gene, also known as melanocyte protein Pmel 17 (PMEL17) or silver (SILV), as mutations in the homologous gene in mice and other species produce phenotypic effects similar to what is observed in the dilute coat colour in rabbit. The rabbit dilute locus is determined by a recessive coat colour mutation that dilutes the black to blue (grey) interacting with the basic colours influenced by the agouti and extension loci. To investigate this candidate gene, we isolated and sequenced cDNAs as well as portions of intronic and exonic regions of the PMEL gene in several rabbits with different coat colours and identified single nucleotide polymorphisms, including several missense mutations. One polymorphism, positioned in intron 7, was genotyped in a family in which there was segregation of the dilute coat colour. The results excluded PMEL as the causative gene for the dilute locus in rabbits, shortening the list of candidate genes that should be analysed to identify the mutation determining this phenotypic trait.

International audience

International audience

L'article est publié par l'American Dairy Science Association; We have previously characterized 2 haplotypes (Fertil+ and Fertil-) of Holstein dairy cows differing in 1 female fertility quantitative trait locus (QTL) located on chromosome 3 (QTL-Fert-F-BTA3) between positions 9.8 and 13.5 cM. This QTL is composed of 124 genes, some of them being involved in metabolism or reproduction. Primiparous Fertil+ and Fertil- cows exhibited 69 and 39% pregnancy rate at first service, respectively. A difference in plasma nonesterified fatty acid concentrations observed between both haplotypes might indicate a difference in adipose tissue mobilization. We compared adipose tissue gene expression in Fertil+ and Fertil- cows during their second lactation, at 2 physiological stages, implying either intense lipid mobilization (1 wk postpartum) or fat storage (5 mo of gestation). We investigated by reverse-transcription quantitative PCR the mRNA gene expression of 5 positional candidate genes located in the QTL-Fert-F-BTA3, as well as 18 other functional candidate genes encoding proteins involved in lipid metabolism and several adipokines. Among them, genes involved in either lipolysis or lipogenesis were chosen as controls because they were previously described in dairy cow adipose tissue. A hierarchical clustering was performed to group genes according to their expression pattern, allowing 2 clusters to be determined. Cluster 1 was composed of genes that were overexpressed during mobilization (ADIPOQ, ADIPOR2, LIPE, FABP4, PLIN1, RARRES, LEPR, and CPT1A) and cluster 2 of genes overexpressed during reconstitution of body reserves (ACACA, FASN, and SCD). Genes belonging to cluster 1 (LIPE, FABP4, PLIN1, and CPT1A) are known to be involved in lipolysis and fatty acid oxidation, and genes belonging to cluster 2 (ACACA, FASN, and SCD) are known to be involved in fatty acid synthesis. The expression of 5 genes from cluster 1 was correlated to plasma nonesterified fatty acid levels and thus to mobilization of body reserves in dairy cows (ADIPOQ, ADIPOR2, LIPE, PLIN1, and FABP4). During the mobilization stage, none of the positional candidate genes belonging to QTL-Fert-F-BTA3 (ADAR, MTX1, SHC1, SPTA1, and PAQR6) showed a difference in expression between the 2 haplotypes. Interestingly, ADIPOQ and ADIPOR2 were the only genes showing a significant mRNA overexpression in Fertil- cows at the mobilization stage. Further studies focusing on plasma adiponectin level and adipokine actions on the ovary are needed to investigate its potential role in dairy cow fertility.