Analyses structurales et fonctionnelles de l'espace génique du chromosome 3B du blé tendre (Triticum aestivum L.)

Genome-wide studies of the bread wheat are a complicated task due to its large size (17 Gb), its allohexaploidy and its high content in repeat sequences (>80%). Using a chromosome-specific approach, the chromosome 3B (995 Mb) was successfully isolated and sequenced leading to the assembly of one pseudomolecule. The work presented in this thesis investigated the impact of the 3B chromosome size on the gene space organization. Production of transcriptomic data was achieved using RNA-Seq approach. The chromosome 3B was annotated and we predicted 7 264 features, including 5 326 full genes and 1 938 pseudogenes. We constructed RNA-Seq libraries for 15 developmental wheat conditions. Using this data we detected expression of 71.4% of the predictions, and 3 692 novel transcribed regions (NTR). We also detected alternative transcripts for 61% of the expressed genes, with 5.8 isoforms on average for one gene. Using these transcriptional data, we highlighted a partitioning of the chromosome 3B gene space. Indeed, transcription was found all along the chromosome, but genes were organized according to an increasing density gradient along the centromere-telomere axis. Based on recombination profile, we segmented the chromosome in 3 major regions: R1, R2 and R3. The region R2 was identified with low or no recombination rate corresponding to the centromeric and peri-centromeric regions (647 Mb). The regions R1 and R3 were associated with a higher recombination rate, both localized on the distal part of the short arm (58 Mb) and the long arm (69 Mb) respectively, where the recombination rate is higher. All three regions showed distinct level and specificity of gene expression as well as unique gene structure (variation size, exon number, intron size). Indeed, genes expressed in a specific condition and with a small number of alternatives transcripts were localized on regions R1 and R3. We showed that two evolutionary model could explain the link between gene structure and the level/specificity of expression : “selection for economy” and “genome design”. In conclusion, a transcriptomic studies was achieved along the 3B chromosome for the first time. This study demonstrated a relationship between gene characteristics (structure, expression level, expression specificity and evolution) and the chromosome 3B organization. Future pseudomolecule assemblies will help us to assess the structural organization of these chromosomes. In order to better understand the cellular mechanisms of gene expression, an epigenomic study of the 3B chromosome was started.De par sa taille (17 Gb), la complexité de son génome (allohexaploïde) ainsi que la forte proportion d’éléments répétés (>80%), l’étude du génome de blé tendre est une tâche particulièrement complexe et s’est souvent retrouvée confrontée aux limites technologies. Grâce une approche de tri de chromosomes, le chromosome 3B (995 Mb) a pu être isolé et séquencé. Ces données ont permis la construction d’une pseudomolécule. Mes travaux de thèse se sont basés sur des données de transcriptomique produites avec une approche RNA-Seq, afin d’investiguer l’impact de la taille de ce chromosome sur l’organisation de l’espace génique. L’annotation du chromosome 3B a permis de mettre en évidence : 5 326 gènes et 1 938 pseudogènes. L’analyse des librairies RNA-Seq pour 15 conditions de développement a permis de mettre en évidence l’expression de 71 % des gènes annotés, ainsi que 3 692 régions nouvellement transcrites (NTR). Nous avons aussi pu détecter des transcrits alternatifs pour 61% des gènes exprimés (en moyenne 6 isoformes). Nous avons donc pu mettre en évidence une structuration de l’espace génique pour le chromosome 3B. En effet, la transcription est répartie sur tout le chromosome, cependant les gènes sont organisés selon un gradient de densité croissant sur l’axe centromère-télomère. En nous basant sur le profil des données de recombinaison, nous avons divisé le chromosome en 3 régions : R1, R2 et R3. La région R2 correspondant à la région centrale du chromosome (647 Mb) où le taux de recombinaison est très faible voir absent. Les régions R1 (58 Mb) et R3 (69 Mb) correspondent respectivement aux parties distales du bras court et du bras long du chromosome, où le taux de recombinaison est le plus fort. Ces trois régions diffèrent par leur niveau et leur spécificité d'expression, ainsi que par leur structure génique (nombre d'exons, taille des introns …). En effet, les gènes ayant une expression tissu-spécifique, ainsi qu’un faible nombre de transcrits alternatifs sont retrouvés dans les régions R1 et R3. Deux modèles peuvent expliquer le lien observé entre la structure des gènes et leur niveau/spécificité d’expression : le modèle de la sélection pour l’économie et le modèle dessin génomique. En conclusion, ce travail a montré et ce, pour la première fois à l’échelle d’un chromosome entier de blé, l’impact de la taille du chromosome sur l’organisation ; mettant en relation la structure des gènes, leur niveau d’expression, leur spécificité d’expression, ainsi que leur nature évolutive. L’assemblage ainsi que l’annotation de pseudomolécules des autres chromosomes permettra de mettre en évidence si cette structure est conservée. Afin de mieux comprendre les mécanismes cellulaires impliqués dans la régulation de l’expression des gènes, une étude du paysage épigénomique a été engagée

Wheat transcriptomic responses to extended feeding by wheat curl mites

The economic importance of wheat and its contribution to human and livestock diets has been already demonstrated. However, wheat production is impacted by pests that induce yield reductions. Among these pests, wheat curl mite (WCM, Aceria tosichella Keifer) impacts wheat all around the world. WCM are tiny pests that feed within the whorl of developing leaves, and their feeding causes leaf curling by preventing them from unfurling. The curling of the leaves provides a protective niche for the WCM. Additionally, WCM are also the vector of serious viruses in wheat. Little is known regarding the impact of the WCM on wheat transcriptome, and to date, only one article has been published describing the wheat transcriptomic changes after 1 day of WCM feeding. To better understand the wheat transcriptome variation after extended feeding by WCM [10 days post infestation (dpi)], we used an RNA-seq approach. We collected WCM-infested and uninfested leaves from two wheat cultivars: Byrd (WCM resistant) and Settler CL (WCM susceptible) at 10 dpi. Our transcriptomic analysis revealed the common and specific transcriptomic variations in WCM resistant and susceptible wheat cultivars, chromosome 3D specific location of the differentially expressed genes with functions involved in defense and stress response, and also identified the gene functions related to lipid signaling and membrane integrity, and phytohormone pathways potentially contributing to WCM resistance. Collectively, our study provides important insights on wheat defense mechanisms against WCM after extended feeding

Temporal transcriptomic profiling elucidates sorghum defense mechanisms against sugarcane aphids

Background The sugarcane aphid (SCA; Melanaphis sacchari) has emerged as a key pest on sorghum in the United States that feeds from the phloem tissue, drains nutrients, and inflicts physical damage to plants. Previously, it has been shown that SCA reproduction was low and high on sorghum SC265 and SC1345 plants, respectively, compared to RTx430, an elite sorghum male parental line (reference line). In this study, we focused on identifying the defense-related genes that confer resistance to SCA at early and late time points in sorghum plants with varied levels of SCA resistance. Results We used RNA-sequencing approach to identify the global transcriptomic responses to aphid infestation on RTx430, SC265, and SC1345 plants at early time points 6, 24, and 48 h post infestation (hpi) and after extended period of SCA feeding for 7 days. Aphid feeding on the SCA-resistant line upregulated the expression of 3827 and 2076 genes at early and late time points, respectively, which was relatively higher compared to RTx430 and SC1345 plants. Co-expression network analysis revealed that aphid infestation modulates sorghum defenses by regulating genes corresponding to phenylpropanoid metabolic pathways, secondary metabolic process, oxidoreductase activity, phytohormones, sugar metabolism and cell wall-related genes. There were 187 genes that were highly expressed during the early time of aphid infestation in the SCA-resistant line, including genes encoding leucine-rich repeat (LRR) proteins, ethylene response factors, cell wall-related, pathogenesis-related proteins, and disease resistance-responsive dirigent-like proteins. At 7 days post infestation (dpi), 173 genes had elevated expression levels in the SCA-resistant line and were involved in sucrose metabolism, callose formation, phospholipid metabolism, and proteinase inhibitors. Conclusions In summary, our results indicate that the SCA-resistant line is better adapted to activate early defense signaling mechanisms in response to SCA infestation because of the rapid activation of the defense mechanisms by regulating genes involved in monolignol biosynthesis pathway, oxidoreductase activity, biosynthesis of phytohormones, and cell wall composition. This study offers further insights to better understand sorghum defenses against aphid herbivory

Small-scale gene duplications played a major role in the recent evolution of wheat chromosome 3B

Background: Bread wheat is not only an important crop, but its large (17 Gb), highly repetitive, and hexaploid genome makes it a good model to study the organization and evolution of complex genomes. Recently, we produced a high quality reference sequence of wheat chromosome 3B (774 Mb), which provides an excellent opportunity to study the evolutionary dynamics of a large and polyploid genome, specifically the impact of single gene duplications.Results: We find that 27 % of the 3B predicted genes are non-syntenic with the orthologous chromosomes of Brachypodium distachyon, Oryza sativa, and Sorghum bicolor, whereas, by applying the same criteria, non-syntenic genes represent on average only 10 % of the predicted genes in these three model grasses. These non-syntenic genes on 3B have high sequence similarity to at least one other gene in the wheat genome, indicating that hexaploid wheat has undergone massive small-scale interchromosomal gene duplications compared to other grasses. Insertions of non-syntenic genes occurred at a similar rate along the chromosome, but these genes tend to be retained at a higher frequency in the distal, recombinogenic regions. The ratio of non-synonymous to synonymous substitution rates showed a more relaxed selection pressure for non-syntenic genes compared to syntenic genes, and gene ontology analysis indicated that non-syntenic genes may be enriched in functions involved in disease resistance.Conclusion: Our results highlight the major impact of single gene duplications on the wheat gene complement and confirm the accelerated evolution of the Triticeae lineage among grasses

Co-Transcriptomic Analysis of the Maize–Western Corn Rootworm Interaction

The Western corn rootworm (WCR; Diabrotica virgifera virgifera) is an economically important belowground pest of maize. Belowground feeding by WCR is damaging because it weakens the roots system, diminishes nutrient uptake, and creates entry points for fungal and bacterial pathogens and increases lodging, all of which can significantly suppress maize yields. Previously, it was demonstrated that belowground herbivory can trigger plant defense responses in the roots and the shoots, thereby impacting intraplant communication. Although several aspects of maize-WCR interactions have been reported, co-transcriptomic remodeling in the plant and insect are yet to be explored. We used a maize genotype, Mp708, that is resistant to a large guild of herbivore pests to study the underlying plant defense signaling network between below and aboveground tissues. We also evaluated WCR compensatory transcriptome responses. Using RNA-seq, we profiled the transcriptome of roots and leaves that interacted with WCR infestation up to 5 days post infestation (dpi). Our results suggest that Mp708 shoots and roots had elevated constitutive and WCR-feeding induced expression of genes related to jasmonic acid and ethylene pathways, respectively, before and after WCR feeding for 1 and 5 days. Similarly, extended feeding by WCR for 5 days in Mp708 roots suppressed many genes involved in the benzoxazinoid pathway, which is a major group of indolederived secondary metabolites that provides resistance to several insect pests in maize. Furthermore, extended feeding by WCR on Mp708 roots revealed several genes that were downregulated in WCR, which include genes related to proteolysis, neuropeptide signaling pathway, defense response, drug catabolic process, and hormone metabolic process. These findings indicate a dynamic transcriptomic dialog between WCR and WCR-infested maize plants

Aboveground Herbivory Influences Belowground Defense Responses in Maize

The European corn borer (ECB; Ostrinia nubilalis) is an economically damaging insect pest of maize (Zea mays L.), an important cereal crop widely grown globally. Among inbred lines, the maize genotype Mp708 has shown resistance to diverse herbivorous insects, although several aspects of the defense mechanisms of Mp708 plants are yet to be explored. Here, the changes in root physiology arising from short-term feeding by ECB on the shoot tissues of Mp708 plants was evaluated directly using transcriptomics, and indirectly by monitoring changes in growth of western corn rootworm (WCR; Diabrotica virgifera virgifera) larvae. Mp708 defense responses negatively impacted both ECB and WCR larval weights, providing evidence for changes in root physiology in response to ECB feeding on shoot tissues. There was a significant downregulation of genes in the root tissues following short-term ECB feeding, including genes needed for direct defense (e.g., proteinase inhibitors and chitinases). Our transcriptomic analysis also revealed specific regulation of the genes involved in hormonal and metabolite pathways in the roots of Mp708 plants subjected to ECB herbivory. These data provide support for the long-distance signaling-mediated defense in Mp708 plants and suggest that altered metabolite profiles of roots in response to ECB feeding of shoots likely negatively impacted WCR growth

Early risk factors of overweight developmental trajectories during middle childhood

Background Research is needed to identify early life risk factors associated with different developmental paths leading to overweight by adolescence. Objectives To model heterogeneity in overweight development during middle childhood and identify factors associated with differing overweight trajectories. Methods Data was drawn from the Quebec Longitudinal Study of Child Development (QLSCD; 1998- 2010). Trained research assistants measured height and weight according to a standardized protocol and conducted yearly home interviews with the child’s caregiver (mother in 98% of cases). Information on several putative early life risk factors for the development of overweight were obtained, including factors related to the child’s perinatal, early behavioral family and social environment. Group-based trajectories of the probability of overweight (6- 12 years) were identified with a semiparametric method (n=1678). Logistic regression analyses were used to identify early risk factors (5 months- 5 years) associated with each trajectory. Results Three trajectories of overweight were identified: “early-onset overweight” (11.0 %), “lateonset overweight” (16.6%) and “never overweight” (72.5%). Multinomial analyses indicated that children in the early and late-onset group, compared to the never overweight group, had 3 common types of risk factors: parental overweight, preschool overweight history, and large size for gestational age. Maternal overprotection (OR= 1.12, CI: 1.01-1.25), short nighttime sleep duration (OR=1.66, CI: 1.07-2.57), and immigrant status (OR=2.01, CI: 1.05-3.84) were factors specific to the early-onset group. Finally, family food insufficiency (OR=1.81, CI: 1.00-3.28) was weakly associated with membership in the late-onset trajectory group. Conclusions The development of overweight in childhood follows two different trajectories, which have common and distinct risk factors that could be the target of early preventive interventions

Phosphate Deficiency Negatively Affects Early Steps of the Symbiosis between Common Bean and Rhizobia

Phosphate (Pi) deficiency reduces nodule formation and development in different legume species including common bean. Despite significant progress in the understanding of the genetic responses underlying the adaptation of nodules to Pi deficiency, it is still unclear whether this nutritional deficiency interferes with the molecular dialogue between legumes and rhizobia. If so, what part of the molecular dialogue is impaired? In this study, we provide evidence demonstrating that Pi deficiency negatively affects critical early molecular and physiological responses that are required for a successful symbiosis between common bean and rhizobia. We demonstrated that the infection thread formation and the expression of PvNSP2, PvNIN, and PvFLOT2, which are genes controlling the nodulation process were significantly reduced in Pi-deficient common bean seedlings. In addition, whole-genome transcriptional analysis revealed that the expression of hormones-related genes is compromised in Pi-deficient seedlings inoculated with rhizobia. Moreover, we showed that regardless of the presence or absence of rhizobia, the expression of PvRIC1 and PvRIC2, two genes participating in the autoregulation of nodule numbers, was higher in Pi-deficient seedlings compared to control seedlings. The data presented in this study provides a mechanistic model to better understand how Pi deficiency impacts the early steps of the symbiosis between common bean and rhizobia