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3. The faba bean pan-transcriptome

Author

Escobar-Herrera, Léandro, Kreplak, Jonathan, Nadzieja, Marcin, Terezol, Morgane, Desmetz, Catherine, Aubert, Grégoire, Uggerhoj Andersen, Stig, ProdInra, Migration, Aarhus University [Aarhus], Agroécologie [Dijon], and Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)

Subjects
[SDV] Life Sciences [q-bio], [SDE] Environmental Sciences, [SDV]Life Sciences [q-bio], [SDE]Environmental Sciences, food and beverages, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SDV.BV] Life Sciences [q-bio]/Vegetal Biology
Abstract

Faba bean (Vicia faba) is a widely adapted nitrogen fixing grain legume that produces seeds with high protein content. It is an agriculturally attractive crop with a good disease resistance profile, but targeted breeding is hampered by the lack of a reference genome and gene set. Here we develop a faba bean gene expression atlas and pan-transcriptome. The pan-transcriptome was generated using data from four different accessions (Hedin, Hiverna, 153b, 2378), including data from both aerial and root tissues. The quality and utility of the pan-transcriptome was assessed by mapping reads from accessions that had not contributed data to the pan-transcriptome. Here, the high mapping rates suggested that the pan-transcriptome represents a comprehensive faba bean reference gene set and that it will be a useful resource for differential gene expression analyses and genome annotation. In addition, the gene expression atlas provides valuable information to support gene function discovery.

Published
2020

4. Studying the interplay between sulfur nutrition and water stress tolerance in pea by proteomics : a focus on seed development and composition

Author

Henriet, Charlotte, Aime, Delphine, Balliau, Thierry, Rossin, Nadia, Serre, Rémy-Félix, Terezol, Morgane, Kreplak, Jonathan, Zivy, Michel, Vernoud, Vanessa, Gallardo, Karine, Agroécologie [Dijon], Université de Bourgogne (UB)-Institut National de la Recherche Agronomique (INRA)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Génétique Quantitative et Evolution - Le Moulon (Génétique Végétale) (GQE-Le Moulon), Centre National de la Recherche Scientifique (CNRS)-AgroParisTech-Université Paris-Sud - Paris 11 (UP11)-Institut National de la Recherche Agronomique (INRA), Génome et Transcriptome - Plateforme Génomique (GeT-PlaGe), Institut National de la Recherche Agronomique (INRA)-Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), and EL Mjiyad, Noureddine

Subjects
[SDE] Environmental Sciences, sulfur nutrition, proteomics, seed composition, pea, [SDE]Environmental Sciences, food and beverages, water stress tolerance, seed development
Abstract

International audience; Water stress and sulfur-deficiency are two constraints increasingly faced by crops due to climatechange and low-input practices. To investigate their interplay in the grain legume pea (Pisum sativumL.), sulfate was depleted at mid-vegetative stage and a moderate 9-day water stress period was imposedduring the early reproductive phase. The combined stress accelerated seed production, lowering yield,one-seed weight and seed number per plant, but rebalanced seed protein composition. In fact, themoderate water stress mitigated the negative effect of sulfur-deficiency on the accumulation of sulfurrichproteins in seeds, probably due to a lower seed sink strength for nitrogen, enabling a readjustmentof the sulfur-poor/sulfur-rich globulin ratio. These results uncovered the importance of sulfur forstabilizing seed yield in pea facing short and moderate water stress episodes, and showed that theadaptive response of sulfur-deprived plants to water stress is much more complicated than a simpleadditive response. Developing seeds were subjected to shotgun proteomics and transcriptomics toadvance our knowledge of the seed response to the single or double stresses. Among the results thatwill be presented is the building of a protein network together with a differential analysis, highlightinghubs potentially implicated in seed development and stress response.

Published
2019

5. Interplay between sulfur nutrition and water stress tolerance in pea : a focus on seed development and composition

Author

Henriet, Charlotte, Aime, Delphine, Terezol, Morgane, Kilandamoko, Anderson, Rossin, Nadia, Combes Soia, Lucie, Labaš, Vladimir, Serre, Rémy-Félix, Prudent, Marion, Kreplak, Jonathan, Vernoud, Vanessa, Gallardo, Karine, Agroécologie [Dijon], Université de Bourgogne (UB)-Institut National de la Recherche Agronomique (INRA)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Physiologie de la reproduction et des comportements [Nouzilly] (PRC), Institut National de la Recherche Agronomique (INRA)-Institut Français du Cheval et de l'Equitation [Saumur]-Université de Tours (UT)-Centre National de la Recherche Scientifique (CNRS), Génome et Transcriptome - Plateforme Génomique (GeT-PlaGe), Institut National de la Recherche Agronomique (INRA)-Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), ICLGG., ProdInra, Migration, Institut National de la Recherche Agronomique (INRA)-Institut Français du Cheval et de l'Equitation [Saumur]-Université de Tours-Centre National de la Recherche Scientifique (CNRS), Université Toulouse III - Paul Sabatier (UT3), and Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3)

Subjects
[SDV] Life Sciences [q-bio], [SDE] Environmental Sciences, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, [SDV.GEN]Life Sciences [q-bio]/Genetics, [SDV]Life Sciences [q-bio], [SDE]Environmental Sciences, food and beverages, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SDV.BV] Life Sciences [q-bio]/Vegetal Biology, [INFO]Computer Science [cs], [SDV.GEN.GA] Life Sciences [q-bio]/Genetics/Animal genetics, [SDV.GEN] Life Sciences [q-bio]/Genetics, [INFO] Computer Science [cs]
Abstract

International audience; Water stress and sulfur-deficiency are two constraints increasingly faced by crops due to climate change and low-input practices. To investigate their interplay in the grain legume pea (Pisum sativum L.), sulfate was depleted at mid-vegetative stage and a moderate 9-day water stress period was imposed during the early reproductive phase. The combined stress accelerated seed production, lowering yield, one-seed weight and seed number per plant, but rebalanced seed globulin composition. In fact, the moderate water stress mitigated the negative effect of sulfur-deficiency on the accumulation of sulfur-rich globulins in seeds, probably due to a lower seed sink strength for nitrogen, enabling a readjustment of the sulfur-poor/sulfur-rich globulin ratio. These results uncovered the importance of sulfur for stabilizing seed yield in pea facing short and moderate water stress episodes, and showed that the adaptive response of sulfur-deprived plants to water stress is much more complicated than a simple additive response. A transcriptome analysis of developing seeds at the end of the combined stress period clearly advanced our knowledge of the seed response to the single or double stresses. Among the results that will be presented is a specific up-regulation of a set of genes in response to the combined stress, indicating the establishment of unique regulatory processes when sulfur-deficiency is combined with water stress and highlighting candidate genes to fine-tune the regulation of globulin synthesis under stressed conditions.

Published
2019

6. Time-series RNA-seq analysis of pea seeds during development under control and drought conditions

Author

Terezol, Morgane, Mazuel, Adrien, Rossin, Nadia, Serre, Rémy-Félix, Kreplak, Jonathan, Vernoud, Vanessa, Agroécologie [Dijon], Université de Bourgogne (UB)-Institut National de la Recherche Agronomique (INRA)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Génome et Transcriptome - Plateforme Génomique (GeT-PlaGe), Institut National de la Recherche Agronomique (INRA)-Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), ProdInra, Migration, Université Toulouse III - Paul Sabatier (UT3), and Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3)

Subjects
[SDV] Life Sciences [q-bio], [SDE] Environmental Sciences, [SDV.GEN]Life Sciences [q-bio]/Genetics, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, [SDV]Life Sciences [q-bio], [SDE]Environmental Sciences, food and beverages, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SDV.BV] Life Sciences [q-bio]/Vegetal Biology, [SDV.GEN] Life Sciences [q-bio]/Genetics, [SDV.GEN.GA] Life Sciences [q-bio]/Genetics/Animal genetics
Abstract

National audience; Pea (Pisum sativum) produces seeds rich in proteins. However, protein content and seed quality can be impacted by environmental factors including drought. Accumulation of seed storage proteins (SSP) during seed filling is a highly regulated process. While proteomics of SSP deposition in pea seeds is well documented, knowledge of the underlying regulatory gene networks, either in control or stress conditions, is lacking. In this study, a RNA-seq based transcriptome analysis of seed development in control and water stress condition was carried out. Developing seeds were collected at six time points, from late embryogenesis to early maturation. RNA-seq was performed on an Illumina Hiseq3000 and reads were mapped on Pisum sativum v1a genome version. A complete RNA-seq workflow analysis including (i) the annotation of new genes using StringTie, (ii) the analysis of unmapped reads (which could represent up to 24% of the total reads in some samples) using RepeatExplorer and Trinity and (iii) the differential expression analysis using Deseq2, will be presented. These data will help us to decipher the transcriptional regulatory network that controls pea seed development, notably during SSP deposition, and how these processes are impacted by drought. This study is funded under the REGULEG ANR Project (ANR-15-CE20-0001-02) coordinated by J. Buitink (INRA, Angers, France)

Published
2019

7. The pan-transcriptome of Vicia faba

Author

Escobar-Herrera, L.A., Kreplak, Jonathan, Nadzieja, M., Terezol, Morgane, Desmetz, Catherine, Aubert, Gregoire, Andersen, S.U., Aarhus University [Aarhus], Agroécologie [Dijon], Université de Bourgogne (UB)-Institut National de la Recherche Agronomique (INRA)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, and ProdInra, Migration

Subjects
[SDV] Life Sciences [q-bio], [SDE] Environmental Sciences, [SDV]Life Sciences [q-bio], [SDE]Environmental Sciences, food and beverages, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SDV.BV] Life Sciences [q-bio]/Vegetal Biology
Abstract

Vicia faba (faba bean) is a nitrogen-fixing protein crop that, in contrast to soya bean, yields well in temperate climates. It is diploid but has a very large genome of ~13 Gb, and genomic resources are currently limited. To provide a high-quality reference gene set and expression atlas, we have carried out RNA-seq of multiple tissues from five faba bean accessions. For each tissue, an assembly was produced using the Trinity software package using both Illumina and PacBio reads. For each accession, the assemblies were then merged to create a more complete reference gene set. The assemblies were of high quality, with more than 95% complete BUSCOs [1] and read mapping rates of ~90%. The assemblies for each accession were then joined to create a comprehensive reference gene set along with an expression atlas describing gene expression patterns across accessions and tissues. These resources will now facilitate gene discovery and characterisation in faba bean and speed up identification of genes associated with important traits including pest and disease resistance and antinutrients such as vicine and convicine.

Published
2019

8. An RNAseq approach towards deciphering mechanisms involved in bruchid tolerance in faba bean

Author

Kreplak, Jonathan, Terezol, Morgane, Desmetz, Catherine, Raffiot, Blandine, Bouchez, Olivier, Marget, Pascal, Burstin, Judith, Aubert, Gregoire, Agroécologie [Dijon], Université de Bourgogne (UB)-Institut National de la Recherche Agronomique (INRA)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Génome et Transcriptome - Plateforme Génomique (GeT-PlaGe), Institut National de la Recherche Agronomique (INRA)-Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Noble Research Institute., Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), and Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse)

Subjects
[SDV.GEN]Life Sciences [q-bio]/Genetics, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, [SDV]Life Sciences [q-bio], [SDE]Environmental Sciences, fungi, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, food and beverages
Abstract

International audience; Broad bean weevil (Bruchus rufimanus) is a major pest of faba bean. Once eggs are laid on the pods, larvae penetrate, develop in the seeds and create damage that affects the quality of the beans. This renders them unsuitable for the human consumption market. Therefore, in the context of reducing pesticide use and in order to develop faba bean varieties resistant to bruchid, the search for tolerant accessions is an important issue. A germplasm screen has identified two accessions with good levels of tolerance, suggesting that these genotypes are less attractive to the insects and/or that their seeds contain compounds toxic for the larvae. In order to understand the underlying molecular mechanisms, we used an RNAseq transcriptomic approach on different plant tissues (leaf, flower, young pod and developing seed) of these two tolerant accessions and one additional sensitive cultivar. As the Vicia faba genome has not yet been sequenced, a de-novo assembly was performed to build a set of genes to be used for differential expression analyses : individual assemblies per tissue and genotype have been done and clustered to eliminate redundancy. A SuperTranscript [1] of 30825 genes (average size of contigs 1945bp) has been obtained with good completeness (97% of BUSCO [2]) representing the transcriptome from the four organs of each of the three genotypes. Differential expression studies using this Unigene have highlighted contrasted response of the three genotypes for specific pathways and will help identifying regulated genes.

Published
2017

9. Les miRNAs jouent un rôle crucial dans la régulation des fonctions cellulaires en particulier en réponse aux contraintes environnementales

Author

Terezol, Morgane, Agroécologie [Dijon], Université de Bourgogne (UB)-Institut National de la Recherche Agronomique (INRA)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Université de Poitiers, and EL Mjiyad, Noureddine

Subjects
[SDV] Life Sciences [q-bio], [SDV]Life Sciences [q-bio]
Published
2016

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