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21 results on '"Sandrine Arribat"'

1. Identification of new potential molecular actors related to fiber quality in flax through Omics

Author

Malika Chabi, Estelle Goulas, Dmitry Galinousky, Anne-Sophie Blervacq, Anca Lucau-Danila, Godfrey Neutelings, Sébastien Grec, Arnaud Day, Brigitte Chabbert, Katharina Haag, Jörg Müssig, Sandrine Arribat, Sébastien Planchon, Jenny Renaut, and Simon Hawkins

Subjects
flax (Linum usitatissimum L.), proteomics, transcriptomics, cell wall, fiber, retting, Plant culture, SB1-1110
Abstract

One of the biggest challenges for a more widespread utilization of plant fibers is to better understand the different molecular factors underlying the variability in fineness and mechanical properties of both elementary and scutched fibers. Accordingly, we analyzed genome-wide transcription profiling from bast fiber bearing tissues of seven different flax varieties (4 spring, 2 winter fiber varieties and 1 winter linseed) and identified 1041 differentially expressed genes between varieties, of which 97 were related to cell wall metabolism. KEGG analysis highlighted a number of different enriched pathways. Subsequent statistical analysis using Partial Least-Squares Discriminant Analysis showed that 73% of the total variance was explained by the first 3 X-variates corresponding to 56 differentially expressed genes. Calculation of Pearson correlations identified 5 genes showing a strong correlation between expression and morphometric data. Two-dimensional gel proteomic analysis on the two varieties showing the most discriminant and significant differences in morphometrics revealed 1490 protein spots of which 108 showed significant differential abundance. Mass spectrometry analysis successfully identified 46 proteins representing 32 non-redundant proteins. Statistical clusterization based on the expression level of genes corresponding to the 32 proteins showed clear discrimination into three separate clusters, reflecting the variety type (spring-/winter-fiber/oil). Four of the 32 proteins were also highly correlated with morphometric features. Examination of predicted functions for the 9 (5 + 4) identified genes highlighted lipid metabolism and senescence process. Calculation of Pearson correlation coefficients between expression data and retted fiber mechanical measurements (strength and maximum force) identified 3 significantly correlated genes. The genes were predicted to be connected to cell wall dynamics, either directly (Expansin-like protein), or indirectly (NAD(P)-binding Rossmann-fold superfamily protein). Taken together, our results have allowed the identification of molecular actors potentially associated with the determination of both in-planta fiber morphometrics, as well as ex-planta fiber mechanical properties, both of which are key parameters for elementary fiber and scutched fiber quality in flax.

Published
2023
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3. Population genomics of apricots unravels domestication history and adaptive events

Author

Alexis Groppi, Shuo Liu, Amandine Cornille, Stéphane Decroocq, Quynh Trang Bui, David Tricon, Corinne Cruaud, Sandrine Arribat, Caroline Belser, William Marande, Jérôme Salse, Cécile Huneau, Nathalie Rodde, Wassim Rhalloussi, Stéphane Cauet, Benjamin Istace, Erwan Denis, Sébastien Carrère, Jean-Marc Audergon, Guillaume Roch, Patrick Lambert, Tetyana Zhebentyayeva, Wei-Sheng Liu, Olivier Bouchez, Céline Lopez-Roques, Rémy-Félix Serre, Robert Debuchy, Joseph Tran, Patrick Wincker, Xilong Chen, Pierre Pétriacq, Aurélien Barre, Macha Nikolski, Jean-Marc Aury, Albert Glenn Abbott, Tatiana Giraud, and Véronique Decroocq

Subjects
Science
Abstract

The evolutionary and domestication history of apricots is poorly understood. Here, the authors provide four apricot high-quality genome assemblies, the genomes of 578 accessions from natural and cultivated populations, and show that Chinese and European apricots constitute two different gene pools, resulting from independent domestication events.

Published
2021
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4. Cantaloupe melon genome reveals 3D chromatin features and structural relationship with the ancestral cucurbitaceae karyotype

Author

Clement Pichot, Anis Djari, Joseph Tran, Marion Verdenaud, William Marande, Cecile Huneau, Veronique Gautier, David Latrasse, Sandrine Arribat, Vivien Sommard, Christelle Troadec, Charles Poncet, Mohammed Bendahmane, Judit Szecsi, Catherine Dogimont, Jerome Salse, Moussa Benhamed, Mohamed Zouine, Adnane Boualem, and Abdelhafid Bendahmane

Subjects
genomics, omics, plant biology, plant evolution, Science
Abstract

Summary: Cucumis melo displays a large diversity of horticultural groups with cantaloupe melon the most cultivated type. Using a combination of single-molecule sequencing, 10X Genomics link-reads, high-density optical and genetic maps, and chromosome conformation capture (Hi-C), we assembled a chromosome scale C. melo var. cantalupensis Charentais mono genome. Integration of RNA-seq, MeDip-seq, ChIP-seq, and Hi-C data revealed a widespread compartmentalization of the melon genome, segregating constitutive heterochromatin and euchromatin. Genome-wide comparative and evolutionary analysis between melon botanical groups identified Charentais mono genome increasingly more divergent from Harukei-3 (reticulatus), Payzawat (inodorus), and HS (ssp. agrestis) genomes. To assess the paleohistory of the Cucurbitaceae, we reconstructed the ancestral Cucurbitaceae karyotype and compared it to sequenced cucurbit genomes. In contrast to other species that experienced massive chromosome shuffling, melon has retained the ancestral genome structure. We provide comprehensive genomic resources and new insights in the diversity of melon horticultural groups and evolution of cucurbits.

Published
2022
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5. Fonio millet genome unlocks African orphan crop diversity for agriculture in a changing climate

Author

Michael Abrouk, Hanin Ibrahim Ahmed, Philippe Cubry, Denisa Šimoníková, Stéphane Cauet, Yveline Pailles, Jan Bettgenhaeuser, Liubov Gapa, Nora Scarcelli, Marie Couderc, Leila Zekraoui, Nagarajan Kathiresan, Jana Čížková, Eva Hřibová, Jaroslav Doležel, Sandrine Arribat, Hélène Bergès, Jan J. Wieringa, Mathieu Gueye, Ndjido A. Kane, Christian Leclerc, Sandrine Causse, Sylvie Vancoppenolle, Claire Billot, Thomas Wicker, Yves Vigouroux, Adeline Barnaud, and Simon G. Krattinger

Subjects
Science
Abstract

Fonio millet is a fast growing orphan cereal crop with a great potential for dryland agriculture. Here, the authors report chromosome-scale reference genome assembly and population genomic resources to shed light on genetic diversity, population structure and domestication of fonio millet.

Published
2020
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6. High-quality genome sequence of white lupin provides insight into soil exploration and seed quality

Author

Bárbara Hufnagel, André Marques, Alexandre Soriano, Laurence Marquès, Fanchon Divol, Patrick Doumas, Erika Sallet, Davide Mancinotti, Sébastien Carrere, William Marande, Sandrine Arribat, Jean Keller, Cécile Huneau, Thomas Blein, Delphine Aimé, Malika Laguerre, Jemma Taylor, Veit Schubert, Matthew Nelson, Fernando Geu-Flores, Martin Crespi, Karine Gallardo, Pierre-Marc Delaux, Jérôme Salse, Hélène Bergès, Romain Guyot, Jérôme Gouzy, and Benjamin Péret

Subjects
Science
Abstract

White lupin is an annual crop cultivated for protein rich seeds and can produce cluster roots for efficient phosphate acquisition. Here, the authors generate high quality genome assemblies of a cultivated accession, a landrace, and a wild relative and provides insight into soil exploration and seed quality.

Published
2020
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7. Molecular Epidemiology of Bacterial Wilt in the Madagascar Highlands Caused by Andean (Phylotype IIB-1) and African (Phylotype III) Brown Rot Strains of the Ralstonia solanacearum Species Complex

Author

Santatra Ravelomanantsoa, Christian Vernière, Adrien Rieux, Laurent Costet, Frédéric Chiroleu, Sandrine Arribat, Gilles Cellier, Olivier Pruvost, Stéphane Poussier, Isabelle Robène, Fabien Guérin, and Philippe Prior

Subjects
Ralstonia solanacearum, genetic diversity, MLVA, population structure, Madagascar, Plant culture, SB1-1110
Abstract

The Ralstonia solanacearum species complex (RSSC) is a highly diverse cluster of bacterial strains found worldwide, many of which are destructive and cause bacterial wilt (BW) in a wide range of host plants. In 2009, potato production in Madagascar was dramatically affected by several BW epidemics. Controlling this disease is critical for Malagasy potato producers. The first important step toward control is the characterization of strains and their putative origins. The genetic diversity and population structure of the RSSC were investigated in the major potato production areas of the Highlands. A large collection of strains (n = 1224) was assigned to RSSC phylotypes based on multiplex polymerase chain reaction (PCR). Phylotypes I and III have been present in Madagascar for a long time but rarely associated with major potato BW outbreaks. The marked increase of BW prevalence was found associated with phylotype IIB sequevar 1 (IIB-1) strains (n = 879). This is the first report of phylotype IIB-1 strains in Madagascar. In addition to reference strains, epidemic IIB-1 strains (n = 255) were genotyped using the existing MultiLocus Variable-Number Tandem Repeat Analysis (MLVA) scheme RS2-MLVA9, producing 31 haplotypes separated into two related clonal complexes (CCs). One major CC included most of the worldwide haplotypes distributed across wide areas. A regional-scale investigation suggested that phylotype IIB-1 strains were introduced and massively spread via latently infected potato seed tubers. Additionally, the genetic structure of phylotype IIB-1 likely resulted from a bottleneck/founder effect. The population structure of phylotype III, described here for the first time in Madagascar, exhibited a different pattern. Phylotype III strains (n = 217) were genotyped using the highly discriminatory MLVA scheme RS3-MLVA16. High genetic diversity was uncovered, with 117 haplotypes grouped into 11 CCs. Malagasy phylotype III strains were highly differentiated from continental African strains, suggesting no recent migration from the continent. Overall, population structure of phylotype III involves individual small CCs that correlate to restricted geographic areas in Madagascar. The evidence suggests, if at all, that African phylotype III strains are not efficiently transmitted through latently infected potato seed tubers.

Published
2018
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8. Tube-Wise Diagnostic Microarray for the Multiplex Characterization of the Complex Plant Pathogen Ralstonia solanacearum

Author

Gilles Cellier, Sandrine Arribat, Frédéric Chiroleu, Philippe Prior, and Isabelle Robène

Subjects
Ralstonia solanacearum, microarray, ArrayTube, multiplexing, diagnostic, Plant culture, SB1-1110
Abstract

Ralstonia solanacearum is a well-known agricultural and ecological threat worldwide. The complexity of the R. solanacearum species complex (Rssc) represents a challenge for the accurate characterization of epidemiological strains by official services and research laboratories. The majority of protocols only focus on a narrow range of strains; however, this species complex includes strains that represent major constraints and are under strict regulation. The main drawback associated with the current methods of detecting and characterizing Rssc strains is their reliance on combining different protocols to properly characterize the strains at the ecotype level, which require time and money. Therefore, we used microarray technology (ArrayTube) to develop a standard protocol, which characterizes 17 major groups of interest in the Rssc, in a single multiplex reaction. These 17 majors groups are linked with a phylogenetic assignation (phylotypes, sequevars), but also with an ecotype assignation associated with a range of hosts (e.g., brown rot, Moko). Probes were designed with a 50-mer length constraint and thoroughly evaluated for any flaws or secondary structures. The strains are characterized based on a DNA extraction from pure culture. Validation data showed strong intra-repeatability, inter-repeatability, and reproducibility as well as good specificity. A hierarchical analysis of the probe groups is suitable for an accurate characterization. Compared with single marker detection tests, the method described in this paper addresses efficiently the issue of combining several tests by testing a large number of phylogenetic markers in a single reaction assay. This custom microarray (RsscAT) represents a significant improvement in the epidemiological monitoring of Rssc strains worldwide, and it has the potential to provide insights for phylogenetic incongruence of Rssc strains based on the host of isolation and may be used to indicate potentially emergent strains.

Published
2017
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9. Is gene transcription involved in seed dry after-ripening?

Author

Patrice Meimoun, Ernest Mordret, Nicolas B Langlade, Sandrine Balzergue, Sandrine Arribat, Christophe Bailly, and Hayat El-Maarouf-Bouteau

Subjects
Medicine, Science
Abstract

Orthodox seeds are living organisms that survive anhydrobiosis and may display dormancy, an inability to germinate at harvest. Seed germination potential can be acquired during a prolonged period of dry storage called after-ripening. The aim of this work was to determine if gene transcription is an underlying regulatory mechanism for dormancy alleviation during after-ripening. To identify changes in gene transcription strictly associated with the acquisition of germination potential but not with storage, we used seed storage at low relative humidity that maintains dormancy as control. Transcriptome profiling was performed using DNA microarray to compare change in gene transcript abundance between dormant (D), after-ripened non-dormant (ND) and after-ripened dormant seeds (control, C). Quantitative real-time polymerase chain reaction (qPCR) was used to confirm gene expression. Comparison between D and ND showed the differential expression of 115 probesets at cut-off values of two-fold change (p

Published
2014
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10. A gene-phenotype network based on genetic variability for drought responses reveals key physiological processes in controlled and natural environments.

Author

David Rengel, Sandrine Arribat, Pierre Maury, Marie-Laure Martin-Magniette, Thibaut Hourlier, Marion Laporte, Didier Varès, Sébastien Carrère, Philippe Grieu, Sandrine Balzergue, Jérôme Gouzy, Patrick Vincourt, and Nicolas B Langlade

Subjects
Medicine, Science
Abstract

Identifying the connections between molecular and physiological processes underlying the diversity of drought stress responses in plants is key for basic and applied science. Drought stress response involves a large number of molecular pathways and subsequent physiological processes. Therefore, it constitutes an archetypical systems biology model. We first inferred a gene-phenotype network exploiting differences in drought responses of eight sunflower (Helianthus annuus) genotypes to two drought stress scenarios. Large transcriptomic data were obtained with the sunflower Affymetrix microarray, comprising 32423 probesets, and were associated to nine morpho-physiological traits (integrated transpired water, leaf transpiration rate, osmotic potential, relative water content, leaf mass per area, carbon isotope discrimination, plant height, number of leaves and collar diameter) using sPLS regression. Overall, we could associate the expression patterns of 1263 probesets to six phenotypic traits and identify if correlations were due to treatment, genotype and/or their interaction. We also identified genes whose expression is affected at moderate and/or intense drought stress together with genes whose expression variation could explain phenotypic and drought tolerance variability among our genetic material. We then used the network model to study phenotypic changes in less tractable agronomical conditions, i.e. sunflower hybrids subjected to different watering regimes in field trials. Mapping this new dataset in the gene-phenotype network allowed us to identify genes whose expression was robustly affected by water deprivation in both controlled and field conditions. The enrichment in genes correlated to relative water content and osmotic potential provides evidence of the importance of these traits in agronomical conditions.

Published
2012
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11. A strongly improved assembly of the pearl millet reference genome using Oxford Nanopore long reads and optical mapping

Author

Marine Salson, Julie Orjuela, Cédric Mariac, Leïla Zekraouï, Marie Couderc, Sandrine Arribat, Nathalie Rodde, Adama Faye, Ndjido A. Kane, Christine Tranchant-Dubreuil, Yves Vigouroux, and Cécile Berthouly-Salazar

Abstract

Pearl millet (Pennisetum glaucum(L.)) R. Br. syn.Cenchrus americanus(L.) Morrone) is an important crop in South Asia and sub-Saharan Africa which contributes to ensure food security. Its genome has an estimated size of 1.76 Gb and displays a high level of repetitiveness above 80%. A first assembly was previously obtained for the Tift 23D2B1-P1-P5 cultivar genotype using short-read sequencing technologies. This assembly is however incomplete and fragmented with around 200 Mb unplaced on chromosomes. We report here an improved quality assembly of the pearl millet Tift 23D2B1-P1-P5 cultivar genotype obtained with an approach combining Oxford Nanopore long reads and Bionano Genomics optical maps. This strategy allowed us to add around 200 Mb at the chromosome-level assembly. Moreover we strongly improved continuity in the order of the contigs and scaffolds wihtin the chromosomes, particularly in the centromeric regions. Notably, we added more than 100 Mb around the centromeric region on chromosome 7. This new assembly also displayed a higher gene completeness with a complete BUSO score of 98.4% using the Poales database. This more complete and higher quality assembly of the Tift 23D2B1-P1-P5 genotype now available to the community will help in the development of research on the role of structural variants, and more broadly in genomics studies and the breeding of pearl millet.

Published
2023

12. Long-read and chromosome-scale assembly of the hexaploid wheat genome achieves high resolution for research and breeding

Author

Patrick Wincker, Stefan Engelen, Nathan Papon, David Grimbichler, Marion Ranoux, Jean-Marc Aury, Frédéric Choulet, Adriana Alberti, Sandrine Arribat, Etienne Paux, Hélène Rimbert, Isabelle Dufau, Pauline Lasserre-Zuber, Benjamin Istace, Caroline Belser, Philippe Leroy, Cécile Monat, Corinne Cruaud, Arnaud Bellec, Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Clermont Auvergne (UCA), CEA- Saclay (CEA), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Centre National de Ressources Génomiques Végétales (CNRGV), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Mésocentre Clermont Auvergne, Université Clermont Auvergne (UCA), GenoscopeCommissariat a l'Energie Atomique et aux Energies Alternatives (CEA)SRESRI/Region Auvergne-Rhone-Alpes, and ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010)

Subjects
[SDV]Life Sciences [q-bio], Health Informatics, haplotype characterization, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Computational biology, Breeding, Biology, Genome, Chromosomes, [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, long-reads, wheat, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, hexaploid genome, Triticum, Selection (genetic algorithm), Whole genome sequencing, Chinese spring, food and beverages, Chromosome, Sequence Analysis, DNA, introgressions, Computer Science Applications, nanopore sequencing, genome assembly, Lower cost, Nanopore sequencing, Reference genome
Abstract

Background The sequencing of the wheat (Triticum aestivum) genome has been a methodological challenge for many years owing to its large size (15.5 Gb), repeat content, and hexaploidy. Many initiatives aiming at obtaining a reference genome of cultivar Chinese Spring have been launched in the past years and it was achieved in 2018 as the result of a huge effort to combine short-read sequencing with many other resources. Reference-quality genome assemblies were then produced for other accessions, but the rapid evolution of sequencing technologies offers opportunities to reach high-quality standards at lower cost. Results Here, we report on an optimized procedure based on long reads produced on the Oxford Nanopore Technology PromethION device to assemble the genome of the French bread wheat cultivar Renan. Conclusions We provide the most contiguous chromosome-scale assembly of a bread wheat genome to date. Coupled with an annotation based on RNA-sequencing data, this resource will be valuable for the crop community and will facilitate the rapid selection of agronomically important traits. We also provide a framework to generate high-quality assemblies of complex genomes using ONT.

Published
2021

13. Population genomics of apricots unravels domestication history and adaptive events

Author

Patrick Wincker, Corinne Cruaud, William Marande, Guillaume Roch, Amandine Cornille, Nathalie Rodde, Jean-Marc Aury, Robert Debuchy, Quynh Trang Bui, David Tricon, Pierre Pétriacq, Jérôme Salse, Rémy Félix Serre, Sandrine Arribat, Tatiana Giraud, Alexis Groppi, Erwan Denis, Wassim Rhalloussi, Céline Lopez-Roques, Véronique Decroocq, Olivier Bouchez, Shuo Liu, Macha Nikolski, Jean Marc Audergon, Sébastien Carrère, Xilong Chen, Patrick Lambert, Caroline Belser, Cecile Huneau, Stéphane Decroocq, Tetyana Zhebentyayeva, Stéphane Cauet, Weisheng Liu, Joseph Tran, Benjamin Istace, Albert G. Abbott, Aurélien Barré, Centre de Bioinformatique de Bordeaux (CBIB), CGFB, Institut de biochimie et génétique cellulaires (IBGC), Université Bordeaux Segalen - Bordeaux 2-Centre National de la Recherche Scientifique (CNRS), Biologie du fruit et pathologie (BFP), Université Bordeaux Segalen - Bordeaux 2-Université Sciences et Technologies - Bordeaux 1-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Research Institute of Pomology (RIP CAAS), Chinese Academy of Agricultural Sciences (CAAS), Génétique Quantitative et Evolution - Le Moulon (Génétique Végétale) (GQE-Le Moulon), AgroParisTech-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Génomique métabolique (UMR 8030), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Centre National de Ressources Génomiques Végétales (CNRGV), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Clermont Auvergne (UCA), Laboratoire des interactions plantes micro-organismes (LIPM), Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Génétique et Amélioration des Fruits et Légumes (GAFL), CEP Innovation, The Schatz Center for Tree Molecular Genetics,Department of Ecosystem Science and Management, The Pennsylvania State University, Génome et Transcriptome - Plateforme Génomique ( GeT-PlaGe), 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)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Ecophysiologie et Génomique Fonctionnelle de la Vigne (UMR EGFV), Université de Bordeaux (UB)-Institut des Sciences de la Vigne et du Vin (ISVV)-Ecole Nationale Supérieure des Sciences Agronomiques de Bordeaux-Aquitaine (Bordeaux Sciences Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Forest Health Research and Education Center,University of Kentucky, (FHC), Ecologie Systématique et Evolution (ESE), AgroParisTech-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), ANR-11-CHEX-0002,ABRIWG,Génomique comparative et fonctionnelle de la résistance à la sharka et des besoins en froid chez les arbres fruitiers à noyaux(2011), Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Laboratoire des Interactions Plantes Microbes Environnement (LIPME), Pennsylvania State University (Penn State), Penn State System, Liaoning Institute of Pomology, 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), University of Kentucky (UK), GET-PACBIO program (« Programme opérationnel FEDER-FSEMIDI-PYRENEES ET GARONNE 2014-2020 »), ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), Gauthier, Muriel, Organisation et montée en puissance d'une Infrastructure Nationale de Génomique - - France-Génomique2010 - ANR-10-INBS-0009 - INBS - VALID, Université Bordeaux Segalen - Bordeaux 2-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Sciences et Technologies - Bordeaux 1, Université de Toulouse (UT)-Université de Toulouse (UT)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-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 de Toulouse (UT)-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 de Toulouse (UT)-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 de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and University of Kentucky

Subjects
0106 biological sciences, 0301 basic medicine, Prunus armeniaca, [SDV]Life Sciences [q-bio], General Physics and Astronomy, adaptation, 01 natural sciences, Gene flow, Population genomics, Plant evolution, [SDV.BV] Life Sciences [q-bio]/Vegetal Biology, Arbre fruitier à noyau, Génétique, Phylogeny, Disease Resistance, Multidisciplinary, biology, Phylogenomics, [SDV] Life Sciences [q-bio], Génomique, Phenotype, [SDV.BV.AP] Life Sciences [q-bio]/Vegetal Biology/Plant breeding, Gene pool, Fruit à noyau, Genome, Plant, Gene Flow, Agricultural genetics, Abricotier, Science, Chromosomes, Plant, Article, General Biochemistry, Genetics and Molecular Biology, Evolution, Molecular, [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, 03 medical and health sciences, domestication, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Selection, Genetic, Domestication, Abricot, Life Cycle Stages, Genetic diversity, [SDV.GEN]Life Sciences [q-bio]/Genetics, Genetic Variation, General Chemistry, Phenotypic trait, biology.organism_classification, [SDV.BV.AP]Life Sciences [q-bio]/Vegetal Biology/Plant breeding, 030104 developmental biology, Evolutionary biology, Fruit, Metagenomics, Adaptation, divergence, 010606 plant biology & botany
Abstract

Among crop fruit trees, the apricot (Prunus armeniaca) provides an excellent model to study divergence and adaptation processes. Here, we obtain nearly 600 Armeniaca apricot genomes and four high-quality assemblies anchored on genetic maps. Chinese and European apricots form two differentiated gene pools with high genetic diversity, resulting from independent domestication events from distinct wild Central Asian populations, and with subsequent gene flow. A relatively low proportion of the genome is affected by selection. Different genomic regions show footprints of selection in European and Chinese cultivated apricots, despite convergent phenotypic traits, with predicted functions in both groups involved in the perennial life cycle, fruit quality and disease resistance. Selection footprints appear more abundant in European apricots, with a hotspot on chromosome 4, while admixture is more pervasive in Chinese cultivated apricots. Our study provides clues to the biology of selected traits and targets for fruit tree research and breeding., The evolutionary and domestication history of apricots is poorly understood. Here, the authors provide four apricot high-quality genome assemblies, the genomes of 578 accessions from natural and cultivated populations, and show that Chinese and European apricots constitute two different gene pools, resulting from independent domestication events.

Published
2021

14. High-quality genome sequence of white lupin provides insight into soil exploration and seed quality

Author

Pierre-Marc Delaux, Romain Guyot, Martin Crespi, Erika Sallet, Malika Laguerre, Fanchon Divol, Sébastien Carrère, Benjamin Péret, Patrick Doumas, Cecile Huneau, Matthew R. Nelson, Jemma Taylor, Alexandre Soriano, Jérôme Salse, Laurence Marquès, Veit Schubert, Fernando Geu-Flores, Davide Mancinotti, Jérôme Gouzy, Sandrine Arribat, Karine Gallardo, André Marques, Thomas Blein, Barbara Hufnagel, William Marande, Delphine Aime, Hélène Bergès, Jean Keller, Biochimie et Physiologie Moléculaire des Plantes (BPMP), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Max Planck Institute for Plant Breeding Research (MPIPZ), Laboratoire des interactions plantes micro-organismes (LIPM), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), University of Copenhagen = Københavns Universitet (KU), Centre National de Ressources Génomiques Végétales (CNRGV), Institut National de la Recherche Agronomique (INRA), Laboratoire de Recherche en Sciences Végétales (LRSV), Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Génétique Diversité et Ecophysiologie des Céréales - Clermont Auvergne (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne (UCA), Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Agroécologie [Dijon], Institut National de la Recherche Agronomique (INRA)-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), Royal Botanic Garden , Kew, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), The University of Western Australia (UWA), Centre IRD de Montpellier (IRD), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire des Interactions Plantes Microbes Environnement (LIPME), Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Génétique Diversité et Ecophysiologie des Céréales (GDEC), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), 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), Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben] (IPK-Gatersleben), Evolution des Interactions Plantes-Microorganismes, Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Institut de Recherche pour le Développement (IRD), VILLUM Foundation : 15476, Innovate UK, FAPEAL/CNPq (Brasil), ANR-11-IDEX-0002,UNITI,Université Fédérale de Toulouse(2011), ANR-10-LABX-0032,LaSIPS,LABORATORY FOR SYSTEMS AND ENGINEERING OF PARIS SACLAY(2010), European Project: 0637420(2007), University of Copenhagen = Københavns Universitet (UCPH), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Royal Botanic Gardens [Kew], and Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3)

Subjects
0106 biological sciences, 0301 basic medicine, Repetitive Sequences, Nucleic Acid/genetics, Plant Roots/genetics, [SDV]Life Sciences [q-bio], Plant genetics, Gene Dosage, General Physics and Astronomy, Sequence assembly, Alkaloids/chemistry, Plant Roots, 01 natural sciences, Genome, Lupinus, Soil, Nutrient, Gene Duplication, lcsh:Science, ComputingMilieux_MISCELLANEOUS, Plant Proteins, Plant Proteins/metabolism, 2. Zero hunger, Multidisciplinary, Ecotype, food and beverages, Transcriptome/genetics, Polymorphism, Single Nucleotide/genetics, Seeds, Genome, Plant, Agricultural genetics, Synteny/genetics, Plant domestication, Science, Centromere, Biology, Lupinus/genetics, Polymorphism, Single Nucleotide, Synteny, Article, General Biochemistry, Genetics and Molecular Biology, Crop, Evolution, Molecular, 03 medical and health sciences, Alkaloids, Seeds/physiology, Centromere/genetics, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Domestication, Repetitive Sequences, Nucleic Acid, Models, Genetic, fungi, Genetic Variation, Molecular Sequence Annotation, General Chemistry, Sequence Analysis, DNA, 15. Life on land, biology.organism_classification, Plant Leaves, 030104 developmental biology, Agronomy, Genomic Structural Variation, lcsh:Q, Plant Leaves/metabolism, Transcriptome, 010606 plant biology & botany
Abstract

White lupin (Lupinus albus L.) is an annual crop cultivated for its protein-rich seeds. It is adapted to poor soils due to the production of cluster roots, which are made of dozens of determinate lateral roots that drastically improve soil exploration and nutrient acquisition (mostly phosphate). Using long-read sequencing technologies, we provide a high-quality genome sequence of a cultivated accession of white lupin (2n = 50, 451 Mb), as well as de novo assemblies of a landrace and a wild relative. We describe a modern accession displaying increased soil exploration capacity through early establishment of lateral and cluster roots. We also show how seed quality may have been impacted by domestication in term of protein profiles and alkaloid content. The availability of a high-quality genome assembly together with companion genomic and transcriptomic resources will enable the development of modern breeding strategies to increase and stabilize white lupin yield., White lupin is an annual crop cultivated for protein rich seeds and can produce cluster roots for efficient phosphate acquisition. Here, the authors generate high quality genome assemblies of a cultivated accession, a landrace, and a wild relative and provides insight into soil exploration and seed quality.

Published
2020

15. Fonio millet genome unlocks African orphan crop diversity for agriculture in a changing climate

Author

Ndjido Ardo Kane, Yves Vigouroux, Denisa Šimoníková, Leila Zekraoui, Jaroslav Dolezel, Nagarajan Kathiresan, Sandrine Causse, Michael Abrouk, Thomas Wicker, Sandrine Arribat, Claire Billot, Stéphane Cauet, Simon G. Krattinger, Jana Cizkova, Sylvie Vancoppenolle, Adeline Barnaud, E. Hribova, Hélène Bergès, Philippe Cubry, Jan Bettgenhaeuser, Mathieu Gueye, Hanin Ibrahim Ahmed, Liubov Gapa, Nora Scarcelli, Yveline Pailles, Jan J. Wieringa, Christian Leclerc, Marie Couderc, University of Zurich, Barnaud, Adeline, Krattinger, Simon G, King Abdullah University of Science and Technology (KAUST), Diversité, adaptation, développement des plantes (UMR DIADE), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Institute of Experimental Botany of the Czech Academy of Sciences (IEB / CAS), Czech Academy of Sciences [Prague] (CAS), Centre National de Ressources Génomiques Végétales (CNRGV), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Naturalis Biodiversity Center [Leiden], Institut Fondamental d'Afrique Noire (IFAN), Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD), Senegalese Agricultural Research Institute, LMI Adaptation des Plantes et microorganismes associés aux Stress Environnementaux [Dakar] (LAPSE), Institut de Recherche pour le Développement (IRD), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Universität Zürich [Zürich] = University of Zurich (UZH), European Regional Development Fund OPVVV project 'Plants as a tool for sustainable development' CZ.02.1.01/0.0/0.0/16_019/0000827, ANR-16-IDEX-0006,MUSE,MUSE(2016), ANR-10-LABX-0001,AGRO,Agricultural Sciences for sustainable Development(2010), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)

Subjects
0106 biological sciences, 0301 basic medicine, [SDV]Life Sciences [q-bio], Digitaria, General Physics and Astronomy, 580 Plants (Botany), 01 natural sciences, Plant breeding, F30 - Génétique et amélioration des plantes, Domestication, 0302 clinical medicine, 10126 Department of Plant and Microbial Biology, lcsh:Science, 2. Zero hunger, Molecular breeding, 0303 health sciences, Multidisciplinary, Diversité génétique (comme ressource), Agroforestry, Domestication des plantes, phytogénétique, food and beverages, Agriculture, 3100 General Physics and Astronomy, Genome, Plant, Agricultural genetics, Plant domestication, Science, Climate Change, Context (language use), 1600 General Chemistry, Genetics and Molecular Biology, Biology, Article, General Biochemistry, Genetics and Molecular Biology, génomique, Evolution, Molecular, 03 medical and health sciences, Ressource génétique végétale, Variation génétique, Species Specificity, 1300 General Biochemistry, Genetics and Molecular Biology, 10211 Zurich-Basel Plant Science Center, Selection, Genetic, 030304 developmental biology, Changement climatique, Genetic diversity, business.industry, Genetic Variation, Molecular Sequence Annotation, Digitaria exilis, General Chemistry, 15. Life on land, biology.organism_classification, Amélioration des plantes, 030104 developmental biology, Crop diversity, 13. Climate action, General Biochemistry, Africa, lcsh:Q, business, Edible Grain, 030217 neurology & neurosurgery, 010606 plant biology & botany
Abstract

Sustainable food production in the context of climate change necessitates diversification of agriculture and a more efficient utilization of plant genetic resources. Fonio millet (Digitaria exilis) is an orphan African cereal crop with a great potential for dryland agriculture. Here, we establish high-quality genomic resources to facilitate fonio improvement through molecular breeding. These include a chromosome-scale reference assembly and deep re-sequencing of 183 cultivated and wild Digitaria accessions, enabling insights into genetic diversity, population structure, and domestication. Fonio diversity is shaped by climatic, geographic, and ethnolinguistic factors. Two genes associated with seed size and shattering showed signatures of selection. Most known domestication genes from other cereal models however have not experienced strong selection in fonio, providing direct targets to rapidly improve this crop for agriculture in hot and dry environments., Fonio millet is a fast growing orphan cereal crop with a great potential for dryland agriculture. Here, the authors report chromosome-scale reference genome assembly and population genomic resources to shed light on genetic diversity, population structure and domestication of fonio millet.

Published
2020

16. Genome sequence of the cluster root forming white lupin;

Author

Barbara Hufnagel, Benjamin Péret, Pierre-Marc Delaux, Patrick Doumas, Romain Guyot, Alexandre Soriano, William Marande, Sandrine Arribat, Hélène Bergès, Laurence Marquès, Malika Laguerre, Thomas Blein, Erika Sallet, Davide Mancinotti, Martin Crespi, Sébastien Carrère, Matthew R. Nelson, Cecile Huneau, Jérôme Salse, Jemma Taylor, Fanchon Divol, Jean Keller, Fernando Geu-Flores, Delphine Aime, Veit Schubert, Karine Gallardo, Jérôme Gouzy, Biochimie et Physiologie Moléculaire des Plantes (BPMP), Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Laboratoire des interactions plantes micro-organismes (LIPM), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), University of Copenhagen = Københavns Universitet (UCPH), Centre National de Ressources Génomiques Végétales (CNRGV), Institut National de la Recherche Agronomique (INRA), Laboratoire de Recherche en Sciences Végétales (LRSV), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Agroécologie [Dijon], Institut National de la Recherche Agronomique (INRA)-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), Royal Botanic Gardens [Kew], Leibniz Institute of Plant Genetics and Crop Plant Research, Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO), Evolution des Interactions Plantes-Microorganismes, Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Institut de Recherche pour le Développement (IRD), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), University of Copenhagen = Københavns Universitet (KU), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), 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, Royal Botanic Gardens, Kew, Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Montpellier (UM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Equipe Développement et Plasticité du Système Racinaire (PLASTICITE), Université de Montpellier (UM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), University of Copenhagen, Frederiksberg C, Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Génétique Diversité et Ecophysiologie des Céréales - Clermont Auvergne (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne (UCA), Université Paris-Sud - Paris 11 (UP11)-Université Paris-Saclay-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)-Institut National de la Recherche Agronomique (INRA), Royal Botanic Garden , Kew, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Interactions plantes-microorganismes et santé végétale, Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (UNS), and Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0106 biological sciences, 2. Zero hunger, Whole genome sequencing, 0303 health sciences, Root system, 15. Life on land, Biology, biology.organism_classification, 010603 evolutionary biology, 01 natural sciences, Genome, 03 medical and health sciences, Lupinus, Symbiosis, Arabidopsis, Botany, Cluster root, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Legume, 030304 developmental biology
Abstract

White lupin (Lupinus albus L.) is a legume that produces seeds recognized for their high protein content and good nutritional value (lowest glycemic index of all grains, high dietary fiber content, and zero gluten or starch)1–5. White lupin can form nitrogen-fixing nodules but has lost the ability to form mycorrhizal symbiosis with fungi6. Nevertheless, its root system is well adapted to poor soils: it produces cluster roots, constituted of dozens of determinate lateral roots that improve soil exploration and phosphate remobilization7. As phosphate is a limited resource that comes from rock reserves8, the production of cluster roots is a trait of interest to improve fertilizers efficiency. Using long reads sequencing technologies, we provide a high-quality genome sequence of a modern variety of white lupin (2n=50, 451 Mb), as well asde novoassemblies of a landrace and a wild relative. We describe how domestication impacted soil exploration capacity through the early establishment of lateral and cluster roots. We identify theAPETALA2transcription factorLaPUCHI-1, homolog of the Arabidopsis morphogenesis coordinator9, as a potential regulator of this trait. Our high-quality genome and companion genomic and transcriptomic resources enable the development of modern breeding strategies to increase and stabilize yield and to develop new varieties with reduced allergenic properties (caused by conglutins10), which would favor the deployment of this promising culture.

Published
2019

17. Molecular Epidemiology of Bacterial Wilt in the Madagascar Highlands Caused by Andean (Phylotype IIB-1) and African (Phylotype III) Brown Rot Strains of the

Author

Santatra, Ravelomanantsoa, Christian, Vernière, Adrien, Rieux, Laurent, Costet, Frédéric, Chiroleu, Sandrine, Arribat, Gilles, Cellier, Olivier, Pruvost, Stéphane, Poussier, Isabelle, Robène, Fabien, Guérin, and Philippe, Prior

Subjects
MLVA, fungi, Ralstonia solanacearum, Madagascar, food and beverages, population structure, Plant Science, genetic diversity, Original Research
Abstract

The Ralstonia solanacearum species complex (RSSC) is a highly diverse cluster of bacterial strains found worldwide, many of which are destructive and cause bacterial wilt (BW) in a wide range of host plants. In 2009, potato production in Madagascar was dramatically affected by several BW epidemics. Controlling this disease is critical for Malagasy potato producers. The first important step toward control is the characterization of strains and their putative origins. The genetic diversity and population structure of the RSSC were investigated in the major potato production areas of the Highlands. A large collection of strains (n = 1224) was assigned to RSSC phylotypes based on multiplex polymerase chain reaction (PCR). Phylotypes I and III have been present in Madagascar for a long time but rarely associated with major potato BW outbreaks. The marked increase of BW prevalence was found associated with phylotype IIB sequevar 1 (IIB-1) strains (n = 879). This is the first report of phylotype IIB-1 strains in Madagascar. In addition to reference strains, epidemic IIB-1 strains (n = 255) were genotyped using the existing MultiLocus Variable-Number Tandem Repeat Analysis (MLVA) scheme RS2-MLVA9, producing 31 haplotypes separated into two related clonal complexes (CCs). One major CC included most of the worldwide haplotypes distributed across wide areas. A regional-scale investigation suggested that phylotype IIB-1 strains were introduced and massively spread via latently infected potato seed tubers. Additionally, the genetic structure of phylotype IIB-1 likely resulted from a bottleneck/founder effect. The population structure of phylotype III, described here for the first time in Madagascar, exhibited a different pattern. Phylotype III strains (n = 217) were genotyped using the highly discriminatory MLVA scheme RS3-MLVA16. High genetic diversity was uncovered, with 117 haplotypes grouped into 11 CCs. Malagasy phylotype III strains were highly differentiated from continental African strains, suggesting no recent migration from the continent. Overall, population structure of phylotype III involves individual small CCs that correlate to restricted geographic areas in Madagascar. The evidence suggests, if at all, that African phylotype III strains are not efficiently transmitted through latently infected potato seed tubers.

Published
2017

18. Targeted mRNA Oxidation Regulates Sunflower Seed Dormancy Alleviation during Dry After-Ripening

Author

Nicolas B. Langlade, Hayat El-Maarouf-Bouteau, Christophe Bailly, Sandrine Balzergue, Sandrine Arribat, Patrick Vincourt, Jérémie Bazin, Université Pierre et Marie Curie - Paris 6 (UPMC), Unité mixte de recherche interactions plantes-microorganismes, Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Unité de recherche en génomique végétale (URGV), Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), and Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0106 biological sciences, [SDV]Life Sciences [q-bio], Plant Science, 01 natural sciences, abscisic acid, alzheimer disease, Protein biosynthesis, Research Articles, Plant Proteins, 2. Zero hunger, 0303 health sciences, food and beverages, vitamin e, Plant Dormancy, Biochemistry, 8-Hydroxy-2'-Deoxyguanosine, Germination, gene expression, arabidopsis thaliana, signal transduction, processing bodies, stress granules, cdna aflp, germination, Seeds, Helianthus, Sunflower seed, Oxidation-Reduction, Polymorphism, Restriction Fragment Length, Molecular Sequence Data, Phosphatase, Biology, 03 medical and health sciences, Helianthus annuus, Animals, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, RNA, Messenger, 030304 developmental biology, Polymorphism, Genetic, Gene Expression Profiling, Deoxyguanosine, Cell Biology, Microarray Analysis, Lyase, Protein Biosynthesis, Dormancy, Imbibition, Transcriptome, 010606 plant biology & botany
Abstract

L'article original est publié par The American Society of Plant Biologists; International audience; After-ripening is the mechanism by which dormant seeds become nondormant during their dry storage after harvest. The absence of free water in mature seeds does not allow detectable metabolism; thus, the processes associated with dormancy release under these conditions are largely unknown. We show here that sunflower (Helianthus annuus) seed alleviation of dormancy during after-ripening is associated with mRNA oxidation and that this oxidation is prevented when seeds are maintained dormant. In vitro approaches demonstrate that mRNA oxidation results in artifacts in cDNA-amplified fragment length polymorphim analysis and alters protein translation. The oxidation of transcripts is not random but selective, and, using microarrays, we identified 24 stored mRNAs that became highly oxidized during after-ripening. Oxidized transcripts mainly correspond to genes involved in responses to stress and in cell signaling. Among them, protein phosphatase 2C PPH1, mitogen-activated protein kinase phosphatase 1, and phenyl ammonia lyase 1 were identified. We propose that targeted mRNA oxidation during dry after-ripening of dormant seeds could be a process that governs cell signaling toward germination in the early steps of seed imbibition.

Published
2011

19. Is Gene Transcription Involved in Seed Dry After-Ripening?

Author

Nicolas B. Langlade, Ernest Mordret, Sandrine Arribat, Sandrine Balzergue, Hayat El-Maarouf-Bouteau, Christophe Bailly, Patrice Meimoun, Laboratoire de Biologie du Développement (LBD), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Biologie Paris Seine (IBPS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Laboratoire des interactions plantes micro-organismes (LIPM), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Unité de recherche en génomique végétale (URGV), Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Ecoseed, KBBE project, Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), and Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)

Subjects
0106 biological sciences, Gene Expression, Plant Science, Plant Genetics, 01 natural sciences, Transcriptomes, Transcriptome, Gene Expression Regulation, Plant, Gene expression, Molecular Cell Biology, Plant Genomics, Flowering Plants, 2. Zero hunger, Regulation of gene expression, Plant Growth and Development, 0303 health sciences, Multidisciplinary, food and beverages, Genomics, Signaling in Selected Disciplines, Plants, Plant Dormancy, Cell biology, Germination, Plant Physiology, Seeds, Medicine, Helianthus, Sunflower seed, DNA microarray, Research Article, Signal Transduction, Science, DNA transcription, Biology, Molecular Genetics, 03 medical and health sciences, Genome Analysis Tools, Plant Signaling, Plant-Environment Interactions, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Botany, Genetics, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Gene Regulation, 030304 developmental biology, Gene Expression Profiling, Plant Ecology, Computational Biology, Humidity, Gene expression profiling, Dormancy, Genome Expression Analysis, 010606 plant biology & botany, Developmental Biology
Abstract

International audience; Orthodox seeds are living organisms that survive anhydrobiosis and may display dormancy, an inability to germinate at harvest. Seed germination potential can be acquired during a prolonged period of dry storage called after-ripening. The aim of this work was to determine if gene transcription is an underlying regulatory mechanism for dormancy alleviation during after-ripening. To identify changes in gene transcription strictly associated with the acquisition of germination potential but not with storage, we used seed storage at low relative humidity that maintains dormancy as control. Transcriptome profiling was performed using DNA microarray to compare change in gene transcript abundance between dormant (D), after-ripened non-dormant (ND) and after-ripened dormant seeds (control, C). Quantitative real-time polymerase chain reaction (qPCR) was used to confirm gene expression. Comparison between D and ND showed the differential expression of 115 probesets at cutoff values of twofold change (p,0.05). Comparisons between both D and C with ND in transcript abundance showed that only 13 transcripts, among 115, could be specific to dormancy alleviation. qPCR confirms the expression pattern of these transcripts but without significant variation between conditions. Here we show that sunflower seed dormancy alleviation in the dry state is not related to regulated changes in gene expression.

Published
2014

20. Bridging physiological and evolutionary time-scales in a gene regulatory network

Author

Sandrine Arribat, Loren H. Rieseberg, Matthieu Vignes, Vân Anh Huynh-Thu, Nicolas B. Langlade, Didier Varès, Patrick Vincourt, David Rengel, Sandrine Balzergue, Pierre Geurts, Gwenaëlle Marchand, Nolan C. Kane, Unité mixte de recherche interactions plantes-microorganismes, Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Université de Liège, Department of Ecology and Evolutionary Biology (Faculty of Biology), University of Science-Vietnam National Universities, Unité de recherche en génomique végétale (URGV), Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Department of Biology, Indiana University [Bloomington], Indiana University System-Indiana University System, Florida Museum of Natural History, Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA), Institut National de la Recherche Agronomique (INRA), OLEOSOL (F.U.I.), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées

Subjects
Physiology, abscisic acid (ABA), Systems biology, [SDV]Life Sciences [q-bio], Gene regulatory network, Plant Science, drought, Biology, CLC-A chloride channel protein, Gene Expression Regulation, Plant, Helianthus annuus, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Gene Regulatory Networks, [INFO]Computer Science [cs], [MATH]Mathematics [math], Gene, Plant Proteins, Genetic diversity, Nitrates, Models, Genetic, Ecology, food and beverages, 15. Life on land, Biological Evolution, Phenotype, NITRATE TRANSPORTER 1.1 (NRT1.1), Droughts, network inference, Nitrate transport, Evolutionary biology, Helianthus, genetic differentiation, Adaptation, Transcriptome, Algorithms, Abscisic Acid
Abstract

International audience; Gene regulatory networks (GRNs) govern phenotypic adaptations and reflect the trade-offs between physiological responses and evolutionary adaptation that act at different time-scales. To identify patterns of molecular function and genetic diversity in GRNs, we studied the drought response of the common sunflower, Helianthus annuus, and how the underlying GRN is related to its evolution. We examined the responses of 32 423 expressed sequences to drought and to abscisic acid (ABA) and selected 145 co-expressed transcripts. We characterized their regulatory relationships in nine kinetic studies based on different hormones. From this, we inferred a GRN by meta-analyses of a Gaussian graphical model and a random forest algorithm and studied the genetic differentiation among populations (FST ) at nodes. We identified two main hubs in the network that transport nitrate in guard cells. This suggests that nitrate transport is a critical aspect of the sunflower physiological response to drought. We observed that differentiation of the network genes in elite sunflower cultivars is correlated with their position and connectivity. This systems biology approach combined molecular data at different time-scales and identified important physiological processes. At the evolutionary level, we propose that network topology could influence responses to human selection and possibly adaptation to dry environments.

Published
2014

21. The hidden legume roots: cluster root development in white lupin

Author

Barbara Hufnagel, André Marques, Erika Sallet, William Marande, Alexandre Soriano, Sandrine Arribat, Matthew Nelson, Fanchon Divol, Laurence MARQUES, Cecilia Gallardo, Jerome Salse, Romain Guyot, Pierre Marc Delaux, Fernando Geu-Flores, Helene Berges, Jerome Gouzy, Benjamin Peret, Biochimie et Physiologie Moléculaire des Plantes (BPMP), Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Laboratoire des interactions plantes micro-organismes (LIPM), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Centre National de Ressources Génomiques Végétales (CNRGV), Institut National de la Recherche Agronomique (INRA), Royal Botanic Gardens [Kew], Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Institut de Recherche pour le Développement (IRD), Evolution des Interactions Plantes-Microorganismes, Laboratoire de Recherche en Sciences Végétales (LRSV), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), University of Copenhagen = Københavns Universitet (UCPH), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Royal Botanic Gardens, Kew, Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), and University of Copenhagen = Københavns Universitet (KU)

Subjects
[SDV]Life Sciences [q-bio], [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

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