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1. Aeschynomene evenia, a Model Plant for Studying the Molecular Genetics of the Nod-Independent Rhizobium-Legume Symbiosis

Author

Jean-François Arrighi, Fabienne Cartieaux, Spencer C. Brown, Marguerite Rodier-Goud, Marc Boursot, Joel Fardoux, Delphine Patrel, Djamel Gully, Sandrine Fabre, Clémence Chaintreuil, and Eric Giraud

Subjects
Microbiology, QR1-502, Botany, QK1-989
Abstract

Research on the nitrogen-fixing symbiosis has been focused, thus far, on two model legumes, Medicago truncatula and Lotus japonicus, which use a sophisticated infection process involving infection thread formation. However, in 25% of the legumes, the bacterial entry occurs more simply in an intercellular fashion. Among them, some Aeschynomene spp. are nodulated by photosynthetic Bradyrhizobium spp. that do not produce Nod factors. This interaction is believed to represent a living testimony of the ancestral state of the rhizobium–legume symbiosis. To decipher the mechanisms of this Nod-independent process, we propose Aeschynomene evenia as a model legume because it presents all the characteristics required for genetic and molecular analysis. It is a short-perennial and autogamous species, with a diploid and relatively small genome (2n = 20; 460 Mb/1C). A. evenia ‘IRFL6945’ is nodulated by the well-characterized photosynthetic Bradyrhizobium sp. strain ORS278 and is efficiently transformed by Agrobacterium rhizogenes. Aeschynomene evenia is genetically homozygous but polymorphic accessions were found. A manual hybridization procedure has been set up, allowing directed crosses. Therefore, it should be relatively straightforward to unravel the molecular determinants of the Nod-independent process in A. evenia. This should shed new light on the evolution of rhizobium–legume symbiosis and could have important agronomic implications.

Published
2012
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2. The banana (Musa acuminata) genome and the evolution of monocotyledonous plants

Author

Gaëtan Droc, Adriana Alberti, Philippe Francois, Rémy Habas, Patrick Wincker, Jaroslav Dolezel, Mouna Jeridi, Cyril Jourda, E. Hribova, Thomas Wicker, Kamel Jabbari, Julie Leclercq, Cees Waalwijk, Olivier Panaud, Benjamin Noel, Marlã̈ne Souquet, Manuel Ruiz, Didier Mbéguié-A-Mbéguié, Margot Correa, Nicolas Roux, Saravanaraj Ayyampalayam, Ronan Rivallan, Spencer Brown, Françoise Carreel, Maria Bernard, Andrzej Kilian, Jose Barbosa, Olivier Jaillon, Olivier Garsmeur, Jean-Marc Aury, Ange-Marie Risterucci, Julie Poulain, Karine Labadie, Xavier Argout, Steeve Joseph, Pat Heslop-Harrison, Jean-Christophe Glaszmann, Ana Maria Rocha de Almeida, Mathieu Rouard, Jean Weissenbach, Stéphanie Bocs, Juliette Lengellé, Nabila Yahiaoui, Eric Lyons, Anne Dievart, Corinne Da Silva, Marguerite Rodier-Goud, Dheema Burthia, Céline Cardi, Michael Freeling, Angélique D'Hont, Claire Poiron, Valentin Guignon, Matthieu Chabannes, Frédéric Bakry, Christophe Jenny, Franc-Christophe Baurens, Michael R. McKain, Miguel A. Dita, Francis Quetier, Diane Burgess, Jim Leebens-Mack, Gert H. J. Kema, Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-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), 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)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Développement et amélioration des plantes (UMR DAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Institut de biologie de l'ENS Paris (IBENS), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut de Génomique d'Evry (IG), Institut de Biologie François JACOB (JACOB), 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)-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, Laboratoire Génome et développement des plantes (LGDP), Université de Perpignan Via Domitia (UPVD)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d’Optique Atmosphérique - UMR 8518 (LOA), Institut national des sciences de l'Univers (INSU - CNRS)-Université de Lille-Centre National de la Recherche Scientifique (CNRS), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Institut des sciences du végétal (ISV), Centre National de la Recherche Scientifique (CNRS), Plant Research International (PRI), Wageningen University and Research [Wageningen] (WUR), 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), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-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), Université Paris-Saclay-Institut de Biologie François JACOB (JACOB), 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 la Recherche Scientifique (CNRS)-Université Montpellier 2 - Sciences et Techniques (UM2)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), École normale supérieure - Paris (ENS Paris)-École normale supérieure - Paris (ENS Paris)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Lille, Wageningen University and Research Centre [Wageningen] (WUR), University of Zurich, and D'Hont, Angélique

Subjects
MESH: Genome, Plant, 0106 biological sciences, Phylogénie, Lineage (evolution), Plant genetics, Évolution, 580 Plants (Botany), Haploidy, resource, in-situ hybridization, Musa acuminata, 01 natural sciences, F30 - Génétique et amélioration des plantes, MESH: Genotype, sequence count data, 10126 Department of Plant and Microbial Biology, Gene Duplication, Musa balbisiana, dna sequences, MESH: Genes, Plant, maximum likelihood, MESH: Phylogeny, Conserved Sequence, Phylogeny, MESH: Evolution, Molecular, 2. Zero hunger, 0303 health sciences, MESH: Conserved Sequence, Multidisciplinary, MESH: Gene Duplication, food and beverages, F70 - Taxonomie végétale et phytogéographie, MESH: Haploidy, MESH: DNA Transposable Elements, Génotype, Genome, Plant, dna-sequences, Séquence nucléotidique, diversification, Poales, Genotype, Molecular Sequence Data, Biology, Poaceae, Genes, Plant, differential expression, Evolution, Molecular, Zingiberales, Biointeractions and Plant Health, 03 medical and health sciences, MESH: Musa, Botany, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, gene, Domestication, 030304 developmental biology, 1000 Multidisciplinary, Génome, MESH: Molecular Sequence Data, Bioint Moleculair Phytopathology, rice, Musa, 15. Life on land, biology.organism_classification, Arecales, DNA Transposable Elements, identification, maximum-likelihood, in situ hybridization, 010606 plant biology & botany
Abstract

International audience; Bananas (Musa spp.), including dessert and cooking types, are giant perennial monocotyledonous herbs of the order Zingiberales, a sister group to the well-studied Poales, which include cereals. Bananas are vital for food security in many tropical and subtropical countries and the most popular fruit in industrialized countries. The Musa domestication process started some 7,000 years ago in Southeast Asia. It involved hybridizations between diverse species and subspecies, fostered by human migrations, and selection of diploid and triploid seedless, parthenocarpic hybrids thereafter widely dispersed by vegetative propagation. Half of the current production relies on somaclones derived from a single triploid genotype (Cavendish). Pests and diseases have gradually become adapted, representing an imminent danger for global banana production. Here we describe the draft sequence of the 523-megabase genome of a Musa acuminata doubled-haploid genotype, providing a crucial stepping-stone for genetic improvement of banana. We detected three rounds of whole-genome duplications in the Musa lineage, independently of those previously described in the Poales lineage and the one we detected in the Arecales lineage. This first monocotyledon high-continuity whole-genome sequence reported outside Poales represents an essential bridge for comparative genome analysis in plants. As such, it clarifies commelinid-monocotyledon phylogenetic relationships, reveals Poaceae-specific features and has led to the discovery of conserved non-coding sequences predating monocotyledon-eudicotyledon divergence.

Published
2012
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3. Bi-fluorescence imaging for estimating accurately the nuclear condition of Rhizoctonia spp

Author

A. J. Caesar, Marie-Claude Bon, Cécile Heraud, Fatiha Guermache, and Marguerite Rodier-Goud

Subjects
0303 health sciences, Fluorescence-lifetime imaging microscopy, biology, 030306 microbiology, fungi, food and beverages, biology.organism_classification, Rhizoctonia, Applied Microbiology and Biotechnology, Fluorescence, Microbiology, Rhizoctonia solani, 03 medical and health sciences, chemistry.chemical_compound, Autofluorescence, chemistry, DAPI, Biological system, 030304 developmental biology
Abstract

Aims: To simplify the determination of the nuclear condition of the pathogenic Rhizoctonia, which currently needs to be performed either using two fluorescent dyes, thus more costly and time-consuming, or using only one fluorescent dye, thus less accurate. Methods and Results: A red primary fluorescence (autofluorescence) of the hyphal cell walls and septa of Rhizoctonia spp. with green excitation is evidenced in Rhizoctonia spp. This property is exploited and combined for the first time with a conventional DAPI fluorescence to accurately determine the nuclear condition of Rhizoctonia. This bi-fluorescence imaging strategy depicted the nuclear condition in Rhizoctonia spp. more accurately than the conventional DAPI fluorescence used alone and was validated against isolates previously genotyped by DNA sequencing. Conclusions: We demonstrated that the bi-fluorescence imaging strategy was safe, accurate and simple to perform and interpret. Significance and Impact of the Study: The developed bi-fluorescence imaging strategy provides a sensitive tool for determining the nuclear condition of Rhizoctonia strains. Its simplicity is a key advantage when there are numerous cultures to be examined.

Published
2012
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4. Isolation of five new monosomic alien addition lines of Gossypium australe F. Muell in G. hirsutum L. by SSR and GISH analyses

Author

André Toussaint, Jean-Marc Lacape, Jean-Marie Jacquemin, Guy Mergeai, Marguerite Rodier-Goud, Rudy Palm, Halima Benbouza, Jean-Pierre Baudoin, D. Sarr, and L. Ahoton

Subjects
biology, Gossypium australe, Botany, Backcrossing, Genetics, Chromosome, Plant Science, Alien, Gossypium, biology.organism_classification, Agronomy and Crop Science, Gossypium hirsutum
Abstract

Gossypium australe F. Muell (2n = 2x = 26) is a wild perennial species possessing agronomic useful traits that would be interesting to introgress into G. hirsutum L. (2n = 4x = 52), the main cultivated cotton species. To isolate monosomic alien addition lines (MAALs) of G. australe in G. hirsutum, the [2(G. hirsutum · G. australe) · G. hirsutum] pentaploid (2n = 5x = 65) was backcrossed as male parent to G. hirsutum. Analysis of 42 BC1 plants and seven alien addition lines, already available, with 150 SSR markers developed from G. hirsutum revealed a cross-species amplification rate of 100% and a polymorphism rate of 56%. Eighty polymorphic SSR markers generated 87 G. australe-specific loci that have been assigned by a hierarchical cluster analysis to 13 linkage groups corresponding to the 13 chromosomes of G. australe. Analysis by SSR markers and genomic in situ hybridization of the self-progeny of disomic alien addition lines, backcross progeny of the pentaploid, allowed the isolation of five new MAALs. (Resume d'auteur)

Published
2010
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5. Evidence for spontaneous polyploidization in cassava Manihot esculenta Crantz

Author

Julie Sardos, Roger Malapa, Vincent Lebot, Jean-Louis Noyer, Dominique Dambier, and Marguerite Rodier-Goud

Subjects
Manihot esculenta, biology, Vegetative reproduction, business.industry, F60 - Physiologie et biochimie végétale, fungi, Euphorbiaceae, food and beverages, F70 - Taxonomie végétale et phytogéographie, Plant Science, biology.organism_classification, Intraspecific competition, F30 - Génétique et amélioration des plantes, Crop, Plant ecology, Agriculture, Botany, Ploidy, business, Cropping, Ecology, Evolution, Behavior and Systematics
Abstract

Cassava, Manihot esculenta Crantz (Euphorbiaceae), is a major tropical crop. It is a diploid and sexually fertile, but confined to vegetative propagation in agriculture. While polyploidization is a major evolutionary process in higher plants and is of importance in the creation of improved crop varieties, spontaneous polyploidization is poorly documented for M. esculenta. Molecular and cytological evidence is provided here for two cases of intraspecific triploidization events that occurred in smallholders' fields in Vanuatu, South Pacific. We then discuss the implications of triploidy for the crop and highlight the importance of this discovery for the evolution of this species in traditional cropping systems.

Published
2009
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6. The genomes of many yam species contain transcriptionally active endogenous geminiviral sequences that may be functionally expressed

Author

Marguerite Rodier-Goud, Maneerat Koohapitagtam, Michel Peterschmitt, Serge Galzi, Darren P. Martin, Stephan Winter, Denis Filloux, Sasha Murrell, Marie Stephanie Vernerey, Angélique D'Hont, Paul Wilkin, Ben Murrell, Philippe Roumagnac, Marilyne Uzest, Charlotte Julian, Michael Golden, Biologie et Génétique des Interactions Plante-Parasite (UMR BGPI), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-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), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Institute of Infectious Diseases and Molecular Medicine (IDM), University of Cape Town, Scripps Research Institute, Prince of Songkla University (PSU), Computational Biology Group, Institute of Infectious Diseases and Molecular Medicine, Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Royal Botanic Gardens, Deutsche Sammlung von Mikroorganismen und Zellkulturen, Leibniz Association, Partenaires INRAE, Department of Medicine, University of California [San Diego] (UC San Diego), University of California-University of California, Roumagnac, Philippe, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (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)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)

Subjects
0106 biological sciences, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, Virologie, ADN, 01 natural sciences, Genome, F30 - Génétique et amélioration des plantes, chemistry.chemical_compound, Expression des gènes, functional protein expression, Clade, endogenous viral sequences, geminivirus, yam, selection analysis, Selection naturelle, Genetics, 0303 health sciences, Vegetal Biology, biology, Dioscorea, Transcription d'ADN, Agricultural sciences, Research Article, Séquence nucléotidique, Phytopathology and phytopharmacy, Microbiology, 03 medical and health sciences, Virology, Plant virus, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Gene, Géminivirus, Virus classification, H20 - Maladies des plantes, 030304 developmental biology, Nicotiana, Génome, Begomovirus, Virus des végétaux, biology.organism_classification, Amélioration des plantes, Phytopathologie et phytopharmacie, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, chemistry, DNA, Sciences agricoles, Biologie végétale, 010606 plant biology & botany
Abstract

BGPI : équipe 2/7; International audience; Endogenous viral sequences are essentially ‘fossil records’ that can sometimes reveal the genomic features of long extinct virus species. Although numerous known instances exist of single-stranded DNA (ssDNA) genomes becoming stably integrated within the genomes of bacteria and animals, there remain very few examples of such integration events in plants. The best studied of these events are those which yielded the geminivirus-related DNA elements found within the nuclear genomes of various Nicotiana species. Although other ssDNA virus-like sequences are included within the draft genomes of various plant species, it is not entirely certain that these are not contaminants. The Nicotiana geminivirus-related DNA elements therefore remain the only definitively proven instances of endogenous plant ssDNA virus sequences. Here, we characterize two new classes of endogenous plant virus sequence that are also apparently derived from ancient geminiviruses in the genus Begomovirus. These two endogenous geminivirus-like elements (EGV1 and EGV2) are present in the Dioscorea spp. of the Enantiophyllum clade. We used fluorescence in situ hybridization to confirm that the EGV1 sequences are integrated in the D. alata genome and showed that one or two ancestral EGV sequences likely became integrated more than 1.4 million years ago during or before the diversification of the Asian and African Enantiophyllum Dioscorea spp. Unexpectedly, we found evidence of natural selection actively favouring the maintenance of EGV-expressed replication-associated protein (Rep) amino acid sequences, which clearly indicates that functional EGV Rep proteins were probably expressed for prolonged periods following endogenization. Further, the detection in D. alata of EGV gene transcripts, small 21–24 nt RNAs that are apparently derived from these transcripts, and expressed Rep proteins, provides evidence that some EGV genes are possibly still functionally expressed in at least some of the Enantiophyllum clade species.

Published
2015
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7. An efficient and rapid protocol for plant nuclear DNA preparation suitable for next generation sequencing methods

Author

Christine Dubreuil-Tranchant, Patrice This, Marguerite Rodier-Goud, Gregory Carrier, Alexandre de Kochko, Sylvain Santoni, Loïc Le Cunff, Jean-Michel Boursiquot, Aurélie Canaguier, Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Géno-vigne® (UMT Géno-vigne®), Institut National de la Recherche Agronomique (INRA)-Institut Français de la Vigne et du Vin (IFV)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Diversité et adaptation des plantes cultivées (UMR DIAPC), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2), Diversité et Adaptation des Plantes Cultivées, Institut de Recherche pour le Développement (IRD [ Madagascar]), Développement et amélioration des plantes (UMR DAP), Centre National de la Recherche Scientifique (CNRS)-Université Montpellier 2 - Sciences et Techniques (UM2)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Unité de recherche en génomique végétale (URGV), Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)-Institut National de la Recherche Agronomique (INRA), UMR 1097 Diversité et Adaptation des Plantes Cultivées, 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)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), 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), Université Montpellier 2 - Sciences et Techniques (UM2)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut Français de la Vigne et du Vin (IFV)-Institut National de la Recherche Agronomique (INRA)

Subjects
0106 biological sciences, Cytoplasm, caféier, nuclei isolation, Plant Science, dna, Coffee, 01 natural sciences, F30 - Génétique et amélioration des plantes, séquenceurs de nouvelle génération, chemistry.chemical_compound, Vitis, 2. Zero hunger, 0303 health sciences, next generation sequencers, adn, coffee tree, viticulture, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, Nuclear DNA, DNA Contamination, isolation, Nucleic Acid Amplification Techniques, Genome, Plant, Méthodologie, coffea, DNA, Plant, Molecular Sequence Data, fruit tree, Computational biology, Biology, fruit arboriculture, DNA sequencing, 03 medical and health sciences, Coffea canephora, vitis vinifera, séquençage, Genetics, Gene, Ecology, Evolution, Behavior and Systematics, Gene Library, nuclear plant DNA extraction, arbre fruitier, 030304 developmental biology, Cell Nucleus, Bacterial artificial chromosome, Base Sequence, business.industry, gène, Multiple displacement amplification, Sequence Analysis, DNA, DNA extraction, grapevine, Biotechnology, isolement des noyaux, arboriculture fruitière, chemistry, nuclei, extraction, extraction de l'ADN nucléaire des plantes, vigne, business, DNA, 010606 plant biology & botany
Abstract

All protocols for Next Generation Sequencers (NGS) start with the preparation of a DNA library from extracted DNA. Quality, number, and length of the sequences produced by NGS all depend on the quality of the library that was prepared, itself dependent on the DNA quality. Generally, when using NGS, one would wish to obtain the genomic information contained in the nucleus without an excessive proportion of cytoplasmic DNA. Multiple copies of cytoplasmic genomes are present in every cell (11 to 70 copies, depending on the developmental stage and/or physiological status) ( Tymms et al., 1983 ). The chloroplast DNA of plants, therefore, represents 17 - 23% of their total DNA ( Boffey and Leech, 1982 ). In this study, we developed a protocol that strongly reduces the amount of cytoplasmic DNA. The improvement in quality makes the method perfectly adapted to library construction for NGS. We applied this extraction method to the grapevine ( Vitis vinifera L.) and coffee tree ( Coffea canephora Pierre ex A. Froehner). These species are known to contain many secondary metabolites, which can generate diffi culties for DNA extraction ( Peterson et al., 1997 ; Mattivi et al., 2006 ). To establish the protocol, we were partially inspired by a classic protocol for nuclear DNA plant extraction destined for the construction of BAC (Bacterial Artifi cial Chromosome) libraries ( Peterson et al., 1997 ). The two stages of the protocol are: (i) isolation of nuclei and (ii) nuclear DNA extraction. Nuclear DNA obtained with this protocol was then sequenced using 454/GS-FLX technology (Roche, Basel, Switzerland) with the Titanium kit. All protocols for Next Generation Sequencers (NGS) start with the preparation of a DNA library from extracted DNA. Quality, number, and length of the sequences produced by NGS all depend on the quality of the library that was prepared, itself dependent on the DNA quality. Generally, when using NGS, one would wish to obtain the genomic information contained in the nucleus without an excessive proportion of cytoplasmic DNA. Multiple copies of cytoplasmic genomes are present in every cell (11 to 70 copies, depending on the developmental stage and/or physiological status) ( Tymms et al., 1983 ). The chloroplast DNA of plants, therefore, represents 17 - 23% of their total DNA ( Boffey and Leech, 1982 ). In this study, we developed a protocol that strongly reduces the amount of cytoplasmic DNA. The improvement in quality makes the method perfectly adapted to library construction for NGS. We applied this extraction method to the grapevine ( Vitis vinifera L.) and coffee tree ( Coffea canephora Pierre ex A. Froehner). These species are known to contain many secondary metabolites, which can generate diffi culties for DNA extraction ( Peterson et al., 1997 ; Mattivi et al., 2006 ). To establish the protocol, we were partially inspired by a classic protocol for nuclear DNA plant extraction destined for the construction of BAC (Bacterial Artifi cial Chromosome) libraries ( Peterson et al., 1997 ). The two stages of the protocol are: (i) isolation of nuclei and (ii) nuclear DNA extraction. Nuclear DNA obtained with this protocol was then sequenced using 454/GS-FLX technology (Roche, Basel, Switzerland) with the Titanium kit.

Published
2010
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8. Radiation of the Nod-independent Aeschynomene relies on multiple allopolyploid speciation events

Author

Marc Boursot, Fabienne Cartieaux, Jean-François Arrighi, Eric Giraud, Marguerite Rodier-Goud, Céline Cardi, Angélique D'Hont, Bernard Dreyfus, Clémence Chaintreuil, Spencer Brown, Laboratoire des symbioses tropicales et méditerranéennes (UMR LSTM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université Montpellier 1 (UM1)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM)-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), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut des sciences du végétal (ISV), and Centre National de la Recherche Scientifique (CNRS)

Subjects
0106 biological sciences, Physiology, Lineage (evolution), [SDV]Life Sciences [q-bio], F62 - Physiologie végétale - Croissance et développement, Plant Science, 01 natural sciences, Genome, F30 - Génétique et amélioration des plantes, TECHNIQUE PCR, nodulation, PHYLOGENIE, In Situ Hybridization, Fluorescence, Phylogeny, Genetics, 0303 health sciences, biology, NODULE RACINAIRE, POLYPLOIDE, food and beverages, Fabaceae, GENOTYPE, GENOME, HYBRIDATION, DNA, Intergenic, Genome, Plant, Species complex, Nuclear gene, Genotype, Genetic Speciation, F60 - Physiologie et biochimie végétale, Pantropical, Mitosis, Genes, Plant, Chromosomes, Plant, Nod-independent symbiosis, Polyploidy, 03 medical and health sciences, Polyploid, Aeschynomene, polyploid complex, Species Specificity, ETUDE COMPARATIVE, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, SYMBIOSE, FLUORESCENCE, Crosses, Genetic, 030304 developmental biology, allopolyploid, LEGUMINEUSE TROPICALE, Cell Nucleus, Ecotype, Base Sequence, Chromosome, BIOLOGIE MOLECULAIRE, biology.organism_classification, Diploidy, ETUDE EXPERIMENTALE, 010606 plant biology & botany, Microsatellite Repeats
Abstract

International audience; The semi-aquatic legumes belonging to the genus Aeschynomene constitute a premium system for investigating the origin and evolution of unusual symbiotic features such as stem nodulation and the presence of a Nod-independent infection process. This latter apparently arose in a single Aeschynomene lineage. But how this unique Nod-independent group then radiated is not yet known. We have investigated the role of polyploidy in Aeschynomene speciation via a case study of the pantropical A. indica and then extended the analysis to the other Nod-independent species. For this, we combined SSR genotyping, genome characterization through flow cytometry, chromosome counting, FISH and GISH experiments, molecular phylogenies using ITS and single nuclear gene sequences, and artificial hybridizations. These analyses demonstrate the existence of an A. indica polyploid species complex comprising A. evenia (C. Wright) (2n = 2x = 20), A. indica L. s. s. (2n = 4x = 40) and a new hexaploid form (2n = 6x = 60). This latter contains the two genomes present in the tetraploid (A. evenia and A. scabra) and another unidentified genome. Two other species, A. pratensis and A. virginica, are also shown to be of allopolyploid origin. This work reveals multiple hybridization/polyploidization events, thus highlighting a prominent role of allopolyploidy in the radiation of the Nod-independent Aeschynomene.

Published
2013
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9. Three Infectious Viral Species Lying in Wait in the Banana Genome

Author

Marie-Stéphanie Vernerey, Franc-Christophe Baurens, Valérie Barbe, Marie-Line Iskra-Caruana, Matthieu Chabannes, Pierre-Olivier Duroy, Stéphanie Bocs, Marguerite Rodier-Goud, Philippe Gayral, Laboratoire des interactions plantes micro-organismes (LIPM), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Biologie et Génétique des Interactions Plante-Parasite (UMR BGPI), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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), Institut de recherche sur la biologie de l'insecte UMR7261 (IRBI), Université de Tours-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Université de Tours (UT)-Centre National de la Recherche Scientifique (CNRS), 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)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-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)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), and 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)

Subjects
0106 biological sciences, Genes, Viral, Gene Dosage, 01 natural sciences, Genome, virus des végétaux, F30 - Génétique et amélioration des plantes, Plant Viruses, banana B genome, Musa balbisiana, Gene Order, Banana streak virus, In Situ Hybridization, Fluorescence, Genomic organization, Genetics, Recombination, Genetic, 0303 health sciences, education.field_of_study, Vegetal Biology, banane, musa balbisiana, infectious, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Genome, Plant, sélection végétale, Genotype, Immunology, Population, endogenous Banana streak virus (eBSV), Genomics, Relation hôte pathogène, Biology, Microbiology, evolution 20 21, 03 medical and health sciences, musa acuminata, Virology, education, Gene, 030304 developmental biology, H20 - Maladies des plantes, amélioration génétique, génome, Haplotype, interaction hôte pathogène, Musa, séquence nucléotidique, biology.organism_classification, maladie des plantes, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, Genetic Diversity and Evolution, Insect Science, Biologie végétale, 010606 plant biology & botany
Abstract

Plant pararetroviruses integrate serendipitously into their host genomes. The banana genome harbors integrated copies of banana streak virus (BSV) named endogenous BSV (eBSV) that are able to release infectious pararetrovirus. In this investigation, we characterized integrants of three BSV species— Goldfinger (eBSGFV), Imove (eBSImV), and Obino l'Ewai (eBSOLV)—in the seedy Musa balbisiana Pisang klutuk wulung (PKW) by studying their molecular structure, genomic organization, genomic landscape, and infectious capacity. All eBSVs exhibit extensive viral genome duplications and rearrangements. eBSV segregation analysis on an F1 population of PKW combined with fluorescent in situ hybridization analysis showed that eBSImV, eBSOLV, and eBSGFV are each present at a single locus. eBSOLV and eBSGFV contain two distinct alleles, whereas eBSImV has two structurally identical alleles. Genotyping of both eBSV and viral particles expressed in the progeny demonstrated that only one allele for each species is infectious. The infectious allele of eBSImV could not be identified since the two alleles are identical. Finally, we demonstrate that eBSGFV and eBSOLV are located on chromosome 1 and eBSImV is located on chromosome 2 of the reference Musa genome published recently. The structure and evolution of eBSVs suggest sequential integration into the plant genome, and haplotype divergence analysis confirms that the three loci display differential evolution. Based on our data, we propose a model for BSV integration and eBSV evolution in the Musa balbisiana genome. The mutual benefits of this unique host-pathogen association are also discussed.

Published
2013
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10. Aeschynomene evenia, a model plant for studying the molecular genetics of the nod-independent rhizobium-legume symbiosis

Author

Sandrine Fabre, Clémence Chaintreuil, Spencer Brown, Fabienne Cartieaux, Joël Fardoux, Jean-François Arrighi, Marc Boursot, Eric Giraud, Djamel Gully, Delphine Patrel, Marguerite Rodier-Goud, Laboratoire des symbioses tropicales et méditerranéennes (UMR LSTM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université Montpellier 1 (UM1)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut des sciences du végétal (ISV), Centre National de la Recherche Scientifique (CNRS), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (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), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), French National Research Agency [ANR-SESAM-2010-BLAN-170801], and ANR-10-BLAN-1708,SESAM,Echange des signaux symbiotiques : analyse des mécanismes moléculaires dans les symbioses fixatrices d'azote Nod-indépendantes(2010)

Subjects
0106 biological sciences, NODULATION, Physiology, Plant genetics, RIBOSOMAL-RNA GENES, Agrobacterium, 01 natural sciences, Plant Root Nodulation, Plant Roots, F30 - Génétique et amélioration des plantes, GENOME STRUCTURE, INFECTION, LOTUS-JAPONICUS, Bradyrhizobium, Pollination, Phylogeny, 0303 health sciences, Plant Stems, food and beverages, Fabaceae, General Medicine, Medicago truncatula, Aeschynomène, ROOT ENDOSYMBIOSES, Phenotype, Rhizobium, ARACHIS-HYPOGAEA, Genome, Plant, Genetic Markers, DNA, Plant, F60 - Physiologie et biochimie végétale, Lotus japonicus, ARBUSCULAR MYCORRHIZA, Flowers, Biology, 03 medical and health sciences, Transformation, Genetic, Symbiosis, Nitrogen Fixation, Botany, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, 030304 developmental biology, Polymorphism, Genetic, Aeschynomene, MEDICAGO-TRUNCATULA, biology.organism_classification, EVOLUTION, Plant Leaves, Seedlings, Agronomy and Crop Science, 010606 plant biology & botany
Abstract

International audience; Research on the nitrogen-fixing symbiosis has been focused, thus far, on two model legumes, Medicago truncatula and Lotus japonicus, which use a sophisticated infection process involving infection thread formation. However, in 25% of the legumes, the bacterial entry occurs more simply in an intercellular fashion. Among them, some Aeschynomene spp. are nodulated by photosynthetic Bradyrhizobium spp. that do not produce Nod factors. This interaction is believed to represent a living testimony of the ancestral state of the rhizobium-legume symbiosis. To decipher the mechanisms of this Nod-independent process, we propose Aeschynomene evenia as a model legume because it presents all the characteristics required for genetic and molecular analysis. It is a short-perennial and autogamous species, with a diploid and relatively small genome (2n=20; 460 Mb/1C). A. evenia 'IRFL6945' is nodulated by the well-characterized photosynthetic Bradyrhizobium sp. strain ORS278 and is efficiently transformed by Agrobacterium rhizogenes. Aeschynomene evenia is genetically homozygous but polymorphic accessions were found. A manual hybridization procedure has been set up, allowing directed crosses. Therefore, it should be relatively straightforward to unravel the molecular determinants of the Nod-independent process in A. evenia. This should shed new light on the evolution of rhizobium-legume symbiosis and could have important agronomic implications.

Published
2012
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11. Highlighting the occurrence of tetraploidy in Acacia senegal (L.) Willd. and genetic variation patterns in its natural range revealed by DNA microsatellite markers

Author

Gilles Bezançon, Aichatou Assoumane, Marguerite Rodier-Goud, Daniel Verhaegen, Alzouma Mayaki Zoubeirou, Bénédicte Favreau, Université Abdou Moumouni [Niamey], Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), IRD Représentation du Niger, 276 Avenue de Maradi, BP 11416 Niamey, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-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 de Recherche pour le Développement (IRD), Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (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)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)

Subjects
0106 biological sciences, Acacia senegal . In situ hybridization . Polyploid complex .Genetic diversity .Genetic structure .SSRmarkers, Range (biology), 01 natural sciences, Genetic diversity, F30 - Génétique et amélioration des plantes, Génétique des populations, Chloroplaste, Marqueur génétique, Genetics, SSR markers, 0303 health sciences, Hybridation, food and beverages, Forestry, Polyploid complex, Polyploïdie, Genetic structure, Microsatellite, Ploidy, In situ hybridization, food.ingredient, Acacia senegal, Horticulture, Biology, 010603 evolutionary biology, 03 medical and health sciences, Variation génétique, food, Nombre chromosomique, Genetic variation, Tétraploïdie, Cytogénétique, Molecular Biology, 030304 developmental biology, fungi, K10 - Production forestière, Evolutionary biology, Gum arabic, Diploïdie, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract

International audience; Acacia senegal (L.) Willd. is the main species producing the internationally traded gum arabic. Genetic studies of this species are rare and until now the chromo- some number was thought to be diploid (2n02x026). Here, using chromosome number counting, we demonstrate for the first time that tetraploids (2n04x052) also occur in A. senegal. Nuclear and chloroplast microsatellite markers were used to estimate and compare genetic variation within this newly described polyploidy complex in the Sudano- Sahelian region in Africa. Genetic diversity was higher in diploids, suggesting that the formation of tetraploids is recent and that mutation-drift equilibrium has not yet been reached. The two cytotypes do not have the same genetic structure and are genetically differentiated. Among tetra- ploids, populations are greatly differentiated and do not share the same chlorotypes. Based on these results, we discuss recurrent formation of tetraploids from different diploid progenitors across the distribution range of A. senegal in the Sudano-Sahelian zone.

Published
2012
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12. A high-resolution map of the Nile tilapia genome: a resource for studying cichlids and other percomorphs

Author

Helena D'Cotta, Nikkie E. M. Van Bers, Jean-François Baroiller, Richard Guyon, Jean Pierre Coutanceau, Thomas D. Kocher, Matthew A. Conte, Lucile Soler, Naoual Azzouzi, Francis Galibert, Marguerite Rodier-Goud, Angélique D'Hont, Christophe Hitte, Céline Bonillo, Michaelle Rakotomanga, Richard P. M. A. Crooijmans, David J. Penman, Elodie Pepey, Catherine Ozouf-Costaz, Galibert, Francis, Institut de Génétique et Développement de Rennes (IGDR), Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Intensification raisonnée et écologique pour une pisciculture durable (UMR INTREPID), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), 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)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Department of Biology, University of Maryland [College Park], University of Maryland System-University of Maryland System, Animal Breeding and Genomics Centre, Wageningen University and Research [Wageningen] (WUR), Institute of Aquaculture, University of Stirling, Systématique, adaptation, évolution (SAE), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), This work was supported by grant to COC, JFB and CH (ANR-07-GANI-005) from ANR (Agence Nationale de la Recherche, France)., ANR-07-GANI-0005,PERCIMAP,Construction of a high-density Tilapia RH map(2007), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-IFR140-Centre National de la Recherche Scientifique (CNRS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Wageningen University and Research Centre [Wageningen] (WUR), Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), ANR-07-GANI-0005,GANI,Construction of a high-density Tilapia RH map(2007), Université de Rennes (UR)-Centre National de la Recherche Scientifique (CNRS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Université de Rennes (UR)-Centre National de la Recherche Scientifique (CNRS)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), De Villemeur, Hervé, and Genanimal - Construction of a high-density Tilapia RH map - - PERCIMAP2007 - ANR-07-GANI-0005 - GANI - VALID

Subjects
tetraodon-nigroviridis, 0106 biological sciences, Chromosomes, Artificial, Bacterial, oreochromis-niloticus, Genetic Linkage, tilapia, Polymorphisme génétique, sex determination, 01 natural sciences, Genome, Nile tilapia, poisson d'élevage, Marqueur génétique, évolution, Expressed Sequence Tags, Genetics, Comparative Genomic Hybridization, 0303 health sciences, Expressed sequence tag, biology, Oreochromis niloticus, Chromosome Mapping, Cichlids, genetic-linkage map, Oreochromis, [SDV.BBM.GTP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Research Article, Biotechnology, construction, Locus des caractères quantitatifs, lcsh:QH426-470, Genotype, Perciformes (199XXXXXXX013), lcsh:Biotechnology, Fish farming, Animal Breeding and Genomics, Quantitative trait locus, Polymorphism, Single Nucleotide, 010603 evolutionary biology, 03 medical and health sciences, Fish physiology, lcsh:TP248.13-248.65, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], evolution, Animals, Fokkerij en Genomica, 14. Life underwater, 030304 developmental biology, Génie génétique, fish, Radiation Hybrid Mapping, génome, Microsatellite, sequence, L10 - Génétique et amélioration des animaux, biology.organism_classification, radiation hybrid map, Haplochromine, lcsh:Genetics, Evolutionary biology, cartographie du génome, Carte génétique, WIAS, M12 - Production de l'aquaculture, zebrafish genome, cichlidae, Microsatellite Repeats
Abstract

Background The Nile tilapia (Oreochromis niloticus) is the second most farmed fish species worldwide. It is also an important model for studies of fish physiology, particularly because of its broad tolerance to an array of environments. It is a good model to study evolutionary mechanisms in vertebrates, because of its close relationship to haplochromine cichlids, which have undergone rapid speciation in East Africa. The existing genomic resources for Nile tilapia include a genetic map, BAC end sequences and ESTs, but comparative genome analysis and maps of quantitative trait loci (QTL) are still limited. Results We have constructed a high-resolution radiation hybrid (RH) panel for the Nile tilapia and genotyped 1358 markers consisting of 850 genes, 82 markers corresponding to BAC end sequences, 154 microsatellites and 272 single nucleotide polymorphisms (SNPs). From these, 1296 markers could be associated in 81 RH groups, while 62 were not linked. The total size of the RH map is 34,084 cR3500 and 937,310 kb. It covers 88% of the entire genome with an estimated inter-marker distance of 742 Kb. Mapping of microsatellites enabled integration to the genetic map. We have merged LG8 and LG24 into a single linkage group, and confirmed that LG16-LG21 are also merged. The orientation and association of RH groups to each chromosome and LG was confirmed by chromosomal in situ hybridizations (FISH) of 55 BACs. Fifty RH groups were localized on the 22 chromosomes while 31 remained small orphan groups. Synteny relationships were determined between Nile tilapia, stickleback, medaka and pufferfish. Conclusion The RH map and associated FISH map provide a valuable gene-ordered resource for gene mapping and QTL studies. All genetic linkage groups with their corresponding RH groups now have a corresponding chromosome which can be identified in the karyotype. Placement of conserved segments indicated that multiple inter-chromosomal rearrangements have occurred between Nile tilapia and the other model fishes. These maps represent a valuable resource for organizing the forthcoming genome sequence of Nile tilapia, and provide a foundation for evolutionary studies of East African cichlid fishes.

Published
2012
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13. Cytogenetic evidence of mixed disomic and polysomic inheritance in an allotetraploid (AABB) Musa genotype

Author

Angélique D'Hont, Frédéric Bakry, Xavier Perrier, Marguerite Rodier-Goud, Mouna Jeridi, and Ali Ferchichi

Subjects
Inheritance Patterns, Plant Science, Musa acuminata, F30 - Génétique et amélioration des plantes, Musa balbisiana, In Situ Hybridization, Fluorescence, Genetics, Likelihood Functions, biology, Nucleic Acid Hybridization, food and beverages, Meiosis, Ploidy, Genome, Plant, Génotype, medicine.medical_specialty, DNA, Plant, Genotype, Gamète, Chromosomes, Plant, Cytogenetics, medicine, Tétraploïdie, Cytogénétique, Hybrid, Chromosome, Héritabilité, Musa, Original Articles, biology.organism_classification, Tetraploidy, Recombinaison, Chromosome Pairing, Appariement chromosomique, Germ Cells, Plant
Abstract

Background and Aims Edible bananas originated mainly from two wild species, Musa acuminata Colla (AA) and Musa balbisiana Colla (BB), and triploid cultivars with an AAA, AAB or ABB genome are the most widely used. In the present study, chromosome pairing affinities are investigated in a sterile AB Indian variety and in its fertile colchicine-induced allotetraploid (AABB) derivative to determine the inheritance pattern of the tetraploid genotype. The potential implications of interspecific recombination and chromosomal composition of diploid gametes for Musa improvement are presented. Methods The pairing of different chromosome sets at diploid and tetraploid levels was investigated through a combination of conventional cytogenetic and genomic in-situ hybridization (GISH) analyses of meiotic chromosomes, leading to a likelihood model of the pairing behaviour. GISH analysis of mitotic chromosomes was also conducted to reveal the chromosome constitution of hybrids derived from crosses involving the allotetraploid genotype. Key Results Analysis of chromosome associations at both ploidy levels suggested that the newly formed allotetraploid behaves as a 'segmental allotetraploid' with three chromosome sets in a tetrasomic pattern, three sets in a likely disomic pattern and the five remaining sets in an intermediate pattern. Balanced and unbalanced diploid gametes were detected in progenies, with the chromosome constitution appearing to be more homogenous in pollen than in ovules. Conclusions Colchicine-induced allotetraploids in Musa provide access to the genetic background of natural AB varieties. The segmental inheritance pattern exhibited by the AABB allotetraploid genotype implies chromosome exchanges between M. acuminata and M. balbisiana species and opens new horizons for reciprocal transfer of valuable alleles. (Resume d'auteur)

Published
2012

14. Homoeologous chromosome pairing between the A and B genomes of Musa spp. revealed by genomic in situ hybridization

Author

Angélique D'Hont, Jacques Escoute, Frédéric Bakry, Ali Ferchichi, Marguerite Rodier-Goud, Mouna Jeridi, Françoise Carreel, Emmanuel Fondi, Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-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), and Université de Gabès

Subjects
0106 biological sciences, DNA, Plant, Gene Transfer, Horizontal, Musa, banana, genomic in situ hybridization, meiosis, homoeologous chromosomes pairing, interspecific hybrid, polyploidy, Plant Science, 01 natural sciences, Genome, Musa acuminata, Chromosomes, Plant, F30 - Génétique et amélioration des plantes, Polyploidy, 03 medical and health sciences, Meiosis, Musa balbisiana, Botany, [SDV.IDA]Life Sciences [q-bio]/Food engineering, [SPI.GPROC]Engineering Sciences [physics]/Chemical and Process Engineering, Cultivar, Metaphase, In Situ Hybridization, 030304 developmental biology, Hybrid, Genetics, 0303 health sciences, biology, fungi, Chromosome, food and beverages, Musa, biology.organism_classification, Chromosome Pairing, Hybridation interspécifique, Hybridization, Genetic, Technical Article, Triploïdie, 010606 plant biology & botany
Abstract

Publis011-agap-037 - UMR 1334 AGAP : Equipe AFEF ‘Architecture et Fonctionnement des Espèces fruitières’ ; Team AFFS ‘Architecture and Functioning of Fruit Species’; International audience; Background and Aims Most cooking banana and several desert bananas are interspecific triploid hybrids between Musa acuminata (A genome) and Musa balbisiana (B genome). In addition, M. balbisiana has agronomical characteristics such as resistance to biotic and abiotic stresses that could be useful to improve monospecific acuminata cultivars. To develop efficient breeding strategies for improving Musa cultivars, it is therefore important to understand the possibility of chromosome exchange between these two species. Methods A protocol was developed to prepare chromosome at meiosis metaphase I suitable for genomic in situ hybridization. A series of technical challenges were encountered, the main ones being the hardness of the cell wall and the density of the microsporocyte's cytoplasm, which hampers accessibility of the probes to the chromosomes. Key parameters in solving these problems were addition of macerozyme in the enzyme mix, the duration of digestion and temperature during the spreading phase. Results and Conclusions This method was applied to analyse chromosome pairing in metaphase from triploid interspecific cultivars, and it was clearly demonstrated that interspecific recombinations between M. acuminata and M. balbisiana chromosomes do occur and may be frequent in triploid hybrids. These results provide new insight into Musa cultivar evolution and have important implications for breeding.

Published
2011
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15. Mechanisms of haplotype divergence at the RGA08 nucleotide-binding leucine-rich repeat gene locus in wild banana (Musa balbisiana)

Author

Stéphanie Bocs, Mathieu Rouard, Nabila Yahiaoui, Takashi Matsumoto, Franc-Christophe Baurens, Roberto Neil Gerard Miller, Marguerite Rodier-Goud, and Didier Mbéguié-A-Mbéguié

Subjects
Identification, Phylogénie, Plant Science, F30 - Génétique et amélioration des plantes, Intergenic region, Gene Expression Regulation, Plant, Musa balbisiana, lcsh:Botany, Gene cluster, Gene Order, Conserved Sequence, Phylogeny, Genetics, Recombination, Genetic, Chromosome Mapping, Banana - doenças e pragas, lcsh:QK1-989, Banana - genética, Génotype, Research Article, Locus des caractères quantitatifs, Séquence nucléotidique, Sequence analysis, Pseudogene, Locus (genetics), Biology, Genes, Plant, Leucine, Haploïdie, Gene family, Alleles, Repetitive Sequences, Nucleic Acid, Génome, Haplotype, Genetic Variation, Musa, biology.organism_classification, Recombinaison, Haplotypes, Gène, Microsatellite Repeats
Abstract

Background Comparative sequence analysis of complex loci such as resistance gene analog clusters allows estimating the degree of sequence conservation and mechanisms of divergence at the intraspecies level. In banana (Musa sp.), two diploid wild species Musa acuminata (A genome) and Musa balbisiana (B genome) contribute to the polyploid genome of many cultivars. The M. balbisiana species is associated with vigour and tolerance to pests and disease and little is known on the genome structure and haplotype diversity within this species. Here, we compare two genomic sequences of 253 and 223 kb corresponding to two haplotypes of the RGA08 resistance gene analog locus in M. balbisiana "Pisang Klutuk Wulung" (PKW). Results Sequence comparison revealed two regions of contrasting features. The first is a highly colinear gene-rich region where the two haplotypes diverge only by single nucleotide polymorphisms and two repetitive element insertions. The second corresponds to a large cluster of RGA08 genes, with 13 and 18 predicted RGA genes and pseudogenes spread over 131 and 152 kb respectively on each haplotype. The RGA08 cluster is enriched in repetitive element insertions, in duplicated non-coding intergenic sequences including low complexity regions and shows structural variations between haplotypes. Although some allelic relationships are retained, a large diversity of RGA08 genes occurs in this single M. balbisiana genotype, with several RGA08 paralogs specific to each haplotype. The RGA08 gene family has evolved by mechanisms of unequal recombination, intragenic sequence exchange and diversifying selection. An unequal recombination event taking place between duplicated non-coding intergenic sequences resulted in a different RGA08 gene content between haplotypes pointing out the role of such duplicated regions in the evolution of RGA clusters. Based on the synonymous substitution rate in coding sequences, we estimated a 1 million year divergence time for these M. balbisiana haplotypes. Conclusions A large RGA08 gene cluster identified in wild banana corresponds to a highly variable genomic region between haplotypes surrounded by conserved flanking regions. High level of sequence identity (70 to 99%) of the genic and intergenic regions suggests a recent and rapid evolution of this cluster in M. balbisiana.

Published
2010

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