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15 results on '"Mathieu Rousseau-Gueutin"'

1. A Modified Meiotic Recombination in Brassica napus Largely Improves Its Breeding Efficiency

Author

Franz Boideau, Alexandre Pelé, Coleen Tanguy, Gwenn Trotoux, Frédérique Eber, Loeiz Maillet, Marie Gilet, Maryse Lodé-Taburel, Virginie Huteau, Jérôme Morice, Olivier Coriton, Cyril Falentin, Régine Delourme, Mathieu Rousseau-Gueutin, and Anne-Marie Chèvre

Subjects
recombination rate and distribution, polyploidy, allotriploidy, Brassica napus, genetic mapping, plant breeding, Biology (General), QH301-705.5
Abstract

Meiotic recombination is the main tool used by breeders to generate biodiversity, allowing genetic reshuffling at each generation. It enables the accumulation of favorable alleles while purging deleterious mutations. However, this mechanism is highly regulated with the formation of one to rarely more than three crossovers, which are not randomly distributed. In this study, we showed that it is possible to modify these controls in oilseed rape (Brassica napus, AACC, 2n = 4x = 38) and that it is linked to AAC allotriploidy and not to polyploidy per se. To that purpose, we compared the frequency and the distribution of crossovers along A chromosomes from hybrids carrying exactly the same A nucleotide sequence, but presenting three different ploidy levels: AA, AAC and AACC. Genetic maps established with 202 SNPs anchored on reference genomes revealed that the crossover rate is 3.6-fold higher in the AAC allotriploid hybrids compared to AA and AACC hybrids. Using a higher SNP density, we demonstrated that smaller and numerous introgressions of B. rapa were present in AAC hybrids compared to AACC allotetraploid hybrids, with 7.6 Mb vs. 16.9 Mb on average and 21 B. rapa regions per plant vs. nine regions, respectively. Therefore, this boost of recombination is highly efficient to reduce the size of QTL carried in cold regions of the oilseed rape genome, as exemplified here for a QTL conferring blackleg resistance.

Published
2021
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2. Haplotype Detection from Next-Generation Sequencing in High-Ploidy-Level Species: 45S rDNA Gene Copies in the Hexaploid Spartina maritima

Author

Julien Boutte, Benoît Aliaga, Oscar Lima, Julie Ferreira de Carvalho, Abdelkader Ainouche, Jiri Macas, Mathieu Rousseau-Gueutin, Olivier Coriton, Malika Ainouche, and Armel Salmon

Subjects
poaceae, duplication, paralogy, polyploidy, bioinformatics, Genetics, QH426-470
Abstract

Gene and whole-genome duplications are widespread in plant nuclear genomes, resulting in sequence heterogeneity. Identification of duplicated genes may be particularly challenging in highly redundant genomes, especially when there are no diploid parents as a reference. Here, we developed a pipeline to detect the different copies in the ribosomal RNA gene family in the hexaploid grass Spartina maritima from next-generation sequencing (Roche-454) reads. The heterogeneity of the different domains of the highly repeated 45S unit was explored by identifying single nucleotide polymorphisms (SNPs) and assembling reads based on shared polymorphisms. SNPs were validated using comparisons with Illumina sequence data sets and by cloning and Sanger (re)sequencing. Using this approach, 29 validated polymorphisms and 11 validated haplotypes were reported (out of 34 and 20, respectively, that were initially predicted by our program). The rDNA domains of S. maritima have similar lengths as those found in other Poaceae, apart from the 5′-ETS, which is approximately two-times longer in S. maritima. Sequence homogeneity was encountered in coding regions and both internal transcribed spacers (ITS), whereas high intragenomic variability was detected in the intergenic spacer (IGS) and the external transcribed spacer (ETS). Molecular cytogenetic analysis by fluorescent in situ hybridization (FISH) revealed the presence of one pair of 45S rDNA signals on the chromosomes of S. maritima instead of three expected pairs for a hexaploid genome, indicating loss of duplicated homeologous loci through the diploidization process. The procedure developed here may be used at any ploidy level and using different sequencing technologies.

Published
2016
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3. Speciation Success of Polyploid Plants Closely Relates to the Regulation of Meiotic Recombination

Author

Alexandre Pelé, Mathieu Rousseau-Gueutin, and Anne-Marie Chèvre

Subjects
polyploidy, genome evolution, diploidization, meiosis, unreduced gametes, recombination, Plant culture, SB1-1110
Abstract

Polyploidization is a widespread phenomenon, especially in flowering plants that have all undergone at least one event of whole genome duplication during their evolutionary history. Consequently, a large range of plants, including many of the world’s crops, combines more than two sets of chromosomes originating from the same (autopolyploids) or related species (allopolyploids). Depending on the polyploid formation pathway, different patterns of recombination will be promoted, conditioning the level of heterozygosity. A polyploid population harboring a high level of heterozygosity will produce more genetically diverse progenies. Some of these individuals may show a better adaptability to different ecological niches, increasing their chance for successful establishment through natural selection. Another condition for young polyploids to survive corresponds to the formation of well-balanced gametes, assuring a sufficient level of fertility. In this review, we discuss the consequences of polyploid formation pathways, meiotic behavior and recombination regulation on the speciation success and maintenance of polyploid species.

Published
2018
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4. Untangling structural factors driving genome stabilization in nascent Brassica napus allopolyploids

Author

Gwenn Trotoux, Maryse Lodé-Taburel, Jérôme Morice, Mathieu Rousseau-Gueutin, Cyril Falentin, Solenn Stoeckel, Frédérique Eber, Anne-Marie Chèvre, Marie-Madeleine Gilet, Julie Ferreira de Carvalho, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, 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), European Union, a Marie Sklodowska-Curie grant [791908], department 'Biology and Plant Breeding' at INRAE, Université de Rennes (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-INSTITUT AGRO Agrocampus Ouest, 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, Physiology, media_common.quotation_subject, Brassica, Fertility, Plant Science, Biology, 01 natural sciences, Genome, 03 medical and health sciences, Polyploid, Meiosis, homoeologous exchanges, Genetic algorithm, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Selection (genetic algorithm), polyploidy, 030304 developmental biology, media_common, 2. Zero hunger, fertility, 0303 health sciences, Brassica napus, food and beverages, biology.organism_classification, Aneuploidy, meiotic behavior, Evolutionary biology, euploid selection, Ploidy, Brassica napus (oilseed rape), Genome, Plant, genome stability, 010606 plant biology & botany
Abstract

International audience; Allopolyploids have globally higher fitness than their diploid progenitors; however, by comparison, most resynthesized allopolyploids have poor fertility and highly unstable genome. Elucidating the evolutionary processes promoting genome stabilization and fertility is thus essential to comprehend allopolyploid success. Using the Brassica model, we mimicked the speciation process of a nascent allopolyploid species by resynthesizing allotetraploid Brassica napus and systematically selecting for euploid individuals over eight generations in four independent allopolyploidization events with contrasted genetic backgrounds, cytoplasmic donors, and polyploid formation type. We evaluated the evolution of meiotic behavior and fertility and identified rearrangements in S-1 to S-9 lineages to explore the positive consequences of euploid selection on B. napus genome stability. Recurrent selection of euploid plants for eight generations drastically reduced the percentage of aneuploid progenies as early as the fourth generation, concomitantly with a decrease in number of newly fixed homoeologous rearrangements. The consequences of homoeologous rearrangements on meiotic behavior and seed number depended strongly on the genetic background and cytoplasm donor. The combined use of both self-fertilization and recurrent euploid selection allowed identification of genomic regions associated with fertility and meiotic behavior, providing complementary evidence to explain B. napus speciation success.

Published
2021
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5. Cytonuclear interactions remain stable during allopolyploid evolution despite repeated whole-genome duplications in Brassica

Author

Patrick Wincker, Jérémy Lucas, Jean-Marc Aury, Gwenn Trotoux, Anne-Marie Chèvre, Fabrice Legeai, Jérôme Morice, Valérie Barbe, Marie Gilet, Maryse Lodé, Zhesi He, Ian Bancroft, Cyril Falentin, Rod J. Snowdon, Julie Ferreira de Carvalho, Jean Keller, Olivier Filangi, Gwenaëlle Deniot, Mathieu Rousseau-Gueutin, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Scalable, Optimized and Parallel Algorithms for Genomics (GenScale), Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-GESTION DES DONNÉES ET DE LA CONNAISSANCE (IRISA-D7), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Rennes 1 (UR1), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), 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), Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Centre National de la Recherche Scientifique (CNRS), Justus-Liebig-Universität Gießen (JLU), University of York [York, UK], Université d'Évry-Val-d'Essonne (UEVE), Institut de Biologie François JACOB (JACOB), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), UK Biotechnology and Biological Sciences Research Council. Grant Number: BB/L027844/1Agreenskills+ FellowshipFrance Génomique National infrastructureAgence Nationale pour la Recherche. Grant Number: ANR‐10‐INBS‐09, ANR-10-INBS-09-01/10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), 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 National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Justus Liebig University, ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), and Justus-Liebig-Universität Gießen = Justus Liebig University (JLU)

Subjects
0106 biological sciences, 0301 basic medicine, Chloroplasts, Genome, Plastid, interspecific hybridization, Plant Science, Brassica, Biology, 01 natural sciences, Genome, allopolyploidy, Evolution, Molecular, Polyploidy, 03 medical and health sciences, Negative selection, chloroplast, Transcription (biology), Gene Duplication, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Genetics, Gene conversion, Plastid, Gene, fungi, Brassica napus, Brassica rapa, duplicated genes, food and beverages, Cell Biology, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, genome inheritance, 030104 developmental biology, Paleopolyploidy, intergenomic conflicts, Brassica oleracea, Ploidy, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], 010606 plant biology & botany
Abstract

International audience; Several plastid macromolecular protein complexes are encoded by both nuclear and plastid genes. Therefore, cytonuclear interactions are held in place to prevent genomic conflicts that may lead to incompatibilities. Allopolyploidy resulting from hybridization and genome doubling of two divergent species, can disrupt these fine-tuned interactions, as newly formed allopolyploid species confront biparental nuclear chromosomes with uniparentally inherited plastid genome. To avoid any deleterious effects of unequal genome inheritance, preferential transcription of the plastid donor over the other one has been hypothesized to occur in allopolyploids. We used Brassica as a model to study the effects of paleopolyploidy in diploid parental species, as well as the effects of recent and ancient allopolyploidy in Brassica napus on genes implicated in plastid protein complexes. We first identified redundant nuclear copies involved in those complexes. Compared to cytosolic protein complexes and to genome-wide retention rates, genes involved in plastid protein complexes show a higher retention of genes in duplicated and triplicated copies. Those redundant copies are functional and undergoing strong purifying selection. We then compared transcription patterns and sequences of those redundant gene copies between resynthesized allopolyploids and their diploid parents. The neo-polyploids showed no biased subgenome expression or maternal homogenization via gene conversion despite presence of some non-synonymous substitutions between plastid genomes of parental progenitors. Instead, subgenome dominance was observed regardless of the maternal progenitor. Our results provide new insights on the evolution of plastid protein complexes which could be tested and generalized in other allopolyploid species. This article is protected by copyright. All rights reserved.

Published
2019
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6. Amplifying recombination genome-wide and reshaping crossover landscapes in Brassicas

Author

Charles Poncet, Frédérique Eber, Mathieu Rousseau-Gueutin, Jérôme Morice, Alexandre Pelé, Sylvain Dechaumet, Gwenn Trotoux, Anne-Marie Chèvre, Maryse Lodé, Virginie Huteau, Thibaut Jousseaume, Sylvie Negre, Marie Gilet, Matthieu Falque, Olivier Coriton, Olivier C. Martin, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Génétique Quantitative et Evolution - Le Moulon (Génétique Végétale) (GQE-Le Moulon), Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-AgroParisTech-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]), Conseil Régional de Bretagne, BAP INRA, BAP INRA Département, ANR-14-CE19-0004,CROC,Contrôle de la fréquence de recombinaison méiotique pour accélérer l'innovation variétales chez les espèces cultivées polyploïdes(2014), AGROCAMPUS OUEST-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Recherche Agronomique (INRA), Centre National de la Recherche Scientifique (CNRS)-AgroParisTech-Université Paris-Sud - Paris 11 (UP11)-Institut National de la Recherche Agronomique (INRA), Écologie et santé des écosystèmes (ESE), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de la Recherche Agronomique (INRA), ANR- 14-CE19-0004, ANR, 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 Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST

Subjects
0301 basic medicine, Cancer Research, [SDV]Life Sciences [q-bio], Interference (genetic), Biochemistry, Chromosomal crossover, Homologous Chromosomes, recombinaison méiotique, chromosome, Cell Cycle and Cell Division, Crossing Over, Genetic, Homologous Recombination, Genetics (clinical), Genetic Interference, Genetics, Recombination, Genetic, education.field_of_study, Chromosome Biology, Chromosome Mapping, genêtic variation, Nucleic acids, Meiosis, Cell Processes, diversité génétique, Ploidy, Genome, Plant, Research Article, lcsh:QH426-470, DNA recombination, Population, crossing over, Brassica, Biology, Research and Analysis Methods, Polymorphism, Single Nucleotide, Chromosomes, [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, Polyploidy, 03 medical and health sciences, Genetic variation, education, Molecular Biology Techniques, genome, Molecular Biology, Ecology, Evolution, Behavior and Systematics, Hybrid, génome, Gene Mapping, Chromosome, Biology and Life Sciences, Genetic Variation, Cell Biology, DNA, Chromosome Pairs, lcsh:Genetics, 030104 developmental biology
Abstract

Meiotic recombination by crossovers (COs) is tightly regulated, limiting its key role in producing genetic diversity. However, while COs are usually restricted in number and not homogenously distributed along chromosomes, we show here how to disrupt these rules in Brassica species by using allotriploid hybrids (AAC, 2n = 3x = 29), resulting from the cross between the allotetraploid rapeseed (B. napus, AACC, 2n = 4x = 38) and one of its diploid progenitors (B. rapa, AA, 2n = 2x = 20). We produced mapping populations from different genotypes of both diploid AA and triploid AAC hybrids, used as female and/or as male. Each population revealed nearly 3,000 COs that we studied with SNP markers well distributed along the A genome (on average 1 SNP per 1.25 Mbp). Compared to the case of diploids, allotriploid hybrids showed 1.7 to 3.4 times more overall COs depending on the sex of meiosis and the genetic background. Most surprisingly, we found that such a rise was always associated with (i) dramatic changes in the shape of recombination landscapes and (ii) a strong decrease of CO interference. Hybrids carrying an additional C genome exhibited COs all along the A chromosomes, even in the vicinity of centromeres that are deprived of COs in diploids as well as in most studied species. Moreover, in male allotriploid hybrids we found that Class I COs are mostly responsible for the changes of CO rates, landscapes and interference. These results offer the opportunity for geneticists and plant breeders to dramatically enhance the generation of diversity in Brassica species by disrupting the linkage drag coming from limits on number and distribution of COs., Author summary In organisms with sexual reproduction, meiosis generates gametes containing half of the genetic material of parents. During this process, the reciprocal exchanges between the homologous chromosomes due to crossovers (COs) ensure their proper segregation as well as the generation of diversity. However, the number of COs is limited and their location is heterogeneous along chromosomes. A major challenge is to overcome these constraints for enhancing the genetic shuffling of alleles. This work demonstrates that it is possible to do so in Brassica hybrids obtained by manual crossings, combining a complete set of homologous chromosomes and a haploid set provided by a related species. Specifically, by studying large segregating populations, we find that in allotriploid Brassica hybrids, more COs are formed all along the homologous chromosomes, especially in regions usually deprived of COs, compared to diploids. These results offer the opportunity for geneticists and plant breeders to dramatically enhance the generation of new diversity.

Published
2017
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7. The impact of open pollination on the structural evolutionary dynamics, meiotic behavior, and fertility of resynthesized allotetraploid Brassica napus L

Author

Virginie Huteau, Gwenn Trotoux, Olivier Coriton, Sylvie Negre, Mathieu Rousseau-Gueutin, Marie Gilet, Sonia Vautrin, Jérôme Morice, Cyril Falentin, Alexandre Pelé, Maryse Lodé, Frédérique Eber, Anne-Marie Chèvre, Hélène Bergès, Joëlle Fourment, Gwennaëlle Deniot, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), AGROCAMPUS OUEST-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Recherche Agronomique (INRA), Centre National de Ressources Génomiques Végétales (CNRGV), Institut National de la Recherche Agronomique (INRA), ANR-10-EQPX-07-01, ERA-CAPS13.017_Evo-Genapus, Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, 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), ANR-10-EQPX-0007,LIGAN PM,Plate forme Lilloise de séquençage du génome humain pour une médecine personnalisée(2010), and Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST

Subjects
0301 basic medicine, Genomics, QH426-470, Biology, Brassica napus, allopolyploidy, genome dynamic, meiotic behavior, fertility, Genome, méïose, brassica napus, Open pollination, 03 medical and health sciences, Meiosis, Polyploid, polyploïdie, Genetics, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Molecular Biology, Genome size, Genetics (clinical), polyploidy, Vegetal Biology, Selfing, Chromosome, food and beverages, 030104 developmental biology, diversité allélique, plante à fleurs, hybridation génomique in situ, Biologie végétale, allopolyploidie
Abstract

Allopolyploidy, which results from the merger and duplication of two divergent genomes, has played a major role in the evolution and diversification of flowering plants. The genomic changes that occur in resynthesized or natural neopolyploids have been extensively studied, but little is known about the effects of the reproductive mode in the initial generations that may precede its successful establishment. To truly reflect the early generations of a nascent polyploid, two resynthesized allotetraploid Brassica napus populations were obtained for the first time by open pollination. In these populations, we detected a much lower level of aneuploidy (third generation) compared with those previously published populations obtained by controlled successive selfing. We specifically studied 33 resynthesized B. napus individuals from our two open pollinated populations, and showed that meiosis was affected in both populations. Their genomes were deeply shuffled after allopolyploidization: up to 8.5 and 3.5% of the C and A subgenomes were deleted in only two generations. The identified deletions occurred mainly at the distal part of the chromosome, and to a significantly greater extent on the C rather than the A subgenome. Using Fluorescent In Situ Hybridization (BAC-FISH), we demonstrated that four of these deletions corresponded to fixed translocations (via homeologous exchanges). We were able to evaluate the size of the structural variations and their impact on the whole genome size, gene content, and allelic diversity. In addition, the evolution of fertility was assessed, to better understand the difficulty encountered by novel polyploid individuals before the putative formation of a novel stable species.

Published
2017
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8. The poor lonesome A subgenome of Brassica napus var. Darmor (AACC) may not survive without its mate

Author

Alexandre Pelé, Cyril Falentin, Mathieu Rousseau-Gueutin, Sylvie Negre, Marie Gilet, Gwenn Trotoux, Jérôme Morice, Gwenaëlle Deniot, Anne-Marie Chèvre, Frédérique Eber, Maryse Lodé, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), AGROCAMPUS OUEST-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Recherche Agronomique (INRA), Chercheur indépendant, BAP INRA, Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, 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 Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST

Subjects
0106 biological sciences, 0301 basic medicine, oilseed rape, Physiology, [SDV]Life Sciences [q-bio], Introgression, Genomics, Context (language use), Plant Science, Biology, 01 natural sciences, Genome, Chromosomes, Plant, allopolyploidy, brassica napus, Polyploidy, 03 medical and health sciences, Polyploid, evolution, Gene, Genetics, génome, subgenome extraction, alloploidy, food and beverages, Biological Evolution, Diploidy, 030104 developmental biology, Genetic marker, évolution du génome, Hybridization, Genetic, Pollen, structural rearrangements, Ploidy, Genome, Plant, alloploidie, 010606 plant biology & botany
Abstract

International audience; Constitutive genomes of allopolyploid species evolve throughout their life span. However, the consequences of long-term alterations on the interdependency between each original genome have not been established. Here, we attempted an approach corresponding to subgenome extraction from a previously sequenced natural allotetraploid, offering a unique opportunity to evaluate plant viability and structural evolution of one of its diploid components. We employed two different strategies to extract the diploid AA component of the Brassica napus variety 'Darmor' (AACC, 2n = 4x = 38) and we assessed the genomic structure of the latest AA plants obtained (after four to five rounds of selection), using a 60K single nucleotide polymorphism Illumina array. Only one strategy was successful and the diploid AA plants that were structurally characterized presented a lower proportion of the B. napus A subgenome extracted than expected. In addition, our analyses revealed that some genes lost in a polyploid context appeared to be compensated for plant survival, either by conservation of genomic regions from B. rapa, used in the initial cross, or by some introgressions from the B. napus C subgenome. We conclude that as little as c. 7500 yr of coevolution could lead to subgenome interdependency in the allotetraploid B. napus as a result of structural modifications.

Published
2017
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9. The Impact of Open Pollination on the Structural Evolutionary Dynamics, Meiotic Behavior, and Fertility of Resynthesized Allotetraploid

Author

Mathieu, Rousseau-Gueutin, Jérôme, Morice, Olivier, Coriton, Virginie, Huteau, Gwenn, Trotoux, Sylvie, Nègre, Cyril, Falentin, Gwennaëlle, Deniot, Marie, Gilet, Frédérique, Eber, Alexandre, Pelé, Sonia, Vautrin, Joëlle, Fourment, Maryse, Lodé, Hélène, Bergès, and Anne-Marie, Chèvre

Subjects
fertility, Brassica napus, food and beverages, Investigations, Chromosomes, Plant, allopolyploidy, Evolution, Molecular, Polyploidy, Meiosis, genome dynamic, meiotic behavior, Hybridization, Genetic, Pollination, Genome, Plant, In Situ Hybridization, Fluorescence
Abstract

Allopolyploidy, which results from the merger and duplication of two divergent genomes, has played a major role in the evolution and diversification of flowering plants. The genomic changes that occur in resynthesized or natural neopolyploids have been extensively studied, but little is known about the effects of the reproductive mode in the initial generations that may precede its successful establishment. To truly reflect the early generations of a nascent polyploid, two resynthesized allotetraploid Brassica napus populations were obtained for the first time by open pollination. In these populations, we detected a much lower level of aneuploidy (third generation) compared with those previously published populations obtained by controlled successive selfing. We specifically studied 33 resynthesized B. napus individuals from our two open pollinated populations, and showed that meiosis was affected in both populations. Their genomes were deeply shuffled after allopolyploidization: up to 8.5 and 3.5% of the C and A subgenomes were deleted in only two generations. The identified deletions occurred mainly at the distal part of the chromosome, and to a significantly greater extent on the C rather than the A subgenome. Using Fluorescent In Situ Hybridization (BAC-FISH), we demonstrated that four of these deletions corresponded to fixed translocations (via homeologous exchanges). We were able to evaluate the size of the structural variations and their impact on the whole genome size, gene content, and allelic diversity. In addition, the evolution of fertility was assessed, to better understand the difficulty encountered by novel polyploid individuals before the putative formation of a novel stable species.

Published
2016

10. Reference Transcriptomes and Detection of Duplicated Copies in Hexaploid and Allododecaploid Spartina Species (Poaceae)

Author

Malika L. Aïnouche, Julien Boutte, Mathieu Rousseau-Gueutin, Corinne Da Silva, Patrick Wincker, Armel Salmon, Julie Ferreira de Carvalho, Julie Poulain, Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, 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 Génomique d'Evry (IG), Université Paris-Saclay-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), LIA Ecological Genomics of Polyploidy, Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Centre National de la Recherche Scientifique (CNRS), 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, Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, and Salmon, Armel

Subjects
0301 basic medicine, homeo-SNPs, transcriptome de novo assembly, K-S distribution, polyploidy, haplotyping, paralogs-orthologs-homeologs, Genotyping Techniques, Genomics, Biology, Poaceae, Genome, Polymorphism, Single Nucleotide, 03 medical and health sciences, paralogs–orthologs–homeologs, Gene Duplication, Gene duplication, Genetics, KS distribution, Ecology, Evolution, Behavior and Systematics, Gene Library, Spartina, Haplotype, food and beverages, Reference Standards, biology.organism_classification, 030104 developmental biology, Haplotypes, Ploidy, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Synonymous substitution, Transcriptome, Reference genome, Research Article
Abstract

International audience; In this study, we report the assembly and annotation of five reference transcriptomes for the European hexaploid Spartina species (S. maritima, S. alterniflora and their homoploid hybrids S. x townsendii and S. x neyrautii) and the allododecaploid invasive species S. anglica. These transcriptomes were constructed from various leaf and root cDNA libraries that were sequenced using both Roche-454 and Illumina technologies. Considering the high ploidy levels of the Spartina genomes under study, and considering the absence of diploid reference genome and the need of an appropriate analytical strategy, we developed generic bioinformatics tools to (1) detect different haplotypes of each gene within each species and (2) assign a parental origin to haplotypes detected in the hexaploid hybrids and the neo-allopolyploid. The approach described here allows the detection of putative homeologs from sets of short reads. Synonymous substitution rate (KS) comparisons between haplotypes from the hexaploid species revealed the presence of one KS peak (likely resulting from the tetraploid duplication event). The procedure developed in this study can be applied for future differential gene expression or genomics experiments to study the fate of duplicated genes in the invasive allododecaploid S. anglica.

Published
2016
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11. Haplotype Detection from Next-Generation Sequencing in High-Ploidy-Level Species: 45S rDNA Gene Copies in the Hexaploid Spartina maritima

Author

Malika L. Aïnouche, Benoît Aliaga, Armel Salmon, Abdelkader Aïnouche, Mathieu Rousseau-Gueutin, Jiri Macas, Oscar Lima, Julien Boutte, Julie Ferreira de Carvalho, Olivier Coriton, Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Inst Plant Mol Biol, Ctr Biol, Czech Academy of Sciences [Prague] (CAS), Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, 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), nternational Associated Laboratory 'Ecological Genomics of Polyploidy' - CNRS (INEE) [UMR CNRS 6553 Ecobio], University of Rennes 1, Iowa State University (Ames, USA), Partner University Funds, Molecular Ecology Platform [UMR CNRS 6553, Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Centre National de la Recherche Scientifique (CNRS), Czech Academy of Sciences [Prague] (ASCR), Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), and Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST

Subjects
0301 basic medicine, [SDV]Life Sciences [q-bio], Genomics, QH426-470, Biology, Investigations, Genes, Plant, Genome, DNA, Ribosomal, Polymorphism, Single Nucleotide, DNA sequencing, Polyploidy, 03 medical and health sciences, Open Reading Frames, Genetics, Coding region, Molecular Biology, Gene, paralogy, Genetics (clinical), In Situ Hybridization, Fluorescence, Phylogeny, poaceae, duplication, polyploidy, bioinformatics, Haplotype, Computational Biology, High-Throughput Nucleotide Sequencing, Reproducibility of Results, Molecular Sequence Annotation, External transcribed spacer, 030104 developmental biology, Haplotypes, RNA, Ribosomal, Ploidy, Genome, Plant
Abstract

Gene and whole-genome duplications are widespread in plant nuclear genomes, resulting in sequence heterogeneity. Identification of duplicated genes may be particularly challenging in highly redundant genomes, especially when there are no diploid parents as a reference. Here, we developed a pipeline to detect the different copies in the ribosomal RNA gene family in the hexaploid grass Spartina maritima from next-generation sequencing (Roche-454) reads. The heterogeneity of the different domains of the highly repeated 45S unit was explored by identifying single nucleotide polymorphisms (SNPs) and assembling reads based on shared polymorphisms. SNPs were validated using comparisons with Illumina sequence data sets and by cloning and Sanger (re)sequencing. Using this approach, 29 validated polymorphisms and 11 validated haplotypes were reported (out of 34 and 20, respectively, that were initially predicted by our program). The rDNA domains of S. maritima have similar lengths as those found in other Poaceae, apart from the 5′-ETS, which is approximately two-times longer in S. maritima. Sequence homogeneity was encountered in coding regions and both internal transcribed spacers (ITS), whereas high intragenomic variability was detected in the intergenic spacer (IGS) and the external transcribed spacer (ETS). Molecular cytogenetic analysis by fluorescent in situ hybridization (FISH) revealed the presence of one pair of 45S rDNA signals on the chromosomes of S. maritima instead of three expected pairs for a hexaploid genome, indicating loss of duplicated homeologous loci through the diploidization process. The procedure developed here may be used at any ploidy level and using different sequencing technologies.

Published
2015
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12. Tracking the evolutionary history of polyploidy in Fragaria L. (strawberry): new insights from phylogenetic analyses of low-copy nuclear genes

Author

Mathieu Rousseau-Gueutin, Malika L. Aïnouche, K. Olbricht, Beatrice Denoyes-Rothan, Amèlia Gaston, G. Staudt, Abdelkader Aïnouche, L. Richard, INRA : UR419, Institut National de la Recherche Agronomique (INRA), Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Centre National de la Recherche Scientifique (CNRS), Federal Research Centre for Cultivated Plants (JKI), Federal Research Centre for Cultivated Plants, Région Aquitaine INRA CIREF -Création variétale Fraises Fruits rouges, Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Station de recherches fruitières, Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), and Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0106 biological sciences, MESH: Genome, Plant, MESH: Sequence Analysis, DNA, MESH: Amino Acid Sequence, DHAR, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, 01 natural sciences, MESH: Genes, Plant, MESH: Fragaria, MESH: Phylogeny, Phylogeny, MESH: Evolution, Molecular, Plant Proteins, Genetics, 0303 health sciences, Duplicated gene, Phylogenetic tree, MESH: Plant Proteins, Fragaria, Reticulate evolution, GBSSI, Ploidy, Oxidoreductases, Genome, Plant, MESH: Cell Nucleus, Nuclear gene, DNA, Plant, Sequence analysis, [SDE.MCG]Environmental Sciences/Global Changes, Molecular Sequence Data, MESH: Sequence Alignment, Low-copy nuclear genes, Biology, Genes, Plant, 010603 evolutionary biology, Evolution, Molecular, Polyploidy, 03 medical and health sciences, Starch Synthase, Species Specificity, Polyploid, Phylogenetics, MESH: Polyploidy, MESH: Species Specificity, Amino Acid Sequence, MESH: Oxidoreductases, MESH: Diploidy, MESH: DNA, Plant, [SDU.ENVI]Sciences of the Universe [physics]/Continental interfaces, environment, Molecular Biology, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Cell Nucleus, MESH: Molecular Sequence Data, Sequence Analysis, DNA, Diploidy, MESH: Starch Synthase, Sequence Alignment
Abstract

International audience; Phylogenetic utility of two nuclear genes (GBSSI-2 and DHAR) was explored in genus Fragaria in order to clarify phylogenetic relationships among taxa and to elucidate the origin of the polyploid species. Orthology of the amplified products was assessed by several methods. Our results strongly suggest the loss of one GBSSI duplicated copy (GBSSI-1) in the Fragariinae subtribe. Phylogenetic analyses provided new insights into the evolutionary history of Fragaria, such as evidence supporting the presence of three main diploid genomic pools in the genus and demonstrating the occurrence of independent events of polyploidisation. In addition, the data provide evidence supporting an allopolyploid origin of the hexaploid F. moschata, and the octoploids F. chiloensis, F. iturupensis and F. virginiana. Accordingly, a new pattern summarizing our present knowledge on the Fragaria evolutionary history is proposed. Additionally, sequence analyses also revealed relaxed constraints on homoeologous copies at high ploidy level, as demonstrated by deletion events within DHAR coding sequences of some allo-octoploid haplotypes.

Published
2009
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13. Use of a reference octoploid map for detecting homoeologous QTLs potentially involved in viability in the cultivated strawberry

Author

N. Pedeprat, Beatrice Denoyes-Rothan, L. Barrot, E. Lerceteau-Köhler, Mathieu Rousseau-Gueutin, Amèlia Gaston, Aurélie Petit, P. Chartier, D. Roca, ProdInra, Migration, Unité de recherches Espèces Fruitières et Vigne (UREFV), Institut National de la Recherche Agronomique (INRA), and Création Variétale Fraises Fruits Rouges (Ciref)

Subjects
0106 biological sciences, QTL, [SDV]Life Sciences [q-bio], Population, POLYPLOIDY, Horticulture, Quantitative trait locus, CARTOGRAPHIE GENETIQUE, 01 natural sciences, Gene mapping, Genetic linkage, Botany, FRAISIER, Rosoideae, education, Genetics, education.field_of_study, biology, fungi, food and beverages, 04 agricultural and veterinary sciences, Fragaria, biology.organism_classification, FRAGARIA, [SDV] Life Sciences [q-bio], 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, Microsatellite, Ploidy, COMPARATIVE GENETIC MAPPING, 010606 plant biology & botany
Abstract

International audience; The construction of a reference map of the complex octoploid cultivated strawberry was optimized by comparative mapping between Fragaria showing different levels of ploidy. In addition, this approach is a powerful tool for improving the detection of QTLs, and for a better understanding of the organization of these QTLs. By identifying the homoeologous linkage groups in the complex octoploid cultivated strawberry, potential homoeologous QTLs in Fragaria can be detected. The comparative mapping was based on two populations belonging to two different levels of Fragaria. The linkage map of the complex octoploid cultivated strawberry (Fragaria × ananassa Duch., 2n=8x=56) was based on a segregating population of 213 individuals of a cross between ‘Capitola’ and ‘CF1116’, two genotypes with many contrasting traits. This genetic map was compared to the diploid one, obtained from an interspecific cross between F. vesca and F. bucharica (Sargent et al., 2006). Based on 56 SSR markers common to both diploid and octoploid genetic maps, almost all linkage groups of the genetic octoploid map were arranged into the seven homoeologous groups (HGs) expected for the genus Fragaria, which belongs to the tribe Rosoideae. For each trait, QTLs can potentially be detected on each linkage group belonging to the same HG. Results showed detection of homoeologous chromosomal regions potentially involved in viability of the plant.

Published
2009

14. Comparative Genetic Mapping Between Octoploid and Diploid Fragaria Species Reveals a High Level of Colinearity Between Their Genomes and the Essentially Disomic Behavior of the Cultivated Octoploid Strawberry

Author

Amparo Monfort, D. W. Simpson, Beatrice Denoyes-Rothan, G. Guérin, E. Lerceteau-Köhler, Pere Arús, Laure Barrot, Mathieu Rousseau-Gueutin, Daniel J. Sargent, European Commission, Région Nouvelle-Aquitaine, Unité de recherches Espèces Fruitières et Vigne (UREFV), Institut National de la Recherche Agronomique (INRA), Création Variétale Fraises Fruits Rouges (Ciref), East Malling Research, and Institute of Agrifood Research and Technology (IRTA)

Subjects
0106 biological sciences, DNA, Plant, Genetic Linkage, Molecular Sequence Data, Biology, CARTOGRAPHIE GENETIQUE, Investigations, 01 natural sciences, Genome, Fragaria, Chromosomes, Plant, Polyploidy, 03 medical and health sciences, Gene mapping, Meiosis, Genetic linkage, Genetics, Reference map, FRAISIER, Crosses, Genetic, 030304 developmental biology, 0303 health sciences, [SDV.GEN]Life Sciences [q-bio]/Genetics, ESPÈCE OCTOPLOÏDE, Chromosome Mapping, ESPÈCE DIPLOÏDE, Diploidy, Close relationship, Ploidy, Genome, Plant, 010606 plant biology & botany, Microsatellite Repeats
Abstract

Macrosynteny and colinearity between Fragaria (strawberry) species showing extreme levels of ploidy have been studied through comparative genetic mapping between the octoploid cultivated strawberry (F. ×ananassa) and its diploid relatives. A comprehensive map of the octoploid strawberry, in which almost all linkage groups are ranged into the seven expected homoeologous groups was obtained, thus providing the first reference map for the octoploid Fragaria. High levels of conserved macrosynteny and colinearity were observed between homo(eo)logous linkage groups and between the octoploid homoeologous groups and their corresponding diploid linkage groups. These results reveal that the polyploidization events that took place along the evolution of the Fragaria genus and the more recent juxtaposition of two octoploid strawberry genomes in the cultivated strawberry did not trigger any major chromosomal rearrangements in genomes involved in F. ×ananassa. They further suggest the existence of a close relationship between the diploid Fragaria genomes. In addition, despite the possible existence of residual levels of polysomic segregation suggested by the observation of large linkage groups in coupling phase only, the prevalence of linkage groups in coupling/repulsion phase clearly demonstrates that the meiotic behavior is mainly disomic in the cultivated strawberry., This work was supported by grants from the Région Aquitaine and the European Community (Fonds Européen de Développement Régional, FEDER funds).

Published
2008
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15. Impact of whole genome triplication on the evolutionary history and the functional dynamics of regulatory genes involved in Brassica self-incompatibility signalling pathway

Author

Maryse Lodé, Jérémy Lucas, Mathieu Rousseau-Gueutin, Sylvie Negre, Julie Ferreira de Carvalho, Gwenn Trotoux, Thanina Azibi, Houria Hadj-Arab, Marie-Madeleine Gilet, Julien Boutte, Xavier Vekemans, Anne-Marie Chèvre, FSTGAT/USTHB, BP 32, El-Alia Bab Ezzouar, 16111, Alger, Algeria, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, 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), Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo), Centre National de la Recherche Scientifique (CNRS)-Université de Lille, 791908, H2020 Marie Skłodowska-Curie Actions, 16MDU952, Accord-Programme of the Algerian-French Convention CMEP-TASSILI, Université des Sciences et de la Technologie Houari Boumediene = University of Sciences and Technology Houari Boumediene [Alger] (USTHB), Université de Rennes (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-INSTITUT AGRO Agrocampus Ouest, 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), Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo (EEP)), and Université de Lille-Centre National de la Recherche Scientifique (CNRS)

Subjects
0106 biological sciences, Brassica, Plant Science, Biology, 01 natural sciences, Genome, Polyploidy, Self-incompatibility, Transcription (biology), Evolutionary dynamics, Gene, Regulator gene, Genetics, Duplicated gene evolution, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], food and beverages, Brassicaceae, Cell Biology, Self-incompatibility signalling pathway, biology.organism_classification, Biological Evolution, Phenotype, Pollen, Ploidy, Genome, Plant, Whole genome triplication (WGT), Signal Transduction, 010606 plant biology & botany
Abstract

International audience; Polyploidy or whole genome duplication is a frequent and recurrent phenomenon in flowering plants that has played a major role in their diversification, adaptation and speciation. The adaptive success of polyploids relates to the different evolutionary fates of duplicated genes. In this study, we explored the impact of the whole genome triplication (WGT) event in the Brassiceae tribe on the genes involved in the self-incompatibility (SI) signalling pathway, a mechanism allowing recognition and rejection of self-pollen in hermaphrodite plants. By taking advantage of the knowledge acquired on this pathway as well as of several reference genomes in Brassicaceae species, we determined copy number of the different genes involved in this pathway and investigated their structural and functional evolutionary dynamics. We could infer that whereas most genes involved in the SI signalling returned to single copies after the WGT event (i.e. ARC1, JDP1, THL1, THL2, Exo70A01) in diploid Brassica species, a few were retained in duplicated (GLO1 and PLDα) or triplicated copies (MLPK). We also carefully studied the gene structure of these latter duplicated genes (including the conservation of functional domains and active sites) and tested their transcription in the stigma to identify which copies seem to be involved in the SI signalling pathway. By taking advantage of these analyses, we then explored the putative origin of a contrasted SI phenotype between two Brassica rapa varieties that have been fully sequenced and shared the same S-allele (S60).

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