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1. Genetic and transcriptomic analyses provide new insights on the early antiviral response to VHSV in resistant and susceptible rainbow trout

Author

Eloi R. Verrier, Carine Genet, Denis Laloë, Florence Jaffrezic, Andrea Rau, Diane Esquerre, Nicolas Dechamp, Céline Ciobotaru, Caroline Hervet, Francine Krieg, Luc Jouneau, Christophe Klopp, Edwige Quillet, and Pierre Boudinot

Subjects
Rainbow trout, VHSV, Antiviral resistance, Transcriptome deep sequencing, QTL, Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background The viral hemorrhagic septicemia virus (VHSV) is a major threat for salmonid farming and for wild fish populations worldwide. Previous studies have highlighted the importance of innate factors regulated by a major quantitative trait locus (QTL) for the natural resistance to waterborne VHSV infection in rainbow trout. The aim of this study was to analyze the early transcriptomic response to VHSV inoculation in cell lines derived from previously described resistant and susceptible homozygous isogenic lines of rainbow trout to obtain insights into the molecular mechanisms responsible for the resistance to the viral infection. Results We first confirmed the presence of the major QTL in a backcross involving a highly resistant fish isogenic line (B57) and a highly susceptible one (A22), and were able to define the confidence interval of the QTL and to identify its precise position. We extended the definition of the QTL since it controls not only resistance to waterborne infection but also the kinetics of mortality after intra-peritoneal injection. Deep sequencing of the transcriptome of B57 and A22 derived cell lines exposed to inactivated VHSV showed a stronger response to virus inoculation in the resistant background. In line with our previous observations, an early and strong induction of interferon and interferon-stimulated genes was correlated with the resistance to VHSV, highlighting the major role of innate immune factors in natural trout resistance to the virus. Interestingly, major factors of the antiviral innate immunity were much more expressed in naive B57 cells compared to naive A22 cells, which likely contributes to the ability of B57 to mount a fast antiviral response after viral infection. These observations were further extended by the identification of several innate immune-related genes localized close to the QTL area on the rainbow trout genome. Conclusions Taken together, our results improve our knowledge in virus-host interactions in vertebrates and provide novel insights in the molecular mechanisms explaining the resistance to VHSV in rainbow trout. Our data also provide a collection of potential markers for resistance and susceptibility of rainbow trout to VHSV infection.

Published
2018
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2. Resistance to a rhabdovirus (VHSV) in rainbow trout: identification of a major QTL related to innate mechanisms.

Author

Eloi R Verrier, Michel Dorson, Stéphane Mauger, Corinne Torhy, Céline Ciobotaru, Caroline Hervet, Nicolas Dechamp, Carine Genet, Pierre Boudinot, and Edwige Quillet

Subjects
Medicine, Science
Abstract

Health control is a major issue in animal breeding and a better knowledge of the genetic bases of resistance to diseases is needed in farm animals including fish. The detection of quantitative trait loci (QTL) will help uncovering the genetic architecture of important traits and understanding the mechanisms involved in resistance to pathogens. We report here the detection of QTL for resistance to Viral Haemorrhagic Septicaemia Virus (VHSV), a major threat for European aquaculture industry. Two induced mitogynogenetic doubled haploid F2 rainbow trout (Oncorhynchus mykiss) families were used. These families combined the genome of susceptible and resistant F0 breeders and contained only fully homozygous individuals. For phenotyping, fish survival after an immersion challenge with the virus was recorded, as well as in vitro virus replication on fin explants. A bidirectional selective genotyping strategy identified seven QTL associated to survival. One of those QTL was significant at the genome-wide level and largely explained both survival and viral replication in fin explants in the different families of the design (up to 65% and 49% of phenotypic variance explained respectively). These results evidence the key role of innate defence in resistance to the virus and pave the way for the identification of the gene(s) responsible for resistance. The identification of a major QTL also opens appealing perspectives for selective breeding of fish with improved resistance.

Published
2013
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3. Prenatal programming by testosterone of follicular theca cell functions in ovary

Author

Stéphane Fabre, Rozenn Dalbies-Tran, Hans Adriaensen, Juliette Cognie, Nathalie di Clemente, Anthony Estienne, Danielle Monniaux, Virginie Maillard, Carine Genet, Christelle Hennequet-Antier, Peggy Jarrier, Corinne Laclie, Florence Plisson-Petit, Pascal Papillier, Anne-Lyse Lainé, Physiologie de la reproduction et des comportements [Nouzilly] (PRC), Institut Français du Cheval et de l'Equitation [Saumur]-Université de Tours (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Biologie des Oiseaux et Aviculture (BOA), Institut National de la Recherche Agronomique (INRA)-Université de Tours (UT), CHU Saint-Antoine [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Institut National de la Santé et de la Recherche Médicale (INSERM), Region Centre and INRA, France - French fellowshipFrench National Research Agency (ANR) - AMHAROC/ANR-12-BSV1-0034-02, Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université de Tours-Institut Français du Cheval et de l'Equitation [Saumur], and Institut National de la Recherche Agronomique (INRA)-Université de Tours

Subjects
collagen, sheep, endocrine system, medicine.medical_specialty, Testosterone Excess, endocrine system diseases, Ovarian Cortex, [SDV]Life Sciences [q-bio], fibrillin, Biology, 03 medical and health sciences, Cellular and Molecular Neuroscience, 0302 clinical medicine, Ovarian Follicle, Pregnancy, Internal medicine, Follicular phase, medicine, Animals, Humans, rna sequencing, Gene Regulatory Networks, Testosterone, Molecular Biology, Cells, Cultured, mri, 030304 developmental biology, Pharmacology, 0303 health sciences, 030219 obstetrics & reproductive medicine, pcos, Theca Cell, Cell Biology, Antral follicle, Follicular fluid, smoc, Endocrinology, Gene Expression Regulation, Theca, Prenatal Exposure Delayed Effects, Theca Cells, amh, Molecular Medicine, Female, Polycystic Ovary Syndrome, Hormone
Abstract

International audience; In mammalian ovaries, the theca layers of growing follicles are critical for maintaining their structural integrity and supporting androgen synthesis. Through combining the postnatal monitoring of ovaries by abdominal magnetic resonance imaging, endocrine profiling, hormonal analysis of the follicular fluid of growing follicles, and transcriptomic analysis of follicular theca cells, we provide evidence that the exposure of ovine fetuses to testosterone excess activates postnatal follicular growth and strongly affects the functions of follicular theca in adulthood. Prenatal exposure to testosterone impaired androgen synthesis in the small antral follicles of adults and affected the expression in their theca cells of a wide array of genes encoding extracellular matrix components, their membrane receptors, and signaling pathways. Most expression changes were uncorrelated with the concentrations of gonadotropins, steroids, and anti-Müllerian hormone in the recent hormonal environment of theca cells, suggesting that these changes rather result from the long-term developmental effects of testosterone on theca cell precursors in fetal ovaries. Disruptions of the extracellular matrix structure and signaling in the follicular theca and ovarian cortex can explain the acceleration of follicle growth through altering the stiffness of ovarian tissue. We propose that these mechanisms participate in the etiology of the polycystic ovarian syndrome, a major reproductive pathology in woman.

Published
2019
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4. A novel homozygous nonsense mutation in ITGB4 gene causes epidermolysis bullosa in Mouton Vendéen sheep

Author

Stéphane Fabre, Florent Woloszyn, Carine Genet, L. Drouilhet, Louise Chantepie, Julien Sarry, Gwenola Tosser-Klopp, Florence Plisson-Petit, Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)

Subjects
Vendéen sheep, Genotype, media_common.quotation_subject, Nonsense mutation, Nonsense, Sheep Diseases, Biology, [SDV.BDLR.RS]Life Sciences [q-bio]/Reproductive Biology/Sexual reproduction, 03 medical and health sciences, 0302 clinical medicine, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Genetics, medicine, Animals, Gene, ComputingMilieux_MISCELLANEOUS, Sheep, Domestic, 030304 developmental biology, media_common, 0303 health sciences, Sheep, Integrin beta4, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, General Medicine, medicine.disease, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, Codon, Nonsense, 030220 oncology & carcinogenesis, Animal Science and Zoology, Epidermolysis bullosa, Epidermolysis Bullosa, Junctional
Abstract

International audience

Published
2020
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5. New Anti-Müllerian Hormone Target Genes Involved in Granulosa Cell Survival in Women With Polycystic Ovary Syndrome

Author

Stéphane Fabre, Alice Pierre, Emmanuelle Mathieu d'Argent, Corinne Vigouroux, Nathalie di Clemente, Carine Genet, Chrystèle Racine, Camille Bourgneuf, Charlotte Dupont, Christelle Hennequet-Antier, Danielle Monniaux, Julien Sarry, Florence Plisson-Petit, Centre de Recherche Saint-Antoine (CRSA), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU), Unité de Recherche sur les Maladies Cardiovasculaires, du Métabolisme et de la Nutrition = Research Unit on Cardiovascular and Metabolic Diseases (ICAN), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Institut de Cardiométabolisme et Nutrition = Institute of Cardiometabolism and Nutrition [CHU Pitié Salpêtrière] (IHU ICAN), CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), CHU Tenon [AP-HP], Physiologie de la reproduction et des comportements [Nouzilly] (PRC), Institut Français du Cheval et de l'Equitation [Saumur] (IFCE)-Université de Tours (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Unité de Biologie Fonctionnelle et Adaptative (BFA (UMR_8251 / U1133)), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Ligue nationale contre le cancerN/ref: RS16/75-41, ANR-12-BSV1-0034,AMHAROC,L'hormone anti-Müllérienne ovarienne : régulation, activité et implication dans le syndrome des ovaires polykystiques(2012), Fabre, Stéphane, BLANC - L'hormone anti-Müllérienne ovarienne : régulation, activité et implication dans le syndrome des ovaires polykystiques - - AMHAROC2012 - ANR-12-BSV1-0034 - BLANC - VALID, Centre de Recherche Saint-Antoine (CR Saint-Antoine), Sorbonne Université (SU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Saint-Antoine [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Unité de Recherche sur les Maladies Cardiovasculaires, du Métabolisme et de la Nutrition = Institute of cardiometabolism and nutrition (ICAN), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pitié-Salpêtrière [AP-HP], Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Institut Français du Cheval et de l'Equitation [Saumur]-Université de Tours-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Sorbonne Université (SU), and Institut Français du Cheval et de l'Equitation [Saumur]-Université de Tours (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)

Subjects
Anti-Mullerian Hormone, endocrine system diseases, Endocrinology, Diabetes and Metabolism, Clinical Biochemistry, Apoptosis, Anti-Müllerian hormone, [SDV.BBM.BM] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Biochemistry, Mice, 0302 clinical medicine, Endocrinology, Cells, Cultured, 0303 health sciences, [SDV.BDLR.RS] Life Sciences [q-bio]/Reproductive Biology/Sexual reproduction, 030219 obstetrics & reproductive medicine, biology, Granulosa cells apoptosis, Polycystic ovary, female genital diseases and pregnancy complications, [SDV.BBM.GTP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Female, hormones, hormone substitutes, and hormone antagonists, Polycystic Ovary Syndrome, Adult, endocrine system, medicine.medical_specialty, Cell Survival, Granulosa cell, Mice, Transgenic, [SDV.GEN.GA] Life Sciences [q-bio]/Genetics/Animal genetics, Follicle atresia, [SDV.BDLR.RS]Life Sciences [q-bio]/Reproductive Biology/Sexual reproduction, 03 medical and health sciences, Follicle, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Internal medicine, medicine, Animals, Humans, Gene, 030304 developmental biology, Cell Proliferation, Granulosa Cells, urogenital system, Biochemistry (medical), [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, medicine.disease, Mice, Inbred C57BL, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, Gene Expression Regulation, Atresia, Case-Control Studies, biology.protein, Target genes, Hormone
Abstract

Purpose A protective effect of anti-Müllerian hormone (AMH) on follicle atresia was recently demonstrated using long-term treatments, but this effect has never been supported by mechanistic studies. This work aimed to gain an insight into the mechanism of action of AMH on follicle atresia and on how this could account for the increased follicle pool observed in women with polycystic ovary syndrome (PCOS). Methods In vivo and in vitro experiments were performed to study the effects of AMH on follicle atresia and on the proliferation and apoptosis of granulosa cells (GCs). RNA-sequencing was carried out to identify new AMH target genes in GCs. The expression of some of these genes in GCs from control and PCOS women was compared using microfluidic real time quantitative RT-PCR. Results A short-term AMH treatment prevented follicle atresia in prepubertal mice. Consistent with this result, AMH inhibited apoptosis and promoted proliferation of different models of GCs. Moreover, integrative biology analyses of 965 AMH target genes identified in 1 of these GC models, confirmed that AMH had initiated a gene expression program favoring cell survival and proliferation. Finally, on 43 genes selected among the most up- and down-regulated AMH targets, 8 were up-regulated in GCs isolated from PCOS women, of which 5 are involved in cell survival. Main conclusions Our results provide for the first time cellular and molecular evidence that AMH protects follicles from atresia by controlling GC survival and suggest that AMH could participate in the increased follicle pool of PCOS patients.

Published
2020
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6. Transcriptome analysis of ovine granulosa cells reveals differences between small antral follicles collected during the follicular and luteal phases

Author

Julien Sarry, Carine Genet, Fazlollah Afraz, Florence Plisson-Petit, A. Ahmadi, Reza Talebi, Stéphane Fabre, Fac Agr, Dept Anim Sci, University of Tabriz, Agr Biotechnol Res Inst North Reg, Partenaires INRAE, Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées

Subjects
0301 basic medicine, [SDV.OT]Life Sciences [q-bio]/Other [q-bio.OT], endocrine system, Granulosa cell, Context (language use), Luteal Phase, Luteal phase, Biology, Andrology, 03 medical and health sciences, Food Animals, Follicular phase, Animals, RNA, Messenger, Small Animals, integrative analyse, Estrous cycle, Granulosa Cells, Sheep, Sequence Analysis, RNA, Equine, estrous cycle, Follicular atresia, RNA sequencing, granulosa cell, Antral follicle, 030104 developmental biology, Follicular Phase, Gene Expression Regulation, Female, Animal Science and Zoology, Folliculogenesis, Transcriptome
Abstract

International audience; Ovarian follicular growth occurs in both the follicular and luteal phases of the estrous cycle but in very different endocrine contexts. In both phases, many small antral follicles with similar morphologic and histologic characteristics are present within the ovaries as a reserve for the terminal folliculogenesis. However, there are several gaps in our molecular knowledge of the gene expression profiles of small antral follicles in the follicular and luteal phases. The aim of the present study was to use RNA sequencing to compare and analyze the global transcriptional profile of ovine granulosa cells collected from small antral follicles (1-3 mm) either during the follicular or the luteal phase of the estrous cycle, with the hypothesis that they should be differential. We identified 663 genes whose mRNA was differentially expressed or accumulated in the granulosa cell layer of small antral follicles in the two phases. A comprehensive interpretation of these data was performed through integrative analyses (Gene Ontology, Ingenuity Pathway Analysis) and the exploitation of already available transcriptomic data on follicular growth and atresia. In particular, we observed that the contrasted endocrine context between follicular and luteal phases may have an impact on estradiol, follicle-stimulating hormone (FSH), and on the activin/inhibin signaling pathways. Furthermore, we reveal the possible initiation of early follicular atresia in small antral follicles during the follicular phase in interaction with the presence of immune cells. This study provides new insights into the gene expression profile in ovine granulosa cells, and we suggest that these molecular changes may have an implication at the time of follicle selection. (C) 2017 Elsevier Inc. All rights reserved.

Published
2018
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8. Comparative Expression Pattern of Two Vestigial-Like 2 Genes in Zebrafish

Author

Xavier Cousin, Francine Rizk, Carine Genet, and Aline Hamade

Subjects
Genetics, animal structures, biology, Mutant, General Medicine, In situ hybridization, biology.organism_classification, Hedgehog signaling pathway, medicine.anatomical_structure, Transcription (biology), Notochord, medicine, Transcription factor, Zebrafish, Gene
Abstract

The vestigial Vg gene, initially characterized in Drosophila, encodes a transcription co-factor which is crucial for wings development. Vg binds via its Sd interaction domain (SID) to the Scalloped (Sd) transcription factor and its vertebrate homolog Tef1. Previous studies identified several vertebrate genes sharing high homology with Drosophila Vg SID such as Vgl (for Vg-like), TONDU (also known as Vgl1) or Vito-1 (also known as Vgl2). In order to investigate the role of vestigial-like 2 (vgll2) in zebrafish muscle development, we managed to clone and characterize two zebrafishVgll2 homolog genes, Vgll2a and Vgll2b. Alignment data showed high sequence homology of Vgll2a to vertebrates Vgll2 sequences. In situ hybridization showed that the two investigated Vgll2 genes had a similar expression pattern: they were first detected in adaxial cells (11 hpf), than expanded laterally in somites and at the end of segmentation, both genes were expressed in additional structures including head muscles and fin buds. In addition, different expression patterns of the two genes were observed. Vgll2a was expressed in bronchial arches precursor streams, derived gill muscles and hypothalamic precursors. Vgll2b was expressed in notochord at 14 hpf and regressed following notochord maturation at 18hpf. Furthermore, the genetic regulation of vgll2 genes was analysed using smu mutants and data revealed that both genes are regulated via the Hedgehog signaling pathway.

Published
2013
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9. A Second Generation Integrated Map of the Rainbow Trout (Oncorhynchus mykiss) Genome: Analysis of Conserved Synteny with Model Fish Genomes

Author

Caird E. Rexroad, Yuqin Hu, Frank M. You, Ming-Cheng Luo, Guangtu Gao, Mekki Boussaha, Yniv Palti, Carine Genet, National Center for Cool and Cold Water Aquaculture, ARS-USDA, United States Department of Agriculture, Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Department of Plant Sciences, University of California, Cereal Research Center, Agriculture and Agri-Food [Ottawa] (AAFC), and USDA-ARS : Agricultural Research Service

Subjects
0106 biological sciences, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, animal structures, Molecular Sequence Data, physical map, Synteny, 01 natural sciences, Applied Microbiology and Biotechnology, Genome, conserved synteny, 03 medical and health sciences, Animals, genetic map, 14. Life underwater, [INFO.INFO-BT]Computer Science [cs]/Biotechnology, 030304 developmental biology, Comparative genomics, Genetics, oncorhynchus mykiss, 0303 health sciences, Bacterial artificial chromosome, Base Sequence, Contig, biology, Chromosome Mapping, Stickleback, Chromosome, biology.organism_classification, Microsatellite, Rainbow trout, comparative genomic, 010606 plant biology & botany
Abstract

Chantier qualité GA; DNA fingerprints and end sequences from bacterial artificial chromosomes (BACs) from two new libraries were generated to improve the first generation integrated physical and genetic map of the rainbow trout (Oncorhynchus mykiss) genome. The current version of the physical map is composed of 167,989 clones of which 158,670 are assembled into contigs and 9,319 are singletons. The number of contigs was reduced from 4,173 to 3,220. End sequencing of clones from the new libraries generated a total of 11,958 high quality sequence reads. The end sequences were used to develop 238 new microsatellites of which 42 were added to the genetic map. Conserved synteny between the rainbow trout genome and model fish genomes was analyzed using 188,443 BAC end sequence (BES) reads. The fractions of BES reads with significant BLASTN hits against the zebrafish, medaka, and stickleback genomes were 8.8%, 9.7%, and 10.5%, respectively, while the fractions of significant BLASTX hits against the zebrafish, medaka, and stickleback protein databases were 6.2%, 5.8%, and 5.5%, respectively. The overall number of unique regions of conserved synteny identified through grouping of the rainbow trout BES into fingerprinting contigs was 2,259, 2,229, and 2,203 for stickleback, medaka, and zebrafish, respectively. These numbers are approximately three to five times greater than those we have previously identified using BAC paired ends. Clustering of the conserved synteny analysis results by linkage groups as derived from the integrated physical and genetic map revealed that despite the low sequence homology, large blocks of macrosynteny are conserved between chromosome arms of rainbow trout and the model fish species.

Published
2011
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10. Retinoic acid activates myogenesis in vivo through Fgf8 signalling

Author

Carine Genet, Laure Bally-Cuif, Gerrit Begemann, Florence Sabatier, Marianne Deries, Anne Bonnieu, Aline Hamade, Xavier Cousin, Différenciation Cellulaire et Croissance (DCC), Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2), University of Konstanz, Institute of Developmental Genetics, Helmholtz-Zentrum München (HZM), Institute of Virology, and Technical University

Subjects
medicine.medical_specialty, Embryo, Nonmammalian, animal structures, Fibroblast Growth Factor 8, SOMITES, [SDV]Life Sciences [q-bio], Retinoic acid, Tretinoin, Biology, Muscle Development, MyoD, MYOGENESIS, ACEREBELLAR, 03 medical and health sciences, chemistry.chemical_compound, 0302 clinical medicine, FGF8, PRESOMITIC MESODERM, Internal medicine, RETINOIC ACID, medicine, Paraxial mesoderm, Animals, [INFO]Computer Science [cs], fgf8, [SDV.BDD]Life Sciences [q-bio]/Development Biology, Molecular Biology, ComputingMilieux_MISCELLANEOUS, Myogenin, MyoD Protein, 030304 developmental biology, 0303 health sciences, ZEBRAFISH, Myogenesis, Gene Expression Regulation, Developmental, Cell Biology, Zebrafish Proteins, myoD, 3. Good health, Cell biology, Gastrulation, Endocrinology, chemistry, Protein Biosynthesis, embryonic structures, MYF5, 030217 neurology & neurosurgery, Signal Transduction, Developmental Biology
Abstract

International audience; Retinoic acid (RA) has been shown to regulate muscle differentiation in vitro. Here, we have investigated the role of RA signalling during embryonic myogenesis in zebrafish. We have altered RA signalling from gastrulation stages onwards by either inhibiting endogenous RA synthesis using an inhibitor of retinaldehyde dehydrogenases (DEAB) or by addition of exogenous RA. DEAB reduces expression of the myogenic markers myoD and myogenin in somites, whereas RA induces increased expression of these genes and strongly induces premature myoD expression in the presomitic mesoderm (psm). The expression dynamics of myf5 in presomitic and somitic mesoderm suggest that RA promotes muscle differentiation, a role supported by the fact that RA activates expression of fast myosin, while DEAB represses it. We identify Fgf8 as a major relay factor in RA-mediated activation of myogenesis. We show that fgf8 expression in somites and anterior psm is regulated by RA, and find that in the absence of Fgf8 signalling in the acerebellar mutant RA fails to promote myoD expression. We propose that, in the developing embryo, localised synthesis of RA by Raldh2 in the anterior psm and in somites activates fgf8 expression which in turn induces the expression of myogenic genes and fast muscle differentiation.

Published
2006
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11. Rna-seq analysis of transcriptome response to VHS-V infection in two target tissues of resistant vs susceptible trout clonal lines

Author

Carine Genet, Verrier, E. R., Céline Ciobotaru, Christophe Klopp, Diane Esquerre, Denis Laloë, Pierre Boudinot, Edwige Quillet, Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, UMR1110, Institut National de la Santé et de la Recherche Médicale (INSERM), Unité de Biométrie et Intelligence Artificielle (UBIA), Institut National de la Recherche Agronomique (INRA), Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT], Unité de recherche Virologie et Immunologie Moléculaires (VIM), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, and Unité de recherche Virologie et Immunologie Moléculaires (VIM (UR 0892))

Subjects
resistance, [SDV]Life Sciences [q-bio], identification, virus, gene, vhs-v, transcriptome, infection
Abstract

absent

Published
2014

12. Identification de gènes différentiellement exprimés dans deux tissus cibles de lignées clonales de truite sensibles ou résistantes à la SHV

Author

Carine Genet, Verrier, E. R., Céline Ciobotaru, Christophe Klopp, Diane Esquerre, Denis Laloë, Pierre Boudinot, Edwige Quillet, Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, UMR1110, Institut National de la Santé et de la Recherche Médicale (INSERM), Unité de Biométrie et Intelligence Artificielle (ancêtre de MIAT) (UBIA), Institut National de la Recherche Agronomique (INRA), Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT], Unité de recherche Virologie et Immunologie Moléculaires (VIM (UR 0892)), ProdInra, Archive Ouverte, Unité de Biométrie et Intelligence Artificielle (UBIA), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Unité de recherche Virologie et Immunologie Moléculaires (VIM), and AgroParisTech-Institut National de la Recherche Agronomique (INRA)

Subjects
[SDV] Life Sciences [q-bio], [SDV]Life Sciences [q-bio]
Abstract

absent

Published
2014

13. Salmonids have an extraordinary complex type I IFN system: characterization of the IFN locus in Rainbow trout [i]Oncorhynchus mykiss[/i] reveals two novel IFN subgroups

Author

Tzong-Yueh Chen, Carine Genet, Jun Zou, Akshaya Panigrahi, Christopher J. Secombes, Young Mao Chen, Mahmood Ul Hassan, Sharif M. Mughal, Po Tsang Lee, Thitiya Summathed, Pierre Boudinot, Bartolomeo Gorgoglione, Nick G.H. Taylor, Scottish Fish Immunology Research Centre, School of Biological Sciences, University of Aberdeen, Weymouth Laboratory, Centre for Environment, Fisheries and Aquaculture Science [Weymouth] (CEFAS), Génétique Animale et Biologie Intégrative (GABI), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Institute of Biotechnology, National Cheng Kung University (NCKU), Zoology Department, Government College University, Faculty of Fisheries and Wild Life, University of Veterinary and Animal Sciences, Unité de recherche Virologie et Immunologie Moléculaires (VIM), Institut National de la Recherche Agronomique (INRA), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, and Unité de recherche Virologie et Immunologie Moléculaires (VIM (UR 0892))

Subjects
Fish Proteins, endocrine system, animal structures, animal diseases, [SDV]Life Sciences [q-bio], Immunology, Molecular Sequence Data, Stimulation, Spleen, Biology, Brown trout, chemistry.chemical_compound, medicine, Immunology and Allergy, Animals, Salmo, Innate immune system, Base Sequence, urogenital system, biology.organism_classification, Molecular biology, 3. Good health, medicine.anatomical_structure, chemistry, Cell culture, Genetic Loci, Organ Specificity, Oncorhynchus mykiss, Interferon Type I, Rainbow trout, Resiquimod
Abstract

Fish type I IFNs are classified into two groups with two (group I) or four (group II) cysteines in the mature peptide and can be further divided into four subgroups, termed IFN-a, -b, -c, and -d. Salmonids possess all four subgroups, whereas other teleost species have one or more but not all groups. In this study, we have discovered two further subgroups (IFN-e and -f) in rainbow trout Oncorhynchus mykiss and analyzed the expression of all six subgroups in rainbow trout and brown trout Salmo trutta. In rainbow trout RTG-2 and RTS-11 cells, polyinosinic-polycytidylic acid stimulation resulted in early activation of IFN-d, whereas the IFN-e subgroup containing the highest number of members showed weak induction. In contrast with the cell lines, remarkable induction of IFN-a, -b, and -c was detected in primary head kidney leukocytes after polyinosinic-polycytidylic acid treatment, whereas a moderate increase of IFNs was observed after stimulation with resiquimod. Infection of brown trout with hemorrhagic septicemia virus resulted in early induction of IFN-d, -e, and -f and a marked increase of IFN-b and IFN-c expression in kidney and spleen. IFN transcripts were found to be strongly correlated with the viral burden and with marker genes of the IFN antiviral cascade. The results demonstrate that the IFN system of salmonids is far more complex than previously realized, and in-depth research is required to fully understand its regulation and function.

Published
2014
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14. The rainbow trout genome provides novel insights into evolution after whole-genome duplication in vertebrates

Author

Patrick Wincker, Pascal Bento, Benjamin Noel, Cédric Cabau, Jean-Marc Aury, Yann Guiguen, Alexandra Louis, Edwige Quillet, Carine Genet, Julien Bobe, Maria Bernard, Mekki Boussaha, Camille Berthelot, Olivier Jaillon, Delphine Galiana, Jean-Nicolas Volff, Christophe Klopp, Domitille Chalopin, Corinne Da Silva, Patrice Dehais, Christine Gaspin, Karine Labadie, Frédéric Brunet, Gary H. Thorgaard, Adriana Alberti, Philippe Bardou, Jérôme Montfort, Amélie Juanchich, Hugues Roest Crollius, René Guyomard, Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), Département de Biologie - ENS Paris, 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), 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), Welcome Trust Genome Campus, Hinxton, European Bioinformatics Institute, École normale supérieure - Lyon (ENS Lyon), Institut de Génomique Fonctionnelle de Lyon (IGFL), École normale supérieure - Lyon (ENS Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Physiologie et Génomique des Poissons (LPGP), Institut National de la Recherche Agronomique (INRA)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Unité de Biométrie et Intelligence Artificielle (UBIA), Institut National de la Recherche Agronomique (INRA), School of Biological Sciences, Washington State University (WSU), Université d'Évry-Val-d'Essonne (UEVE), Génomique métabolique (UMR 8030), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), ANR (Genotrout project, ANR-09-GENM-001) Génomique et Biotechnologies Végétales, Institut de biologie de l'ENS Paris (IBENS), 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), École normale supérieure de Lyon (ENS de Lyon), École normale supérieure de Lyon (ENS de Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-École nationale supérieure agronomique de Toulouse (ENSAT), Université de Toulouse (UT)-Université de Toulouse (UT), Unité de Biométrie et Intelligence Artificielle (ancêtre de MIAT) (UBIA), Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris)-École normale supérieure - Paris (ENS Paris)-Centre National de la Recherche Scientifique (CNRS), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT], ProdInra, Archive Ouverte, 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)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), 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), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-École normale supérieure - Lyon (ENS Lyon), Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Institut National de la Recherche Agronomique (INRA), AgroParisTech-Institut National de la Recherche Agronomique (INRA), 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), 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), and 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 National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)

Subjects
phylogénétique, [SDV]Life Sciences [q-bio], séquençage du génome complet, General Physics and Astronomy, Whole genome duplication, Vertebrate genome, Biology, Gene Deletions, Genome, Article, General Biochemistry, Genetics and Molecular Biology, Evolution, Molecular, poisson, Gene Duplication, biology.animal, phylogénie, Animals, analyse génomique, duplication des génomes, Gene, salmonidae, Genetics, oncorhynchus mykiss, Multidisciplinary, génome, évolution animale, Vertebrate, General Chemistry, biology.organism_classification, Spotted gar, [SDV] Life Sciences [q-bio], évolution des espèces, Vertebrates, Rainbow trout, analyse génétique, truite arc en ciel, expression des gènes
Abstract

Vertebrate evolution has been shaped by several rounds of whole-genome duplications (WGDs) that are often suggested to be associated with adaptive radiations and evolutionary innovations. Due to an additional round of WGD, the rainbow trout genome offers a unique opportunity to investigate the early evolutionary fate of a duplicated vertebrate genome. Here we show that after 100 million years of evolution the two ancestral subgenomes have remained extremely collinear, despite the loss of half of the duplicated protein-coding genes, mostly through pseudogenization. In striking contrast is the fate of miRNA genes that have almost all been retained as duplicated copies. The slow and stepwise rediploidization process characterized here challenges the current hypothesis that WGD is followed by massive and rapid genomic reorganizations and gene deletions., Although whole-genome duplications (WGDs) are rare events, they have an important role in shaping vertebrate evolution. Here, the authors sequence the rainbow trout genome and show that rediploidization after WGD occurs in a slow and stepwise manner.

Published
2014
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15. Resistance to a Rhabdovirus (VHSV) in Rainbow Trout: Identification of a Major QTL Related to Innate Mechanisms

Author

M. Dorson, Nicolas Dechamp, Corinne Torhy, Pierre Boudinot, Stéphane Mauger, Caroline Hervet, Carine Genet, Céline Ciobotaru, Edwige Quillet, Eloi R. Verrier, Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Unité de recherche Virologie et Immunologie Moléculaires (VIM), Institut National de la Recherche Agronomique (INRA), European Community (IFOP), French Ministry of Research [2004/190], European Community's SeventhFramework Programme (FP7), Research Infrastructures action [FP7-228394], Animal Genetics and Animal Health Divisions of INRA, Unité de recherche Virologie et Immunologie Moléculaires (VIM (UR 0892)), and Quillet, Edwige

Subjects
Male, Aquaculture, Virus Replication, Tissue Culture Techniques, Hemorrhagic Septicemia, Viral, Animal Breeding, Animal Management, Genetics, 0303 health sciences, Novirhabdovirus, trout, Genome, Multidisciplinary, biology, qtl, Homozygote, Chromosome Mapping, Agriculture, 04 agricultural and veterinary sciences, Sciences du Vivant [q-bio]/Microbiologie et Parasitologie, Survival Rate, Trout, Phenotype, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Veterinary Diseases, Oncorhynchus mykiss, fish, Medicine, Female, Fish Farming, rhabdovirus, Ichthyology, Research Article, Genotype, Science, Quantitative Trait Loci, Quantitative trait locus, Selective breeding, 03 medical and health sciences, Animals, 14. Life underwater, Biology, Gene, 030304 developmental biology, Veterinary Virology, biology.organism_classification, Immunity, Innate, Genetic architecture, Genetics of Disease, 040102 fisheries, Doubled haploidy, 0401 agriculture, forestry, and fisheries, Veterinary Science, Rainbow trout, Animal Genetics, Zoology, truite arc en ciel
Abstract

Chantier qualité GA; Health control is a major issue in animal breeding and a better knowledge of the genetic bases of resistance to diseases is needed in farm animals including fish. The detection of quantitative trait loci (QTL) will help uncovering the genetic architecture of important traits and understanding the mechanisms involved in resistance to pathogens. We report here the detection of QTL for resistance to Viral Haemorrhagic Septicaemia Virus (VHSV), a major threat for European aquaculture industry. Two induced mitogynogenetic doubled haploid F2 rainbow trout (Oncorhynchus mykiss) families were used. These families combined the genome of susceptible and resistant F0 breeders and contained only fully homozygous individuals. For phenotyping, fish survival after an immersion challenge with the virus was recorded, as well as in vitro virus replication on fin explants. A bidirectional selective genotyping strategy identified seven QTL associated to survival. One of those QTL was significant at the genome-wide level and largely explained both survival and viral replication in fin explants in the different families of the design (up to 65% and 49% of phenotypic variance explained respectively). These results evidence the key role of innate defence in resistance to the virus and pave the way for the identification of the gene(s) responsible for resistance. The identification of a major QTL also opens appealing perspectives for selective breeding of fish with improved resistance.

Published
2013
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16. Gynogenetic clonal lines of rainbow trout O. mykiss, a model for the identification of new antiviral pathways

Author

Eloi Verrier, Michel Dorson, Nicolas Dechamp, Corinne Torhy, Sandrine Le Guillou, Céline Ciobotaru, Carine Genet, Pierre Boudinot, Edwige Quillet, Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, 0892 Unité de Virologie et Immunologie Moléculaires, Institut National de la Recherche Agronomique (INRA), Unité de recherche Virologie et Immunologie Moléculaires (VIM), Virologie et Immunologie Moléculaires (VIM (UR 0892)), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Unité de recherche Virologie et Immunologie Moléculaires (VIM (UR 0892)), AgroParisTech-Institut National de la Recherche Agronomique (INRA), and Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)

Subjects
[SDV]Life Sciences [q-bio]
Abstract

absent

Published
2012

17. Analysis of BAC-end sequences in rainbow trout: Content characterization and assessment of synteny between trout and other fish genomes

Author

Frédérick Gavory, Edwige Quillet, Patrick Wincker, Carine Genet, Yniv Palti, Patrice Dehais, Mekki Boussaha, Guangtu Gao, Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Laboratoire de Génétique Cellulaire (LGC), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, National Center for Cool and Cold Water Aquaculture, ARS-USDA, USDA-ARS : Agricultural Research Service, Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Recherche Agronomique (INRA), United States Department of Agriculture, 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 de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT), AgroParisTech-Institut National de la Recherche Agronomique (INRA), and Genet, Carine

Subjects
0106 biological sciences, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, Chromosomes, Artificial, Bacterial, genomic tool, animal structures, Positional cloning, lcsh:QH426-470, Sequence analysis, lcsh:Biotechnology, Minisatellite Repeats, Computational biology, Synteny, 01 natural sciences, Genome, 03 medical and health sciences, Sequence Homology, Nucleic Acid, lcsh:TP248.13-248.65, Genetics, Animals, 14. Life underwater, rainbow trout, bac-end sequence, Cloning, Molecular, 030304 developmental biology, Whole genome sequencing, Comparative genomics, 0303 health sciences, biology, Sequence Analysis, DNA, biology.organism_classification, Trout, lcsh:Genetics, Oncorhynchus mykiss, Rainbow trout, Research Article, 010606 plant biology & botany, Biotechnology
Abstract

Background Rainbow trout (Oncorhynchus mykiss) are cultivated worldwide for aquaculture production and are widely used as a model species to gain knowledge of many aspects of fish biology. The common ancestor of the salmonids experienced a whole genome duplication event, making extant salmonids such as the rainbow trout an excellent model for studying the evolution of tetraploidization and re-diploidization in vertebrates. However, the lack of a reference genome sequence hampers research progress for both academic and applied purposes. In order to enrich the genomic tools already available in this species and provide further insight on the complexity of its genome, we sequenced a large number of rainbow trout BAC-end sequences (BES) and characterized their contents. Results A total of 176,485 high quality BES, were generated, representing approximately 4% of the trout genome. BES analyses identified 6,848 simple sequence repeats (SSRs), of which 3,854 had high quality flanking sequences for PCR primers design. The first rainbow trout repeat elements database (INRA RT rep1.0) containing 735 putative repeat elements was developed, and identified almost 59.5% of the BES database in base-pairs as repetitive sequence. Approximately 55% of the BES reads (97,846) had more than 100 base pairs of contiguous non-repetitive sequences. The fractions of the 97,846 non-repetitive trout BES reads that had significant BLASTN hits against the zebrafish, medaka and stickleback genome databases were 15%, 16.2% and 17.9%, respectively, while the fractions of the non-repetitive BES reads that had significant BLASTX hits against the zebrafish, medaka, and stickleback protein databases were 10.7%, 9.5% and 9.5%, respectively. Comparative genomics using paired BAC-ends revealed several regions of conserved synteny across all the fish species analyzed in this study. Conclusions The characterization of BES provided insights on the rainbow trout genome. The discovery of specific repeat elements will facilitate analyses of sequence content (e.g. for SNPs discovery and for transcriptome characterization) and future genome sequence assemblies. The numerous microsatellites will facilitate integration of the linkage and physical maps and serve as valuable resource for fine mapping QTL and positional cloning of genes affecting aquaculture production traits. Furthermore, comparative genomics through BES can be used for identifying positional candidate genes from QTL mapping studies, aid in future assembly of a reference genome sequence and elucidating sequence content and complexity in the rainbow trout genome.

Published
2011
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18. A first generation BAC-based physical map of the rainbow trout genome

Author

Carine Genet, Gary H. Thorgaard, Roger L. Vallejo, Ming-Cheng Luo, Frank M. You, Paul A. Wheeler, Yuqin Hu, Caird E. Rexroad, Yniv Palti, National Center for Cool and Cold Water Aquaculture, University of California, Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, School of Biological Sciences and Center for Reproductive Biology, Washington State University (WSU), AgroParisTech-Institut National de la Recherche Agronomique (INRA), National Center for Cool and Cold Water Aquaculture, ARS-USDA, and USDA-ARS : Agricultural Research Service

Subjects
Genetic Markers, 0106 biological sciences, Chromosomes, Artificial, Bacterial, carte physique, lcsh:QH426-470, Genotype, Positional cloning, lcsh:Biotechnology, [SDV]Life Sciences [q-bio], trout, physical map, bac, Quantitative Trait Loci, Computational biology, truite, Quantitative trait locus, 01 natural sciences, Contig Mapping, 03 medical and health sciences, Gene mapping, lcsh:TP248.13-248.65, Genetics, Animals, 14. Life underwater, 030304 developmental biology, 0303 health sciences, Genome, biology, Contig, food and beverages, Sequence Analysis, DNA, biology.organism_classification, DNA Fingerprinting, lcsh:Genetics, Trout, Oncorhynchus mykiss, Rainbow trout, Research Article, Microsatellite Repeats, 010606 plant biology & botany, Biotechnology, Reference genome
Abstract

Background Rainbow trout (Oncorhynchus mykiss) are the most-widely cultivated cold freshwater fish in the world and an important model species for many research areas. Coupling great interest in this species as a research model with the need for genetic improvement of aquaculture production efficiency traits justifies the continued development of genomics research resources. Many quantitative trait loci (QTL) have been identified for production and life-history traits in rainbow trout. A bacterial artificial chromosome (BAC) physical map is needed to facilitate fine mapping of QTL and the selection of positional candidate genes for incorporation in marker-assisted selection (MAS) for improving rainbow trout aquaculture production. This resource will also facilitate efforts to obtain and assemble a whole-genome reference sequence for this species. Results The physical map was constructed from DNA fingerprinting of 192,096 BAC clones using the 4-color high-information content fingerprinting (HICF) method. The clones were assembled into physical map contigs using the finger-printing contig (FPC) program. The map is composed of 4,173 contigs and 9,379 singletons. The total number of unique fingerprinting fragments (consensus bands) in contigs is 1,185,157, which corresponds to an estimated physical length of 2.0 Gb. The map assembly was validated by 1) comparison with probe hybridization results and agarose gel fingerprinting contigs; and 2) anchoring large contigs to the microsatellite-based genetic linkage map. Conclusion The production and validation of the first BAC physical map of the rainbow trout genome is described in this paper. We are currently integrating this map with the NCCCWA genetic map using more than 200 microsatellites isolated from BAC end sequences and by identifying BACs that harbor more than 300 previously mapped markers. The availability of an integrated physical and genetic map will enable detailed comparative genome analyses, fine mapping of QTL, positional cloning, selection of positional candidate genes for economically important traits and the incorporation of MAS into rainbow trout breeding programs.

Published
2009
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19. A Type I and Type II microsatellite linkage map of Rainbow trout (Oncorhynchus mykiss) with presumptive coverage of all chromosome arms

Author

René Guyomard, Stéphane Mauger, Edwige Quillet, Sylvain Martineau, Kamila Tabet-Canale, Francine Krieg, Carine Genet, Unité de recherche Génétique des Poissons (UGP), Institut National de la Recherche Agronomique (INRA), and French AGENAE program and was supported by INRA (Institut Interprofessionnel des Produits de l'Aquaculture), French Ministry of Agriculture and Fisheries and EU (contract n°A0248)

Subjects
Fish Proteins, 0106 biological sciences, microsatellite, carte génétique, lcsh:QH426-470, [SDV]Life Sciences [q-bio], lcsh:Biotechnology, truite, Quantitative trait locus, Biology, Synteny, 01 natural sciences, Chromosomes, 03 medical and health sciences, Genetic linkage, lcsh:TP248.13-248.65, Centromere, Gene orders, Genetics, Animals, Zebrafish, 030304 developmental biology, Linkage (software), 0303 health sciences, Genome, Chromosome Mapping, Chromosome, lcsh:Genetics, GENETIC MAPS, Oncorhynchus mykiss, TROUTS, MICROSATELLITE, Microsatellite, Rainbow trout, Microsatellite Repeats, Research Article, 010606 plant biology & botany, Biotechnology
Abstract

Background The development of large genomic resources has become a prerequisite to elucidate the wide-scale evolution of genomes and the molecular basis of complex traits. Linkage maps represent a first level of integration and utilization of such resources and the primary framework for molecular analyses of quantitative traits. Previously published linkage maps have already outlined the main peculiarities of the rainbow trout meiosis and a correspondance between linkage groups and chromosome arms has been recently established using fluorescent in situ hybridization. The number of chromosome arms which were covered by these maps remained unknown. Results We report an updated linkage map based on segregation analysis of more than nine hundred microsatellite markers in two doubled haploid gynogenetic lines. These markers segregated into 31 linkage groups spanning an approximate total map length of 2750 cM. Centromeres were mapped for all the linkage groups using meiogenetic lines. For each of the 31 linkage groups, the meta or acrocentric structure infered from centromere mapping was identical with those recently found with fluorescent in situ hybridization results. The present map is therefore assumed to cover the 52 chromosome arms which constitute the rainbow trout karyotype. Our data confirm the occurrence of a high interference level in this species. Homeologous regions were identified in eleven linkage groups, reflecting the tetraploid nature of the salmonid genome. The data supported the assumption that gene orders are conserved between duplicated groups and that each group is located on a single chromosome arm. Overall, a high congruence with already published rainbow trout linkage maps was found for both gene syntenies and orders. Conclusion This new map is likely to cover the whole set of chromosome arms and should provide a useful framework to integrate existing or forthcoming rainbow trout linkage maps and other genomic resources. Since very large numbers of EST containing microsatellite sequences are available in databases, it becomes feasible to construct high-density linkage maps localizing known genes. This will facilitate comparative mapping and, eventually, identification of candidate genes in QTL studies.

Published
2006
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20. Retinoic acid controls muscle differentiation in vivo through Fgf8 signaling pathway

Author

Hamade, A., Carine Genet, Deries, M., Laure Bally-Cuif, Begemann, G., Florence Sabatier, Anne Bonnieu, Xavier Cousin, Différenciation Cellulaire et Croissance (DCC), Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2), German Research Center for Environmental Health - Helmholtz Center München (GmbH), and University of Konstanz

Subjects
MYOGENESIS, ZEBRAFISH, [SDV]Life Sciences [q-bio], RETINOIC ACID, [INFO]Computer Science [cs], ComputingMilieux_MISCELLANEOUS, Fgf8
Abstract

International audience

Published
2005

21. Retinoic acid activates zebrafish myogenesis through Fgf8 signaling pathway

Author

Anne Bonnieu, Hamade, A., Deries, M., Laure Bally-Cuif, Begemann, G., Carine Genet, Florence Sabatier, Xavier Cousin, Différenciation Cellulaire et Croissance (DCC), Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2), Institute of Developmental Genetics, Helmholtz-Zentrum München (HZM), and University of Konstanz

Subjects
MYOGENESIS, animal structures, ZEBRAFISH, [SDV]Life Sciences [q-bio], embryonic structures, RETINOIC ACID, [INFO]Computer Science [cs], Fgf8
Abstract

National audience; Retinoic acid (RA) is involved in the control of a variety of differentiation processes. In vitro experiments have clearly shown that RA blocks myoblast proliferation and induces their differentiation. We are studying RA function in myogenesis control during zebrafish development. To determine whether RA acts on muscle development in vivo, we altered RA signaling by treating zebrafish embryos either with exogenous RA or with retinaldehyde dehydrogenase inhibitors (DEAB or Citral), or with a pan-RA receptor antagonist, reagent BMS493. We have shown that RA is able to induce expression of early and late muscle differentiation factors (MyoD, myohenin, mef2c...). On the contrary, in DEABor BMS493-treated embryos expression of these myogenic genes was reduced. Analysis of expression patterns suggests that RA could participate to the establishment of a differentiation zone in the anterior presomitic mesoderm (psm). We have analysed “classical” muscle signalling pathways and showed that neither Hh/hedgehog nor Wnt/wingless pathway seems to be involved. We have analysed the expression of fgf8 gene and showed that fgf8 expression is controlled in a similar way as myogenic factors albeit at earlier stages and independently of an intermediate translation. Furthermore we showed that in ace mutants (the zebrafish mutant acerebellar (ace) is devoid of fgf8), RA activation of myogenic factors is blocked. Taken together these elements strongly suggest that Fgf8 mediates the differentiating effect of RA on myogenesis. We are currently investigating the involvement of other Fgfs and of other gene networks through a functional genomic systematic analysis.

Published
2005

22. Identification of gene networks involved in retinoic acid control of muscle differentiation

Author

L. Yang, Carine Genet, J. Jaekel, Uwe Strähle, M. San Cristobal, Aline Hamade, Xavier Cousin, Anne Bonnieu, ProdInra, Migration, Différenciation Cellulaire et Croissance (DCC), Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2), Institut für Toxikologie und Genetik, Partenaires INRAE, Laboratoire de Génétique Cellulaire (LGC), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Institut National de la Recherche Agronomique (INRA), INRA- PHASE, MRT (CG) and AFM (AB and XC), GENET, Carine, Karlsruhe Institute of Technology (KIT), Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), Ecole Nationale Vétérinaire de Toulouse (ENVT), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)

Subjects
[SDV]Life Sciences [q-bio], [SDV.BA]Life Sciences [q-bio]/Animal biology, Gene regulatory network, Retinoic acid, Retinoic acid receptor beta, STATISTICAL ANALYSIS, Retinoic acid receptor gamma, Aquatic Science, Biology, [INFO] Computer Science [cs], Retinoid X receptor gamma, GENE, Retinoic acid-inducible orphan G protein-coupled receptor, Cell biology, MYOGENESIS, [SDV] Life Sciences [q-bio], chemistry.chemical_compound, Retinoic acid receptor, chemistry, Retinoic acid receptor alpha, [SDV.BDD] Life Sciences [q-bio]/Development Biology, RETINOIC ACID, [INFO]Computer Science [cs], [SDV.BDD]Life Sciences [q-bio]/Development Biology, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2005
Full Text
View/download PDF

23. Identification de régions du génome répondant à la sélection dans une lignée porcine sino-européenne : la Tai zumu

Author

Denis Milan, Olivier Demeure, Guillaume Laval, Nathalie Iannuccelli, Carine Genet, Agnès Bonnet, Germaine Burgaud, Juliette Riquet, Gasnier, C., Jean Pierre Bidanel, Laboratoire de Génétique Cellulaire (LGC), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT), Génétique Animale (GARen), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST-Ecole Nationale Supérieure Agronomique de Rennes, Laboratoire de radiobiologie et d'étude du génome (LREG), Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Génétique Expérimentale en Productions Animales (GEPA), Institut National de la Recherche Agronomique (INRA), Station de Génétique Quantitative et Appliquée (SGQA), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Institut National de la Recherche Agronomique (INRA)-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)-Ecole Nationale Supérieure Agronomique de Rennes, and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Recherche Agronomique (INRA)

Subjects
SELECTION, GENETIC MARKERS, ALLELE FREQUENCY, FREQUENCES ALLELIQUES, [SDV]Life Sciences [q-bio], PIGS, ComputingMilieux_MISCELLANEOUS
Abstract

Chantier qualité spécifique "Auteurs Externes" département de Génétique animale : uniquement liaison auteur au référentiel HR-Access; International audience

Published
2003

24. Construction of a physical map along the porcine chromosome 7q

Author

Barbosa, A., Christine Renard, Celine Urien, Bourgeaux, N., J-Claude Save, Carine Genet, Denis Milan, Francois PIUMI, Claire Rogel-Gaillard, Patrick Chardon, Laboratoire de radiobiologie et d'étude du génome (LREG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Recherche Agronomique (INRA), Laboratoire de Génétique Cellulaire (LGC), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, ProdInra, Migration, Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), and Université de Toulouse (UT)-Université de Toulouse (UT)

Subjects
[SDV] Life Sciences [q-bio], pig, chromosome porcin 7q, pig chromosome 7q, [SDV]Life Sciences [q-bio], physical map, ComputingMilieux_MISCELLANEOUS
Abstract

Chantier qualité spécifique "Auteurs Externes" département de Génétique animale : uniquement liaison auteur au référentiel HR-Access; International audience

Published
2002

25. Mapping of 10 genes to porcine chromosome 13 and refining the regions of conserved syntheny with human chromosome 3

Author

Poucke, M., Manon Yerle, Francois PIUMI, Jacobs, K., Carine Genet, Mattheeuws, M., Zeveren, A., Peelman, L. J., Laboratoire de radiobiologie et d'étude du génome (LREG), and Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)

Subjects
GENETIC MAPS, [SDV]Life Sciences [q-bio], COMPARATIVE GENETICS, PIGS, MEN
Abstract

Chantier qualité spécifique "Auteurs Externes" département de Génétique animale : uniquement liaison auteur au référentiel HR-Access

Published
2002

26. Cytogenetic and radiation hybrid mapping reveals conserved synteny and gene order between human chromosome 21 and pig chromosome 13

Author

Patrick Chardon, Ibis Sanchez-Serrano, Christopher K. Tuggle, Carine Genet, Martine Yerle, Denis Milan, Xianwei Shi, and Grant Cravens

Subjects
Genetics, Radiation Hybrid Mapping, Chromosomes, Human, Pair 21, Swine, Biology, Quantitative trait locus, Human genetics, Chromosome Painting, Sequence-tagged site, Order (biology), Quantitative Trait, Heritable, Sequence Homology, Nucleic Acid, Gene Order, Animals, Birth Weight, Humans, Radiation hybrid mapping, Lod Score, Chromosome 21, Gene, Conserved Sequence, Chromosome 13, Sequence Tagged Sites
Published
2000

27. Mapping of QTL involved in growth, backfat thickness and intramuscular fat content in pigs. Regional RH mapping in the QTL region identified on chromosome 7

Author

Carine Genet, Jean Pierre Bidanel, Christine Renard, Nathalie Iannuccelli, Claude Caritez, J., Gruand, J., Bourgeois, F., Yves Amigues, Claire Rogel-Gaillard, Juliette Riquet, Jacques Mourot, Barbosa, A., Claude Chevalet, Ollivier, L., Joël Gellin, Denis Milan, Laboratoire de Génétique Cellulaire (LGC), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Station de Génétique Quantitative et Appliquée (SGQA), Institut National de la Recherche Agronomique (INRA), Laboratoire de radiobiologie et d'étude du génome (LREG), Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Génétique Expérimentale en Productions Animales (GEPA), Unité mixte de recherche veau et porc (UMR VP), Ecole Nationale Supérieure Agronomique de Rennes-Institut National de la Recherche Agronomique (INRA), ProdInra, Migration, Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT), and Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Supérieure Agronomique de Rennes

Subjects
[SDV] Life Sciences [q-bio], pig, hybrid, irradiation, qtl, [SDV]Life Sciences [q-bio], genetic map, [INFO]Computer Science [cs], chromosome, [INFO] Computer Science [cs], ComputingMilieux_MISCELLANEOUS
Abstract

"Chantier qualité spécifique "Auteurs Externes" département de Génétique animale : uniquement liaison auteur au référentiel HR-Access "; International audience

Published
2000

28. Combined approaches at INRA to fine map QTL influencing growth, fatness and carcass composition traits in pig

Author

Juliette Riquet, Marie Pierre Sanchez, Olivier Demeure, Nathalie Iannuccelli, Katia Feve, Hélène Gilbert, Carine Genet, Agnès Bonnet, Christophe Péry, Yvon Billon, Jean-Marcel Gogué, Claude Caritez, J., Pascale Le Roy, Christine Renard, Jean Pierre Bidanel, Denis Milan, ProdInra, Migration, Laboratoire de Génétique Cellulaire (LGC), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Station de Génétique Quantitative et Appliquée (SGQA), Institut National de la Recherche Agronomique (INRA), Génétique Animale (GARen), Institut National de la Recherche Agronomique (INRA)-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)-Ecole Nationale Supérieure Agronomique de Rennes, Laboratoire de radiobiologie et d'étude du génome (LREG), Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Domaine expérimental Bourges-La Sapinière (BOURGES), Génétique Expérimentale en Productions Animales (GEPA), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Recherche Agronomique (INRA), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT), and Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST-Ecole Nationale Supérieure Agronomique de Rennes

Subjects
CARCASSES, [SDV] Life Sciences [q-bio], FATNESS, QTL, [SDV]Life Sciences [q-bio], GROWTH, PIGS, FINE MAPPING
Abstract

Chantier qualité spécifique "Auteurs Externes" département de Génétique animale : uniquement liaison auteur au référentiel HR-Access

29. Progress in QTL mapping for growth and fatness traits on porcine chromosome 7

Author

Olivier Demeure, Nathalie Iannuccelli, Guillaume Laval, Christine Renard, Juliette Riquet, Carine Genet, Gasnier, C., Jean Pierre Bidanel, Denis Milan, Génétique Animale (GARen), Institut National de la Recherche Agronomique (INRA)-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)-Ecole Nationale Supérieure Agronomique de Rennes, Laboratoire de Génétique Cellulaire (LGC), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Laboratoire de radiobiologie et d'étude du génome (LREG), Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Station de Génétique Quantitative et Appliquée (SGQA), Institut National de la Recherche Agronomique (INRA), ProdInra, Migration, Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST-Ecole Nationale Supérieure Agronomique de Rennes, Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), and Université de Toulouse (UT)-Université de Toulouse (UT)

Subjects
[SDV] Life Sciences [q-bio], PIG CHROMOSOME 7, FATNESS, QTL, [SDV]Life Sciences [q-bio], GROWTH, PIGS, CHROMOSOME PORCIN 7
Abstract

Chantier qualité spécifique "Auteurs Externes" département de Génétique animale : uniquement liaison auteur au référentiel HR-Access

30. Gynogenetic clonal lines of rainbow trout[i] O. mykiss[/i], a model for the identification of new antiviral pathways

Author

Eloi Verrier, Michel Dorson, Christelle Langevin, Nicolas Dechamp, Corinne Torhy, Stéphane Mauger, Sandrine Le Guillou, Céline Ciobotaru, Carine Genet, Pierre Boudinot, Edwige Quillet, Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Unité de recherche Virologie et Immunologie Moléculaires (VIM (UR 0892)), Institut National de la Recherche Agronomique (INRA), AgroParisTech-Institut National de la Recherche Agronomique (INRA), and Unité de recherche Virologie et Immunologie Moléculaires (VIM)

Subjects
[SDV.SA]Life Sciences [q-bio]/Agricultural sciences
Abstract

absent

31. Uncovering the genetic architecture of response to VHSV in rainbow trout O. mykiss

Author

Eloi Verrier, Michel Dorson, Nicolas Dechamp, Sandrine Le Guillou, Carine Genet, Céline Ciobotaru, Corinne Torhy, Pierre Boudinot, Edwige Quillet, Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Unité de recherche Virologie et Immunologie Moléculaires (VIM (UR 0892)), Institut National de la Recherche Agronomique (INRA), and Unité de recherche Virologie et Immunologie Moléculaires (VIM)

Subjects
[SDV]Life Sciences [q-bio]
Abstract

absent

32. GENOTROUT - Apport des nouvelles technologies de séquençage (NGS) à l'analyse du génome de la truite arc-en-ciel (2010-2013)

Author

Yann Guiguen, Carine Genet, Edwige Quillet, mekki boussaha, Jean-Nicolas Volff, Domitille Chalopin, Delphine Galiana-Arnoux, Hugues Roest-Crollius, Camille Berthelot, Maria Bernard, Olivier Jaillon, Patrick Wincker, Station commune de Recherches en Ichtyophysiologie, Biodiversité et Environnement (SCRIBE), Institut National de la Recherche Agronomique (INRA)-IFR140, Génétique Animale et Biologie Intégrative (GABI), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Institut de Génomique Fonctionnelle de Lyon (IGFL), École normale supérieure - Lyon (ENS Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), DYnamique et Organisation des GENomes - Equipe de l'IBENS (DYOGEN), Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), Département de Biologie - ENS Paris, 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)-Département de Biologie - ENS Paris, 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), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Laboratoire de Physiologie et Génomique des Poissons (LPGP), Institut National de la Recherche Agronomique (INRA)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), École normale supérieure de Lyon (ENS de Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Institut de biologie de l'ENS Paris (IBENS), 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)-Département de Biologie - ENS Paris, 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 Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-École normale supérieure - Lyon (ENS Lyon), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris), 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), 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), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - 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)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, and 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)

Subjects
[SDV.SA]Life Sciences [q-bio]/Agricultural sciences, SEQUENCAGE, GENOMIQUE, SALMONIDE
Abstract

absent

33. Transcortin: a strong positional candidate for a QTL associated with cortisol levels and carcass composition in pigs

Author

Ousova, O., Nathalie Iannuccelli, Denis Milan, Jean Pierre Bidanel, Carine Genet, Martine Bouissou-Matet Yerle, Joël Gellin, Patrick Chardon, Pierre Mormede, Marie-Pierre Moisan, Laboratoire de Génétique Cellulaire (LGC), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Station de Génétique Quantitative et Appliquée (SGQA), Institut National de la Recherche Agronomique (INRA), Laboratoire de radiobiologie et d'étude du génome (LREG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Recherche Agronomique (INRA), Neurogénétique et Stress (NS), Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT), and Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)

Subjects
BODY COMPOSITION, QTL, CORTISOL, [SDV]Life Sciences [q-bio], PIGS, CANDIDATE GENES
Abstract

"Chantier qualité spécifique "Auteurs Externes" département de Génétique animale : uniquement liaison auteur au référentiel HR-Access "

34. Obtention de la carte génétique du canard Barbarie et du canard Pékin

Author

Carine Genet, Alain Vignal, Catherine Larzul, Laboratoire de Génétique Cellulaire (LGC), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Station d'Amélioration Génétique des Animaux (SAGA), Institut National de la Recherche Agronomique (INRA), and ProdInra, Migration

Subjects
[SDV] Life Sciences [q-bio], GENETIQUE ANIMALE, [SDV]Life Sciences [q-bio], ComputingMilieux_MISCELLANEOUS
Abstract

National audience

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