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2. Tissue Resources for the Functional Annotation of Animal Genomes

Author

Tixier-Boichard, Michèle, Fabre, Stéphane, Dhorne-Pollet, Sophie, Goubil, Adeline, Acloque, Hervé, Vincent-Naulleau, Silvia, Ross, Pablo, Wang, Ying, Chanthavixay, Ganrea, Cheng, Hans, Ernst, Catherine, Leesburg, Vicki, Giuffra, Elisabetta, Zhou, Huaijun, Group, Collaborative Working, Taragnat, Catherine, Berri, Cecile, Jardet, Déborah, Godet, Estelle, Laurent, Fabrice, Gomot, Gilles, Dardente, Hughes, Grasseau, Isabelle, Dubois, Jean-Philippe, Gautron, Joel, Gérard, Nadine, Quéré, Pascale, Lavocat, Roger-Paul, Dalbies-Tran, Rozenn, Métayer, Sonia, Marthey, Sylvain, Coustham, Vincent, and Druart, Xavier

Subjects
Biological Sciences, Genetics, tissue sampling, repository, mammals, bird, cryopreservation, genome, Collaborative Working Group, Clinical Sciences, Law
Abstract

In order to generate an atlas of the functional elements driving genome expression in domestic animals, the Functional Annotation of Animal Genome (FAANG) strategy was to sample many tissues from a few animals of different species, sexes, ages, and production stages. This article presents the collection of tissue samples for four species produced by two pilot projects, at INRAE (National Research Institute for Agriculture, Food and Environment) and the University of California, Davis. There were three mammals (cattle, goat, and pig) and one bird (chicken). It describes the metadata characterizing these reference sets (1) for animals with origin and selection history, physiological status, and environmental conditions; (2) for samples with collection site and tissue/cell processing; (3) for quality control; and (4) for storage and further distribution. Three sets are identified: set 1 comprises tissues for which collection can be standardized and for which representative aliquots can be easily distributed (liver, spleen, lung, heart, fat depot, skin, muscle, and peripheral blood mononuclear cells); set 2 comprises tissues requiring special protocols because of their cellular heterogeneity (brain, digestive tract, secretory organs, gonads and gametes, reproductive tract, immune tissues, cartilage); set 3 comprises specific cell preparations (immune cells, tracheal epithelial cells). Dedicated sampling protocols were established and uploaded in https://data.faang.org/protocol/samples. Specificities between mammals and chicken are described when relevant. A total of 73 different tissues or tissue sections were collected, and 21 are common to the four species. Having a common set of tissues will facilitate the transfer of knowledge within and between species and will contribute to decrease animal experimentation. Combining data on the same samples will facilitate data integration. Quality control was performed on some tissues with RNA extraction and RNA quality control. More than 5,000 samples have been stored with unique identifiers, and more than 4,000 were uploaded onto the Biosamples database, provided that standard ontologies were available to describe the sample. Many tissues have already been used to implement FAANG assays, with published results. All samples are available without restriction for further assays. The requesting procedure is described. Members of FAANG are encouraged to apply a range of molecular assays to characterize the functional status of collected samples and share their results, in line with the FAIR (Findable, Accessible, Interoperable, and Reusable) data principles.

Published
2021

7. Multi-species annotation of transcriptome and chromatin structure in domesticated animals

Author

Foissac, Sylvain, Djebali, Sarah, Munyard, Kylie, Vialaneix, Nathalie, Rau, Andrea, Muret, Kevin, Esquerré, Diane, Zytnicki, Matthias, Derrien, Thomas, Bardou, Philippe, Blanc, Fany, Cabau, Cédric, Crisci, Elisa, Dhorne-Pollet, Sophie, Drouet, Françoise, Faraut, Thomas, Gonzalez, Ignacio, Goubil, Adeline, Lacroix-Lamandé, Sonia, Laurent, Fabrice, Marthey, Sylvain, Marti-Marimon, Maria, Momal-Leisenring, Raphaelle, Mompart, Florence, Quéré, Pascale, Robelin, David, Cristobal, Magali San, Tosser-Klopp, Gwenola, Vincent-Naulleau, Silvia, Fabre, Stéphane, Pinard-Van der Laan, Marie-Hélène, Klopp, Christophe, Tixier-Boichard, Michèle, Acloque, Hervé, Lagarrigue, Sandrine, and Giuffra, Elisabetta

Published
2019
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8. Présentation du portail d'accès aux ressources biologiques du pilier animal de RARe

Author

Marthey, Sylvain, Delavaud, Aurélie, Marthey, Nicolas, Méal, Camille, Tixier-Boichard, Michèle, and MARTHEY, Sylvain

Subjects
fish, access to genetic resources, [INFO.INFO-WB] Computer Science [cs]/Web, [SDV.BA.MVSA] Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health, [SDV.GEN.GA] Life Sciences [q-bio]/Genetics/Animal genetics, Information system, Etl, [SDV] Life Sciences [q-bio], shellfish, [INFO.INFO-BT] Computer Science [cs]/Biotechnology, birds, Système d'information, [SDV.GEN.GPO] Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], [INFO.INFO-DB] Computer Science [cs]/Databases [cs.DB], [SDV.BBM.GTP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], mammals, Mammifères domestiques, [SDV.BDLR] Life Sciences [q-bio]/Reproductive Biology, [SDV.BID] Life Sciences [q-bio]/Biodiversity
Abstract

Le portail web https://crb-anim.fr/access-to-collection/# a été élaboré entre 2015 et 2017 grâce au soutien du projet Investissements d'Avenir CRB-Anim. Il permet de consulter le catalogue des collections de 5 CRBs concernant les espèces animales domestiques, de gérer les demandes d'entrée ou de sortie d'échantillons et d'accéder aux données associées. Cet article présente les étapes de la création du portail : définition des descripteurs standard, spécificités fonctionnelles et sélection d'un prestataire après appel d'offres, développement du portail, réalisation de connecteurs pour alimenter le portail. Depuis son ouverture en 2017, le portail est maintenu en amélioration continue.

Published
2022

11. Bioinformatic Mining and Structure-Activity Profiling of Baeyer-Villiger Monooxygenases from Mycobacterium tuberculosis

Author

Tomas, Nicolas, primary, Leonelli, Dimitri, additional, Campoy, Martin, additional, Marthey, Sylvain, additional, Le, Nguyen-Hung, additional, Rengel, David, additional, Martin, Véronique, additional, Pál, Adrian, additional, Korduláková, Jana, additional, Eynard, Nathalie, additional, Guillet, Valérie, additional, Mourey, Lionel, additional, Daffé, Mamadou, additional, Lemassu, Anne, additional, André, Gwenaëlle, additional, and Marrakchi, Hedia, additional

Published
2022
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12. Additional file of Identification of differentially expressed genes in chickens differing in muscle glycogen content and meat quality

Author

Vonick Sibut, Hennequet-Antier, Christelle, Bihan-Duval, Elisabeth Le, Marthey, Sylvain, Duclos, Michel J, and Berri, Cécile

Subjects
animal structures, food and beverages
Abstract

Additional file of Identification of differentially expressed genes in chickens differing in muscle glycogen content and meat quality

Published
2020
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13. Additional file 3 of Identification of differentially expressed genes in chickens differing in muscle glycogen content and meat quality

Author

Vonick Sibut, Hennequet-Antier, Christelle, Bihan-Duval, Elisabeth Le, Marthey, Sylvain, Duclos, Michel J, and Berri, Cécile

Subjects
animal structures, embryonic structures
Abstract

Additional file 3:List of the common genes that were differentially expressed in the two models (Fat vs. Lean chickens and G+ vs. G- chickens generated from the F2FL population). (DOC 34 KB)

Published
2020
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18. Characterization of Holstein and Normande whole milk miRNomes highlights breed specificities

Author

Le Guillou, Sandrine, Leduc, Arlette, Laubier, Johann, Barbey, Sarah, Rossignol, Marie-Noëlle, Lefebvre, Rachel, Marthey, Sylvain, Laloë, Denis, Le Provost, Fabienne, Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Université Paris Saclay (COmUE), Domaine expérimental animal du Pin (SEA), and Institut National de la Recherche Agronomique (INRA)

Subjects
Epigenomics, [SDV.GEN]Life Sciences [q-bio]/Genetics, [SDV]Life Sciences [q-bio], lcsh:R, Age Factors, lcsh:Medicine, food and beverages, Computational Biology, High-Throughput Nucleotide Sequencing, Breeding, Article, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, MicroRNAs, fluids and secretions, Milk, Species Specificity, Next-generation sequencing, Animals, lcsh:Q, Cattle, Gene expression, lcsh:Science, Transcriptome, Genetic Background
Abstract

International audience; The concept of milk as a healthy food has opened the way for studies on milk components, from nutrients to microRNAs, molecules with broad regulatory properties present in large quantities in milk. Characterization of these components has been performed in several species, such as humans and bovine, depending on the stages of lactation. Here, we have studied the variation in milk microRNA composition according to genetic background. Using high throughput sequencing, we have characterized and compared the milk miRNomes of Holstein and Normande cattle, dairy breeds with distinct milk production features, in order to highlight microRNAs that are essential for regulation of the lactation process. In Holstein and Normande milk, 2,038 and 2,030 microRNAs were identified, respectively, with 1,771 common microRNAs, of which 1,049 were annotated and 722 were predicted. The comparison of the milk miRNomes of two breeds allowed to highlight 182 microRNAs displaying significant differences in the abundance. They are involved in the regulation of lipid metabolism and mammary morphogenesis and development, which affects lactation. Our results provide new insights into the regulation of molecular mechanisms involved in milk production.

Published
2019
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19. Influence of genetic background to the bovine milk microRNA composition

Author

Le Guillou, Sandrine, Laubier, Johann, Leduc, Antoine, Launay, Frédéric, Barbey, Sarah, Lefebvre, Rachel, Rossignol, Marie-Noëlle, Marthey, Sylvain, Laloë, Denis, Le Provost, Fabienne, Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Université Paris Saclay (COmUE), Domaine expérimental animal du Pin (SEA), and Institut National de la Recherche Agronomique (INRA)

Subjects
[SDV.GEN]Life Sciences [q-bio]/Genetics, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, [SDV]Life Sciences [q-bio], ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2019

20. Characterization of Holstein and Normande whole milk miRNomes highlights breed specificities

Author

Leduc, Arlette, Laubier, Johann, Barbey, Sarah, Rossignol, Marie-Noelle, Lefebvre, Rachel, Marthey, Sylvain, Laloë, Denis, Le Provost, Fabienne, and Le Guillou, Sandrine

Subjects
composant du lait, fluids and secretions, origine génétique, variabilité génétique animale, micro arn, food and beverages, race holstein, race normande
Abstract

The concept of milk as a healthy food has opened the way for studies on milk components, from nutrients to microRNAs, molecules with broad regulatory properties present in large quantities in milk. Characterization of these components has been performed in several species, such as humans and bovine, depending on the stages of lactation. Here, we have studied the variation in milk microRNA composition according to genetic background. Using high throughput sequencing, we have characterized and compared the milk miRNomes of Holstein and Normande cattle, dairy breeds with distinct milk production features, in order to highlight microRNAs that are essential for regulation of the lactation process. In Holstein and Normande milk, 2,038 and 2,030 microRNAs were identified, respectively, with 1,771 common microRNAs, of which 1,049 were annotated and 722 were predicted. The comparison of the milk miRNomes of two breeds allowed to highlight 182 microRNAs displaying significant differences in the abundance. They are involved in the regulation of lipid metabolism and mammary morphogenesis and development, which affects lactation. Our results provide new insights into the regulation of molecular mechanisms involved in milk production.

Published
2019

21. MOESM1 of Multi-species annotation of transcriptome and chromatin structure in domesticated animals

Author

Foissac, Sylvain, Djebali, Sarah, Munyard, Kylie, Vialaneix, Nathalie, Rau, Andrea, Muret, Kevin, Esquerré, Diane, Zytnicki, Matthias, Derrien, Thomas, Bardou, Philippe, Blanc, Fany, Cabau, Cédric, Crisci, Elisa, Dhorne-Pollet, Sophie, Drouet, Françoise, Faraut, Thomas, Gonzalez, Ignacio, Goubil, Adeline, Lacroix-Lamandé, Sonia, Laurent, Fabrice, Marthey, Sylvain, Marti-Marimon, Maria, Raphaelle Momal-Leisenring, Mompart, Florence, Quéré, Pascale, Robelin, David, Cristobal, Magali, Tosser-Klopp, Gwenola, Vincent-Naulleau, Silvia, Fabre, Stéphane, Marie-Hélène Pinard-Van Der Laan, Klopp, Christophe, Tixier-Boichard, Michèle, Acloque, Hervé, Lagarrigue, Sandrine, and Giuffra, Elisabetta

Abstract

Additional file 1 Additional file 1: Supplementary figures (S1-S26) and tables (S1-S15).

Published
2019
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22. A missense mutation in TYRP1 causes the chocolate plumage color in chicken and alters melanosome structure

Author

Li, Jingyi, Bed'hom, Bertrand, Marthey, Sylvain, Valade, Mathieu, Dureux, Audrey, Moroldo, Marco, Pechoux, Christine, Coville, Jean-Luc, Gourichon, David, Vieaud, Agathe, Dorshorst, Ben, Andersson, Leif, Tixier-Boichard, Michele, Li, Jingyi, Bed'hom, Bertrand, Marthey, Sylvain, Valade, Mathieu, Dureux, Audrey, Moroldo, Marco, Pechoux, Christine, Coville, Jean-Luc, Gourichon, David, Vieaud, Agathe, Dorshorst, Ben, Andersson, Leif, and Tixier-Boichard, Michele

Abstract

The chocolate plumage color in chickens is due to a sex-linked recessive mutation, choc, which dilutes eumelanin pigmentation. Because TYRP1 is sex-linked in chickens, and TYRP1 mutations determine brown coat color in mammals, TYRP1 appeared as the obvious candidate gene for the choc mutation. By combining gene mapping with gene capture, a complete association was identified between the chocolate phenotype and a missense mutation leading to a His214Asn change in the ZnA zinc-binding domain of the protein. A diagnostic test confirmed complete association by screening 428 non-chocolate chickens of various origins. This is the first TYRP1 mutation described in the chicken. Electron microscopy analysis showed that melanosomes were more numerous in feather follicles of chocolate chickens but exhibited an abnormal structure characterized by a granular content and an irregular shape. A similar altered morphology was observed on melanosomes of another TYRP1 mutant in birds, the roux mutation of the quail.

Published
2019
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24. Les microARNs de la glande mammaire et du lait. Convergence vers la définition d'une signature multi-espèces spécifique de la fonction de lactation

Author

Le Guillou, Sandrine, Mobuchon, Lenha, Marthey, Sylvain, Laloë, Denis, Bourdon, Céline, Boussaha, Mekki, Tosser, Gwenola, Gele, Marine, Boutinaud, Marion, Leroux, Christine, Le Provost, Fabienne, Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Université Paris Saclay (COmUE), Institut de l'élevage (IDELE), Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage [Rennes] (PEGASE), 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), Unité Mixte de Recherche sur les Herbivores - UMR 1213 (UMRH), Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, AgroParisTech-Institut National de la Recherche Agronomique (INRA), and VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Institut National de la Recherche Agronomique (INRA)

Subjects
[SDV.GEN]Life Sciences [q-bio]/Genetics, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, [SDV]Life Sciences [q-bio], [INFO]Computer Science [cs], ComputingMilieux_MISCELLANEOUS, [SHS]Humanities and Social Sciences
Abstract

National audience

Published
2018

25. The CRB-Anim web portal: access to biological resources for animal sciences

Author

Tixier-Boichard, Michele, Marthey, Sylvain, MARTHEY, Nicolas, Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Université Paris Saclay (COmUE), and PIA CRB-Anim

Subjects
ressources génétiques, [SDV.GEN]Life Sciences [q-bio]/Genetics, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, [SDV]Life Sciences [q-bio], portail web, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2018

26. Bull sperm sncRNAs: A new source for potential fertility biomarkers?

Author

Sellem, Eli, Marthey, Sylvain, Kiefer, Hélène, Le Danvic, Chrystelle, Allais-Bonnet , Aurélie, Jouneau, Luc, Jammes, Hélène, Schibler, Laurent, Rau, Andrea, Allice, Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Biologie du Développement et Reproduction (BDR), École nationale vétérinaire d'Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA), ANR SeQuamol - APIS- GENE, and British Society of Animal Science (BSAS). GBR.

Subjects
Reproductive Biology, sperme, Biologie du développement, Biologie de la reproduction, taureau, [SDV.BDLR]Life Sciences [q-bio]/Reproductive Biology, Development Biology, biomarqueur, [SDV.BDD]Life Sciences [q-bio]/Development Biology, gestion de la fertilité, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2018

27. Influence des races bovines sur la composition en microARN du lait

Author

Le Guillou, Sandrine, Laubier, Johann, Leduc, Antoine, Gallard, Yves, Barbey, Sarah, Lefebvre, Rachel, Rossignol, Marie-Noelle, Marthey, Sylvain, Laloë, Denis, Le Provost, Fabienne, Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Université Paris Saclay (COmUE), Domaine expérimental animal du Pin (SEA), and Institut National de la Recherche Agronomique (INRA)

Subjects
[SDV.GEN]Life Sciences [q-bio]/Genetics, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, [SDV]Life Sciences [q-bio], ComputingMilieux_MISCELLANEOUS
Abstract

National audience

Published
2018

28. Milk microRNA composition depends on dairy cow breed

Author

Le Guillou, Sandrine, Laubier, Johann, Leduc, Antoine, Gallard, Yves, Barbey, Sarah, Lefebvre, Rachel, Krupova, Zuzana, Rossignol, Marie-Noelle, Marthey, Sylvain, Laloë, Denis, Le Provost, Fabienne, Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Université Paris Saclay (COmUE), Domaine expérimental animal du Pin (SEA), Institut National de la Recherche Agronomique (INRA), Excilone [Elancourt], and International Milk Genomics Consortium (IMGC).

Subjects
[SDV.GEN]Life Sciences [q-bio]/Genetics, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, [SDV]Life Sciences [q-bio], ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2018

29. Livestock genome annotation: transcriptome and chromatin structure profiling in cattle, goat, chicken and pig

Author

Foissac, Sylvain, Djebali, Sarah, Munyard, Kylie, Vialaneix, Nathalie, Rau, Andrea, Muret, Kévin, Esquerré, Diane, Zytnicki, Matthias, Derrien, Thomas, Bardou, Philippe, Blanc, Fany, Cabau, Cédric, CRISCI, Elisa, Dhorne-Pollet, Sophie, Drouet, Françoise, González, Ignacio, Goubil, Adeline, Lacroix-Lamandé, Sonia, Laurent, Fabrice, Marthey, Sylvain, Marti-Marimon, Maria, Momal-Leisenring, Raphaëlle, Mompart, Florence, Quéré, Pascale, Robelin, David, San Cristobal, Magali, Tosser-Klopp, Gwenola, Vincent-Naulleau, Silvia, Fabre, Stéphane, Pinard - Van Der Laan, Marie-Helene, Klopp, Christophe, Tixier-Boichard, Michele, ACLOQUE, Hervé, Lagarrigue, Sandrine, Giuffra, Elisabetta, 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 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), Curtin University [Perth], Planning and Transport Research Centre (PATREC), Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA), Institut National de la Recherche Agronomique (INRA), Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage [Rennes] (PEGASE), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Institut de Génétique et Développement de Rennes (IGDR), Université de Rennes (UR)-Centre National de la Recherche Scientifique (CNRS)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Infectiologie et Santé Publique (UMR ISP), Institut National de la Recherche Agronomique (INRA)-Université de Tours (UT), iRCM, Commissariat à l'énergie atomique et aux énergies alternatives (CEA), 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-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), and Institut National de la Recherche Agronomique (INRA)-Université de Tours

Subjects
[SDV.GEN]Life Sciences [q-bio]/Genetics, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, Livestock, Hi-C, [SDV]Life Sciences [q-bio], Functional annotation, [INFO]Computer Science [cs], ATAC-seq, RNA-seq, [MATH]Mathematics [math]
Abstract

Article publié dans BMC Biology. Disponible ici : https://prodinra.inra.fr/record/491694; Functional annotation of livestock genomes is a critical step to decipher the genotype-to-phenotype relationship underlying complex traits. As part of the Functional Annotation of Animal Genomes (FAANG) action, the FR-AgENCODE project aims at profiling the landscape of transcription (RNA-seq) and chromatin accessibility and conformation (ATAC-seq and Hi-C) in four livestock species representing ruminants (cattle, goat), monogastrics (pig) and birds (chicken), using three target samples related to metabolism (liver) and immunity (CD4+ and CD8+ T cells). Standardized protocols were applied to produce transcriptome and chromatin datasets for the four species. RNA-seq assays allowed to considerably extend the available catalog of protein-coding and non-coding transcripts. Gene expression profiles were consistent with known metabolic/immune functions and revealed differentially expressed transcripts with unknown function, including new lncRNAs in syntenic regions. The majority of ATAC-seq peaks of chromatin accessibility mapped to putative regulatory regions, with an enrichment of predicted transcription factor binding sites in differentially accessible peaks. Hi-C provided the first set of genome-wide maps of three-dimensional interactions across livestock and showed consistency with results from gene expression and chromatin accessibility in topological compartments of the genomes. We report the first multi-species and multi-assay genome annotation results obtained by a FAANG pilot project. The global consistency between gene expression and chromatin structure data in these four livestock species adds up to previous findings in model animals. Overall, these results emphasize the value of FAANG for the research on domesticated animals and strengthen the importance of future meta-analyses of the reference datasets being generated by this community on different species.

Published
2018
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30. Identification of differentially expressed genes in chickens differing in muscle glycogen content and meat quality

Author

Marthey Sylvain, Le Bihan-Duval Elisabeth, Hennequet-Antier Christelle, Sibut Vonick, Duclos Michel J, and Berri Cécile

Subjects
Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background The processing ability of poultry meat is highly related to its ultimate pH, the latter being mainly determined by the amount of glycogen in the muscle at death. The genetic determinism of glycogen and related meat quality traits has been established in the chicken but the molecular mechanisms involved in variations in these traits remain to be fully described. In this study, Chicken Genome Arrays (20 K) were used to compare muscle gene expression profiles of chickens from Fat (F) and Lean (L) lines that exhibited high and low muscle glycogen content, respectively, and of individuals exhibiting extremely high (G+) or low (G-) muscle glycogen content originating from the F2 cross between the Fat and Lean lines. Real-time RT-PCR was subsequently performed to validate the differential expression of genes either selected from the microarray analysis or whose function in regulating glycogen metabolism was well known. Results Among the genes found to be expressed in chicken P. major muscle, 197 and 254 transcripts appeared to be differentially expressed on microarrays for the F vs. L and the G+ vs. G- comparisons, respectively. Some involved particularly in lipid and carbohydrate metabolism were selected for further validation studies by real-time RT-PCR. We confirmed that, as in mammals, the down-regulation of CEBPB and RGS2 coincides with a decrease in peripheral adiposity in the chicken, but these genes are also suggested to affect muscle glycogen turnover through their role in the cAMP-dependent signalling pathway. Several other genes were suggested to have roles in the regulation of glycogen storage in chicken muscle. PDK4 may act as a glycogen sensor in muscle, UGDH may compete for glycogen synthesis by using UDP-glucose for glucoronidation, and PRKAB1, PRKAG2, and PHKD may impact on glycogen turnover in muscle, through AMP-activated signalling pathways. Conclusions This study is the first stage in the understanding of molecular mechanisms underlying variations in poultry meat quality. Large scale analyses are now required to validate the role of the genes identified and ultimately to find molecular markers that can be used for selection or to optimize rearing practices.

Published
2011
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31. FUNYBASE: a FUNgal phYlogenomic dataBASE

Author

Lopez-Villavicencio Manuela, Fournier Elisabeth, Giraud Tatiana, Gendrault Annie, Rodolphe François, Aguileta Gabriela, Marthey Sylvain, Gautier Angélique, Lebrun Marc-Henri, and Chiapello Hélène

Subjects
Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5
Abstract

Abstract Background The increasing availability of fungal genome sequences provides large numbers of proteins for evolutionary and phylogenetic analyses. However the heterogeneity of data, including the quality of genome annotation and the difficulty of retrieving true orthologs, makes such investigations challenging. The aim of this study was to provide a reliable and integrated resource of orthologous gene families to perform comparative and phylogenetic analyses in fungi. Description FUNYBASE is a database dedicated to the analysis of fungal single-copy genes extracted from available fungal genomes sequences, their classification into reliable clusters of orthologs, and the assessment of their informative value for phylogenetic reconstruction based on amino acid sequences. The current release of FUNYBASE contains two types of protein data: (i) a complete set of protein sequences extracted from 30 public fungal genomes and classified into clusters of orthologs using a robust automated procedure, and (ii) a subset of 246 reliable ortholog clusters present as single copy genes in 21 fungal genomes. For each of these 246 ortholog clusters, phylogenetic trees were reconstructed based on their amino acid sequences. To assess the informative value of each ortholog cluster, each was compared to a reference species tree constructed using a concatenation of roughly half of the 246 sequences that are best approximated by the WAG evolutionary model. The orthologs were classified according to a topological score, which measures their ability to recover the same topology as the reference species tree. The full results of these analyses are available on-line with a user-friendly interface that allows for searches to be performed by species name, the ortholog cluster, various keywords, or using the BLAST algorithm. Examples of fruitful utilization of FUNYBASE for investigation of fungal phylogenetics are also presented. Conclusion FUNYBASE constitutes a novel and useful resource for two types of analyses: (i) comparative studies can be greatly facilitated by reliable clusters of orthologs across sets of user-defined fungal genomes, and (ii) phylogenetic reconstruction can be improved by identifying genes with the highest informative value at the desired taxonomic level.

Published
2008
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32. Expressed sequences tags of the anther smut fungus, Microbotryum violaceum, identify mating and pathogenicity genes

Author

Devier Benjamin, Rodolphe François, Hood Michael E, Gendrault Annie, Chiapello Hélène, Marthey Sylvain, Yockteng Roxana, Wincker Patrick, Dossat Carole, and Giraud Tatiana

Subjects
Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background The basidiomycete fungus Microbotryum violaceum is responsible for the anther-smut disease in many plants of the Caryophyllaceae family and is a model in genetics and evolutionary biology. Infection is initiated by dikaryotic hyphae produced after the conjugation of two haploid sporidia of opposite mating type. This study describes M. violaceum ESTs corresponding to nuclear genes expressed during conjugation and early hyphal production. Results A normalized cDNA library generated 24,128 sequences, which were assembled into 7,765 unique genes; 25.2% of them displayed significant similarity to annotated proteins from other organisms, 74.3% a weak similarity to the same set of known proteins, and 0.5% were orphans. We identified putative pheromone receptors and genes that in other fungi are involved in the mating process. We also identified many sequences similar to genes known to be involved in pathogenicity in other fungi. The M. violaceum EST database, MICROBASE, is available on the Web and provides access to the sequences, assembled contigs, annotations and programs to compare similarities against MICROBASE. Conclusion This study provides a basis for cloning the mating type locus, for further investigation of pathogenicity genes in the anther smut fungi, and for comparative genomics.

Published
2007
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33. Profiling the landscape of transcription, chromatin accessibility and chromosome conformation of cattle, pig, chicken and goat genomes [FAANG pilot project]

Author

Foissac, Sylvain, Djebali Quelen, Sarah, ACLOQUE, Hervé, Bardou, Philippe, Blanc, Fany, Cabau, Cédric, Derrien, Thomas, Drouet, Françoise, Esquerre, Diane, Fabre, Stéphane, Gaspin, Christine, GONZALEZ, Ignacio, Goubil, Adeline, Klopp, Christophe, Laurent, Fabrice, Marthey, Sylvain, Marti-Marimon, Maria, Mompart, Florence, Munyard, Kylie, Muret, Kévin, Pollet, Sophie, Quéré, Pascale, Rau, Andrea, Robelin, David, San Cristobal, Magali, Tixier-Boichard, Michele, Tosser-Klopp, Gwenola, Villa-Vialaneix, Nathalie, Vincent-Naulleau, Silvia, Zytnicki, Matthias, Pinard - Van Der Laan, Marie-Helene, Lagarrigue, Sandrine, Giuffra, Elisabetta, Institut National de la Recherche Agronomique - INRA (FRANCE), Institut National Polytechnique de Toulouse - INPT (FRANCE), 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], Génétique Animale et Biologie Intégrative (GABI), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Infectiologie Animale et Santé Publique - IASP (Nouzilly, France), Institut National de la Recherche Agronomique (INRA), Dynamiques Forestières dans l'Espace Rural (DYNAFOR), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Supérieure Agronomique de Toulouse-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA), Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage [Rennes] (PEGASE), AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA), FR-AgENCODE, Institut National Polytechnique de Toulouse - Toulouse INP (FRANCE), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Infectiologie et Santé Publique (UMR ISP), Institut National de la Recherche Agronomique (INRA)-Université de Tours (UT), Institut National de la Recherche Agronomique (INRA)-École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National Polytechnique (Toulouse) (Toulouse INP), 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), and Institut National de la Recherche Agronomique (INRA)-Université de Tours

Subjects
multispecies, Hi-C, [SDV]Life Sciences [q-bio], Multispecies, Biologie animale, Functional annotation of animal genome (FAANG), functional annotation of animal genome (FAANG), ATAC-seq, RNA-seq
Abstract

Functional annotation of livestock genomes is a critical and obvious next step to derive maximum benefit for agriculture, animal science, animal welfare and human health. The aim of the Fr-AgENCODE project is to generate multi-species functional genome annotations by applying high-throughput molecular assays on three target tissues/cells relevant to the study of immune and metabolic traits. An extensive collection of stored samples from other tissues is available for further use (FAANG Biosamples ‘FR-AGENCODE’). From each of two males and two females per species (pig, cattle, goat, chicken), strand-oriented RNA-seq and chromatin accessibility ATAC-seq assays were performed on liver tissue and on two T-cell types (CD3+CD4+&CD3+CD8+) sorted from blood (mammals) or spleen (chicken). Chromosome Conformation Capture (in situ Hi-C) was also carried out on liver. Sequencing reads from the 3 assays were processed using standard processing pipelines. While most (50–70%) RNA-seq reads mapped to annotated exons, thousands of novel transcripts and genes were found, including extensions of annotated protein-coding genes and new lncRNAs (see abstract #69857). Consistency of ATAC-seq results was confirmed by the significant proportion of called peaks in promoter regions (36–66%) and by the specific accumulation pattern of peaks around gene starts (TSS) v. gene ends (TTS). Principal Component Analyses for RNA-seq (based on quantified gene expression) and ATAC-seq (based on quantified chromatin accessibility) highlighted clusters characterised by cell type and sex in all species. From Hi-C data, we generated 40kb-resolution interaction maps, profiled a genome-wide Directionality Index and identified from 4,100 (chicken) to 12,100 (pig) topologically-associating do- mains (TADs). Correlations were reported between RNA-seq and ATAC-seq results (see abstract #71581). In summary, we present here an overview of the first multi-species and -tissue annotations of chromatin accessibility and genome architecture related to gene expression for farm animals.

Published
2017

34. Les petits ARN non codants du spermatozoïde bovin, de potentiels biomarqueurs de la fertilité mâle ?

Author

Sellem, Eli, Marthey, Sylvain, Kiefer, Hélène, Le Danvic, Chrystelle, Allais-Bonnet , Aurélie, Perrier, Jean-Philippe, Jouneau, Luc, Rau, Andréa, Jammes, Hélène, Schibler, Laurent, Département R&D, CRYOLOG S.A, Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Université Paris-Saclay, Biologie du développement et reproduction (BDR), École nationale vétérinaire d'Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), ANR et APIS GENE (Labcom SeQuaMol), Biologie du Développement et Reproduction (BDR), and École nationale vétérinaire d'Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA)

Subjects
fertilité, arn non codant, bovin, sncRNA, taureau, biomarker, spermatozoïde, biomarqueur, [SDV.BDD]Life Sciences [q-bio]/Development Biology, miRNA
Abstract

Le spermatozoïde a longtemps été considéré comme un taxi, protégeant et transportant son patrimoine génétique jusqu’à la délivrance dans l’ovocyte. Mais depuis quelques années de nouveaux arguments, autour des mécanismes épigénétiques, tels que les petits ARN non codants (sncRNA), proposent une nouvelle vision de la fonction du spermatozoïde par son implication dans le développement précoce de l’embryon (Gapp et al., 2014 ; Kotaja 2014 ; Boissonnas et al., 2013 ; Stopka et al., 2003 ; Liu et al., 2012). Or, chez les animaux de rente et en particulier chez les bovins, le contrôle de la fertilité est un élément central pour une diffusion optimale du progrès génétique. L’analyse des paramètres fonctionnels, traduisant la qualité du spermatozoïde, a longtemps été considérée comme une source importante de biomarqueurs du pouvoir fécondant de la semence. Mais malgré des résultats intéressants, la prédiction de la fertilité reste aujourd’hui inefficace (Sellem et al., 2015). C’est pourquoi la recherche de nouveaux biomarqueurs, tels que les sncRNA du spermatozoïde, a été entrepris. Notre étude a été conduite afin d’une part d’établir un catalogue exhaustif du contenu en sncRNA du spermatozoïde bovin et d’autre part de mettre en évidence de potentiels miRNA liés à la fertilité des taureaux. De l'ARN total a été extrait de 40 éjaculats provenant de taureaux Holstein et Montbeliard avec des fertilités contrastées, en utilisant un nouveau protocole amélioré. Deux contrôles qualité ont été effectués sur l'ARN extrait, afin de mesurer les quantités d'ARN (technologie Qubit) et de vérifier si un miARN de référence (miR125) a pu être détecté par RTqPCR. Les 40 banques NGS ont été préparées avec une sélection de taille (

Published
2017

35. Sunflower oil supplementation affects the expression of miR-20a-5p and miR-142-5p in the lactating bovine mammary gland

Author

Mobuchon, Lenha, Le Guillou, Sandrine, Marthey, Sylvain, Laubier, Johann, Laloë, Denis, Bes, Sébastien, Le Provost, Fabienne, Leroux, Christine, Unité Mixte de Recherche sur les Herbivores - UMR 1213 (UMRH), Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, INRA, ApisGene under the NutriMirMa project, AIP BioRessources, VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Institut National de la Recherche Agronomique (INRA), and AgroParisTech-Institut National de la Recherche Agronomique (INRA)

Subjects
bovin, Physiology, [SDV]Life Sciences [q-bio], lcsh:Medicine, Biochemistry, [SHS]Humanities and Social Sciences, Plant Products, Medicine and Health Sciences, Sunflower Oil, lcsh:Science, Flowering Plants, Reverse Transcriptase Polymerase Chain Reaction, Eukaryota, Agriculture, Plants, Mammary Glands, Lipids, Body Fluids, Nucleic acids, Sunflower, Milk, Female, Anatomy, expression des gènes, Research Article, Real-Time Polymerase Chain Reaction, Vegetable Oils, huile de tournesol, Beverages, Mammary Glands, Animal, Exocrine Glands, Genetics, Animals, Lactation, [INFO]Computer Science [cs], Non-coding RNA, Nutrition, [SDV.GEN]Life Sciences [q-bio]/Genetics, Biology and life sciences, lcsh:R, Reproductive System, Organisms, Lipid Metabolism, Agronomy, Gene regulation, Diet, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, MicroRNAs, Metabolism, glande mammaire, RNA, lcsh:Q, Cattle, Gene expression, Breast Tissue, Crop Science
Abstract

International audience; Oil supplementation in dairy cattle diets is used to modulate milk fat composition, as well as the expression of mammary lipogenic genes, whose regulation remains unclear. MiRNAs are small non-coding RNA considered as crucial regulators of gene expression, offering clues to explain the mechanism underlying gene nutriregulation. The present study was designed to identify miRNAs whose expression in the cow mammary gland is modulated by sunflower oil supplementation. MiRNomes were obtained using RNAseq technology from the mammary gland of lactating cows receiving a low forage diet, supplemented or not with 4% sunflower oil. Among the 272 miRNAs characterized, eight were selected for RT-qPCR validations, showing the significant down-regulation of miR-142-5p and miR-20a-5p by sunflower supplementation. These two miRNAs are predicted to target genes whose expression was reported as differentially expressed by sunflower supplementation. Among their putative targets, ELOVL6 gene involved in lipid metabolism has been studied. However, a first analysis did not show its significant down-regulation, in response to the over-expression of miR-142-5p, of miR-20a-5p, or both, in a bovine mammary epithelial cell line. However, a clearer understanding of the miRNA expression by lipid supplementation would help to decipher the regulation of lactating cow mammary gland in response to nutrition.

Published
2017
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36. Horizontal delivery of microRNAs via food-mother-pup axis

Author

Le Provost, Fabienne, Laubier, Johann, Marthey, Sylvain, Castille, Johan, Le Guillou, Sandrine, Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, and Université Paris Saclay (COmUE)

Subjects
[SDV.GEN]Life Sciences [q-bio]/Genetics, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, [SDV]Life Sciences [q-bio], ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2017

37. Small non coding RNA from frozen bull sperm cells: A Biomarkers panel of male fertility

Author

Sellem, Eli, Marthey, Sylvain, Kiefer, Hélène, Le Danvic, Chrystelle, Allais-Bonnet , Aurélie, Perrier, Jean-Philippe, Jouneau, Luc, Rau, Andrea, Jammes, Hélène, Schibler, Laurent, Allice, Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Université Paris Saclay (COmUE), Biologie du Développement et Reproduction (BDR), École nationale vétérinaire d'Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA), and International Plant and Animal Genome.

Subjects
[SDV.BDD]Life Sciences [q-bio]/Development Biology
Abstract

International audience; New sperm function in embryo development have emerged recently, relying on their small noncoding RNAs (sncRNAs) content. Indeed, involvement of sperm-borne miRNAs in mouse epigenetic inheritance has been evidenced and paternal sncRNAs have been shown to be dispensable for fertilization but crucial for the development of zygotes and 2 cells-embryos. Our study was conducted to unravel the sncRNA content from bull frozen sperm cells and identify miRNA associated with fertility. Total RNA was extracted from 40 ejaculates originating from Holstein and Montbeliard bulls with contrasting fertility, using a novel enhanced protocol. The two quality controls were done on RNA to measure RNAs quantities (Qubit technology) and check whether a reference miRNA (miR125) could be detected by RTqPCR. NGS sequencing libraries were prepared using small RNA (

Published
2017

38. Small non coding RNA from frozen bull sperm cells: biomarkers of male fertility?

Author

Sellem, Eli, Marthey, Sylvain, Kiefer, Hélène, Le Danvic, Chrystelle, Allais-Bonnet , Aurélie, Perrier, Jean-Philippe, Jouneau, Luc, Rau, Andrea, Jammes, Hélène, Schibler, Laurent, Allice, Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Université Paris Saclay (COmUE), Biologie du Développement et Reproduction (BDR), École nationale vétérinaire d'Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA), International Plant and Animal Genome., ANR and APIS-GENE (Labcom SeQuaMol), and International Society for Animal Genetics (ISAG). INT.

Subjects
fertility, [SDV.GEN]Life Sciences [q-bio]/Genetics, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, [SDV]Life Sciences [q-bio], [SDV.BDLR]Life Sciences [q-bio]/Reproductive Biology, [INFO]Computer Science [cs], microARN, bull sperm cell, [SDV.BDD]Life Sciences [q-bio]/Development Biology, ComputingMilieux_MISCELLANEOUS
Abstract

International audience; The sperm cell has been generally considered as a cab driver, carrying and protecting his genetic heritage, but a new vision of its functions has emerged recently. Indeed, sperm cells also carry small noncoding RNAs (sncRNAs) into oocytes during fertilization. Although their roles remain largely unclear, involvement of sperm-borne miRNAs in mouse epigenetic inheritance has been evidenced and paternal miRNAs and/or endo-siRNAs have been shown to be dispensable for fertilization but crucial for the transcriptomic homeostasis and the developmental of zygotes and 2 cells-embryos. This study aimed at unraveling the sncRNA content from bull frozen sperm cells and identifying miRNA or piRNAs associated with fertility. Total RNA has been produced from 40 ejaculates originating from Holstein and Montbeliard bulls with contrasting fertility. To achieve this task, a novel protocol has been developed to ensure good quality and reproducibility. Quality control was ensured by total RNA quantification using the RNA HS Qubit Assay kit, as well as miR125 quantitation by RTqPCR (miRCURY LNA Universal RT microRNA PCR kit; Exiqon). Starting from 77 million of frozen sperm cells on average, RNA yield was 51 ± 15ng, leading to miR125 Cycle Threshold values in a 19 - 20 range. Only small RNA (

Published
2017

39. A missense mutation inTYRP1causes the chocolate plumage color in chicken and alters melanosome structure

Author

Li, Jingyi, primary, Bed’hom, Bertrand, additional, Marthey, Sylvain, additional, Valade, Mathieu, additional, Dureux, Audrey, additional, Moroldo, Marco, additional, Péchoux, Christine, additional, Coville, Jean‐Luc, additional, Gourichon, David, additional, Vieaud, Agathe, additional, Dorshorst, Ben, additional, Andersson, Leif, additional, and Tixier‐Boichard, Michèle, additional

Published
2018
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40. Transcriptome and chromatin structure annotation of liver, CD4+ and CD8+ T cells from four livestock species

Author

Foissac, Sylvain, primary, Djebali, Sarah, additional, Munyard, Kylie, additional, Vialaneix, Nathalie, additional, Rau, Andrea, additional, Muret, Kevin, additional, Esquerré, Diane, additional, Zytnicki, Matthias, additional, Derrien, Thomas, additional, Bardou, Philippe, additional, Blanc, Fany, additional, Cabau, Cèdric, additional, Crisci, Elisa, additional, Dhorne-Pollet, Sophie, additional, Drouet, Françoise, additional, Faraut, Thomas, additional, Gonzalez, Ignacio, additional, Goubil, Adeline, additional, Lacroix-Lamandé, Sonia, additional, Laurent, Fabrice, additional, Marthey, Sylvain, additional, Marti-Marimon, Maria, additional, Momal-Leisenring, Raphaelle, additional, Mompart, Florence, additional, Quéré, Pascale, additional, Robelin, David, additional, Cristobal, Magali San, additional, Tosser-Klopp, Gwenola, additional, Vincent-Naulleau, Silvia, additional, Fabre, Stéphane, additional, der Laan, Marie-Hélène Pinard-Van, additional, Klopp, Christophe, additional, Tixier-Boichard, Michelè, additional, Acloque, Hervé, additional, Lagarrigue, Sandrine, additional, and Giuffra, Elisabetta, additional

Published
2018
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41. Evolution of the Major Histocompatibility Complex class I in wild pigs and peccaries

Author

Lee, Carol, Moroldo, Marco, Perdomo, Alvaro, Mach Casellas, Nuria, Marthey, Sylvain, Lecardonnel, Jerôme, Wahlberg, Per, Chong, Amanda, Estelle Fabrellas, Jordi, Gaillard, Claire, GONGORA, Jaime, University of Sydney, Génétique Animale et Biologie Intégrative (GABI), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Chercheur indépendant, and Institut National de la Recherche Agronomique (INRA)-AgroParisTech

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

Evolution of the Major Histocompatibility Complex class I in wild pigs and peccaries. Annual Meeting of the Society for Molecular Biology and Evolution (SMBE)

Published
2016

42. Small non coding RNA from Frozen bull sperm cells

Author

Sellem, Eli, Marthey, Sylvain, Kiefer, Hélène, Le Danvic, Chrystelle, Allais-Bonnet , Aurélie, Schibler, Laurent, Jammes, Hélène, Allice, Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Université Paris Saclay (COmUE), Biologie du Développement et Reproduction (BDR), École nationale vétérinaire d'Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA), ANR (Labcom SeQuaMol), and International Organisation on Animal Reproduction. FRA.

Subjects
[SDV.BDLR]Life Sciences [q-bio]/Reproductive Biology, [SDV.BDD]Life Sciences [q-bio]/Development Biology, ComputingMilieux_MISCELLANEOUS
Abstract

National audience

Published
2016

43. Genetic determinism of feather colour: how to fill the puzzle?

Author

Tixier-Boichard, Michele, Bed'Hom, Bertrand, Valade, Mathieu, Marthey, Sylvain, Moroldo, Marco, Gourichon, David, Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Pôle d'Expérimentation Avicole de Tours (PEAT), Institut National de la Recherche Agronomique (INRA), Pôle d'Expérimentation Avicole de Tours (UE PEAT), and AgroParisTech-Institut National de la Recherche Agronomique (INRA)

Subjects
[SDV]Life Sciences [q-bio], Feather, Genetics, Chicken, Colour
Abstract

Genetic determinism of feather colour: how to fill the puzzle?. Avian Model Systems 9

Published
2016

44. Inferring the evolution of the major histocompatibility complex of wild pigs and peccaries using hybridisation DNA capture-based sequencing

Author

Lee, Carol, primary, Moroldo, Marco, additional, Perdomo-Sabogal, Alvaro, additional, Mach, Núria, additional, Marthey, Sylvain, additional, Lecardonnel, Jérôme, additional, Wahlberg, Per, additional, Chong, Amanda Y., additional, Estellé, Jordi, additional, Ho, Simon Y. W., additional, Rogel-Gaillard, Claire, additional, and Gongora, Jaime, additional

Published
2017
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45. Food deprivation affects the goat mammary miRNome

Author

Mobuchon, Lenha, Marthey, Sylvain, Le Guillou, Sandrine, Laloë, Denis, Le Provost, Fabienne, Leroux, Christine, Unité Mixte de Recherche sur les Herbivores - UMR 1213 (UMRH), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Institut National de la Recherche Agronomique (INRA), Génétique Animale et Biologie Intégrative (GABI), AgroParisTech-Institut National de la Recherche Agronomique (INRA), ProdInra, Migration, Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, and Institut National de la Recherche Agronomique (INRA)-AgroParisTech

Subjects
[SDV] Life Sciences [q-bio], [SDV]Life Sciences [q-bio], [INFO]Computer Science [cs], [SHS] Humanities and Social Sciences, [INFO] Computer Science [cs], ComputingMilieux_MISCELLANEOUS, [SHS]Humanities and Social Sciences
Abstract

International audience

Published
2015

46. Draft Anaplasma phagocytophilum Genome Sequences from Five Cows, Two Horses, and One Roe Deer Collected in Europe

Author

Dugat, Thibaud, primary, Rossignol, Marie-Noëlle, additional, Rué, Olivier, additional, Loux, Valentin, additional, Marthey, Sylvain, additional, Moroldo, Marco, additional, Silaghi, Cornelia, additional, Höper, Dirk, additional, Fröhlich, Julia, additional, Pfeffer, Martin, additional, Zweygarth, Erich, additional, Lagrée, Anne-Claire, additional, Boulouis, Henri-Jean, additional, and Haddad, Nadia, additional

Published
2016
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47. Selective sweeps using hapFLK combined with genome re-sequencing data reveals strong candidate mutations in QTL regions in divergent chicken lines

Author

Roux, Pierre-François, Boitard, Simon, DJARI, Anis, Esquerre, Diane, Marthey, Sylvain, Désert, Colette, Lecerf, Frédéric, Duval, Elisabeth, Martin, Pascal G.P., Klopp, Christophe, Moroldo, Marco, Servin, Bertrand, Demeure, Olivier, Lagarrigue, Sandrine, Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage [Rennes] (PEGASE), AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA), Laboratoire de Génétique Cellulaire (LGC), 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), Unité de Biométrie et Intelligence Artificielle (UBIA), Institut National de la Recherche Agronomique (INRA), Génétique Animale et Biologie Intégrative (GABI), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Recherches Avicoles (SRA), Unité de recherche Pharmacologie-Toxicologie (UPT), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, 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), 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 Recherches Avicoles (URA), and World's Poultry Science Association (WPSA). INT.

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

Session 1: Genomics and contemporary resources and methodologies; In the context of genome wide re-sequencing using NGS technologies, we analyzed selective sweeps in two divergent chicken lines selected for abdominal fat weight (AF). We applied a new statistic, hapFLK, to analyze the 9.4 M of SNP observed for the whole genome of 20 chickens. This genome scan revealed 129 significant selective sweeps with a size of 86 kb that contained 839 SNP and 2.2 genes, on average. These selective sweeps colocalize with different QTL responsible for abdominal fat and muscle weight, and drastically reduce their size. We then performed three complementary analyses for positional genes in these regions: 1) analysis of their biological functions to select functional candidate genes; 2) analysis in different tissues of their differential expression between both lines to argue in favor of a candidate mutation in regulatory or coding regions; 3) analysis of their polymorphism from DNA-seq and RNA-seq data to identify candidate mutations. The combination of these approaches reveals several strong candidate genes and mutations associated with the traits of interest.

Published
2013

48. Using NGS data to characterize genetics of meet-type and egg-type chicken lines

Author

Roux, Pierre-François, Lecerf, Frédéric, Djari, Anis, Esquerre, Diane, Marthey, Sylvain, Zerjal, Tatiana, Le Bihan-Duval, Elisabeth, Klopp, Christophe, Moroldo, Marco, Estelle, Jordi, Désert, Colette, Bed'Hom, Bertrand, Tixier Boichard, Michèle, Demeure, Olivier, Lagarrigue, Sandrine, Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage [Rennes] (PEGASE), 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), Unité de Biométrie et Intelligence Artificielle (UBIA), Institut National de la Recherche Agronomique (INRA), 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, Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Unité de Recherches Avicoles (URA), Génétique Physiologie et Systèmes d'Elevage, AgroParisTech-Institut National de la Recherche Agronomique (INRA), Recherches Avicoles (SRA), and AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA)

Subjects
[SDV.SA]Life Sciences [q-bio]/Agricultural sciences, analyse de génome, adiposité, sélection génétique, caractérisation génomique, poulet, efficience alimentaire
Abstract

Session 25. Free communications - molecular genetics; absent

Published
2013

49. Identification of candidate polymorphism in a QTL region by combining eQTL mapping with NGS data

Author

Roux, Pierre-François, Blum, Yuna, Désert, Colette, Djari, Anis, Esquerre, Diane, Le Bihan-Duval, Elisabeth, Bed'Hom, Bertrand, Le Roy, Pascale, Lecerf, Frédéric, Moroldo, Marco, Marthey, Sylvain, Klopp, Christophe, Lagarrigue, Sandrine, Demeure, Olivier, Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage [Rennes] (PEGASE), 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), Unité de Biométrie et Intelligence Artificielle (UBIA), Institut National de la Recherche Agronomique (INRA), 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 Recherches Avicoles (URA), Génétique Animale et Biologie Intégrative (GABI), AgroParisTech-Institut National de la Recherche Agronomique (INRA), AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA), Génétique Physiologie et Systèmes d'Elevage, Recherches Avicoles (SRA), and Institut National de la Recherche Agronomique (INRA)-AgroParisTech

Subjects
[SDV.SA]Life Sciences [q-bio]/Agricultural sciences, cartographie de qtl, adiposité, poulet, approche génomique
Abstract

Session 25. Free communications - molecular genetics; absent

Published
2013

50. MiRNAs profile of cutaneous melanoma undergoing complete spontaneous regression in MeLiM pigs

Author

BACO, Michael, Yang, Y.-T., Marthey, Sylvain, Chiang, Y.-S., Le Provost, Fabienne, Chu, C.-Y., Vincent-Naulleau, S., Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, College of Life Science, Institute of Zoology, National Taiwan University [Taiwan] (NTU), College of Life Science, Technology Commons / Center for Systems Biology, Department of Dermatology, Institut de radiobiologie cellulaire et moléculaire (iRCM), Service de radiobiologie expérimentale et innovation technologiques (SREIT), Laboratoire de Radiologie et d'Etude du génome, Commissariat à l'énergie atomique et aux énergies alternatives (CEA), and AgroParisTech-Institut National de la Recherche Agronomique (INRA)

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

absent

Published
2013

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