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4. Epigénétique, gènes et environnement : quelle importance pour les pratiques d’élevage et les méthodes de sélection des volailles ?

Author

COUSTHAM, Vincent, primary, ANDRIEUX, Charlotte, additional, CERUTTI, Chloé, additional, COLLIN, Anne, additional, DAVID, Ingrid, additional, DEMARS, Julie, additional, DEVAILLY, Guillaume, additional, MORISSON, Mireille, additional, HOUSSIER, Marianne, additional, LAGARRIGUE, Sandrine, additional, MÉTAYER-COUSTARD, Sonia, additional, MIGNON-GRASTEAU, Sandrine, additional, PANSERAT, Stéphane, additional, PETIT, Angélique, additional, VITORINO CARVALHO, Anaïs, additional, ZERJAL, Tatiana, additional, and PITEL, Frédérique, additional

Published
2023
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5. Divergent selection for feed efficiency in pigs altered the duodenum transcriptomic response to feed intake and its DNA methylation profiles.

Author

Devailly, Guillaume, Fève, Katia, Saci, Safia, Sarry, Julien, Valière, Sophie, Lluch, Jérôme, Bouchez, Olivier, Ravon, Laure, Billon, Yvon, Gilbert, Hélène, Riquet, Juliette, Beaumont, Martin, and Demars, Julie

Subjects
DNA methylation, DUODENUM, SWINE farms, TRANSCRIPTOMES, SWINE, TIGHT junctions
Abstract

Feed efficiency is a trait of interest in pigs as it contributes to lowering the ecological and economical costs of pig production. A divergent genetic selection experiment from a Large White pig population was performed for 10 generations, leading to pig lines with relatively low-(LRFI) and high- (HRFI) residual feed intake (RFI). Feeding behavior and metabolic differences have been previously reported between the two lines. We hypothesized that part of these differences could be related to differential sensing and absorption of nutrients in the proximal intestine. We investigated the duodenum transcriptome and DNA methylation profiles comparing overnight fasting with ad libitum feeding in LRFI and HRFI pigs (n = 24). We identified 1,106 differentially expressed genes between the two lines, notably affecting pathways of the transmembrane transport activity and related to mitosis or chromosome separation. The LRFI line showed a greater transcriptomic response to feed intake than the HRFI line. Feed intake affected genes from both anabolic and catabolic pathways in the pig duodenum, such as rRNA production and autophagy. Several nutrient transporter and tight junction genes were differentially expressed between lines and/or by short-term feed intake. We also identified 409 differentially methylated regions in the duodenum mucosa between the two lines, while this epigenetic mark was less affected by feeding. Our findings highlighted that the genetic selection for feed efficiency in pigs changed the transcriptome profiles of the duodenum, and notably its response to feed intake, suggesting key roles for this proximal gut segment in mechanisms underlying feed efficiency. [ABSTRACT FROM AUTHOR]

Published
2024
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7. A methyl-seq tool to capture genomic imprinted loci

Author

Hubert Jean-Noël, Iannuccelli Nathalie, Cabau Cédric, Jacomet Eva, Billon Yvon, Serre Rémy-Felix, Vandecasteele Céline, Donnadieu Cécile, and Demars Julie

Abstract

Genomic imprinting represents an original model of epigenetic regulation resulting in a parent-of-origin expression. Despite the critical role of imprinted genes in mammalian growth, metabolism and neuronal function, there is no molecular tool specifically targeting them for a systematic evaluation. Here, we optimized and compared to bisulfite-based standard a novel methyl-seq system to capture 165 candidate regions for genomic imprinting and ultimately detect parent-of-origin methylation, the main hallmark of imprinting.

Published
2023

8. GENOME-WIDE ASSOCIATION STUDY FOR GROWTH AND FEED EFFICIENCY TRAITS IN RABBITS.

Author

Garreau, Hervé, Labrune, Yann, Chapuis, Hervé, Ruesche, Julien, Riquet, Juliette, Demars, Julie, Benitez, Florence, Richard, François, Drouilhet, Laurence, Zemb, Olivier, and Gilbert, Hélène

Subjects
GENOME-wide association studies, RABBITS, SINGLE nucleotide polymorphisms, ANIMAL feeds, ANIMAL breeding, ANIMAL breeds
Abstract

Feed efficiency is a major production trait in animal genetic breeding schemes. To further investigate the genetic control of feed efficiency in rabbits, we performed a genome-wide association study (GWAS) for growth and feed efficiency on 679 rabbits genotyped with the Affimetrix Axiom Rabbit 200K Genotyping Array. After quality control, 127 847 single-nucleotide polymorphisms (SNP) were retained for association analyses. The GWAS were performed using GEMMA software, applying a mixed univariate animal model with a linear regression on each SNP allele. The traits analysed were weight at weaning and at 63 days of age, average daily gain, total individual feed intake, feed conversion ratio and residual feed intake. No significant SNP was found for growth traits or feed intake. Fifteen genome-wide significant SNPs were detected for feed conversion ratio on OCU7, spanning from 124.8 Mbp to 126.3 Mbp, plus two isolated SNP on OCU2 (77.3 Mbp) and OCU8 (16.5 Mbp). For residual feed intake, a region on OCU18 (46.1-53.0 Mbp) was detected, which contained a putative functional candidate gene, GOT1. [ABSTRACT FROM AUTHOR]

Published
2023
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10. Stronger transcriptomic response to feed intake in the duodenum of pig with high feed efficiency from a divergent selection experiment

Author

Devailly, Guillaume, primary, Feve, Katia, additional, Saci, Safia, additional, Sarry, Julien, additional, Valiere, Sophie, additional, Lluch, Jerome, additional, Bouchez, Olivier, additional, Ravon, Laure, additional, Billon, Yvon, additional, Gilbert, Helene, additional, Beaumont, Martin, additional, and Demars, Julie, additional

Published
2022
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11. Genetics of body weight and length of Large White piglets and relationship to maternal performance

Author

Canario, L, Billon, Y, Hébrard, W, Demars, Julie, and Demars, Julie

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

Body weight and body metrics of newborn piglets reflect their level of development. We studied a Large White population raised in a single experimental herd. Survival and growth performance of 10,101 piglets originating from 689 litters were analysed. In 440 of these litters, 1,320 piglets contrasting for birth weight were recorded for body length and circumference. At piglet level, the estimated direct and maternal heritability values were were h²d=0.02 and h²m=0.13 for birth weight, h²d=0.65 and h²m=0.21 for the ponderal index and h²d=0.23 and h²m=0.01 for the ratio of circumference to body length. The genetic correlation between the ponderal index and litter size and gestation length tended to be negative.

Published
2022

15. GENOME WIDE ASSOCIATION STUDY OF GROWTH AND FEED EFFICIENCY TRAITS IN RABBITS

Author

Garreau, Hervé, Labrune, Yann, Chapuis, Hervé, Ruesche, Julien, Riquet, Juliette, Demars, Julie, Benitez, Florence, Richard, François, Gilbert, Hélène, Drouilhet, Laurence, Zemb, Olivier, Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), 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)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), H2020 Feed-a-Gene, ITAVI-INRAE, and European Project: 633531,H2020,H2020-SFS-2014-2,Feed-a-Gene(2015)

Subjects
[SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, [SDV]Life Sciences [q-bio], feed efficiency, rabbit, SNP, GWAS, genetics, feed efficiency SNP GWAS genetics rabbit
Abstract

International audience; We performed a genome wide association study for growth and feed efficiency using the GEMMA software on 679 rabbits genotyped with the Affimetrix Axiom Rabbit 200K Genotyping Array. No significant SNP was found for growth traits or feed intake. Two and 89 chromosome-wide significant SNPs were detected for feed conversion ratio and residual feed intake, respectively. The 89 significant SNPs for residual feed intake were all located on chromosome 18, where the putative functional candidate gene GOT1 could be identified.

Published
2021

16. Heterologous hybridization using the human exome - a molecular tool to target and identify major genes

Author

Iannuccelli, Nathalie, Cabau, Cédric, Sarry, Julien, Bouchez, Olivier, Billon, Yvon, Riquet, Juliette, Allain, Daniel, Demars, Julie, 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
[SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, human+exome+capture+sequencing+variants
Abstract

International audience; Identifying causal mutations responsible of phenotypes in a time and cost-effective manner remains a challenge still for all species. Although the portfolio of next-generation sequencing methodologies offers a broad range of opportunities nowadays, having the right and suitable molecular genetic tools in non-model organisms is often an issue. For the European rabbit (Oryctolagus cuniculus), considered as an animal model for experimental research, the OryCun2.0 reference genome was released in 2009 and the Affymetrix AxiomOrcun SNP Array was made available in 2016. This novel beadchip gives the possibility to develop conveniently genome-wide association studies (GWAS) in rabbits without however freeing itself from the subsequent steps of causal mutation characterization. Whole exome sequencing (WES) appears as a direct and suitable strategy to target and sequence variants all at once. Unfortunately, no exome enrichment tool exist for rabbits. Here, we proposed to capture the rabbit exome using the marketed human panel since human and rabbit genomes are closely related on the phylogenetic tree of species. We performed heterologous hybridization for 48 rabbits from 7 different populations and generated 2 billion sequencing reads for the whole dataset. The quality of the heterologous hybridization allowed the capture of the rabbit exome and enabled a dataset of 40,000 confident variants that specifically target both protein-coding and extended exons. This method also presents a unique opportunity to investigate both (i) the genetic diversity of different rabbits’ breeds and (ii) the mendelian determinism of specific phenotypes in rabbits without resorting to costly customized tools.

Published
2021

18. The importance of annotations (reference genome and parent gene) for the study of circRNAs

Author

robic, annie, Faraut, Thomas, Cerutti, Chloé, Demars, Julie, Kühn, Christa, robic, annie, 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), Leibniz Institute for Farm Animal Biology (FBN), and University of Rostock

Subjects
[SDV] Life Sciences [q-bio], FAANG, annotation, [SDV]Life Sciences [q-bio], circular RNA, livestock species, ComputingMilieux_MISCELLANEOUS, noncoding RNA
Abstract

International audience

Published
2021

19. New perspective on intergenerational transmission of characters

Author

David, Ingrid, Aliakbari, Amir, Canario, Laurianne, Combes, Sylvie, Demars, Julie, Déru, Vanille, Garreau, Herve, Gilbert, Hélène, Ricard, Anne, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and DAVID, Ingrid

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

International audience

Published
2020

23. A Long Read project to find optimal technologic combinations for genome assembly and variability, epigenetic marks detection and metagenomic analysis

Author

Iampietro, Carole, Eché, Camille, Castinel, Adrien, Serre, Rémy-Félix, Klopp, Christophe, Denis, Erwan, Bouchez, Olivier, Kuchly, Claire, Vandecasteele, Céline, BROHA, Amandine, THERVILLE, Romain, Di Franco, Arnaud, Djebali Quelen, Sarah, DREAU, Andreea, Hoede, Claire, KOROVINA, Oleksandra, BIRBES, CLEMENT, Laborie, Didier, Mainguy, Jean, Noirot, Céline, Salin, Gerald, Terzian, Paul, Trotard, Marie-Stéphane, Boichard, Didier, Boussaha, Mekki, Grohs, Cécile, Charcosset, Alain, Belcram, Harry, Joets, Johann, Combes, Sylvie, Pascal, Géraldine, Pitel, Frederique, Leroux, Sophie, Riquet, Juliette, Demars, Julie, Tosser-Klopp, Gwenola, Vitte, Clémentine, Iannuccelli, Nathalie, Lluch, Jérôme, Lopez-Roques, Celine, Faraut, Thomas, Zytnicki, Matthias, Gaspin, Christine, Milan, Denis, Donnadieu, Cécile, Génome et Transcriptome - Plateforme Génomique (GeT-PlaGe), Institut National de la Recherche Agronomique (INRA)-Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA), 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), 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), Génétique Animale et Biologie Intégrative (GABI), Université Paris-Saclay-AgroParisTech-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Génétique Quantitative et Evolution - Le Moulon (Génétique Végétale) (GQE-Le Moulon), AgroParisTech-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), FEDER-Région Occitanie, Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), and AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)

Subjects
[SDV.GEN]Life Sciences [q-bio]/Genetics, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, [SDV]Life Sciences [q-bio], [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [INFO]Computer Science [cs], ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2020

28. Les gènes de coloration et leurs interactions, le modèle lapin Himalayan

Author

Demars, Julie, 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, and ProdInra, Migration

Subjects
[SDV.OT]Life Sciences [q-bio]/Other [q-bio.OT], [SDV.OT] Life Sciences [q-bio]/Other [q-bio.OT], interaction, ComputingMilieux_MISCELLANEOUS, génétique
Abstract

National audience

Published
2018

29. High resolution physical map of porcine chromosome 7 QTL region and comparative mapping of this region among vertebrate genomes

Author

Demeure Olivier, Morisson Mireille, Gautier Mathieu, Feve Katia, Riquet Juliette, Demars Julie, Renard Christine, Chardon Patrick, and Milan Denis

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

Abstract Background On porcine chromosome 7, the region surrounding the Major Histocompatibility Complex (MHC) contains several Quantitative Trait Loci (QTL) influencing many traits including growth, back fat thickness and carcass composition. Previous studies highlighted that a fragment of ~3.7 Mb is located within the Swine Leucocyte Antigen (SLA) complex. Internal rearrangements of this fragment were suggested, and partial contigs had been built, but further characterization of this region and identification of all human chromosomal fragments orthologous to this porcine fragment had to be carried out. Results A whole physical map of the region was constructed by integrating Radiation Hybrid (RH) mapping, BAC fingerprinting data of the INRA BAC library and anchoring BAC end sequences on the human genome. 17 genes and 2 reference microsatellites were ordered on the high resolution IMNpRH212000rad Radiation Hybrid panel. A 1000:1 framework map covering 550 cR12000 was established and a complete contig of the region was developed. New micro rearrangements were highlighted between the porcine and human genomes. A bovine RH map was also developed in this region by mapping 16 genes. Comparison of the organization of this region in pig, cattle, human, mouse, dog and chicken genomes revealed that 1) the translocation of the fragment described previously is observed only on the bovine and porcine genomes and 2) the new internal micro rearrangements are specific of the porcine genome. Conclusion We estimate that the region contains several rearrangements and covers 5.2 Mb of the porcine genome. The study of this complete BAC contig showed that human chromosomal fragments homologs of this heavily rearranged QTL region are all located in the region of HSA6 that surrounds the centromere. This work allows us to define a list of all candidate genes that could explain these QTL effects.

Published
2006
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30. EIF2S2 Retroposition into IRF2BP2 Underlies Fleece Variation in Sheep through the Formation of a Long Endogenous Double-Stranded RNA

Author

Demars, Julie, Cano, Margarita, Drouilhet, Laurence, Fabre, Stéphane, Servin, Bertrand, Mulsant, Philippe, Tosser-Klopp, Gwenola, Allain, Daniel, 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, and Instituto Nacional de Tecnología Agropecuaria (INTA)

Subjects
Animal biology, sheep, phenotypic, selection, fiber, production, [SDV.BA]Life Sciences [q-bio]/Animal biology, Biologie animale
Abstract

International audience; Fleece variation, in composition and structure, observed in mammals is a consequence of a strong selective pressure for fiber production after domestication. Wild species with double coated fleece produced a variety of breeds with single coated fleece. In sheep, these two categories discriminate primitive sheep from woolly modern sheep (Ovis aries). Nowadays, fleece variation is segregating in the Romane breed with lambs owning a coat either long and hairy (characteristic of ancestral sheep) or short and woolly (typical to domestic sheep). Here we report that the “woolly” allele results from the insertion of an antisense EIF2S2 (Eukaryotic Translation Initiation Factor 2, Subunit 2 Beta) retrogene (called asEIF2S2) into the 3’ UTR of the IRF2BP2 (Interferon Regulatory Factor 2 Binding Protein 2) gene leading to an abnormal IRF2BP2 transcript. We provide evidence that this chimeric IRF2BP2/asEIF2S2 messenger, by targeting the genuine sense EIF2S2 RNA and creating a long endogenous double-stranded RNA, alters the expression of EIF2S2 mRNA. This is the first example, to our knowledge of a phenotype arising from the modulation of messengers accumulation via a RNA-RNA hybrid itself generated through a retroposition gene mechanism. Altogether our results bring new insights on (i) the mammalian hair morphogenesis with the identification of EIF2S2 and IRF2BP2 as novel key regulators and (ii) the sheep population history thanks to the characterization of the molecular origin of an evolutionary phenotypic variation. Furthermore, these findings will contribute to a sustainable sheep production system since lambs carrying a hairy fleece are more adapted and robust to environmental harsh conditions.

Published
2017

32. Impact du rationnement alimentaire sur le phénotype Himalayan

Author

Demars, Julie, 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, and Institut National de Recherche Agronomique (INRA). UAR Département Physiologie Animale et Systèmes d'Elevage (0558).

Subjects
[SDV]Life Sciences [q-bio], [INFO]Computer Science [cs]
Abstract

National audience; Perspectives de travaux à venir Suite à des observations faites sur les lapins de la lignée 1001, des différences de coloration et de surfaces de zones colorées ont été constatées. Ces variations sont principalement observées au niveau des oreilles, du museau et des pattes. Ce phénotype particulier appelé « Himalayan » est également retrouvé chez la souris, le chat et le cobaye. Chez le lapin, un variant dans le gène de la tyrosinase (Tyr) a été identifié mais aucune étude récente n’a permis de valider son implication dans le déterminisme génétique du phénotype et aucune étude n’a permis de montrer que la gamme de variation de la coloration était déterminée par cette mutation. Des données disponibles chez la souris pour le gène Asip indiquent que pour un même génotype des variations phénotypiques de la coloration pouvaient être déterminées par des différences de méthylation en amont de la séquence du gène et qu’un stress alimentaire pouvait induire, via un pattern de méthylation variable, des différences de couleur des animaux. On émet donc l’hypothèse que le phénotype « Himalayan » pourrait être déterminé, en plus de la mutation décrite, par des modifications de type épigénétique et que le rationnement pourrait influencer l’expression du gène responsable de la coloration des extrémités du lapin.

Published
2016

33. Genome-Wide Identification of the Mutation Underlying Fleece Variation and Discriminating Ancestral Hairy Species from Modern Woolly Sheep

Author

Demars, Julie, primary, Cano, Margarita, additional, Drouilhet, Laurence, additional, Plisson-Petit, Florence, additional, Bardou, Philippe, additional, Fabre, Stéphane, additional, Servin, Bertrand, additional, Sarry, Julien, additional, Woloszyn, Florent, additional, Mulsant, Philippe, additional, Foulquier, Didier, additional, Carrière, Fabien, additional, Aletru, Mathias, additional, Rodde, Nathalie, additional, Cauet, Stéphane, additional, Bouchez, Olivier, additional, Pirson, Maarten, additional, Tosser-Klopp, Gwenola, additional, and Allain, Daniel, additional

Published
2017
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34. Validation of QTL affecting resistance to nematodes in Sheep identified in a Back-Cross design in a pure breed population

Author

Moreno, Carole, Jacquiet, Philippe, Bouvier, Frédéric, Cortet, Jacques, Blanchard-Letort, Alexandra, Guégnard, Fabrice, François, Dominique, Bourdillon, Yves, Grisez, Christelle, Prévot, Françoise, Averadere, Audrey, Demars, Julie, Sarry, Julien, Stella, Alessandra, Woloszyn, Florent, Canale-Tabet, Kamila, Cabaret, Jacques, Tosser-Klopp, Gwenola, Sallé, Guillaume, 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, Interactions hôtes-agents pathogènes [Toulouse] (IHAP), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Domaine expérimental Bourges-La Sapinière (BOURGES), Institut National de la Recherche Agronomique (INRA), Infectiologie et Santé Publique (UMR ISP), Institut National de la Recherche Agronomique (INRA)-Université de Tours (UT), Parco Tecnologico Padano, and Institut National de la Recherche Agronomique (INRA)-Université de Tours

Subjects
resistance, sheep, nematode, snp, [SDV]Life Sciences [q-bio], [INFO]Computer Science [cs]
Abstract

International audience; Gastro-intestinal nematodes are of major concern to sheep health worldwide. Identifying the causative genes responsible for resistance would augment the efficiency of selection. Previously, back-cross (BC) sheep (Black Belly * Romane breeds) were genotyped with a 50K SNP chip and were measured for faecal egg count after two successive experimental challenges by H. contortus. The most significant QTL were identified on chromosomes 5, 12, 13, 21. A customized assay including 1000 SNP was created to increase the density ofmarker coverage in these regions and others major QTL regions affecting parasitism resistance in natural infection conditions. In the present study, 277 Romane lambs were experimentally challenged with H contortusand genotyped with the dedicated 1000 SNP. Six out of the eight tested QTL regions have an effect in the Romane pure Breed population.

Published
2014

35. Fine mapping of birthcoat type in the Romanov breed sheep

Author

Cano, Margarita, Allain, Daniel, Foulquié, Didier, Moreno, Carole, Mulsant, Philippe, François, Dominique, Demars, Julie, Tosser-Klopp, Gwenola, Instituto Nacional de Tecnología Agropecuaria (INTA), Station d'Amélioration Génétique des Animaux (SAGA), Institut National de la Recherche Agronomique (INRA), Domaine expérimental de La Fage (LA FAGE), 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), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées

Subjects
marker, genomic, romane breed sheep, qtl, [SDV]Life Sciences [q-bio], birthcoat, snp, genetic, ComputingMilieux_MISCELLANEOUS
Abstract

National audience

Published
2013

36. Mapping a putative autosomal gene controlling ovulation rate and infertility in Cambridge sheep

Author

Keane, O.M., HANRAHAN, J.P., Tosser-Klopp, Gwenola, Sarry, Julien, Fabre, Stéphane, Demars, Julie, Bodin, Loys, Teagasc Agriculture and Food Development Authority (Teagasc), 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, Physiologie de la reproduction et des comportements [Nouzilly] (PRC), Institut National de la Recherche Agronomique (INRA)-Institut Français du Cheval et de l'Equitation [Saumur]-Université de Tours-Centre National de la Recherche Scientifique (CNRS), Station d'Amélioration Génétique des Animaux (SAGA), Institut National de la Recherche Agronomique (INRA), and Institut National de la Recherche Agronomique (INRA)-Institut Français du Cheval et de l'Equitation [Saumur]-Université de Tours (UT)-Centre National de la Recherche Scientifique (CNRS)

Subjects
cambridge sheep, [SDV]Life Sciences [q-bio], selection, [INFO]Computer Science [cs], genetic, identifi, ComputingMilieux_MISCELLANEOUS
Abstract

National audience

Published
2013

37. Two new mutations affecting ovulation rate in sheep

Author

Demars, Julie, Fabre, Stéphane, Rossetti, Raffaella, Persani, Luca, Tosser-Klopp, Gwenola, Mulsant, Philippe, Nowak, Zuzanna, Drobick, W., Martyniuk, E., Bodin, Loys, 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, Physiologie de la reproduction et des comportements [Nouzilly] (PRC), Institut National de la Recherche Agronomique (INRA)-Institut Français du Cheval et de l'Equitation [Saumur]-Université de Tours (UT)-Centre National de la Recherche Scientifique (CNRS), Laboratorio di Ricerche Endocrino-Metaboliche, Istituto Auxologico Italiano, Università degli Studi di Milano [Milano] (UNIMI), Warsaw University of Life Sciences (SGGW), Station d'Amélioration Génétique des Animaux (SAGA), Institut National de la Recherche Agronomique (INRA), ANR Monopoly, and Institut National de la Recherche Agronomique (INRA)-Institut Français du Cheval et de l'Equitation [Saumur]-Université de Tours-Centre National de la Recherche Scientifique (CNRS)

Subjects
reproduction, sheep, [SDV]Life Sciences [q-bio], snp, [INFO]Computer Science [cs], genetic, mutation, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2012

38. Novel mutations controlling ovulation rate in sheep

Author

Bodin, Loys, Demars, Julie, Drobik, W., Fabre, Stéphane, HANRAHAN, J.P., Keane, O., Martyniuk, E., Mulsant, Philippe, Nowak, Z., Persani, L., Rossetti, R., Sarry, Julien, Tosser-Klopp, Gwenola, Station d'Amélioration Génétique des Animaux (SAGA), 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, Warsaw University of Life Sciences (SGGW), Physiologie de la reproduction et des comportements [Nouzilly] (PRC), Institut National de la Recherche Agronomique (INRA)-Institut Français du Cheval et de l'Equitation [Saumur]-Université de Tours-Centre National de la Recherche Scientifique (CNRS), Teagasc Agriculture and Food Development Authority (Teagasc), Warsaw Agricultural University, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Università degli Studi di Milano [Milano] (UNIMI), and Institut National de la Recherche Agronomique (INRA)-Institut Français du Cheval et de l'Equitation [Saumur]-Université de Tours (UT)-Centre National de la Recherche Scientifique (CNRS)

Subjects
sheep, [SDV.OT]Life Sciences [q-bio]/Other [q-bio.OT], ovulation, mutation, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2012

39. Towards candidate genes affecting body fatness at the SSC7 QTL by expression analyses

Author

Gondret, Florence, Riquet, Juliette, Tacher, Sandrine, Demars, Julie, Sanchez, Marie Pierre, Billon, Yvon, Robic, Annie, Bidanel, Jean Pierre, Milan, Denis, Systèmes d'Elevage, Nutrition Animale et Humaine (SENAH), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Supérieure Agronomique de Rennes, 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), Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Génétique Expérimentale en Productions Animales (GEPA), Institut National de la Recherche Agronomique (INRA), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, and AgroParisTech-Institut National de la Recherche Agronomique (INRA)

Subjects
[SDV.SA]Life Sciences [q-bio]/Agricultural sciences, qtl, ppard, cdkn1a, adipogenesis, swine chromosome 7
Abstract

A quantitative trait locus (QTL) affecting fatness in a way opposite to expectations based on breed means was mapped to swine chromosome 7 (SSC7) using crosses between Large White (LW) and Meishan (MS) founders. Defining the molecular fatness trait more explicitly would allow deducing positional candidate genes, for which expression differences must be analysed in experimental populations. First, mRNA levels of genes representing sequential steps in adipogenesis or involved in lipid metabolism were studied in backfat of pigs having homozygous LWQTL7/LWQTL7 or heterozygous LWQTL7/MSQTL7 alleles and considered at two ages. mRNA level of DLK1 expressed in preadipocytes was greater in MSQTL7/LWQTL7 pigs than in homozygous pigs at 28 days. Transcript abundances of CEBPA involved in differentiation, the prolipogenic FASN gene and the adipocyte-specific marker FABP4 were lower in MSQTL7/LWQTL7 pigs compared with LWQTL7/LWQTL7 pigs at 150 days. Because these results suggest a lag time in terminal differentiation associated with the MS allele, seven genes in the QTL interval were deduced as promising candidates for the QTL effect by bioinformatics analysis. Among them, PPARD and CDKN1A had lower expression levels in MSQTL7/LWQTL7 pigs at both ages. Genotype-related differences were observed in mRNA levels of PPARD target genes involved in cell differentiation (FZD7) or fatty acid oxidation (ACADL and ACOX1) at 150 days. These results re-evaluate the potential of PPARD to explain part of variation in pig adiposity.

Published
2012

40. Genetic variants within the second intron of theKCNQ1gene affect CTCF binding and confer a risk of Beckwith–Wiedemann syndrome upon maternal transmission

Author

Demars, Julie, primary, Shmela, Mansur Ennuri, additional, Khan, Abdul Waheed, additional, Lee, Kai Syin, additional, Azzi, Salah, additional, Dehais, Patrice, additional, Netchine, Irène, additional, Rossignol, Sylvie, additional, Le Bouc, Yves, additional, El-Osta, Assam, additional, and Gicquel, Christine, additional

Published
2014
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41. Genome-Wide Association Studies Identify Two Novel BMP15 Mutations Responsible for an Atypical Hyperprolificacy Phenotype in Sheep

Author

Demars, Julie, primary, Fabre, Stéphane, additional, Sarry, Julien, additional, Rossetti, Raffaella, additional, Gilbert, Hélène, additional, Persani, Luca, additional, Tosser-Klopp, Gwenola, additional, Mulsant, Philippe, additional, Nowak, Zuzanna, additional, Drobik, Wioleta, additional, Martyniuk, Elzbieta, additional, and Bodin, Loys, additional

Published
2013
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42. Analysis of the IGF2/H19 imprinting control region uncovers new genetic defects, including mutations of OCT-binding sequences, in patients with 11p15 fetal growth disorders

Author

Demars, Julie, primary, Shmela, Mansur Ennuri, additional, Rossignol, Sylvie, additional, Okabe, Jun, additional, Netchine, Irène, additional, Azzi, Salah, additional, Cabrol, Sylvie, additional, Le Caignec, Cédric, additional, David, Albert, additional, Le Bouc, Yves, additional, El-Osta, Assam, additional, and Gicquel, Christine, additional

Published
2009
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43. Metabolic and histochemical characteristics of fat and muscle tissues in homozygous or heterozygous pigs for the body composition QTL located on chromosome 7

Author

Demars, Julie, primary, Riquet, Juliette, additional, Sanchez, Marie-Pierre, additional, Billon, Yvon, additional, Hocquette, Jean-François, additional, Lebret, Bénédicte, additional, Iannuccelli, Nathalie, additional, Bidanel, Jean-Pierre, additional, Milan, Denis, additional, and Gondret, Florence, additional

Published
2007
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45. A genome-wide epistatic network underlies the molecular architecture of continuous color variation of body extremities

Author

Julie Demars, Yann Labrune, Nathalie Iannuccelli, Alice Deshayes, Sophie Leroux, Hélène Gilbert, Patrick Aymard, Florence Benitez, Juliette Riquet, Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), 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)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Stabilité génétique, cellules souches et radiations (SGCSR (U_1274 / UMR_E_008)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris-Saclay-Université Paris Cité (UPCité), Département Génétique Animale, INRAE, Laboratoire GenPhySE - Génétique Physiologie et Systèmes d'Elevage, Centro Nacional de Genotipado (CeGen), GenoToul bioinformatics, European Project: 633531,H2020,H2020-SFS-2014-2,Feed-a-Gene(2015), 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), Demars, Julie, and Adapting the feed, the animal and the feeding techniques to improve the efficiency and sustainability of monogastric livestock production systems - Feed-a-Gene - - H20202015-03-01 - 2020-02-29 - 633531 - VALID

Subjects
epistasis, Melanogenesis, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, LD, epistasis Melanogenesis Recessivity BAF, CNV, LRR, SNP, local false sign rate, Oryctolagus cuniculus, Coat coloration Copy number variation, credible set, single nucleotide polymorphism, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Genetics, LFSR, GWAS, B allele frequency, genome wide association study, [SDV.BA.MVSA]Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health, Copy number variation, Recessivity, [SDV.BA.MVSA] Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health, PIP, posterior inclusion probability, [SDV.BIO] Life Sciences [q-bio]/Biotechnology, Coat coloration, [SDV.BBM.GTP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], CS, Ocu, linkage disequilibrium, log R ratio
Abstract

International audience; Deciphering the molecular architecture of coat coloration for a better understanding of the biological mechanisms underlying pigmentation still remains a challenge. We took advantage of a rabbit French experimental population in which both a pattern and a gradient of coloration from white to brown segregated within the himalayan phenotype. The whole experimental design was genotyped using the high density Affymetrix® AxiomOrcun™ SNP Array and phenotyped into 6 different groups ordered from the lighter to the darker. Genome-wide association analyses pinpointed an oligogenic determinism, under recessive and additive inheritance, involving genes already known in melanogenesis (ASIP, KIT, MC1R, TYR), and likely processed pseudogenes linked to ribosomal function, RPS20 and RPS14. We also identified (i) gene-gene interactions through ASIP:MC1R affecting light cream/beige phenotypes while KIT:RPS responsible of dark chocolate/brown colors and (ii) a genome-wide epistatic network involving several others coloration genes such as POT1 or HPS5. Finally, we determined the recessive inheritance of the English spotting phenotype likely involving a copy number variation affecting at least the end of the coding sequence of the KIT gene. Our analyses of coloration as a continuous trait allowed us to go beyond much of the established knowledge through the detection of additional genes and gene-gene interactions that may contribute to the molecular architecture of the coloration phenotype.

Published
2022

46. Deciphering the molecular architecture of the coat colour variability in a European rabbit population

Author

Julie Demars, Yann Labrune, Nathalie Iannuccelli, Patrick Aymard, Florence Benitez, Sophie Leroux, Hélène Gilbert, Juliette Riquet, and Demars, Julie

Subjects
coloration+interaction+epistasis+GWAS+rabbit+recessive, [SDV.GEN.GA] Life Sciences [q-bio]/Genetics/Animal genetics
Abstract

Understanding the molecular mechanism of coloration has been the goal of many genetic and evolutionary studies in a broad number of species. Nevertheless, most of our current knowledge is restricted to colour traits exhibiting relatively simple discrete variation and inheritance patterns. More than a hundred of genes are involved in coloration traits in rodents and many mutations have been identified. In the European rabbit (Oryctolagus cuniculus), different coat colours have been selected through domestication and are nowadays fixed in specific breeds. Although numerous mutations affecting coat colour have been discovered in various rabbit breeds, additional variants have still to be identified. Despite the evolution of technologies through the genomics era, understanding the molecular architecture of such complex phenotypes still remains a challenge. Here, we propose a genome-wide investigation of coat colour using rabbit high-density SNP array. We performed genome-wide association studies (GWAS) considering the variation of coat colour as quantitative and binary phenotypes. We identified several significant SNPs marking loci already known to affect coat colour as well as in a few other chromosome regions not yet described to affect this phenotype in rabbits (e.g. a genomic region on chromosome 14). Moreover, we determined the best model of inheritance for each region associated to coat colour. Our results bring new insights into the molecular architecture of the coloration phenotype pinpointing its oligogenic determinism.

Published
2021

47. New Insights into the Melanophilin (MLPH) Gene Affecting Coat Color Dilution in Rabbits

Author

Julie Demars, Juliette Riquet, Luca Fontanesi, Nathalie Iannuccelli, Valerio Joe Utzeri, D. Allain, Gérard Auvinet, Demars, Julie, Iannuccelli, Nathalie, Utzeri, Valerio Joe, Auvinet, Gerard, Riquet, Juliette, Fontanesi, Luca, Allain, Daniel, 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, Alma Mater Studiorum Università di Bologna [Bologna] (UNIBO), Génétique, Expérimentation et Système Innovants (GenESI), and Institut National de la Recherche Agronomique (INRA)

Subjects
0301 basic medicine, Candidate gene, Coat, [SDV.OT]Life Sciences [q-bio]/Other [q-bio.OT], lcsh:QH426-470, coat color dilution, rabbit, Biology, Frameshift mutation, 03 medical and health sciences, Exon, Genetic, Genetics, Allele, Gene, Genetics (clinical), melanophilin, 0402 animal and dairy science, Wild type, 04 agricultural and veterinary sciences, 040201 dairy & animal science, 3. Good health, lcsh:Genetics, 030104 developmental biology, Melanophilin, sense organs, Autre (Sciences du Vivant)
Abstract

Coat color dilution corresponds to a specific pigmentation phenotype that leads to a dilution of wild type pigments. It affects both eumelanin and pheomelanin containing melanosomes. The mode of inheritance of the dilution phenotype is autosomal recessive. Candidate gene approaches focused on the melanophilin (MLPH) gene highlighted two variants associated with the dilution phenotype in rabbits: The c.111-5C&gt, A variant that is located in an acceptor splice site or the c.585delG variant, a frameshift mutation. On the transcript level, the skipping of two exons has been reported as the molecular mechanism responsible for the coat color dilution. To clarify, which of the two variants represents the causal variant, (i) we analyzed their allelic segregation by genotyping Castor and Chinchilla populations, and (ii) we evaluated their functional effects on the stability of MLPH transcripts in skin samples of animals with diluted or wild type coat color. Firstly, we showed that the c.585delG variant showed perfect association with the dilution phenotype in contrast to the intronic c.111-5C&gt, A variant. Secondly, we identified three different MLPH isoforms including the wild type isoform, the exon-skipping isoform and a retained intron isoform. Thirdly, we observed a drastic and significant decrease of MLPH transcript levels in rabbits with a coat color dilution (p-values ranging from 10&minus, 03 to 10&minus, 06). Together, our results bring new insights into the coat color dilution trait.

Published
2018

48. Genome-Wide Association Studies Identify Two Novel BMP15 Mutations Responsible for an Atypical Hyperprolificacy Phenotype in Sheep

Author

Wioleta Drobik, Julie Demars, Raffaella Rossetti, Stéphane Fabre, Julien Sarry, Gwenola Tosser-Klopp, Hélène Gilbert, E. Martyniuk, Zuzanna Nowak, Philippe Mulsant, Luca Persani, Loys Bodin, 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, Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National de la Recherche Agronomique (INRA), Physiologie de la reproduction et des comportements [Nouzilly] (PRC), Institut National de la Recherche Agronomique (INRA)-Institut Français du Cheval et de l'Equitation [Saumur]-Université de Tours (UT)-Centre National de la Recherche Scientifique (CNRS), Université Francois Rabelais [Tours], Institut Français du Cheval et de l'Equitation, Università degli Studi di Milano [Milano] (UNIMI), Warsaw University of Life Sciences (SGGW), Station d'Amélioration Génétique des Animaux (SAGA), This work was supported by grants from France via Agence National pour la Recherche (http://www.agence-nationale-recherche.fr /) (ANR 2010 BLANC grant 160801, MONOPOLY) and EC (FP7/2007–2013), grant 245140, '3SR', Sustainable Solutions for Small Ruminants (http://www.3srbreeding.eu/), WP4 (this publication reflects only the authors' views and the EC is not liable for any use that may be made of the information contained herein), and the DEGERAM Program (FNADT, FEDER, CR Midi Pyrénées, Auvergne et Limousin). This work was partially supported by Telethon Foundation, Italy (grant GGP09126 to LP)., Institut National de la Recherche Agronomique (INRA)-Institut Français du Cheval et de l'Equitation [Saumur]-Université de Tours-Centre National de la Recherche Scientifique (CNRS), and Demars, Julie

Subjects
rasa aragonesa sheep, Cancer Research, Candidate gene, Anatomy and Physiology, Litter Size, [SDV]Life Sciences [q-bio], Genome-wide association study, medicine.disease_cause, Genetic analysis, Genotype, Genetics (clinical), Genetics, 0303 health sciences, Mutation, 04 agricultural and veterinary sciences, Phenotype, Medicine, Bone Morphogenetic Protein 15, increased prolificacy, Research Article, Ovulation, statistical method, lcsh:QH426-470, premature ovarian failure, Biology, haplotype reconstruction, 03 medical and health sciences, granulosa, Genetic Mutation, Genetic variation, Genome-Wide Association Studies, medicine, Animals, Humans, increased ovulation rate, bone morphogenetic protein 15, growth differentiation factor 9, cell function, phenotype, Allele, Molecular Biology, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Sheep, Reproductive System, 0402 animal and dairy science, 040201 dairy & animal science, lcsh:Genetics, Haplotypes, Genetic marker, Genetic Polymorphism, Animal Genetics, Population Genetics, Genome-Wide Association Study
Abstract

Some sheep breeds are naturally prolific, and they are very informative for the studies of reproductive genetics and physiology. Major genes increasing litter size (LS) and ovulation rate (OR) were suspected in the French Grivette and the Polish Olkuska sheep populations, respectively. To identify genetic variants responsible for the highly prolific phenotype in these two breeds, genome-wide association studies (GWAS) followed by complementary genetic and functional analyses were performed. Highly prolific ewes (cases) and normal prolific ewes (controls) from each breed were genotyped using the Illumina OvineSNP50 Genotyping Beadchip. In both populations, an X chromosome region, close to the BMP15 gene, harbored clusters of markers with suggestive evidence of association at significance levels between 1E−05 and 1E−07. The BMP15 candidate gene was then sequenced, and two novel non-conservative mutations called FecXGr and FecXO were identified in the Grivette and Olkuska breeds, respectively. The two mutations were associated with the highly prolific phenotype (pFecXGr = 5.98E−06 and pFecXO = 2.55E−08). Homozygous ewes for the mutated allele showed a significantly increased prolificacy (FecXGr/FecXGr, LS = 2.50±0.65 versus FecX+/FecXGr, LS = 1.93±0.42, p, Author Summary Although causes altering reproductive function and leading to several fertility syndromes in women are various, a clear association between mutations in some members of the TGFβ family (BMP15 and GDF9) and abnormal ovarian phenotype has established the importance of these factors for normal female fertility. Some sheep breeds are naturally prolific since they carry major genes affecting ovulation rate and litter size. These species are therefore unique informative models for the study of reproductive genetics and physiology. Through a GWAS conducted in two sheep breeds using highly prolific ewes as cases and normal prolific ewes as controls, we identified an X chromosome locus close to the BMP15 gene in both breeds. Two novel non-conservative BMP15 mutations, one in each population, located in very well conserved domains of the protein were associated with the phenotype at heterozygous and homozygous status. Moreover, we showed that both mutations altered the BMP15 signaling activity, suggesting a novel kind of BMP15 variant responsible for an atypical high prolificacy, in contrast to all other BMP15 variants described so far. Our findings suggest an additional role of the BMP15 protein in folliculogenesis and could contribute to a better understanding of the pathogenesis of women′s fertility disorders.

Published
2013

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