Search

Your search keyword '"Djari A"' showing total 15 results
Start Over Author "Djari A" Topic research article
15 results on '"Djari A"'

1. Protein kinase A drives paracrine crisis and WNT4-dependent testis tumor in Carney complex

Author

Anne-Marie Lefrançois-Martinez, Amandine Septier, Amanda Swain, Jean-Christophe Pointud, Constantine A. Stratakis, Fabio R. Faucz, Florian Guillou, James Wilmouth, Antoine-Guy Lopez, Adrien Levasseur, Ingrid Plotton, Cyril Djari, Seppo Vainio, Crystal Kamilaris, Isabelle Sahut-Barnola, Hervé Lefebvre, Damien Dufour, Pierre Val, Nathanaëlle Montanier, Antoine Martinez, Igor Tauveron, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre National de la Recherche Scientifique (CNRS), Génétique, Reproduction et Développement (GReD), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne (UCA), Hospices Civils de Lyon (HCL), CHU Clermont-Ferrand, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), Différenciation et communication neuronale et neuroendocrine (DC2N), Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Physiologie de la reproduction et des comportements [Nouzilly] (PRC), Institut Français du Cheval et de l'Equitation [Saumur] (IFCE)-Université de Tours (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), The institute of cancer research [London], and University of Oulu

Subjects
Male, Somatic cell, [SDV]Life Sciences [q-bio], Apoptosis, Mice, 0302 clinical medicine, Wnt4 Protein, Testis, WNT4, Genes, Tumor Suppressor, PRKAR1A, ComputingMilieux_MISCELLANEOUS, Oligonucleotide Array Sequence Analysis, Mice, Knockout, 0303 health sciences, Pigmentation, General Medicine, Seminiferous Tubules, [SDV.MHEP.EM]Life Sciences [q-bio]/Human health and pathology/Endocrinology and metabolism, Sertoli cell, Phenotype, medicine.anatomical_structure, 030220 oncology & carcinogenesis, Research Article, Cell type, Stromal cell, Cyclic AMP-Dependent Protein Kinase RIalpha Subunit, [SDV.CAN]Life Sciences [q-bio]/Cancer, Biology, 03 medical and health sciences, Paracrine signalling, Testicular Neoplasms, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Paracrine Communication, medicine, Animals, Humans, Carney Complex, Carney complex, 030304 developmental biology, Sertoli Cells, Gene Expression Profiling, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, medicine.disease, Cyclic AMP-Dependent Protein Kinases, Disease Models, Animal, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, [SDV.BDD.EO]Life Sciences [q-bio]/Development Biology/Embryology and Organogenesis, Mutation, Cancer research, Transcriptome
Abstract

International audience; Large-cell calcifying Sertoli cell tumors (LCCSCTs) are among the most frequent lesions occurring in male Carney complex (CNC) patients. Although they constitute a key diagnostic criterion for this rare multiple neoplasia syndrome resulting from inactivating mutations of the tumor suppressor PRKAR1A, leading to unrepressed PKA activity, LCCSCT pathogenesis and origin remain elusive. Mouse models targeting Prkar1a inactivation in all somatic populations or separately in each cell type were generated to decipher the molecular and paracrine networks involved in the induction of CNC testis lesions. We demonstrate that the Prkar1a mutation was required in both stromal and Sertoli cells for the occurrence of LCCSCTs. Integrative analyses comparing transcriptomic, immunohistological data and phenotype of mutant mouse combinations led to the understanding of human LCCSCT pathogenesis and demonstrated PKA-induced paracrine molecular circuits in which the aberrant WNT4 signal production is a limiting step in shaping intratubular lesions and tumor expansion both in a mouse model and in human CNC testes.

Published
2021

2. Expanding Duplication of Free Fatty Acid Receptor-2 (GPR43) Genes in the Chicken Genome

Author

Pascal Froment, Philippe Monget, Sophie Leroux, Isabelle Callebaut, Camille Meslin, Florence Gondret, Christophe Klopp, Sandrine Lagarrigue, Edith Guilbert, Colette Désert, Frédérique Pitel, Pascal G.P. Martin, Anis Djari, Physiologie de la reproduction et des comportements [Nouzilly] (PRC), Centre National de la Recherche Scientifique (CNRS)-Université de Tours-Institut Français du Cheval et de l'Equitation [Saumur]-Institut National de la Recherche Agronomique (INRA), Université Francois Rabelais [Tours], Institut Francais du Cheval et de l’Equitation, UMR 1348 Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage, Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST-Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage [Rennes] (PEGASE), AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA)-Institut National de la Recherche Agronomique (INRA)-Génétique animale (G.A.)-Physiologie Animale et Systèmes d'Elevage (PHASE), Institut National de la Recherche Agronomique (INRA), Institut de minéralogie, de physique des matériaux et de cosmochimie (IMPMC), Institut de recherche pour le développement [IRD] : UR206-Centre National de la Recherche Scientifique (CNRS)-Muséum national d'Histoire naturelle (MNHN)-Université Pierre et Marie Curie - Paris 6 (UPMC), INRA, INRA, BIA, Unité de Biométrie et Intelligence Artificielle de Toulouse [Castanet-Tolosan] (UBIA), Institut National de la Recherche Agronomique (INRA)-Plateforme bioinformatique du GIS GENOTOUL - Génopole Toulouse Midi-Pyrénées, Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT], Unité de recherche Pharmacologie-Toxicologie (UPT), 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 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), Institut Français du Cheval et de l'Equitation [Saumur], Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage [Rennes] (PEGASE), 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), Muséum national d'Histoire naturelle (MNHN)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de recherche pour le développement [IRD] : UR206-Centre National de la Recherche Scientifique (CNRS), Unité de recherche sur les Biopolymères, Interactions Assemblages (BIA), ANT FATINTEGER - ANR EpiBird, Institut National de la Recherche Agronomique (INRA)-Institut Français du Cheval et de l'Equitation [Saumur] (IFCE)-Université de Tours (UT)-Centre National de la Recherche Scientifique (CNRS), Institut Français du Cheval et de l'Equitation [Saumur] (IFCE), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Unité de Biométrie et Intelligence Artificielle (ancêtre de MIAT) (UBIA), 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 la Recherche Agronomique (INRA)-Institut Français du Cheval et de l'Equitation [Saumur]-Université de Tours-Centre National de la Recherche Scientifique (CNRS), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), and Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de recherche pour le développement [IRD] : UR206-Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Nonsynonymous substitution, Male, animal structures, Swine, [SDV]Life Sciences [q-bio], chicken, poulet, génomique fonctionnelle, FFAR, Biology, métabolisme des lipides, Genome, Receptors, G-Protein-Coupled, Avian Proteins, Evolution, Molecular, 03 medical and health sciences, régulation, positive selection, Gene Duplication, Gene duplication, evolution, Genetics, Animals, Tissue Distribution, Gene conversion, Copy-number variation, acide gras libre, Gene, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, 0303 health sciences, gene conversion, 0402 animal and dairy science, 04 agricultural and veterinary sciences, 040201 dairy & animal science, genomic DNA, adiposité, duplication, Multigene Family, Female, Synonymous substitution, récepteur, Chickens, Research Article
Abstract

International audience; Free fatty acid receptors (FFAR) belong to a family of five G-protein coupled receptors that are involved in the regulation of lipidmetabolism, so that their loss of function increases the risk of obesity. The aim of this study was to determine the expansion of genesencoding paralogs of FFAR2 in the chicken, considered as amodel organism for developmental biology and biomedical research. Byestimating the gene copy number using quantitative polymerase chain reaction, genomic DNA resequencing, and RNA sequencingdata, we showed the existence of 23 ±1.5 genes encoding FFAR2 paralogs in the chicken genome. The FFAR2 paralogs shared anidentity from 87.2%up to 99%. Extensive gene conversion was responsible for this high degree of sequence similarities betweenthese genes, and this concerned especially the four amino acids known to be critical for ligand binding. Moreover, elevated nonsynonymous/synonymous substitutionratios onsomeamino acids withinor inclose-vicinity of the ligand-bindinggroove suggest thatpositive selectionmay have reduced the effective rate of gene conversion in this region, thus contributing to diversify the function ofsome FFAR2 paralogs. All the FFAR2 paralogs were located on a microchromosome in a same linkage group. FFAR2 genes wereexpressed in different tissues and cells such as spleen, peripheral blood mononuclear cells, abdominal adipose tissue, intestine, andlung, with the highest rate of expression in testis. Further investigations are needed to determine whether these chicken-specificevents along evolution are the consequence of domestication and may play a role in regulating lipid metabolism in this species.

Published
2015

3. Genome-Wide Characterization of RNA Editing in Chicken Embryos Reveals Common Features among Vertebrates

Author

Sandrine Lagarrigue, David Gourichon, Diane Esquerre, Sophie Leroux, Frédérique Pitel, Stéphane Fabre, Pierre-François Roux, Christophe Klopp, Anis Djari, Patrice Dehais, Laure Fresard, 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, 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), SIGENAE, Pôle d'Expérimentation Avicole de Tours (UE PEAT), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT], and Pôle d'Expérimentation Avicole de Tours (PEAT)

Subjects
Genome evolution, human transcriptome, Sequence analysis, [SDV]Life Sciences [q-bio], lcsh:Medicine, Sequence alignment, Chick Embryo, Computational biology, Biology, DNA sequencing, dna sequence, b messenger-rna, widespread rna, accurate identification, gaba (a) receptor, seq data, adenosine, evolution, Evolution, Molecular, Transcription (biology), Animals, lcsh:Science, Genetics, Genome, Multidisciplinary, Sequence Analysis, RNA, lcsh:R, Intron, Computational Biology, High-Throughput Nucleotide Sequencing, RNA, DNA, Sequence Analysis, DNA, RNA editing, lcsh:Q, RNA Editing, Chickens, Research Article
Abstract

RNA editing results in a post-transcriptional nucleotide change in the RNA sequence that creates an alternative nucleotide not present in the DNA sequence. This leads to a diversification of transcription products with potential functional consequences. Two nucleotide substitutions are mainly described in animals, from adenosine to inosine (A-to-I) and from cytidine to uridine (C-to-U). This phenomenon is described in more details in mammals, notably since the availability of next generation sequencing technologies allowing whole genome screening of RNA-DNA differences. The number of studies recording RNA editing in other vertebrates like chicken is still limited. We chose to use high throughput sequencing technologies to search for RNA editing in chicken, and to extend the knowledge of its conservation among vertebrates. We performed sequencing of RNA and DNA from 8 embryos. Being aware of common pitfalls inherent to sequence analyses that lead to false positive discovery, we stringently filtered our datasets and found fewer than 40 reliable candidates. Conservation of particular sites of RNA editing was attested by the presence of 3 edited sites previously detected in mammals. We then characterized editing levels for selected candidates in several tissues and at different time points, from 4.5 days of embryonic development to adults, and observed a clear tissue-specificity and a gradual increase of editing level with time. By characterizing the RNA editing landscape in chicken, our results highlight the extent of evolutionary conservation of this phenomenon within vertebrates, attest to its tissue and stage specificity and provide support of the absence of non A-to-I events from the chicken transcriptome.

Published
2015

4. Genome-wide study of structural variants in bovine Holstein, Montbéliarde and Normande dairy breeds

Author

Alain Pinton, Frédéric Escudié, Maria Bernard, Anis Djari, Alain Roulet, Mekki Boussaha, Franck Samson, Diane Esquerre, Cécile Grohs, Johanna Barbieri, Sébastien Fritz, Rabia Letaief, Christophe Klopp, Gerald Salin, Didier Boichard, Dominique Rocha, Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Unité de Biométrie et Intelligence Artificielle (UBIA), Institut National de la Recherche Agronomique (INRA), Union nationale des coopératives d’élevage et d’insémination animale (UNCEIA), Unité Mathématique, Informatique et Génome (MIG), ANR-Apisgene Cartoseq, Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT], and Union Nationale des Coopératives Agricoles d'Elevage et d'Insémination Animale

Subjects
bovin, Genotype, variants structuraux, [SDV]Life Sciences [q-bio], Quantitative Trait Loci, Genomic Structural Variation, lcsh:Medicine, Single-nucleotide polymorphism, Genome-wide association study, Quantitative trait locus, Biology, Genome, Structural variation, Animals, Copy-number variation, lcsh:Science, 2. Zero hunger, Genetics, Multidisciplinary, génome, lcsh:R, Dairying, Bovine genome, lcsh:Q, Cattle, Animals, Inbred Strains, Genome-Wide Association Study, Research Article
Abstract

High-throughput sequencing technologies have offered in recent years new opportunities to study genome variations. These studies have mostly focused on single nucleotide polymorphisms, small insertions or deletions and on copy number variants. Other structural variants, such as large insertions or deletions, tandem duplications, translocations, and inversions are less well-studied, despite that some have an important impact on phenotypes. In the present study, we performed a large-scale survey of structural variants in cattle. We report the identification of 6,426 putative structural variants in cattle extracted from whole-genome sequence data of 62 bulls representing the three major French dairy breeds. These genomic variants affect DNA segments greater than 50 base pairs and correspond to deletions, inversions and tandem duplications. Out of these, we identified a total of 547 deletions and 410 tandem duplications which could potentially code for CNVs. Experimental validation was carried out on 331 structural variants using a novel high-throughput genotyping method. Out of these, 255 structural variants (77%) generated good quality genotypes and 191 (75%) of them were validated. Gene content analyses in structural variant regions revealed 941 large deletions removing completely one or several genes, including 10 single-copy genes. In addition, some of the structural variants are located within quantitative trait loci for dairy traits. This study is a pan-genome assessment of genomic variations in cattle and may provide a new glimpse into the bovine genome architecture. Our results may also help to study the effects of structural variants on gene expression and consequently their effect on certain phenotypes of interest.

Published
2015

5. Identification of large intergenic non-coding RNAs in bovine muscle using next-generation transcriptomic sequencing

Author

Diane Esquerre, Coline Billerey, Dominique Rocha, Mekki Boussaha, Daniel Gautheret, Emmanuelle Rebours, Anis Djari, Cédric Meersseman, Christophe Klopp, Rocha, Dominique, Institut de génétique et microbiologie [Orsay] (IGM), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), Génétique Animale et Biologie Intégrative (GABI), AgroParisTech-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, Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA), Institut National de la Recherche Agronomique (INRA), INRA Animal Genetics Department (BovRNA-Seq project), Agence Nationale de la Recherche [ANR-05-GANI-005, ANR-05-GANI-017-01, ANR-11-INSB-0013], APIS GENE [01-2005-QualviGenA-02], Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Laboratoire de Génétique Cellulaire, and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT)

Subjects
RNA-Seq, Biology, Quantitative trait locus, 03 medical and health sciences, 0302 clinical medicine, Genetics, Animals, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Gene, 030304 developmental biology, 2. Zero hunger, Regulation of gene expression, 0303 health sciences, Gene Expression Profiling, Muscles, Computational Biology, High-Throughput Nucleotide Sequencing, Reproducibility of Results, Long non-coding RNA, Gene expression profiling, Bovine genome, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Gene Expression Regulation, 030220 oncology & carcinogenesis, Muscle, Cattle, RNA, Long Noncoding, DNA microarray, Beef, Transcriptome, Biotechnology, Research Article
Abstract

Background The advent of large-scale gene expression technologies has helped to reveal in eukaryotic cells, the existence of thousands of non-coding transcripts, whose function and significance remain mostly poorly understood. Among these non-coding transcripts, long non-coding RNAs (lncRNAs) are the least well-studied but are emerging as key regulators of diverse cellular processes. In the present study, we performed a survey in bovine Longissimus thoraci of lincRNAs (long intergenic non-coding RNAs not overlapping protein-coding transcripts). To our knowledge, this represents the first such study in bovine muscle. Results To identify lincRNAs, we used paired-end RNA sequencing (RNA-Seq) to explore the transcriptomes of Longissimus thoraci from nine Limousin bull calves. Approximately 14–45 million paired-end reads were obtained per library. A total of 30,548 different transcripts were identified. Using a computational pipeline, we defined a stringent set of 584 different lincRNAs with 418 lincRNAs found in all nine muscle samples. Bovine lincRNAs share characteristics seen in their mammalian counterparts: relatively short transcript and gene lengths, low exon number and significantly lower expression, compared to protein-encoding genes. As for the first time, our study identified lincRNAs from nine different samples from the same tissue, it is possible to analyse the inter-individual variability of the gene expression level of the identified lincRNAs. Interestingly, there was a significant difference when we compared the expression variation of the 418 lincRNAs with the 10,775 known selected protein-encoding genes found in all muscle samples. In addition, we found 2,083 pairs of lincRNA/protein-encoding genes showing a highly significant correlated expression. Fourteen lincRNAs were selected and 13 were validated by RT-PCR. Some of the lincRNAs expressed in muscle are located within quantitative trait loci for meat quality traits. Conclusions Our study provides a glimpse into the lincRNA content of bovine muscle and will facilitate future experimental studies to unravel the function of these molecules. It may prove useful to elucidate their effect on mechanisms underlying the genetic variability of meat quality traits. This catalog will complement the list of lincRNAs already discovered in cattle and therefore will help to better annotate the bovine genome. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-499) contains supplementary material, which is available to authorized users.

Published
2014

6. Re-sequencing data for refining candidate genes and polymorphisms in QTL regions affecting adiposity in chicken

Author

Anis Djari, Diane Esquerre, Colette Désert, Sandrine Lagarrigue, Christophe Klopp, Morgane Boutin, Olivier Demeure, Pierre-François Roux, Demeure, Olivier, Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage [Rennes] (PEGASE), AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA), Université européenne de Bretagne - European University of Brittany (UEB), SIGENAE, Institut National de la Recherche Agronomique (INRA), Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT], 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), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées

Subjects
Candidate gene, Heredity, Genetic Linkage, [SDV]Life Sciences [q-bio], génomique fonctionnelle, lcsh:Medicine, tissu adipeux, 0302 clinical medicine, INDEL Mutation, Genome Sequencing, lcsh:Science, Adiposity, Genetics, 0303 health sciences, Multidisciplinary, Chromosome Mapping, High-Throughput Nucleotide Sequencing, food and beverages, Genome project, Genomics, Genetic Mapping, Linkage Analysis, annotation fonctionnelle, Research Article, cartographie de qtl, Genotype, Quantitative Trait Loci, poulet, Single-nucleotide polymorphism, Quantitative trait locus, Biology, Research and Analysis Methods, Polymorphism, Single Nucleotide, 03 medical and health sciences, Genetic linkage, Animals, Obesity, Indel, Molecular Biology Techniques, Sequencing Techniques, Gene, Molecular Biology, Genetic Association Studies, 030304 developmental biology, Evolutionary Biology, Population Biology, High Throughput Sequencing, lcsh:R, Biology and Life Sciences, Computational Biology, Molecular Sequence Annotation, Genome Analysis, Genetic Polymorphism, lcsh:Q, Chickens, 030217 neurology & neurosurgery, Population Genetics
Abstract

In this study, we propose an approach aiming at fine-mapping adiposity QTL in chicken, integrating whole genome re-sequencing data. First, two QTL regions for adiposity were identified by performing a classical linkage analysis on 1362 offspring in 11 sire families obtained by crossing two meat-type chicken lines divergently selected for abdominal fat weight. Those regions, located on chromosome 7 and 19, contained a total of 77 and 84 genes, respectively. Then, SNPs and indels in these regions were identified by re-sequencing sires. Considering issues related to polymorphism annotations for regulatory regions, we focused on the 120 and 104 polymorphisms having an impact on protein sequence, and located in coding regions of 35 and 42 genes situated in the two QTL regions. Subsequently, a filter was applied on SNPs considering their potential impact on the protein function based on conservation criteria. For the two regions, we identified 42 and 34 functional polymorphisms carried by 18 and 24 genes, and likely to deeply impact protein, including 3 coding indels and 4 nonsense SNPs. Finally, using gene functional annotation, a short list of 17 and 4 polymorphisms in 6 and 4 functional genes has been defined. Even if we cannot exclude that the causal polymorphisms may be located in regulatory regions, this strategy gives a complete overview of the candidate polymorphisms in coding regions and prioritize them on conservation- and functional-based arguments.

Published
2014

7. RNAbrowse: RNA-Seq de novo assembly results browser

Author

Christophe Klopp, Anis Djari, Philippe Bardou, Cédric Cabau, Jérôme Mariette, Céline Noirot, Claire Hoede, Ibounyamine Nabihoudine, Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA), Institut National de la Recherche Agronomique (INRA), Plateforme Bio-Informatique - Génotoul, 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 Plateforme SIGENAE

Subjects
Computer science, [SDV]Life Sciences [q-bio], Sequence assembly, lcsh:Medicine, RNA-Seq, 010501 environmental sciences, Bioinformatics, computer.software_genre, 01 natural sciences, Computer Applications, Transcriptome, User-Computer Interface, [MATH]Mathematics [math], lcsh:Science, 0303 health sciences, Multidisciplinary, Contig, Programming language, Software Engineering, Genome project, Genomics, Web-Based Applications, RNA extraction, Transcriptome Analysis, Research Article, Computer and Information Sciences, Sequence analysis, Gene prediction, Sequence alignment, 03 medical and health sciences, Genetics, Humans, [INFO]Computer Science [cs], 030304 developmental biology, 0105 earth and related environmental sciences, Internet, Sequence Assembly Tools, Software Tools, Sequence Analysis, RNA, Gene Expression Profiling, lcsh:R, RNA, Biology and Life Sciences, Computational Biology, Genome Analysis, Gene expression profiling, lcsh:Q, Genome Expression Analysis, computer, Software
Abstract

International audience; Transcriptome analysis based on a de novo assembly of next generation RNA sequences is now performed routinely in many laboratories. The generated results, including contig sequences, quantification figures, functional annotations and variation discovery outputs are usually bulky and quite diverse. This article presents a user oriented storage and visualisation environment permitting to explore the data in a top-down manner, going from general graphical views to all possible details. The software package is based on biomart, easy to install and populate with local data. The software package is available under the GNU General Public License (GPL) at http://bioinfo.genotoul.fr/RNAbrowse.

Published
2014

8. Novel Insights into the Bovine Polled Phenotype and Horn Ontogenesis in Bovidae

Author

Aurélien Capitan, Michel Fouchet, Stefan Krebs, Alexander Graf, Mekki Boussaha, Laura Salas-Cortes, Gunnfríður Elín Hreiðarsdóttir, Bernard Weiss, Dominique Thépot, Pierre Roy, Aurélia Baur, Olivier Catros, Marie-Noelle Rossignol, Sébastien Fritz, Helmut Blum, Yves Gallard, Sophie Rothammer, André Eggen, Cécile Grohs, L. Journaux, Emilie Cobo, Daniel Le Bourhis, Claire Ponsart, Aurélie Allais-Bonnet, Eric Pailhoux, Dominique Dozias, Laetitia Clément, Eric Venot, Este Van Marle-Koster, Christophe Klopp, Per Wahlberg, Carine Bernard-Capel, Ingolf Russ, Florence Phocas, Dominique Rocha, Patrick Reversé, Maëlle Pannetier, Jean-Luc Marchand, Marie-Noëlle Fouilloux, Brigitte Marquant-Leguienne, Anis Djari, Sarah Barbey, Diane Esquerre, Ivica Medugorac, Doris Seichter, Stephan Bouet, Pascal Soulas, Chris Hoze, Didier Boichard, 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), Génétique Animale et Biologie Intégrative (GABI), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Chair of Animal Genetics and Husbandry, Ludwig-Maximilians-Universität München (LMU), Laboratory for Functional Genome Analysis, Gene Center, Unité de Biométrie et Intelligence Artificielle (UBIA), 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, Laboratoire d'Analyse Génétique pour les Espèces Animales (LABOGENA), Department of Animal & Wildlife Sciences, University of Pretoria [South Africa], Domaine expérimental animal du Pin (SEA), This project was funded by Apis Gène 'Hornout' and Institut National de la Recherche Agronomique-DGA 'Interpolled' and 'Hornaseq' grants., Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Biologie du Développement et Reproduction (BDR), Ecole Nationale Vétérinaire de Toulouse (ENVT), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Recherche Agronomique (INRA)

Subjects
[SDV.SA]Life Sciences [q-bio]/Agricultural sciences, corne, Anatomy and Physiology, Veterinary Anatomy and Physiology, Receptors, G-Protein-Coupled, bovidae, 0302 clinical medicine, Gene expression, Morphogenesis, Basic Helix-Loop-Helix Transcription Factors, Animal Breeding, Animal Management, Skin, Horns, Genetics, 0303 health sciences, Multidisciplinary, Goats, Chromosome Mapping, Gene Expression Regulation, Developmental, Agriculture, Forkhead Transcription Factors, Phenotype, phénotype, ontogénèse, Autosomal Dominant, 030220 oncology & carcinogenesis, Medicine, Research Article, Genotype, Science, Genomics, Locus (genetics), Biology, OLIG2, 03 medical and health sciences, Animals, Allele, Alleles, 030304 developmental biology, Growth Control, Clinical Genetics, Sheep, Haplotype, Genetic Variation, Body Plan Organization, Animal Skin Anatomy, Mutation, Ectopic expression, Veterinary Science, Cattle, Animal Genetics, Developmental Biology
Abstract

Chantier qualité GA; Despite massive research efforts, the molecular etiology of bovine polledness and the developmental pathways involved in horn ontogenesis are still poorly understood. In a recent article, we provided evidence for the existence of at least two different alleles at the Polled locus and identified candidate mutations for each of them. None of these mutations was located in known coding or regulatory regions, thus adding to the complexity of understanding the molecular basis of polledness. We confirm previous results here and exhaustively identify the causative mutation for the Celtic allele (PC) and four candidate mutations for the Friesian allele (PF). We describe a previously unreported eyelash-and-eyelid phenotype associated with regular polledness, and present unique histological and gene expression data on bovine horn bud differentiation in fetuses affected by three different horn defect syndromes, as well as in wild-type controls. We propose the ectopic expression of a lincRNA in PC/p horn buds as a probable cause of horn bud agenesis. In addition, we provide evidence for an involvement of OLIG2, FOXL2 and RXFP2 in horn bud differentiation, and draw a first link between bovine, ovine and caprine Polled loci. Our results represent a first and important step in understanding the genetic pathways and key process involved in horn bud differentiation in Bovidae.

Published
2013

9. Detection of Haplotypes Associated with Prenatal Death in Dairy Cattle and Identification of Deleterious Mutations in GART, SHBG and SLC37A2

Author

Mekki Boussaha, Cécile Grohs, Sabrina Rodriguez, Dominique Rocha, Diane Esquerre, Aurélien Capitan, Didier Boichard, Aurélia Baur, Anis Djari, Bernard Weiss, Anne Barbat, Christophe Klopp, Sébastien Fritz, Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Unité de Biométrie et Intelligence Artificielle (UBIA), 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), ARN Apisgene Cartoseq, Boichard, Didier, Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées

Subjects
Male, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, bovin, lcsh:Medicine, Breeding, medicine.disease_cause, Antiporters, Autosomal Recessive, embryo mortality, cattle, fertility, gart gene, shbg gene, slc37a2 gene, Animal Breeding, Carbon-Nitrogen Ligases, lcsh:Science, Animal Management, 2. Zero hunger, Genetics, 0303 health sciences, Mutation, Multidisciplinary, Homozygote, Obstetrics and Gynecology, Agriculture, 04 agricultural and veterinary sciences, Breed, Dairying, Embryo Loss, Medicine, Female, gène gart, Inbreeding, Research Article, Animal Types, Receptors, Cell Surface, Large Animals, Biology, mortalité embryonnaire, 03 medical and health sciences, Animal Production, medicine, Animals, Genetic Testing, Gene, Genotyping, Genetic Association Studies, Dairy cattle, 030304 developmental biology, Clinical Genetics, Evolutionary Biology, Population Biology, Point mutation, lcsh:R, Haplotype, fertilité animale, 0402 animal and dairy science, Female Subfertility, 040201 dairy & animal science, Haplotypes, gène shbg, Genetic Polymorphism, lcsh:Q, Veterinary Science, Animal Genetics, Population Genetics
Abstract

Chantier qualité GA; The regular decrease of female fertility over time is a major concern in modern dairy cattle industry. Only half of this decrease is explained by indirect response to selection on milk production, suggesting the existence of other factors such as embryonic lethal genetic defects. Genomic regions harboring recessive deleterious mutations were detected in three dairy cattle breeds by identifying frequent haplotypes (.1%) showing a deficit in homozygotes among Illumina Bovine 50k Beadchip haplotyping data from the French genomic selection database (47,878 Holstein, 16,833 Montbe' liarde, and 11,466 Normande animals). Thirty-four candidate haplotypes (p,1024) including previously reported regions associated with Brachyspina, CVM, HH1, and HH3 in Holstein breed were identified. Haplotype length varied from 1 to 4.8 Mb and frequencies from 1.7 up to 9%. A significant negative effect on calving rate, consistent in heifers and in lactating cows, was observed for 9 of these haplotypes in matings between carrier bulls and daughters of carrier sires, confirming their association with embryonic lethal mutations. Eight regions were further investigated using whole genome sequencing data from heterozygous bull carriers and control animals (45 animals in total). Six strong candidate causative mutations including polymorphisms previously reported in FANCI (Brachyspina), SLC35A3 (CVM), APAF1 (HH1) and three novel mutations with very damaging effect on the protein structure, according to SIFT and Polyphen-2, were detected in GART, SHBG and SLC37A2 genes. In conclusion, this study reveals a yet hidden consequence of the important inbreeding rate observed in intensively selected and specialized cattle breeds. Counter-selection of these mutations and management of matings will have positive consequences on female fertility in dairy cattle.

Published
2013

10. Genome-Wide Study of Structural Variants in Bovine Holstein, Montbéliarde and Normande Dairy Breeds.

Author

Boussaha, Mekki, Esquerré, Diane, Barbieri, Johanna, Djari, Anis, Pinton, Alain, Letaief, Rabia, Salin, Gérald, Escudié, Frédéric, Roulet, Alain, Fritz, Sébastien, Samson, Franck, Grohs, Cécile, Bernard, Maria, Klopp, Christophe, Boichard, Didier, and Rocha, Dominique

Subjects
HOLSTEIN-Friesian cattle, MONTBELIARDE cattle, DAIRY cattle breeds, SINGLE nucleotide polymorphisms, DELETION mutation, CHROMOSOMAL translocation
Abstract

High-throughput sequencing technologies have offered in recent years new opportunities to study genome variations. These studies have mostly focused on single nucleotide polymorphisms, small insertions or deletions and on copy number variants. Other structural variants, such as large insertions or deletions, tandem duplications, translocations, and inversions are less well-studied, despite that some have an important impact on phenotypes. In the present study, we performed a large-scale survey of structural variants in cattle. We report the identification of 6,426 putative structural variants in cattle extracted from whole-genome sequence data of 62 bulls representing the three major French dairy breeds. These genomic variants affect DNA segments greater than 50 base pairs and correspond to deletions, inversions and tandem duplications. Out of these, we identified a total of 547 deletions and 410 tandem duplications which could potentially code for CNVs. Experimental validation was carried out on 331 structural variants using a novel high-throughput genotyping method. Out of these, 255 structural variants (77%) generated good quality genotypes and 191 (75%) of them were validated. Gene content analyses in structural variant regions revealed 941 large deletions removing completely one or several genes, including 10 single-copy genes. In addition, some of the structural variants are located within quantitative trait loci for dairy traits. This study is a pan-genome assessment of genomic variations in cattle and may provide a new glimpse into the bovine genome architecture. Our results may also help to study the effects of structural variants on gene expression and consequently their effect on certain phenotypes of interest. [ABSTRACT FROM AUTHOR]

Published
2015
Full Text
View/download PDF

11. Genome-Wide Characterization of RNA Editing in Chicken Embryos Reveals Common Features among Vertebrates.

Author

Frésard, Laure, Leroux, Sophie, Roux, Pierre-François, Klopp, Christophe, Fabre, Stéphane, Esquerré, Diane, Dehais, Patrice, Djari, Anis, Gourichon, David, Lagarrigue, Sandrine, and Pitel, Frédérique

Subjects
CHICKEN embryos, NUCLEOTIDE sequence, GENETIC transcription, BIOLOGICAL evolution, RNA editing, MAMMALS
Abstract

RNA editing results in a post-transcriptional nucleotide change in the RNA sequence that creates an alternative nucleotide not present in the DNA sequence. This leads to a diversification of transcription products with potential functional consequences. Two nucleotide substitutions are mainly described in animals, from adenosine to inosine (A-to-I) and from cytidine to uridine (C-to-U). This phenomenon is described in more details in mammals, notably since the availability of next generation sequencing technologies allowing whole genome screening of RNA-DNA differences. The number of studies recording RNA editing in other vertebrates like chicken is still limited. We chose to use high throughput sequencing technologies to search for RNA editing in chicken, and to extend the knowledge of its conservation among vertebrates. We performed sequencing of RNA and DNA from 8 embryos. Being aware of common pitfalls inherent to sequence analyses that lead to false positive discovery, we stringently filtered our datasets and found fewer than 40 reliable candidates. Conservation of particular sites of RNA editing was attested by the presence of 3 edited sites previously detected in mammals. We then characterized editing levels for selected candidates in several tissues and at different time points, from 4.5 days of embryonic development to adults, and observed a clear tissue-specificity and a gradual increase of editing level with time. By characterizing the RNA editing landscape in chicken, our results highlight the extent of evolutionary conservation of this phenomenon within vertebrates, attest to its tissue and stage specificity and provide support of the absence of non A-to-I events from the chicken transcriptome. [ABSTRACT FROM AUTHOR]

Published
2015
Full Text
View/download PDF

12. Re-Sequencing Data for Refining Candidate Genes and Polymorphisms in QTL Regions Affecting Adiposity in Chicken.

Author

Roux, Pierre-François, Boutin, Morgane, Désert, Colette, Djari, Anis, Esquerré, Diane, Klopp, Christophe, Lagarrigue, Sandrine, and Demeure, Olivier

Subjects
OBESITY, NUCLEOTIDE sequence, GENOMES, CHICKENS, ANIMAL experimentation
Abstract

In this study, we propose an approach aiming at fine-mapping adiposity QTL in chicken, integrating whole genome re-sequencing data. First, two QTL regions for adiposity were identified by performing a classical linkage analysis on 1362 offspring in 11 sire families obtained by crossing two meat-type chicken lines divergently selected for abdominal fat weight. Those regions, located on chromosome 7 and 19, contained a total of 77 and 84 genes, respectively. Then, SNPs and indels in these regions were identified by re-sequencing sires. Considering issues related to polymorphism annotations for regulatory regions, we focused on the 120 and 104 polymorphisms having an impact on protein sequence, and located in coding regions of 35 and 42 genes situated in the two QTL regions. Subsequently, a filter was applied on SNPs considering their potential impact on the protein function based on conservation criteria. For the two regions, we identified 42 and 34 functional polymorphisms carried by 18 and 24 genes, and likely to deeply impact protein, including 3 coding indels and 4 nonsense SNPs. Finally, using gene functional annotation, a short list of 17 and 4 polymorphisms in 6 and 4 functional genes has been defined. Even if we cannot exclude that the causal polymorphisms may be located in regulatory regions, this strategy gives a complete overview of the candidate polymorphisms in coding regions and prioritize them on conservation- and functional-based arguments. [ABSTRACT FROM AUTHOR]

Published
2014
Full Text
View/download PDF

13. RNAbrowse: RNA-Seq De Novo Assembly Results Browser.

Author

Mariette, Jérôme, Noirot, Céline, Nabihoudine, Ibounyamine, Bardou, Philippe, Hoede, Claire, Djari, Anis, Cabau, Cédric, and Klopp, Christophe

Subjects
RNA sequencing, NUCLEOTIDE sequence, VISUALIZATION, RNA analysis, TRANSCRIPTION factors
Abstract

Transcriptome analysis based on a de novo assembly of next generation RNA sequences is now performed routinely in many laboratories. The generated results, including contig sequences, quantification figures, functional annotations and variation discovery outputs are usually bulky and quite diverse. This article presents a user oriented storage and visualisation environment permitting to explore the data in a top-down manner, going from general graphical views to all possible details. The software package is based on biomart, easy to install and populate with local data. The software package is available under the GNU General Public License (GPL) at http://bioinfo.genotoul.fr/RNAbrowse. [ABSTRACT FROM AUTHOR]

Published
2014
Full Text
View/download PDF

14. Detection of Haplotypes Associated with Prenatal Death in Dairy Cattle and Identification of Deleterious Mutations in GART, SHBG and SLC37A2.

Author

Fritz, Sébastien, Capitan, Aurelien, Djari, Anis, Rodriguez, Sabrina C., Barbat, Anne, Baur, Aurélia, Grohs, Cécile, Weiss, Bernard, Boussaha, Mekki, Esquerré, Diane, Klopp, Christophe, Rocha, Dominique, and Boichard, Didier

Subjects
HAPLOTYPES, DAIRY cattle genetics, GENETIC mutation, GENETIC polymorphisms, POPULATION biology, MEDICAL genetics, VETERINARY medicine
Abstract

The regular decrease of female fertility over time is a major concern in modern dairy cattle industry. Only half of this decrease is explained by indirect response to selection on milk production, suggesting the existence of other factors such as embryonic lethal genetic defects. Genomic regions harboring recessive deleterious mutations were detected in three dairy cattle breeds by identifying frequent haplotypes (>1%) showing a deficit in homozygotes among Illumina Bovine 50k Beadchip haplotyping data from the French genomic selection database (47,878 Holstein, 16,833 Montbéliarde, and 11,466 Normande animals). Thirty-four candidate haplotypes (p<10−4) including previously reported regions associated with Brachyspina, CVM, HH1, and HH3 in Holstein breed were identified. Haplotype length varied from 1 to 4.8 Mb and frequencies from 1.7 up to 9%. A significant negative effect on calving rate, consistent in heifers and in lactating cows, was observed for 9 of these haplotypes in matings between carrier bulls and daughters of carrier sires, confirming their association with embryonic lethal mutations. Eight regions were further investigated using whole genome sequencing data from heterozygous bull carriers and control animals (45 animals in total). Six strong candidate causative mutations including polymorphisms previously reported in FANCI (Brachyspina), SLC35A3 (CVM), APAF1 (HH1) and three novel mutations with very damaging effect on the protein structure, according to SIFT and Polyphen-2, were detected in GART, SHBG and SLC37A2 genes. In conclusion, this study reveals a yet hidden consequence of the important inbreeding rate observed in intensively selected and specialized cattle breeds. Counter-selection of these mutations and management of matings will have positive consequences on female fertility in dairy cattle. [ABSTRACT FROM AUTHOR]

Published
2013
Full Text
View/download PDF

15. Novel Insights into the Bovine Polled Phenotype and Horn Ontogenesis in Bovidae

Author

Allais-Bonnet, Aurélie, Grohs, Cécile, Medugorac, Ivica, Krebs, Stefan, Djari, Anis, Graf, Alexander, Fritz, Sébastien, Seichter, Doris, Baur, Aurélia, Russ, Ingolf, Bouet, Stéphan, Rothammer, Sophie, Wahlberg, Per, Esquerré, Diane, Hoze, Chris, Boussaha, Mekki, Weiss, Bernard, Thépot, Dominique, Fouilloux, Marie-Noëlle, and Rossignol, Marie-Noëlle

Subjects
BOVIDAE, PHENOTYPES, ONTOGENY, DEVELOPMENTAL genetics, MOLECULAR biology, ETIOLOGY of diseases, BIOLOGICAL evolution, GENETICS, ANIMAL morphology
Abstract

Despite massive research efforts, the molecular etiology of bovine polledness and the developmental pathways involved in horn ontogenesis are still poorly understood. In a recent article, we provided evidence for the existence of at least two different alleles at the Polled locus and identified candidate mutations for each of them. None of these mutations was located in known coding or regulatory regions, thus adding to the complexity of understanding the molecular basis of polledness. We confirm previous results here and exhaustively identify the causative mutation for the Celtic allele (PC) and four candidate mutations for the Friesian allele (PF). We describe a previously unreported eyelash-and-eyelid phenotype associated with regular polledness, and present unique histological and gene expression data on bovine horn bud differentiation in fetuses affected by three different horn defect syndromes, as well as in wild-type controls. We propose the ectopic expression of a lincRNA in PC/p horn buds as a probable cause of horn bud agenesis. In addition, we provide evidence for an involvement of OLIG2, FOXL2 and RXFP2 in horn bud differentiation, and draw a first link between bovine, ovine and caprine Polled loci. Our results represent a first and important step in understanding the genetic pathways and key process involved in horn bud differentiation in Bovidae. [ABSTRACT FROM AUTHOR]

Published
2013
Full Text
View/download PDF

Catalog

Books, media, physical & digital resources
See catalog results