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11. A frame-shift mutation in COMTD1 is associated with impaired pheomelanin pigmentation in chicken

Author

Bi, Huijuan, primary, Tranell, Jonas, additional, Harper, Dawn C., additional, Lin, Weifeng, additional, Li, Jingyi, additional, Hellström, Anders R., additional, Larsson, Mårten, additional, Rubin, Carl-Johan, additional, Wang, Chao, additional, Sayyab, Shumaila, additional, Kerje, Susanne, additional, Bed’hom, Bertrand, additional, Gourichon, David, additional, Ito, Shosuke, additional, Wakamatsu, Kazumasa, additional, Tixier-Boichard, Michèle, additional, Marks, Michael S., additional, Globisch, Daniel, additional, and Andersson, Leif, additional

Published
2023
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12. A frame-shift mutation in COMTD1 is associated with impaired pheomelanin pigmentation in chicken

Author

Bi, Huijuan, Tranell, Jonas, Harper, Dawn C., Lin, Weifeng, Li, Jingyi, Hellström, Anders R., Larsson, Mårten, Rubin, Carl-Johan, Wang, Chao, Sayyab, Shumaila, Kerje, Susanne, Bed'hom, Bertrand, Gourichon, David, Ito, Shosuke, Wakamatsu, Kazumasa, Tixier-Boichard, Michele, Marks, Michael S., Globisch, Daniel, Andersson, Leif, Bi, Huijuan, Tranell, Jonas, Harper, Dawn C., Lin, Weifeng, Li, Jingyi, Hellström, Anders R., Larsson, Mårten, Rubin, Carl-Johan, Wang, Chao, Sayyab, Shumaila, Kerje, Susanne, Bed'hom, Bertrand, Gourichon, David, Ito, Shosuke, Wakamatsu, Kazumasa, Tixier-Boichard, Michele, Marks, Michael S., Globisch, Daniel, and Andersson, Leif

Abstract

The biochemical pathway regulating the synthesis of yellow/red pheomelanin is less well characterized than the synthesis of black/brown eumelanin. Inhibitor of gold (IG phenotype) is a plumage colour variant in chicken that provides an opportunity to further explore this pathway since the recessive allele (IG) at this locus is associated with a defect in the production of pheomelanin. IG/IG homozygotes display a marked dilution of red pheomelanin pigmentation, whilst black pigmentation (eumelanin) is only slightly affected. Here we show that a 2-base pair insertion (frame-shift mutation) in the 5th exon of the Catechol-O-methyltransferase containing domain 1 gene (COMTD1), expected to cause a complete or partial loss-of-function of the COMTD1 enzyme, shows complete concordance with the IG phenotype within and across breeds. We show that the COMTD1 protein is localized to mitochondria in pigment cells. Knockout of Comtd1 in a mouse melanocytic cell line results in a reduction in pheomelanin metabolites and significant alterations in metabolites of glutamate/glutathione, riboflavin, and the tricarboxylic acid cycle. Furthermore, COMTD1 overexpression enhanced cellular proliferation following chemical-induced transfection, a potential inducer of oxidative stress. These observations suggest that COMTD1 plays a protective role for melanocytes against oxidative stress and that this supports their ability to produce pheomelanin., De två första författarna delar förstaförfattarskapet.

Published
2023
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13. Improved Basic Cytogenetics Challenges Holocentricity of Butterfly Chromosomes

Author

Dutrillaux, Bernard, Dutrillaux, Anne-marie, Mcclure, Mélanie, Gèze, Marc, Elias, Marianne, Bed’hom, Bertrand, Dutrillaux, Bernard, Dutrillaux, Anne-marie, Mcclure, Mélanie, Gèze, Marc, Elias, Marianne, and Bed’hom, Bertrand

Abstract

Mitotic chromosomes of butterflies, which look like dots or short filaments in most published data, are generally considered to lack localised centromeres and thus to be holokinetic. This particularity, observed in a number of other invertebrates, is associated with meiotic particularities known as “inverted meiosis,” in which the first division is equational, i.e., centromere splitting-up and segregation of sister chromatids instead of homologous chromosomes. However, the accurate analysis of butterfly chromosomes is difficult because (1) their size is very small, equivalent to 2 bands of a mammalian metaphase chromosome, and (2) they lack satellite DNA/heterochromatin in putative centromere regions and therefore marked primary constrictions. Our improved conditions for basic chromosome preparations, here applied to 6 butterfly species belonging to families Nymphalidae and Pieridae challenges the holocentricity of their chromosomes: in spite of the absence of primary constrictions, sister chromatids are recurrently held together at definite positions during mitotic metaphase, which makes possible to establish karyotypes composed of acrocentric and submetacentric chromosomes. The total number of chromosomes per karyotype is roughly inversely proportional to that of non-acrocentric chromosomes, which suggests the occurrence of frequent robertsonian-like fusions or fissions during evolution. Furthermore, the behaviour and morphological changes of chromosomes along the various phases of meiosis do not seem to differ much from those of canonical meiosis. In particular, at metaphase II chromosomes clearly have 2 sister chromatids, which refutes that anaphase I was equational. Thus, we propose an alternative mechanism to holocentricity for explaining the large variations in chromosome numbers in butterflies: (1) in the ancestral karyotype, composed of about 62 mostly acrocentric chromosomes, the centromeres, devoid of centromeric heterochromatin/satellite DNA, were locate

Published
2023
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14. The European Reference Genome Atlas:piloting a decentralised approach to equitable biodiversity genomics

Author

Mc Cartney, Ann M, Formenti, Giulio, Mouton, Alice, Panis, Diego De, Marins, Luisa S, Leitão, Henrique G, Diedericks, Genevieve, Kirangwa, Joseph, Morselli, Marco, Salces-Ortiz, Judit, Escudero, Nuria, Iannucci, Alessio, Natali, Chiara, Svardal, Hannes, Fernández, Rosa, Pooter, Tim De, Joris, Geert, Strazisar, Mojca, Wood, Jo, Herron, Katie E, Seehausen, Ole, Watts, Phillip C, Shaw, Felix, Davey, Robert P, Minotto, Alice, Fernández, José M, Böhne, Astrid, Alegria, Carla, Alioto, Tyler, Alves, Paulo C, Amorim, Isabel R, Aury, Jean-Marc, Backstrom, Niclas, Baldrian, Petr, Baltrunaite, Laima, Barta, Endre, Bed’Hom, Bertrand, Belser, Caroline, Bergsten, Johannes, Bertrand, Laurie, Bilandžija, Helena, Binzer-Panchal, Mahesh, Bista, Iliana, Blaxter, Mark, Borges, Paulo AV, Dias, Guilherme Borges, Bosse, Mirte, Garg, Shilpa, Madsen, Ole, Stiller, Josefin, Mc Cartney, Ann M, Formenti, Giulio, Mouton, Alice, Panis, Diego De, Marins, Luisa S, Leitão, Henrique G, Diedericks, Genevieve, Kirangwa, Joseph, Morselli, Marco, Salces-Ortiz, Judit, Escudero, Nuria, Iannucci, Alessio, Natali, Chiara, Svardal, Hannes, Fernández, Rosa, Pooter, Tim De, Joris, Geert, Strazisar, Mojca, Wood, Jo, Herron, Katie E, Seehausen, Ole, Watts, Phillip C, Shaw, Felix, Davey, Robert P, Minotto, Alice, Fernández, José M, Böhne, Astrid, Alegria, Carla, Alioto, Tyler, Alves, Paulo C, Amorim, Isabel R, Aury, Jean-Marc, Backstrom, Niclas, Baldrian, Petr, Baltrunaite, Laima, Barta, Endre, Bed’Hom, Bertrand, Belser, Caroline, Bergsten, Johannes, Bertrand, Laurie, Bilandžija, Helena, Binzer-Panchal, Mahesh, Bista, Iliana, Blaxter, Mark, Borges, Paulo AV, Dias, Guilherme Borges, Bosse, Mirte, Garg, Shilpa, Madsen, Ole, and Stiller, Josefin

Abstract

A global genome database of all of Earth’s species diversity could be a treasure trove of scientific discoveries. However, regardless of the major advances in genome sequencing technologies, only a tiny fraction of species have genomic information available. To contribute to a more complete planetary genomic database, scientists and institutions across the world have united under the Earth BioGenome Project (EBP), which plans to sequence and assemble high-quality reference genomes for all 1.5 million recognized eukaryotic species through a stepwise phased approach. As the initiative transitions into Phase II, where 150,000 species are to be sequenced in just four years, worldwide participation in the project will be fundamental to success. As the European node of the EBP, the European Reference Genome Atlas (ERGA) seeks to implement a new decentralised, accessible, equitable and inclusive model for producing high-quality reference genomes, which will inform EBP as it scales. To embark on this mission, ERGA launched a Pilot Project to establish a network across Europe to develop and test the first infrastructure of its kind for the coordinated and distributed reference genome production on 98 European eukaryotic species from sample providers across 33 European countries. Here we outline the process and challenges faced during the development of a pilot infrastructure for the production of reference genome resources, and explore the effectiveness of this approach in terms of high-quality reference genome production, considering also equity and inclusion. The outcomes and lessons learned during this pilot provide a solid foundation for ERGA while offering key learnings to other transnational and national genomic resource projects.Competing Interest StatementThe authors have declared no competing interest.Biodiversity genomicsThe application of genomic methods to research biodiversity.BUSCOA bioinformatic method (Benchmarking Universal Single-Copy Orthologues) used to e

Published
2023

16. European mink (Mustela lutreola) reference genome and population genomics

Author

Mouton, Alice, Fournier-Chambrillon, Christine, Fournier, Pascal, Skorupski, Jakub, Śmietana, Przemysław, Vacherie, Benoît, Guérin, Thomas, Payen, Emilie, Bertrand, Laurie, Magdelenat, Ghislaine, Mairey, Barbara, Hamon, Chadia, Leprêtre, Marine, Martins, Nathalie, Brun, Elodie, Beluche, Odette, Lebled, Sandrine, Milani, Claire, Istace, Benjamin, Belser, Caroline, Labadie, Karine, Cruaud, Corinne, Oliveira, Pedro, Aury, Jean-Marc, Wincker, Patrick, Põdra, Madis, Gerbault-Seureau, Michèle, Marchand, Ingrid, Marinov, Mihai, Maran, Tiit, Bellanger, Christelle, Bed’hom, Bertrand, Michaux, Johan, Integrative Biological Sciences (InBioS), Université de Liège, Groupe de Recherche et d’Etude pour la Gestion de l’Environnement (GREGE), University of Szczecin, Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), TRAGSATEC, Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Ligue pour la Protection des Oiseaux (LPO), « Danube Delta » National Institute for Research and Development [Tulcea], Estonian University of Life Sciences (EMU), and Office français de la biodiversité (OFB)

Subjects
[SDV.GEN]Life Sciences [q-bio]/Genetics, [SDV.BA]Life Sciences [q-bio]/Animal biology, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy
Abstract

International audience; The European mink (Mustela lutreola) is considered as critically endangered in the IUCN red list, and is already extinct in large parts of its ancestral range. A chromosome-scale reference genome has been recently produced during the ERGA (European Reference Genome Atlas) pilot project, from an individual sampled in 2006 in Dordogne (France) in the framework of the first National Action Plan for European Mink. A fibroblast cell culture was derived from a skin biopsy on this animal, and then cryopreserved in liquid nitrogen in the Paris National Museum of Natural History cell collection. This frozen sample was used to generate fresh cell cultures for the production of high-quality DNA that was subsequently sequenced and assembled into a high-quality reference genome. This reference can now be used for genomic studies of this species that presents a very high risk of inbreeding depression especially in the western part of its geographic distribution. Inbreeding depression is a critical concern for conservation efforts as it is common in small, declining or fragmented populations. Demographic history of a population can also have an impact on inbreeding depression and shape the levels of genetic load. Interestingly, small populations with extremely low genetic diversity do not always present evidence of Inbreeding depression and may persist thanks to the purging of strong deleterious variants. One way to measure the extent of inbreeding is to scan genomes for runs of homozygosity (ROH). This method is becoming more commonly used to estimate inbreeding and could become a new index for conservation status in wild animals. For this study, we selected two European mink from France (LIFE VISON et PNA Vison), two from Romania, two from Estonia and two from Spain for whole genome re-sequencing (> 25x), each genomic sequence being compared to the reference genome. We expect to find long stretches of ROH that would indicate recent events of inbreeding. The results might have a direct impact on the current conservation program for the European mink.

Published
2022

17. Comparative analysis of the caecal tonsil transcriptome in two chicken lines experimentally infected with Salmonella Enteritidis

Author

Cazals, Anaïs, primary, Rau, Andrea, additional, Estellé, Jordi, additional, Bruneau, Nicolas, additional, Coville, Jean-Luc, additional, Menanteau, Pierrette, additional, Rossignol, Marie-Noëlle, additional, Jardet, Deborah, additional, Bevilacqua, Claudia, additional, Bed’Hom, Bertrand, additional, Velge, Philippe, additional, and Calenge, Fanny, additional

Published
2022
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18. Comparative analysis of the caecal tonsil transcriptome in two hen lines experimentally infected withSalmonellaEnteritidis

Author

Cazals, Anaïs, primary, Rau, Andrea, additional, Estellé, Jordi, additional, Bruneau, Nicolas, additional, Coville, Jean-Luc, additional, Menanteau, Pierrette, additional, Rossignol, Marie-Noëlle, additional, Jardet, Deborah, additional, Bevilacqua, Claudia, additional, Bed’hom, Bertrand, additional, Velge, Philippe, additional, and Calenge, Fanny, additional

Published
2022
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21. Pasteurella multocida experimental infection 1): resistance and hematological response

Author

Gunia, Mélanie, Lantier, Frédéric, Bed’Hom, Bertrand, Guitton, Edouard, Helies, Virginie, Helloin, Emmanuelle, Herbert, Caroline, Maupin, Mickaël, Riou, Mickaël, Robert, Raphaël, Garreau, Herve, 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), Infectiologie et Santé Publique (UMR ISP), Université de Tours (UT)-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), Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Plateforme d'Infectiologie Expérimentale (PFIE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Hycole Sarl, Hypharm, and Université de Tours-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)

Subjects
resistance, blood cell counts, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, hematology, rabbit, Pasteurellosis
Abstract

International audience; Pasteurellosis is the first cause of female mortality in rabbit farms. During the RELAPA project (Genomics for the Genetic Resistance of Rabbits to Pasteurellosis), 953 rabbits were inoculated at 6 weeks of age with a pyogenic strain of Pasteurella multocida (Pm) and were monitored during 14 days. Disease response was very variable among animals, with 7% of resistant animals and 11% of highly susceptible rabbits. Blood cell counts were performed at day 14 after inoculation on 574 inoculated and 28 control rabbits. Significant differences in white blood cell, red blood cell, and platelet counts were observed according to the disease resistance score. Susceptible rabbits have a lower red blood cell count, probably due to the hemolytic and hemorrhagic activity of Pm. They also have a higher percentage of monocytes, neutrophils and eosinophils (mainly involved in the innate immune system and inflammatory responses) and, conversely, a lower percentage of lymphocytes (mainly involved in the adaptive immune response) compared to highly resistant and control rabbits. They do not seem able to mount an effective immune response to control the infection.

Published
2021

22. Pasteurella multocida experimental infection (2): genetic parameters

Author

Gunia, Mélanie, Lantier, Frédéric, Bed’Hom, Bertrand, Guitton, Edouard, Helies, Virginie, Helloin, Emmanuelle, Herbert, Caroline, Maupin, Mickaël, Riou, Mickaël, Robert, Raphaël, Shrestha, Merina, Garreau, Herve, 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), Infectiologie et Santé Publique (UMR ISP), Université de Tours-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), Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Plateforme d'Infectiologie Expérimentale (PFIE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Hycole Sarl, Hypharm, and Université de Tours (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)

Subjects
resistance, blood cell counts, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, hematology, rabbit, Pasteurellosis
Abstract

International audience; In this study, we experimentally infected 953 crossbred rabbits from 6 sire lines with Pasteurella multocida, and diagnosed their response to Pasteurellosis. We recorded abscess and bacterial dissemination, growth before and after inoculation, and performed blood cell counts 14 days post inoculation. The heritabilities were low to moderate for all traits, except for the eosinophils percentage, which does not seem to be heritable. There were positive genetic correlations between the Resistance score and the red blood cell count, the hematocrit, hemoglobin and lymphocyte percentages. On the opposite, there were negative genetic correlations between the Resistance score and the platelets, the white blood cells, the neutrophil and monocytes percentages. Among the hematological traits, lymphocyte percentage could be a potential selection criterion to breed for Pasteurellosis resistance. Its heritability was relatively high (0.24 ± 0.09) compared to the other traits and its correlation with the Resistance score was also high (0.83). This is the first analyses of the genetic parameters of hematological traits in experimentally infected rabbits.

Published
2021

24. Impact of strong selection for the PrP major gene on genetic variability of four French sheep breeds (Open Access publication)

Author

Pantano Thais, Cribiu Edmond, Leymarie Cyril, Neuts Étienne, Bed'hom Bertrand, Amigues Yves, Laloë Denis, Moazami-Goudarzi Katayoun, Brochard Mickaël, Palhiere Isabelle, Bibé Bernard, and Verrier Étienne

Subjects
genetic variability, scrapie resistance, molecular marker, pedigree, sheep, Animal culture, SF1-1100, Genetics, QH426-470
Abstract

Abstract Effective selection on the PrP gene has been implemented since October 2001 in all French sheep breeds. After four years, the ARR "resistant" allele frequency increased by about 35% in young males. The aim of this study was to evaluate the impact of this strong selection on genetic variability. It is focussed on four French sheep breeds and based on the comparison of two groups of 94 animals within each breed: the first group of animals was born before the selection began, and the second, 3–4 years later. Genetic variability was assessed using genealogical and molecular data (29 microsatellite markers). The expected loss of genetic variability on the PrP gene was confirmed. Moreover, among the five markers located in the PrP region, only the three closest ones were affected. The evolution of the number of alleles, heterozygote deficiency within population, expected heterozygosity and the Reynolds distances agreed with the criteria from pedigree and pointed out that neutral genetic variability was not much affected. This trend depended on breed, i.e. on their initial states (population size, PrP frequencies) and on the selection strategies for improving scrapie resistance while carrying out selection for production traits.

Published
2008
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25. Evolution of the polymorphism at molecular markers in QTL and non-QTL regions in selected chicken lines (Open Access publication)

Author

Bijma Piter, Verrier Étienne, Pitel Frédérique, Pinard-van der Laan Marie-Hélène, Bed'hom Bertrand, and Loywyck Valérie

Subjects
selection, quantitative trait loci, hitchhiking, chicken, genetic diversity, Animal culture, SF1-1100, Genetics, QH426-470
Abstract

Abstract We investigated the joint evolution of neutral and selected genomic regions in three chicken lines selected for immune response and in one control line. We compared the evolution of polymorphism of 21 supposedly neutral microsatellite markers versus 30 microsatellite markers located in seven quantitative trait loci (QTL) regions. Divergence of lines was observed by factor analysis. Five supposedly neutral markers and 12 markers in theQTL regions showed Fst values greater than 0.15. However, the non-significant difference (P > 0.05) between matrices of genetic distances based on genotypes at supposedly neutral markers on the one hand, and at markers in QTL regions, on the other hand, showed that none of the markers in the QTL regions were influenced by selection. A supposedly neutral marker and a marker located in the QTL region on chromosome 14 showed temporal variations in allele frequencies that could not be explained by drift only. Finally, to confirm thatmarkers located inQTL regions on chromosomes 1, 7 and 14were under the influence of selection, simulations were performed using haplotype dropping along the existing pedigree. In the zone located on chromosome 14, the simulation results confirmed that selection had an effect on the evolution of polymorphism of markers within the zone.

Published
2008
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28. RNA-Seq Data for Reliable SNP Detection and Genotype Calling: Interest for Coding Variant Characterization and Cis-Regulation Analysis by Allele-Specific Expression in Livestock Species

Author

Jehl, Frédéric, primary, Degalez, Fabien, additional, Bernard, Maria, additional, Lecerf, Frédéric, additional, Lagoutte, Laetitia, additional, Désert, Colette, additional, Coulée, Manon, additional, Bouchez, Olivier, additional, Leroux, Sophie, additional, Abasht, Behnam, additional, Tixier-Boichard, Michèle, additional, Bed’hom, Bertrand, additional, Burlot, Thierry, additional, Gourichon, David, additional, Bardou, Philippe, additional, Acloque, Hervé, additional, Foissac, Sylvain, additional, Djebali, Sarah, additional, Giuffra, Elisabetta, additional, Zerjal, Tatiana, additional, Pitel, Frédérique, additional, Klopp, Christophe, additional, and Lagarrigue, Sandrine, additional

Published
2021
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31. Additional file 3 of Assessment of trade-offs between feed efficiency, growth-related traits, and immune activity in experimental lines of layer chickens

Author

Zerjal, Tatiana, Härtle, Sonja, Gourichon, David, Vanaïque Guillory, Bruneau, Nicolas, Laloë, Denis, Marie-Hélène Pinard-Van Der Laan, Trapp, Sascha, Bed’hom, Bertrand, and Quéré, Pascale

Abstract

Additional file 3: Table S2. Whole blood leucocyte counts (× 103 cells) in vaccinated ND3 and CTR chicken lines.

Published
2021
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32. Additional file 2 of Assessment of trade-offs between feed efficiency, growth-related traits, and immune activity in experimental lines of layer chickens

Author

Zerjal, Tatiana, Härtle, Sonja, Gourichon, David, Vanaïque Guillory, Bruneau, Nicolas, Laloë, Denis, Marie-Hélène Pinard-Van Der Laan, Trapp, Sascha, Bed’hom, Bertrand, and Quéré, Pascale

Subjects
animal structures, sense organs, eye diseases
Abstract

Additional file 2: Table S1. Humoral antibody response after vaccination in the R+ and R− chicken lines.

Published
2021
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33. Additional file 1 of Assessment of trade-offs between feed efficiency, growth-related traits, and immune activity in experimental lines of layer chickens

Author

Zerjal, Tatiana, Härtle, Sonja, Gourichon, David, Vanaïque Guillory, Bruneau, Nicolas, Laloë, Denis, Marie-Hélène Pinard-Van Der Laan, Trapp, Sascha, Bed’hom, Bertrand, and Quéré, Pascale

Abstract

Additional file 1: Figure S1. RFI divergence between female and male R+ and R− chickens over 40 generations.

Published
2021
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35. Evaluation of PReimplantation embryo Aptitude for DEvelopment (EPRADE)

Author

Baertschi, Bernard, Bed’hom, Bertrand, Dosquet, Christine, Grosset, Marie, Dubart-Kupperschmitt, Anne, Jouannet, Pierre, Lemaitre, Christine, Moutel, Grégoire, Nisand, Israël, Remy-Jouet, Isabelle, Duchange, Nathalie, Comité d'éthique de l'Inserm (CEI), Institut National de la Santé et de la Recherche Médicale (INSERM), Université de Genève = University of Geneva (UNIGE), Muséum national d'Histoire naturelle (MNHN), Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), AP -Comité d'évaluation éthique de l'Inserm, Physiopathologie et traitement des maladies du foie, Hôpital Paul Brousse-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris-Saclay, Fertilité et reproduction humaines- Université Paris 5, CHU Caen, Normandie Université (NU)-Tumorothèque de Caen Basse-Normandie (TCBN), Espace régional de réflexion éthique de Normandie (EREN), Biologie de la reproduction, Université de Strasbourg (UNISTRA), and Inserm - Assurance qualité, technologies pour la santé

Subjects
Note Inserm Ethics Committee, Note Comité Ethique Inserm, IEC, CEI, [SDV.ETH] Life Sciences [q-bio]/Ethics, [SDV.ETH]Life Sciences [q-bio]/Ethics
Abstract

Memo by the Inserm Ethics Committee. Embryo and Developmental Group. Written by: Bernard Baertschi and Pierre Jouannet

Published
2021

37. Additional file 2 of Integrative mapping analysis of chicken microchromosome 16 organization

Author

Solinhac, Romain, Leroux, Sophie, Galkina, Svetlana, Chazara, Olympe, Feve, Katia, Vignoles, Florence, Morisson, Mireille, Derjusheva, Svetlana, Bed'hom, Bertrand, Vignal, Alain, Fillon, Valérie, and Pitel, Frédérique

Abstract

Additional File 2:454 contigs distribution on the chicken sequence assembly. The 454 contigs ( http://genome.wustl.edu/genomes/view/gallus_gallus/ ) were aligned to the available chicken sequence assembly (galGal 3, http://genome.ucsc.edu/index.html ). The 7 matching contigs are represented along the GGA16 sequence. File format: PowerPoint (PPT 42 KB)

Published
2021
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39. L’évaluation préimplantatoire de l’aptitude au développement embryonnaire (EPRADE)

Author

Baertschi, Bernard, Bed’hom, Bertrand, Dosquet, Christine, Grosset, Marie, Dubart-Kupperschmitt, Anne, Jouannet, Pierre, Lemaitre, Christine, Moutel, Grégoire, Nisand, Israël, Rémy-Jouet, Isabelle, Duchange, Nathalie, Comité d'éthique de l'Inserm (CEI), Institut National de la Santé et de la Recherche Médicale (INSERM), Université de Genève = University of Geneva (UNIGE), Muséum national d'Histoire naturelle (MNHN), Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), AP -Comité d'évaluation éthique de l'Inserm, Physiopathologie et traitement des maladies du foie, Université Paris-Sud - Paris 11 (UP11)-Hôpital Paul Brousse-Institut National de la Santé et de la Recherche Médicale (INSERM), Fertilité et reproduction humaines- Université Paris 5, CHU Caen, Normandie Université (NU)-Tumorothèque de Caen Basse-Normandie (TCBN), Espace régional de réflexion éthique de Normandie (EREN), Biologie de la reproduction, Université de Strasbourg (UNISTRA), and Inserm - Assurance qualité, technologies pour la santé

Subjects
DPI, Procréation médicalement assistée, Comité Ethique Inserm, Diagnostic préimplantatoire, Assistance médicale à la procréation, CEI, [SDV.ETH] Life Sciences [q-bio]/Ethics, Embryon, FIV, PMA, AMP, Fécondation in vitro, [SDV.ETH]Life Sciences [q-bio]/Ethics
Abstract

Note du groupe « Embryon et développement » du Comité d'Éthique de l'INSERM. Rédaction: Bernard Baertschi et Pierre Jouannet

Published
2021

41. The feather pattern autosomal barring in chicken is strongly associated with segregation at the MC1R locus

Author

Thalmann, Doreen Schwochow, Bornelov, Susanne, Jiang, Tingxin, Li, Jingyi, Gourichon, David, Bed'Hom, Bertrand, Dorshorst, Benjamin J., Chuong, Cheng-Ming, Tixier-Boichard, Michele, Andersson, Leif, Thalmann, Doreen Schwochow, Bornelov, Susanne, Jiang, Tingxin, Li, Jingyi, Gourichon, David, Bed'Hom, Bertrand, Dorshorst, Benjamin J., Chuong, Cheng-Ming, Tixier-Boichard, Michele, and Andersson, Leif

Abstract

Color patterns within individual feathers are common in birds but little is known about the genetic mechanisms causing such patterns. Here, we investigate the genetic basis for autosomal barring in chicken, a horizontal striping pattern on individual feathers. Using an informative backcross, we demonstrate that the MC1R locus is strongly associated with this phenotype. A deletion at SOX10, underlying the dark brown phenotype on its own, affects the manifestation of the barring pattern. The coding variant L133Q in MC1R is the most likely causal mutation for autosomal barring in this pedigree. Furthermore, a genetic screen across six different breeds showing different patterning phenotypes revealed that the most striking shared characteristics among these breeds were that they all carried the MC1R alleles Birchen or brown. Our data suggest that the presence of activating MC1R mutations enhancing pigment synthesis is an important mechanism underlying pigmentation patterns on individual feathers in chicken. We propose that MC1R and its antagonist ASIP play a critical role for determining within-feather pigmentation patterns in birds by acting as activator and inhibitor possibly in a Turing reaction-diffusion model.

Published
2021
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42. The feather pattern autosomal barring in chicken is strongly associated with segregation at the MC1R locus

Author

Schwochow, Doreen, Bornelöv, Susanne, Jiang, Tingxing, Li, Jingyi, Gourichon, David, Bed'Hom, Bertrand, Dorshorst, Ben J., Chuong, Cheng-Ming, Tixier-Boichard, Michele, Andersson, Leif, Schwochow, Doreen, Bornelöv, Susanne, Jiang, Tingxing, Li, Jingyi, Gourichon, David, Bed'Hom, Bertrand, Dorshorst, Ben J., Chuong, Cheng-Ming, Tixier-Boichard, Michele, and Andersson, Leif

Abstract

Color patterns within individual feathers are common in birds but little is known about the genetic mechanisms causing such patterns. Here, we investigate the genetic basis for autosomal barring in chicken, a horizontal striping pattern on individual feathers. Using an informative backcross, we demonstrate that the MC1R locus is strongly associated with this phenotype. A deletion at SOX10, underlying the dark brown phenotype on its own, affects the manifestation of the barring pattern. The coding variant L133Q in MC1R is the most likely causal mutation for autosomal barring in this pedigree. Furthermore, a genetic screen across six different breeds showing different patterning phenotypes revealed that the most striking shared characteristics among these breeds were that they all carried the MC1R alleles Birchen or brown. Our data suggest that the presence of activating MC1R mutations enhancing pigment synthesis is an important mechanism underlying pigmentation patterns on individual feathers in chicken. We propose that MC1R and its antagonist ASIP play a critical role for determining within-feather pigmentation patterns in birds by acting as activator and inhibitor possibly in a Turing reaction-diffusion model.

Published
2021
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43. The feather pattern autosomal barring in chicken is strongly associated with segregation at the MC1R locus

Author

Animal and Poultry Sciences, Thalmann, Doreen Schwochow, Bornelov, Susanne, Jiang, Tingxin, Li, Jingyi, Gourichon, David, Bed'Hom, Bertrand, Dorshorst, Benjamin J., Chuong, Cheng-Ming, Tixier-Boichard, Michele, Andersson, Leif, Animal and Poultry Sciences, Thalmann, Doreen Schwochow, Bornelov, Susanne, Jiang, Tingxin, Li, Jingyi, Gourichon, David, Bed'Hom, Bertrand, Dorshorst, Benjamin J., Chuong, Cheng-Ming, Tixier-Boichard, Michele, and Andersson, Leif

Abstract

Color patterns within individual feathers are common in birds but little is known about the genetic mechanisms causing such patterns. Here, we investigate the genetic basis for autosomal barring in chicken, a horizontal striping pattern on individual feathers. Using an informative backcross, we demonstrate that the MC1R locus is strongly associated with this phenotype. A deletion at SOX10, underlying the dark brown phenotype on its own, affects the manifestation of the barring pattern. The coding variant L133Q in MC1R is the most likely causal mutation for autosomal barring in this pedigree. Furthermore, a genetic screen across six different breeds showing different patterning phenotypes revealed that the most striking shared characteristics among these breeds were that they all carried the MC1R alleles Birchen or brown. Our data suggest that the presence of activating MC1R mutations enhancing pigment synthesis is an important mechanism underlying pigmentation patterns on individual feathers in chicken. We propose that MC1R and its antagonist ASIP play a critical role for determining within-feather pigmentation patterns in birds by acting as activator and inhibitor possibly in a Turing reaction-diffusion model.

Published
2021

45. Whole-genome resequencing reveals loci under selection during chicken domestication

Author

Rubin, Carl-Johan, Zody, Michael C., Eriksson, Jonas, Meadows, Jennifer R.S., Sherwood, Ellen, Webster, Matthew T., Jiang, Lin, Ingman, Max, Sharpe, Ted, Ka, Sojeong, Hallbook, Finn, Besnier, Francois, Carlborg, Orjan, Bed'hom, Bertrand, Tixier-Boichard, Michele, Jensen, Per, Siegel, Paul, Lindblad-Toh, Kerstin, and Andersson, Leif

Subjects
Thyrotropin -- Physiological aspects -- Genetic aspects -- Research -- Models, Hormone receptors -- Physiological aspects -- Genetic aspects -- Research -- Models, Single nucleotide polymorphisms -- Research -- Physiological aspects -- Models -- Genetic aspects, Chickens -- Models -- Genetic aspects -- Research -- Physiological aspects
Abstract

Domestic animals are excellent models for genetic studies of phenotypic evolution (1-3). They have evolved genetic adaptations to a new environment, the farm, and have been subjected to strong human-driven selection leading to remarkable phenotypic changes in morphology, physiology and behaviour. Identifying the genetic changes underlying these developments provides new insight into general mechanisms by which genetic variation shapes phenotypic diversity. Here we describe the use of massively parallel sequencing to identify selective sweeps of favourable alleles and candidate mutations that have had a prominent role in the domestication of chickens (Gallus gallus domesticus) and their subsequent specialization into broiler (meat-producing) and layer (egg-producing) chickens. We have generated 44.5-fold coverage of the chicken genome using pools of genomic DNA representing eight different populations of domestic chickens as well as red jungle fowl (Gallus gallus), the major wild ancestor (4). We report more than 7,000,000 single nucleotide polymorphisms, almost 1,300 deletions and a number of putative selective sweeps. One of the most striking selective sweeps found in all domestic chickens occurred at the locus for thyroid stimulating hormone receptor (TSHR), which has a pivotal role in metabolic regulation and photoperiod control of reproduction in vertebrates. Several of the selective sweeps detected in broilers overlapped genes associated with growth, appetite and metabolic regulation. We found little evidence that selection for loss-of-function mutations had a prominent role in chicken domestication, but we detected two deletions in coding sequences that we suggest are functionally important. This study has direct application to animal breeding and enhances the importance of the domestic chicken as a model organism for biomedical research., For most of their history, domestic chicken populations have been bred for two purposes, egg laying and meat production (5). The effective chicken population size must have been huge in [...]

Published
2010
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46. Improved Basic Cytogenetics Challenges Holocentricity of Butterfly Chromosomes.

Author

Dutrillaux, Bernard, Dutrillaux, Anne-Marie, McClure, Mélanie, Gèze, Marc, Elias, Marianne, and Bed'hom, Bertrand

Subjects
KARYOTYPES, HOMOLOGOUS chromosomes, CHROMOSOMES, CYTOGENETICS, SATELLITE DNA, CHROMOSOME analysis
Abstract

Mitotic chromosomes of butterflies, which look like dots or short filaments in most published data, are generally considered to lack localised centromeres and thus to be holokinetic. This particularity, observed in a number of other invertebrates, is associated with meiotic particularities known as "inverted meiosis," in which the first division is equational, i.e., centromere splitting-up and segregation of sister chromatids instead of homologous chromosomes. However, the accurate analysis of butterfly chromosomes is difficult because (1) their size is very small, equivalent to 2 bands of a mammalian metaphase chromosome, and (2) they lack satellite DNA/heterochromatin in putative centromere regions and therefore marked primary constrictions. Our improved conditions for basic chromosome preparations, here applied to 6 butterfly species belonging to families Nymphalidae and Pieridae challenges the holocentricity of their chromosomes: in spite of the absence of primary constrictions, sister chromatids are recurrently held together at definite positions during mitotic metaphase, which makes possible to establish karyotypes composed of acrocentric and submetacentric chromosomes. The total number of chromosomes per karyotype is roughly inversely proportional to that of non-acrocentric chromosomes, which suggests the occurrence of frequent robertsonian-like fusions or fissions during evolution. Furthermore, the behaviour and morphological changes of chromosomes along the various phases of meiosis do not seem to differ much from those of canonical meiosis. In particular, at metaphase II chromosomes clearly have 2 sister chromatids, which refutes that anaphase I was equational. Thus, we propose an alternative mechanism to holocentricity for explaining the large variations in chromosome numbers in butterflies: (1) in the ancestral karyotype, composed of about 62 mostly acrocentric chromosomes, the centromeres, devoid of centromeric heterochromatin/satellite DNA, were located at contact with telomeric heterochromatin; (2) the instability of telomeric heterochromatin largely contributed to drive the multiple rearrangements, principally chromosome fusions, which occurred during butterfly evolution. [ABSTRACT FROM AUTHOR]

Published
2022
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48. Organoids Research: What are the ethical issues?

Author

Baertschi, Bernard, Atlan, Henri, Botbol-Baum, Mylène, Bed’hom, Bertrand, Combrisson, Hélène, Dosquet, Christine, Dubart-Kupperschmitt, Anne, Hirsch, François, Jouannet, Pierre, Remy-Jouet, Isabelle, Lemaitre, Christine, Moutel, Grégoire, Duchange, Nathalie, The Inserm Ethics Committee (IEC), Institut National de la Santé et de la Recherche Médicale (INSERM), Université de Genève = University of Geneva (UNIGE), École des hautes études en sciences sociales (EHESS), Université Catholique de Louvain = Catholic University of Louvain (UCL), Muséum national d'Histoire naturelle (MNHN), Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), École nationale vétérinaire - Alfort (ENVA), AP -Comité d'évaluation éthique de l'Inserm, Physiopathologie et traitement des maladies du foie, Université Paris-Sud - Paris 11 (UP11)-Hôpital Paul Brousse-Institut National de la Santé et de la Recherche Médicale (INSERM), Inserm - Ethique des sciences de la vie, éthique de la recherche dans les pays du Sud, Fertilité et reproduction humaines- Université Paris 5, Inserm - Assurance qualité, technologies pour la santé, Inserm - Institut Biologie cellulaire, développement et évolution, CHU Caen, Normandie Université (NU)-Tumorothèque de Caen Basse-Normandie (TCBN), and Espace régional de réflexion éthique de Normandie (EREN)

Subjects
Note Inserm Ethics Committee, Note Comité Ethique Inserm, IEC, CEI, [SDV.ETH] Life Sciences [q-bio]/Ethics, [SDV.ETH]Life Sciences [q-bio]/Ethics
Abstract

Note from the Ethics committee.

Published
2020

49. La recherche sur les organoïdes: quels enjeux éthiques?

Author

Baertschi, Bernard, Atlan, Henri, Botbol-Baum, Mylène, Bed’hom, Bertrand, Combrisson, Hélène, Dosquet, Christine, Dubart-Kupperschmitt, Anne, Hirsch, François, Jouannet, Pierre, Remy-Jouet, Isabelle, Lemaitre, Christine, Moutel, Grégoire, Duchange, Nathalie, Comité d'éthique de l'Inserm (CEI), Institut National de la Santé et de la Recherche Médicale (INSERM), Université de Genève = University of Geneva (UNIGE), École des hautes études en sciences sociales (EHESS), Université Catholique de Louvain = Catholic University of Louvain (UCL), Muséum national d'Histoire naturelle (MNHN), Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), École nationale vétérinaire - Alfort (ENVA), AP -Comité d'évaluation éthique de l'Inserm, Physiopathologie et traitement des maladies du foie, Université Paris-Sud - Paris 11 (UP11)-Hôpital Paul Brousse-Institut National de la Santé et de la Recherche Médicale (INSERM), Inserm - Ethique des sciences de la vie, éthique de la recherche dans les pays du Sud, Fertilité et reproduction humaines- Université Paris 5, Inserm - Assurance qualité, technologies pour la santé, Inserm - Institut Biologie cellulaire, développement et évolution, CHU Caen, Normandie Université (NU)-Tumorothèque de Caen Basse-Normandie (TCBN), and Espace régional de réflexion éthique de Normandie (EREN)

Subjects
Note Comité Ethique Inserm, iPS, MEUS, cellules souches, organe, CEI, organoïdes, [SDV.ETH] Life Sciences [q-bio]/Ethics, [SDV.ETH]Life Sciences [q-bio]/Ethics
Abstract

Note du Comité. Groupe "Recherche sur les organoïdes"

Published
2020

50. Mutations in SLC45A2 cause plumage color variation in chicken and Japanese quail

Author

Gunnarsson, Ulrika, Hellstrom, Anders R., Tixier-Boichard, Michele, Minvielle, Francis, Bed'hom, Bertrand, Ito, Shin'ichi, Jensen, Per, Rattink, Annemieke, Vereijken, Addie, and Andersson, Leif

Subjects
Chickens -- Genetic aspects, Chromosomes -- Research, Chromosomes -- Structure, Sex-linkage (Genetics) -- Research, Japanese quail -- Genetic aspects, Color of animals -- Research, Biological sciences
Abstract

S*S (Silver), S*N (wild type/gold), and S*AL (sex-linked imperfect albinism) form a series of alleles at the S (Silver) locus on chicken (Gallus gallus) chromosome Z. Similarly, sex-linked imperfect albinism (AL*A) is the bottom recessive allele at the orthologous AL locus in Japanese quail (Coturnix japonica). The solute carrier family 45, member 2, protein (SLC45A2), previously denoted membrane-associated transporter protein (MATP), has an important role in vesicle sorting in the melanocytes. Here we report five SLC45A2 mutations. The 106delT mutation in the chicken S*AL allele results in a frameshift and a premature stop codon and the corresponding mRNA appears to be degraded by nonsense-mediated mRNA decay. A splice-site mutation in the Japanese quail AL*A allele causes in-frame skipping of exon 4. Two independent missense mutations (Tyr277Cys and Leu347Met) were associated with the Silver allele in chicken. The functional significance of the former mutation, associated only with Silver in White Leghorn, is unclear. Ala72Asp was associated with the cinnamon allele (AL*C) in the Japanese quail. The most interesting feature concerning the SLC45A2 variants documented in this study is the specific inhibition of expression of red pheomelanin in Silver chickens. This phenotypic effect cannot be explained on the basis of the current, incomplete, understanding of SLC45A2 function. It is an enigma why recessive null mutations at this locus cause an almost complete absence of both eumelanin and pheomelanin whereas some missense mutations are dominant and cause a specific inhibition of pheomelanin production.

Published
2007

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