Author: "Bardou, Philippe" - Searchworks@Jio Institute Digital Library Search Results

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185 results on '"Bardou, Philippe"'

1. Searching for homozygous haplotype deficiency in Manech Tête Rousse dairy sheep revealed a nonsense variant in the MMUT gene affecting newborn lamb viability

Author: Ben Braiek, Maxime, Moreno-Romieux, Carole, André, Céline, Astruc, Jean-Michel, Bardou, Philippe, Bordes, Arnaud, Debat, Frédéric, Fidelle, Francis, Granado-Tajada, Itsasne, Hozé, Chris, Plisson-Petit, Florence, Rivemale, François, Sarry, Julien, Tadi, Némuel, Woloszyn, Florent, and Fabre, Stéphane
Published: 2024
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2. A pangenome graph reference of 30 chicken genomes allows genotyping of large and complex structural variants

Author: Rice, Edward S., Alberdi, Antton, Alfieri, James, Athrey, Giridhar, Balacco, Jennifer R., Bardou, Philippe, Blackmon, Heath, Charles, Mathieu, Cheng, Hans H., Fedrigo, Olivier, Fiddaman, Steven R., Formenti, Giulio, Frantz, Laurent A. F., Gilbert, M. Thomas P., Hearn, Cari J., Jarvis, Erich D., Klopp, Christophe, Marcos, Sofia, Mason, Andrew S., Velez-Irizarry, Deborah, Xu, Luohao, and Warren, Wesley C.
Published: 2023
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3. Whole genome sequencing reveals signals of adaptive admixture in Creole cattle

Author: Ben-Jemaa, Slim, Adam, Gabriele, Boussaha, Mekki, Bardou, Philippe, Klopp, Christophe, Mandonnet, Nathalie, and Naves, Michel
Published: 2023
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4. Restriction site-associated DNA sequencing technologies as an alternative to low-density SNP chips for genomic selection: a simulation study in layer chickens

Author: Herry, Florian, Hérault, Frédéric, Lecerf, Frédéric, Lagoutte, Laëtitia, Doublet, Mathilde, Picard-Druet, David, Bardou, Philippe, Varenne, Amandine, Burlot, Thierry, Le Roy, Pascale, and Allais, Sophie
Published: 2023
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5. Using sequence variants of a QTL region improves the accuracy of genomic evaluation in French Saanen goats

Author: Talouarn, Estelle, Teissier, Marc, Bardou, Philippe, Larroque, Hélène, Clément, Virginie, Palhière, Isabelle, Tosser-Klopp, Gwenola, Rupp, Rachel, and Robert-Granié, Christèle
Published: 2021
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6. GEGA (Gallus Enriched Gene Annotation): an online tool providing genomics and functional information across 47 tissues for a chicken gene-enriched atlas gathering Ensembl and Refseq genome annotations.

Author: Degalez, Fabien, Bardou, Philippe, and Lagarrigue, Sandrine
Published: 2024
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7. Uncovering structural variants in Creole cattle from Guadeloupe and their impact on environmental adaptation through whole genome sequencing.

Author: Ben-Jemaa, Slim, Boussaha, Mekki, Mandonnet, Nathalie, Bardou, Philippe, and Naves, Michel
Subjects: WHOLE genome sequencing, BODY temperature regulation, CHROMOSOMAL rearrangement, MUSCLE tone, GENETIC variation, TRANSFER RNA, OLFACTORY receptors
Abstract: Structural variants play an important role in evolutionary processes. Besides, they constitute a large source of inter individual genetic variation that might represent a major factor in the aetiology of complex, multifactorial traits. Their importance in adaptation is becoming increasingly evident in literature. Yet, the characterization of the genomic landscape of structural variants in local breeds remains scarce to date. Herein, we investigate patterns and gene annotation of structural variants in the Creole cattle from Guadeloupe breed using whole genome sequences from 23 bulls representative of the population. In total, we detected 32821 ascertained SV defining 15258 regions, representing ~ 17% of the Creole cattle genome. Among these, 6639 regions have not been previously reported in the Database of Genomic Variants archive. Average number of structural variants detected per individual in the studied population is in the same order of magnitude of that observed in indicine populations and higher than that reported in taurine breeds. We observe an important within-individual variability where approximately half of the detected structural variants have low frequency (MAF < 0.25). Most of the detected structural variants (55%) occurred in intergenic regions. Genic structural variants overlapped with 7793 genes and the predicted effect of most of them is ranked as "modifier". Among the structural variants that were predicted to have a high functional impact on the protein, a 5.5 Kb in length, highly frequent deletion on chromosome 2, affects ALPI, a gene associated with the interaction between gut microbiota and host immune system. The 6639 newly identified structural variants regions include three deletions and three duplications shared by more than 80% of individuals that are significantly enriched for genes related to tRNA threonylcarbamoyladenosine metabolic process, important for temperature adaptation in thermophilic organisms, therefore suggesting a potential role in the thermotolerance of Creole cattle from Guadeloupe cattle to tropical climate. Overall, highly frequent structural variants that are specific to the Creole cattle population encompass olfactory receptor and immunity genes as well as genes involved in muscle tone, muscle development and contraction. Beyond mapping and characterizing structural variants in the Creole cattle from Guadeloupe breed, this study provides valuable information for a better understanding of the potential role of chromosomal rearrangements in adaptive traits in cattle. [ABSTRACT FROM AUTHOR]
Published: 2024
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8. A single base pair duplication in the SLC33A1 gene is associated with fetal losses and neonatal lethality in Manech Tête Rousse dairy sheep.

Author: Ben Braiek, Maxime, Szymczak, Soline, André, Céline, Bardou, Philippe, Fidelle, Francis, Granado‐Tajada, Itsasne, Plisson‐Petit, Florence, Sarry, Julien, Woloszyn, Florent, Moreno‐Romieux, Carole, and Fabre, Stéphane
Subjects: BASE pairs, GENETIC variation, GENE expression, CHROMOSOME duplication, SHEEP, CATTLE fertility, FRAMESHIFT mutation
Abstract: We recently discovered that the Manech Tête Rousse (MTR) deficient homozygous haplotype 2 (MTRDHH2) probably carries a recessive lethal mutation in sheep. In this study, we fine‐mapped this region through whole‐genome sequencing of five MTRDHH2 heterozygous carriers and 95 non‐carriers from various ovine breeds. We identified a single base pair duplication within the SLC33A1 gene, leading to a frameshift mutation and a premature stop codon (p.Arg246Alafs*3). SLC33A1 encodes a transmembrane transporter of acetyl‐coenzyme A that is crucial for cellular metabolism. To investigate the lethality of this mutation in homozygous MTR sheep, we performed at‐risk matings using artificial insemination (AI) between heterozygous SLC33A1 variant carriers (SLC33A1_dupG). Pregnancy was confirmed 15 days post‐AI using a blood test measuring interferon Tau‐stimulated MX1 gene expression. Ultrasonography between 45 and 60 days post‐AI revealed a 12% reduction in AI success compared with safe matings, indicating embryonic/fetal loss. This was supported by the MX1 differential expression test suggesting fetal losses between 15 and 60 days of gestation. We also observed a 34.7% pre‐weaning mortality rate in 49 lambs born from at‐risk matings. Homozygous SLC33A1_dupG lambs accounted for 47% of this mortality, with deaths occurring mostly within the first 5 days without visible clinical signs. Therefore, appropriate management of SLC33A1_dupG with an allele frequency of 0.04 in the MTR selection scheme would help increase overall fertility and lamb survival. [ABSTRACT FROM AUTHOR]
Published: 2024
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9. GEGA (Gallus Enriched Gene Annotation): an online tool providing genomics and functional information across 47 tissues for a chicken gene-enriched atlas gathering Ensembl & Refseq genome annotations

Author: Degalez, Fabien, primary, Bardou, Philippe, additional, and Lagarrigue, Sandrine, additional
Published: 2024
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10. The BioMart community portal: an innovative alternative to large, centralized data repositories.

Author: Smedley, Damian, Haider, Syed, Durinck, Steffen, Pandini, Luca, Provero, Paolo, Allen, James, Arnaiz, Olivier, Awedh, Mohammad Hamza, Baldock, Richard, Barbiera, Giulia, Bardou, Philippe, Beck, Tim, Blake, Andrew, Bonierbale, Merideth, Brookes, Anthony J, Bucci, Gabriele, Buetti, Iwan, Burge, Sarah, Cabau, Cédric, Carlson, Joseph W, Chelala, Claude, Chrysostomou, Charalambos, Cittaro, Davide, Collin, Olivier, Cordova, Raul, Cutts, Rosalind J, Dassi, Erik, Di Genova, Alex, Djari, Anis, Esposito, Anthony, Estrella, Heather, Eyras, Eduardo, Fernandez-Banet, Julio, Forbes, Simon, Free, Robert C, Fujisawa, Takatomo, Gadaleta, Emanuela, Garcia-Manteiga, Jose M, Goodstein, David, Gray, Kristian, Guerra-Assunção, José Afonso, Haggarty, Bernard, Han, Dong-Jin, Han, Byung Woo, Harris, Todd, Harshbarger, Jayson, Hastings, Robert K, Hayes, Richard D, Hoede, Claire, Hu, Shen, Hu, Zhi-Liang, Hutchins, Lucie, Kan, Zhengyan, Kawaji, Hideya, Keliet, Aminah, Kerhornou, Arnaud, Kim, Sunghoon, Kinsella, Rhoda, Klopp, Christophe, Kong, Lei, Lawson, Daniel, Lazarevic, Dejan, Lee, Ji-Hyun, Letellier, Thomas, Li, Chuan-Yun, Lio, Pietro, Liu, Chu-Jun, Luo, Jie, Maass, Alejandro, Mariette, Jerome, Maurel, Thomas, Merella, Stefania, Mohamed, Azza Mostafa, Moreews, Francois, Nabihoudine, Ibounyamine, Ndegwa, Nelson, Noirot, Céline, Perez-Llamas, Cristian, Primig, Michael, Quattrone, Alessandro, Quesneville, Hadi, Rambaldi, Davide, Reecy, James, Riba, Michela, Rosanoff, Steven, Saddiq, Amna Ali, Salas, Elisa, Sallou, Olivier, Shepherd, Rebecca, Simon, Reinhard, Sperling, Linda, Spooner, William, Staines, Daniel M, Steinbach, Delphine, Stone, Kevin, Stupka, Elia, Teague, Jon W, Dayem Ullah, Abu Z, Wang, Jun, and Ware, Doreen
Subjects: Humans, Neoplasms, Proteomics, Genomics, Internet, Database Management Systems, Developmental Biology, Environmental Sciences, Biological Sciences, Information and Computing Sciences
Abstract: The BioMart Community Portal (www.biomart.org) is a community-driven effort to provide a unified interface to biomedical databases that are distributed worldwide. The portal provides access to numerous database projects supported by 30 scientific organizations. It includes over 800 different biological datasets spanning genomics, proteomics, model organisms, cancer data, ontology information and more. All resources available through the portal are independently administered and funded by their host organizations. The BioMart data federation technology provides a unified interface to all the available data. The latest version of the portal comes with many new databases that have been created by our ever-growing community. It also comes with better support and extensibility for data analysis and visualization tools. A new addition to our toolbox, the enrichment analysis tool is now accessible through graphical and web service interface. The BioMart community portal averages over one million requests per day. Building on this level of service and the wealth of information that has become available, the BioMart Community Portal has introduced a new, more scalable and cheaper alternative to the large data stores maintained by specialized organizations.
Published: 2015

11. In silico identification of variations in microRNAs with a potential impact on dairy traits using whole ruminant genome SNP datasets

Author: Bourdon, Céline, Boussaha, Mekki, Bardou, Philippe, Sanchez, Marie-Pierre, Le Guillou, Sandrine, Tribout, Thierry, Larroque, Hélène, Boichard, Didier, Rupp, Rachel, Le Provost, Fabienne, and Tosser-Klopp, Gwenola
Published: 2021
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12. Multi-species annotation of transcriptome and chromatin structure in domesticated animals

Author: Foissac, Sylvain, Djebali, Sarah, Munyard, Kylie, Vialaneix, Nathalie, Rau, Andrea, Muret, Kevin, Esquerré, Diane, Zytnicki, Matthias, Derrien, Thomas, Bardou, Philippe, Blanc, Fany, Cabau, Cédric, Crisci, Elisa, Dhorne-Pollet, Sophie, Drouet, Françoise, Faraut, Thomas, Gonzalez, Ignacio, Goubil, Adeline, Lacroix-Lamandé, Sonia, Laurent, Fabrice, Marthey, Sylvain, Marti-Marimon, Maria, Momal-Leisenring, Raphaelle, Mompart, Florence, Quéré, Pascale, Robelin, David, Cristobal, Magali San, Tosser-Klopp, Gwenola, Vincent-Naulleau, Silvia, Fabre, Stéphane, Pinard-Van der Laan, Marie-Hélène, Klopp, Christophe, Tixier-Boichard, Michèle, Acloque, Hervé, Lagarrigue, Sandrine, and Giuffra, Elisabetta
Published: 2019
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13. Fourth Report on Chicken Genes and Chromosomes 2022

Author: Smith, Jacqueline, Alfieri, James M., Anthony, Nick, Arensburger, Peter, Athrey, Giridhar N., Balacco, Jennifer, Balic, Adam, Bardou, Philippe, Barela, Paul, Bigot, Yves, Blackmon, Heath, Borodin, Pavel M., Carroll, Rachel, Casono, Meya C., Charles, Mathieu, Cheng, Hans, Chiodi, Maddie, Cigan, Lacey, Coghill, Lyndon M., Crooijmans, Richard, Das, Neelabja, Davey, Sean, Davidian, Asya, Degalez, Fabien, Dekkers, Jack M., Derks, Martijn, Diack, Abigail B., Djikeng, Appolinaire, Drechsler, Yvonne, Dyomin, Alexander, Fedrigo, Olivier, Fiddaman, Steven R., Formenti, Giulio, Frantz, Laurent A.F., Fulton, Janet E., Gaginskaya, Elena, Galkina, Svetlana, Gallardo, Rodrigo A., Geibel, Johannes, Gheyas, Almas A., Godinez, Cyrill John P., Goodell, Ashton, Graves, Jennifer A.M., Griffin, Darren K., Haase, Bettina, Han, Jian Lin, Hanotte, Olivier, Henderson, Lindsay J., Hou, Zhuo Cheng, Howe, Kerstin, Huynh, Lan, Ilatsia, Evans, Jarvis, Erich D., Johnson, Sarah M., Kaufman, Jim, Kelly, Terra, Kemp, Steve, Kern, Colin, Keroack, Jacob H., Klopp, Christophe, Lagarrigue, Sandrine, Lamont, Susan J., Lange, Margaret, Lanke, Anika, Larkin, Denis M., Larson, Greger, Layos, John King N., Lebrasseur, Ophélie, Malinovskaya, Lyubov P., Martin, Rebecca J., Cerezo, Maria Luisa Martin, Mason, Andrew S., McCarthy, Fiona M., McGrew, Michael J., Mountcastle, Jacquelyn, Muhonja, Christine Kamidi, Muir, William, Muret, Kévin, Murphy, Terence D., Ng'ang'a, Ismael, Nishibori, Masahide, O'Connor, Rebecca E., Ogugo, Moses, Okimoto, Ron, Ouko, Ochieng, Patel, Hardip R., Perini, Francesco, Pigozzi, María Ines, Potter, Krista C., Price, Peter D., Reimer, Christian, Rice, Edward S., Rocos, Nicolas, Rogers, Thea F., Saelao, Perot, Schauer, Jens, Schnabel, Robert D., Schneider, Valerie A., Simianer, Henner, Smith, Adrian, Stevens, Mark P., Stiers, Kyle, Tiambo, Christian Keambou, Tixier-Boichard, Michele, Torgasheva, Anna A., Tracey, Alan, Tregaskes, Clive A., Vervelde, Lonneke, Wang, Ying, Warren, Wesley C., Waters, Paul D., Webb, David, Weigend, Steffen, Wolc, Anna, Wright, Alison E., Wright, Dominic, Wu, Zhou, Yamagata, Masahito, Yang, Chentao, Yin, Zhong Tao, Young, Michelle C., Zhang, Guojie, Zhao, Bingru, Zhou, Huaijun, Smith, Jacqueline, Alfieri, James M., Anthony, Nick, Arensburger, Peter, Athrey, Giridhar N., Balacco, Jennifer, Balic, Adam, Bardou, Philippe, Barela, Paul, Bigot, Yves, Blackmon, Heath, Borodin, Pavel M., Carroll, Rachel, Casono, Meya C., Charles, Mathieu, Cheng, Hans, Chiodi, Maddie, Cigan, Lacey, Coghill, Lyndon M., Crooijmans, Richard, Das, Neelabja, Davey, Sean, Davidian, Asya, Degalez, Fabien, Dekkers, Jack M., Derks, Martijn, Diack, Abigail B., Djikeng, Appolinaire, Drechsler, Yvonne, Dyomin, Alexander, Fedrigo, Olivier, Fiddaman, Steven R., Formenti, Giulio, Frantz, Laurent A.F., Fulton, Janet E., Gaginskaya, Elena, Galkina, Svetlana, Gallardo, Rodrigo A., Geibel, Johannes, Gheyas, Almas A., Godinez, Cyrill John P., Goodell, Ashton, Graves, Jennifer A.M., Griffin, Darren K., Haase, Bettina, Han, Jian Lin, Hanotte, Olivier, Henderson, Lindsay J., Hou, Zhuo Cheng, Howe, Kerstin, Huynh, Lan, Ilatsia, Evans, Jarvis, Erich D., Johnson, Sarah M., Kaufman, Jim, Kelly, Terra, Kemp, Steve, Kern, Colin, Keroack, Jacob H., Klopp, Christophe, Lagarrigue, Sandrine, Lamont, Susan J., Lange, Margaret, Lanke, Anika, Larkin, Denis M., Larson, Greger, Layos, John King N., Lebrasseur, Ophélie, Malinovskaya, Lyubov P., Martin, Rebecca J., Cerezo, Maria Luisa Martin, Mason, Andrew S., McCarthy, Fiona M., McGrew, Michael J., Mountcastle, Jacquelyn, Muhonja, Christine Kamidi, Muir, William, Muret, Kévin, Murphy, Terence D., Ng'ang'a, Ismael, Nishibori, Masahide, O'Connor, Rebecca E., Ogugo, Moses, Okimoto, Ron, Ouko, Ochieng, Patel, Hardip R., Perini, Francesco, Pigozzi, María Ines, Potter, Krista C., Price, Peter D., Reimer, Christian, Rice, Edward S., Rocos, Nicolas, Rogers, Thea F., Saelao, Perot, Schauer, Jens, Schnabel, Robert D., Schneider, Valerie A., Simianer, Henner, Smith, Adrian, Stevens, Mark P., Stiers, Kyle, Tiambo, Christian Keambou, Tixier-Boichard, Michele, Torgasheva, Anna A., Tracey, Alan, Tregaskes, Clive A., Vervelde, Lonneke, Wang, Ying, Warren, Wesley C., Waters, Paul D., Webb, David, Weigend, Steffen, Wolc, Anna, Wright, Alison E., Wright, Dominic, Wu, Zhou, Yamagata, Masahito, Yang, Chentao, Yin, Zhong Tao, Young, Michelle C., Zhang, Guojie, Zhao, Bingru, and Zhou, Huaijun
Abstract: Chicken Genomic Diversity consortium: large-scale genomics to unravel the origins and adaptations of chickens
Published: 2023

14. A single base pair duplication inSLC33A1gene causes fetal losses and neonatal lethality in Manech Tête Rousse dairy sheep

Author: Braiek, Maxime Ben, primary, Szymczak, Soline, additional, André, Céline, additional, Bardou, Philippe, additional, Fidelle, Francis, additional, Plisson-Petit, Florence, additional, Sarry, Julien, additional, Woloszyn, Florent, additional, Moreno-Romieux, Carole, additional, and Fabre, Stéphane, additional
Published: 2023
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15. Homozygous haplotype deficiency in Manech Tête Rousse dairy sheep revealed a nonsense variant inMMUTgene affecting newborn lamb viability

Author: Braiek, Maxime Ben, primary, Moreno-Romieux, Carole, additional, André, Céline, additional, Astruc, Jean-Michel, additional, Bardou, Philippe, additional, Bordes, Arnaud, additional, Debat, Frédéric, additional, Fidelle, Francis, additional, Hozé, Chris, additional, Plisson-Petit, Florence, additional, Rivemale, François, additional, Sarry, Julien, additional, Tadi, Némuel, additional, Woloszyn, Florent, additional, and Fabre, Stéphane, additional
Published: 2023
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16. Chicken Genomic Diversity consortium: large-scale genomics to unravel the origins and adaptations of chickens

Author: Fiddaman, Steven R, Klopp, Christophe, Charles, Mathieu, Bardou, Philippe, Lebrasseur, Ophélie, Derks, Martijn F. L., Schauer, Jens, Reimer, Christian, Geibel, Johannes, Gheyas, Almas, Smith, Adrian L., Schnabel, Robert, Cerezo, Maria Luisa Martin, Nishibori, Masahide, Godinez, Cyrill John P., Layos, John King N., Alfieri, James M., Blackmon, Heath, Athrey, Giridhar N., Larson, Greger, Ng’ang’a, Ismael, Muir, William, Lange, Margaret, Wright, Dominic, Cheng, Hans H, Simianer, Henner, Weigend, Steffen, Warren, Wesley, Crooijmans, Richard P. M. A., Hanotte, Olivier, Smith, Jacqueline, Tixier-Boichard, Michele, and Frantz, Laurent Af
Abstract: On October 25-26, 2019, a satellite meeting devoted to the preparation of a Chicken Genome Diversity Consortium was organised after the 11th European Symposium of Poultry Genetics in Prague. Researchers involved in chicken genomics from Europe, Africa and China, discussed the objectives of such a consortium with some presenting their data. However, the technical aspects of how to share and jointly analyse the data were not finalized, nor was the funding model for the cost of data storage and computation. In 2021, an opportunity arose with the call for projects of the SuperMUC computing cluster of the Leibniz-Rechenzentrum in Germany. A new consortium of scientists re-launched the discussion to establish a project with the aim to explore how the high-throughput genomics age can be harnessed to answer evolutionary questions surrounding the chicken. The FARMGENOMIC project (23826) was accepted for funding in autumn 2021, gathering around 20 members from 10 institutions in Europe, North America, and Africa. This newly formed Chicken Genomic Diversity consortium brings together members from a variety of disciplines, including genomics, palaeogenetics, animal breeding, immunology, organismal biology, evolutionary biology, and archaeology. Central to the consortium are the concepts of inclusivity and openness – all data are to be made available to all members of the consortium, and later distributed to the wider community, and collaborations between groups are fostered and actively encouraged. It is hoped this state-of-the-art resource, curated in-house by bioinformaticians, will enable the community to answer previously intractable questions in chicken evolution.
Published: 2023
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17. Fourth Report on Chicken Genes and Chromosomes 2022

Author: Smith, Jacqueline, primary, Alfieri, James M., additional, Anthony, Nick, additional, Arensburger, Peter, additional, Athrey, Giridhar N., additional, Balacco, Jennifer, additional, Balic, Adam, additional, Bardou, Philippe, additional, Barela, Paul, additional, Bigot, Yves, additional, Blackmon, Heath, additional, Borodin, Pavel M., additional, Carroll, Rachel, additional, Casono, Meya C., additional, Charles, Mathieu, additional, Cheng, Hans, additional, Chiodi, Maddie, additional, Cigan, Lacey, additional, Coghill, Lyndon M., additional, Crooijmans, Richard, additional, Das, Neelabja, additional, Davey, Sean, additional, Davidian, Asya, additional, Degalez, Fabien, additional, Dekkers, Jack M., additional, Derks, Martijn, additional, Diack, Abigail B., additional, Djikeng, Appolinaire, additional, Drechsler, Yvonne, additional, Dyomin, Alexander, additional, Fedrigo, Olivier, additional, Fiddaman, Steven R., additional, Formenti, Giulio, additional, Frantz, Laurent A.F., additional, Fulton, Janet E., additional, Gaginskaya, Elena, additional, Galkina, Svetlana, additional, Gallardo, Rodrigo A., additional, Geibel, Johannes, additional, Gheyas, Almas, additional, Godinez, Cyrill John P., additional, Goodell, Ashton, additional, Graves, Jennifer A. M., additional, Griffin, Daren K., additional, Haase, Bettina, additional, Han, Jian-Lin, additional, Hanotte, Olivier, additional, Henderson, Lindsay J., additional, Hou, Zhuo-Cheng, additional, Howe, Kerstin, additional, Huynh, Lan, additional, Ilatsia, Evans, additional, Jarvis, Erich, additional, Johnson, Sarah M., additional, Kaufman, Jim, additional, Kelly, Terra, additional, Kemp, Steve, additional, Kern, Colin, additional, Keroack, Jacob H., additional, Klopp, Christophe, additional, Lagarrigue, Sandrine, additional, Lamont, Susan J., additional, Lange, Margaret, additional, Lanke, Anika, additional, Larkin, Denis M., additional, Larson, Greger, additional, Layos, John King N., additional, Lebrasseur, Ophélie, additional, Malinovskaya, Lyubov P., additional, Martin, Rebecca J., additional, Martin Cerezo, Maria Luisa, additional, Mason, Andrew S., additional, McCarthy, Fiona M., additional, McGrew, Michael J., additional, Mountcastle, Jacquelyn, additional, Muhonja, Christine Kamidi, additional, Muir, William, additional, Muret, Kévin, additional, Murphy, Terence, additional, Ng’ang’a, Ismael, additional, Nishibori, Masahide, additional, O’Connor, Rebecca E., additional, Ogugo, Moses, additional, Okimoto, Ron, additional, Ouko, Ochieng, additional, Patel, Hardip R., additional, Perini, Francesco, additional, Pigozzi, María Ines, additional, Potter, Krista C., additional, Price, Peter D., additional, Reimer, Christian, additional, Rice, Edward S., additional, Rocos, Nicolas, additional, Rogers, Thea F., additional, Saelao, Perot, additional, Schauer, Jens, additional, Schnabel, Robert, additional, Schneider, Valerie, additional, Simianer, Henner, additional, Smith, Adrian, additional, Stevens, Mark P., additional, Stiers, Kyle, additional, Tiambo, Christian Keambou, additional, Tixier-Boichard, Michele, additional, Torgasheva, Anna A., additional, Tracey, Alan, additional, Tregaskes, Clive A., additional, Vervelde, Lonneke, additional, Wang, Ying, additional, Warren, Wesley C., additional, Waters, Paul D., additional, Webb, David, additional, Weigend, Steffen, additional, Wolc, Anna, additional, Wright, Alison E., additional, Wright, Dominic, additional, Wu, Zhou, additional, Yamagata, Masahito, additional, Yang, Chentao, additional, Yin, Zhong-Tao, additional, Young, Michelle C., additional, Zhang, Guojie, additional, Zhao, Bingru, additional, and Zhou, Huaijun, additional
Published: 2023
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18. An open-source tool to assess the carbon footprint of research

Author: Mariette, Jérôme, primary, Blanchard, Odile, additional, Berné, Olivier, additional, Aumont, Olivier, additional, Carrey, Julian, additional, Ligozat, AnneLaure, additional, Lellouch, Emmanuel, additional, Roche, Philippe-Emmanuel, additional, Guennebaud, Gaël, additional, Thanwerdas, Joel, additional, Bardou, Philippe, additional, Salin, Gérald, additional, Maigne, Elise, additional, Servan, Sophie, additional, and Ben-Ari, Tamara, additional
Published: 2022
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19. Geographical contrasts of Y-chromosomal haplogroups from wild and domestic goats reveal ancient migrations and recent introgressions

Author: Consortium, Vargoats, primary, Nijman, Isaäc, additional, Rosen, Benjamin, additional, Bardou, Philippe, additional, Faraut, Thomas, additional, Cumer, Tristan, additional, Daly, Kevin, additional, Zheng, Zhuqing, additional, Cai, Yudong, additional, Asadollahpour, Hojjat, additional, Cinar-Kul, Bengi, additional, Zhang, Wei-Yi, additional, e, guangxin, additional, Ayin, A, additional, Baird, Hayley, additional, Bakhtin, Meirat, additional, Balteanu, Valentin, additional, Barfield, Diana, additional, Berger, Beate, additional, Blichfeldt, Thor, additional, Boink, Geert, additional, Bugiwati, Sri Rachma, additional, Cai, Zexi, additional, Carolan, Sean, additional, Clark, Emily, additional, Curik, Vladka Cubrić, additional, Dagong, Muhammad, additional, Dorji, Tashi, additional, Drew, Louise, additional, Guo, Jiazhong, additional, Hallsson, Jón, additional, Horvat, Simon, additional, Kantanen, Juha, additional, Kawaguchi, Fuki, additional, Kazymbet, Polat, additional, khayatzadeh, Negar, additional, Kim, Namshin, additional, Shah, Manoj Kumar, additional, Liao, Yuying, additional, Martinez, Amparo, additional, Masangkay, Joseph, additional, Masaoka, Maho, additional, Mazza, Raffaele, additional, McEwan, John, additional, Milanesi, Marco, additional, Faruque, Md Omar, additional, Nomura, Yuto, additional, Ouchene-Khelifi, Nadjet-Amina, additional, Pereira, Filipe, additional, Sahana, Goutam, additional, Salavati, Mazdak, additional, Sasazaki, Shinji, additional, SILVA, Anne DA, additional, Simčič, Mojca, additional, Soelkner, Johann, additional, Sutherland, Alison, additional, Tigchelaar, Johannes, additional, Zhang, Hongping, additional, Consortium, Econogene, additional, Marsan, Paolo Ajmone, additional, Bradley, Daniel, additional, Colli, Licia, additional, Drögemüller, Cord, additional, Jiang, Yu, additional, Lei, chuzhao, additional, Mannen, H, additional, Pompanon, Francois, additional, TOSSER-KLOPP, GWENOLA, additional, and Lenstra, Johannes A., additional
Published: 2022
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20. Y-chromosomal haplotypes in domestic and wild goats reveal ancient paternal bottlenecks and recent introgressions

Author: Vargoats Consortium, Nijman, Isaäc, Rosen, Benjamin, Faraut, Thomas, Bardou, Philippe, Cumer, Tristan, Daly, Kevin, Zheng, Zhuqing, Yu, Jiang, Lei, Chuzhao, Cai, Yudong, Bâlteanu, Valentin, Barfield, Diana, Beard, Hailey, Berger, Beate, Blichfeldt, Thor, Boink, Geert, Carolan, Sean, Colli, Licia, Cubric Curik, Vlatka, Drew, Louise, Droegemueller, Cord, and Kantanen, Juha
Subjects: Y chromosome, Haplotypes, Domestic and wild goats
Abstract: By its paternal transmission, Y-chromosomal haplotypes are sensitive markers of population history and male-mediated introgression. Previous studies have identified in domestic goats four major Y chromosomal haplotypes Y1A, Y1B, Y2A and Y2B with a marked geographic differentiation and several regional variants. In this study we combine whole-genome sequences (WGSs) of 392 male goats from 64 modern breeds and 7 wild goat species generated by the Vargoats goat genome project, 136 entries in the Short-Read Archive and genotypes of diagnostic SNPs of several modern and ancient samples. We identified single-copy male- specific SNPs in four scaffolds, containing SRY, ZFY, DBY with SSX3Y and UTY, and USP9Y with UMN2001, respectively. Phylogenetic analyses indicated haplogroups corresponding to Y1B, Y2A and Y2B, respectively, but Y1A is split into Y1AA and Y1AB. All these haplogroups were detected in ancient DNA samples from southeast Europe. In different branches of the tree, the haplotypes from domestic goats, Iranian bezoars and Anatolian bezoars, respectively, have separate positions. Notably, the Anatolian haplotypes are near the roots of the tree or of subtrees, suggesting that the Iranian bezoars are closer to the wild ancestors of domestic sheep. Haplogroup distributions for 150 domestic breeds indicates on all three continents ancient paternal population bottlenecks, especially during the migration into northern Europe. In addition, sharing of haplogroups reveals male-mediated introgression of Boer goat into Uganda, Kenya, Tanzania, Malawi and Zimbabwe, and of European goats into the native Korean goat population. This study illustrates the power of the Y-chromosomal variation for the reconstructing the history of mammalian species with a wide geographic range.
Published: 2022

21. Jflow: a workflow management system for web applications

Author: Mariette, Jérôme, Escudié, Frédéric, Bardou, Philippe, Nabihoudine, Ibouniyamine, Noirot, Céline, Trotard, Marie-Stéphane, Gaspin, Christine, and Klopp, Christophe
Published: 2016
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22. FishmiRNA: An Evolutionarily Supported MicroRNA Annotation and Expression Database for Ray-Finned Fishes

Author: Desvignes, Thomas, primary, Bardou, Philippe, additional, Montfort, Jérôme, additional, Sydes, Jason, additional, Guyomar, Cervin, additional, George, Simon, additional, Postlethwait, John H, additional, and Bobe, Julien, additional
Published: 2022
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23. MINTIA: a metagenomic INserT integrated assembly and annotation tool

Author: Bardou, Philippe, Laguerre, Sandrine, Maman Haddad, Sarah, Legoueix Rodriguez, Sabrina, Laville, Elisabeth, Dumon, Claire, Potocki-Veronese, Gabrielle, Klopp, Christophe, 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), Toulouse Biotechnology Institute (TBI), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Toulouse White Biotechnology (TWB), Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-École nationale supérieure agronomique de Toulouse (ENSAT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRAE)
Subjects: [SDV.BIO]Life Sciences [q-bio]/Biotechnology, Bioinformatics, Activity-based metagenomics, Functional annotation, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Biodiversity, Software package, Biochemistry, Microbiology, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Medicine, Functional metagenomics, Biotechnology, Metagenomic fosmid, Sequence assembly
Abstract: International audience; The earth harbors trillions of bacterial species adapted to very diverse ecosystems thanks to specific metabolic function acquisition. Most of the genes responsible for these functions belong to uncultured bacteria and are still to be discovered. Functional metagenomics based on activity screening is a classical way to retrieve these genes from microbiomes. This approach is based on the insertion of large metagenomic DNA fragments into a vector and transformation of a host to express heterologous genes. Metagenomic libraries are then screened for activities of interest, and the metagenomic DNA inserts of active clones are extracted to be sequenced and analysed to identify genes that are responsible for the detected activity. Hundreds of metagenomics sequences found using this strategy have already been published in public databases. Here we present the MINTIA software package enabling biologists to easily generate and analyze large metagenomic sequence sets, retrieved after activity-based screening. It filters reads, performs assembly, removes cloning vector, annotates open reading frames and generates user friendly reports as well as files ready for submission to international sequence repositories. The software package can be downloaded from https://github.com/Bios4Biol/MINTIA .
Published: 2021
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24. A Nonsense Variant in CCDC65 Gene Causes Respiratory Failure Associated with Increased Lamb Mortality in French Lacaune Dairy Sheep

Author: Ben Braiek, Maxime, primary, Moreno-Romieux, Carole, additional, Allain, Charlotte, additional, Bardou, Philippe, additional, Bordes, Arnaud, additional, Debat, Frédéric, additional, Drögemüller, Cord, additional, Plisson-Petit, Florence, additional, Portes, David, additional, Sarry, Julien, additional, Tadi, Némuel, additional, Woloszyn, Florent, additional, and Fabre, Stéphane, additional
Published: 2021
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25. Fourth Report on Chicken Genes and Chromosomes 2022.

Author: Smith, Jacqueline, Alfieri, James M., Anthony, Nick, Arensburger, Peter, Athrey, Giridhar N., Balacco, Jennifer, Balic, Adam, Bardou, Philippe, Barela, Paul, Bigot, Yves, Blackmon, Heath, Borodin, Pavel M., Carroll, Rachel, Casono, Meya C., Charles, Mathieu, Cheng, Hans, Chiodi, Maddie, Cigan, Lacey, Coghill, Lyndon M., and Crooijmans, Richard
Subjects: KARYOTYPES, CHROMOSOMES, CHICKENS, BIOLOGICAL evolution, CHICKEN breeds, GENETIC determinism, LOCUS (Genetics), MASS extinctions
Abstract: Bird whole-genome alignments. a Alignment of chicken to zebra finch [Rhie et al., 2021], Anna's hummingbird [Rhie et al., 2021], superb fairywren [Penalba et al., 2020], and the ancestral emu genome [Liu J et al., 2021]. b Alignment of the chicken genome to species that have undergone significant chromosome rearrangement: saker falcon, California condor [Robinson et al., 2021], and golden eagle [Mead et al., 2021]. The Bird 10,000 Genomes (B10K) Project [Zhang et al., 2015] has generated insightful results and the future bird T2T genome and pan-genome will undoubtedly reveal more genes. The chicken genome aligns very well with the emu genome, which is considered to represent the ancestral bird genome [Liu J et al., 2021]. Chicken as a Model for Bird Genome Alignments (Prepared by P.D. Waters, J.A.M. Graves, and H.R. Patel) Chicken has long been a model for bird genomes [International Chicken Genome Sequencing Consortium, 2004], but it is only in recent years that a chromosome-level assembly has been available that includes the gene-dense microchromosomes. The GC content of most of these "missing" genes is more than 60%, and few genes even have over 80% (the median GC content of the chicken genome is 42.22% and the median GC content of the duck genome is 41.99%) [Hron et al., 2015; Bornelov et al., 2017; Botero-Castro et al., 2017; Yin et al., 2019b]. [Extracted from the article]
Published: 2022
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26. Additional file 9 of VarGoats project: a dataset of 1159 whole-genome sequences to dissect Capra hircus global diversity

Author: Denoyelle, Laure, Talouarn, Estelle, Bardou, Philippe, Colli, Licia, Alberti, Adriana, Danchin, Coralie, Del Corvo, Marcello, Engelen, St��fan, Orvain, C��line, Palhi��re, Isabelle, Rupp, Rachel, Sarry, Julien, Salavati, Mazdak, Amills, Marcel, Clark, Emily, Crepaldi, Paola, Faraut, Thomas, Masiga, Clet Wandui, Pompanon, Fran��ois, Rosen, Benjamin D., Stella, Alessandra, Van Tassell, Curtis P., and Tosser-Klopp, Gwenola
Abstract: Additional file 9: Figure S5. Sex assignment for the 1159 goats sampled in VarGoats. Representation of the ratio of read number between the autosomes and the X chromosome and the read number on the Y chromosome for each animal to determine its sex. The horizontal bar corresponds to the threshold of 25 reads from the Y scaffold allowing to differentiate males from females.
Published: 2021
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27. Additional file 6 of VarGoats project: a dataset of 1159 whole-genome sequences to dissect Capra hircus global diversity

Author: Denoyelle, Laure, Talouarn, Estelle, Bardou, Philippe, Colli, Licia, Alberti, Adriana, Danchin, Coralie, Del Corvo, Marcello, Engelen, St��fan, Orvain, C��line, Palhi��re, Isabelle, Rupp, Rachel, Sarry, Julien, Salavati, Mazdak, Amills, Marcel, Clark, Emily, Crepaldi, Paola, Faraut, Thomas, Masiga, Clet Wandui, Pompanon, Fran��ois, Rosen, Benjamin D., Stella, Alessandra, Van Tassell, Curtis P., and Tosser-Klopp, Gwenola
Abstract: Additional file 6: Figure S4. Tranche plot produced by VariantRecalibrator for SNPs. Description: Partition of the call sets into quality tranches. The tranches correspond to certain levels of sensitivity relative to the truth sets (the highest tranche corresponds to a high accuracy call set but with the lowest value of sensitivity).
Published: 2021
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28. Additional file 3 of VarGoats project: a dataset of 1159 whole-genome sequences to dissect Capra hircus global diversity

Author: Denoyelle, Laure, Talouarn, Estelle, Bardou, Philippe, Colli, Licia, Alberti, Adriana, Danchin, Coralie, Del Corvo, Marcello, Engelen, St��fan, Orvain, C��line, Palhi��re, Isabelle, Rupp, Rachel, Sarry, Julien, Salavati, Mazdak, Amills, Marcel, Clark, Emily, Crepaldi, Paola, Faraut, Thomas, Masiga, Clet Wandui, Pompanon, Fran��ois, Rosen, Benjamin D., Stella, Alessandra, Van Tassell, Curtis P., and Tosser-Klopp, Gwenola
Abstract: Additional file 3: Figure S1. Distribution of the concordance rates. Concordance rates (CR) between sequence variants and 50 k genotypes for 457 individuals. The figure shows a clear disruption in the distribution of CR, thus we found it easy and relevant to discard the samples below a concordance rate of 70% between sequence and chip SNP data.
Published: 2021
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29. Additional file 5 of VarGoats project: a dataset of 1159 whole-genome sequences to dissect Capra hircus global diversity

Author: Denoyelle, Laure, Talouarn, Estelle, Bardou, Philippe, Colli, Licia, Alberti, Adriana, Danchin, Coralie, Del Corvo, Marcello, Engelen, St��fan, Orvain, C��line, Palhi��re, Isabelle, Rupp, Rachel, Sarry, Julien, Salavati, Mazdak, Amills, Marcel, Clark, Emily, Crepaldi, Paola, Faraut, Thomas, Masiga, Clet Wandui, Pompanon, Fran��ois, Rosen, Benjamin D., Stella, Alessandra, Van Tassell, Curtis P., and Tosser-Klopp, Gwenola
Abstract: Additional file 5: Figure S3. Pairwise comparisons of the annotations chosen in VQSR for InDels. Description: Modeling report generated by GATK VariantRecalibrator for every pairwise combination of annotations used (QD, DP, FS, MQRankSum, ReadPosRankSum and SOR), with a 2D projection of the Gaussian mixture model.
Published: 2021
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30. 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. Geographical contrasts of Y‐chromosomal haplogroups from wild and domestic goats reveal ancient migrations and recent introgressions.

Author: Nijman, Isaäc J., Rosen, Benjamin D., Bardou, Philippe, Faraut, Thomas, Cumer, Tristan, Daly, Kevin G., Zheng, Zhuqing, Cai, Yudong, Asadollahpour, Hojjat, Kul, Bengi Çınar, Zhang, Wei‐Yi, E., Guangxin, Ayin, A., Baird, Hayley, Bakhtin, Meirat, Bâlteanu, Valentin A., Barfield, Diana, Berger, Beate, Blichfeldt, Thor, and Boink, Geert
Subjects: GOATS, HAPLOGROUPS, HAPLOTYPES, GENE flow, FOSSIL DNA, CROSSBREEDING
Abstract: By their paternal transmission, Y‐chromosomal haplotypes are sensitive markers of population history and male‐mediated introgression. Previous studies identified biallelic single‐nucleotide variants in the SRY, ZFY and DDX3Y genes, which in domestic goats identified four major Y‐chromosomal haplotypes, Y1A, Y1B, Y2A and Y2B, with a marked geographical partitioning. Here, we extracted goat Y‐chromosomal variants from whole‐genome sequences of 386 domestic goats (75 breeds) and seven wild goat species, which were generated by the VarGoats goat genome project. Phylogenetic analyses indicated domestic haplogroups corresponding to Y1B, Y2A and Y2B, respectively, whereas Y1A is split into Y1AA and Y1AB. All five haplogroups were detected in 26 ancient DNA samples from southeast Europe or Asia. Haplotypes from present‐day bezoars are not shared with domestic goats and are attached to deep nodes of the trees and networks. Haplogroup distributions for 186 domestic breeds indicate ancient paternal population bottlenecks and expansions during migrations into northern Europe, eastern and southern Asia, and Africa south of the Sahara. In addition, sharing of haplogroups indicates male‐mediated introgressions, most notably an early gene flow from Asian goats into Madagascar and the crossbreeding that in the 19th century resulted in the popular Boer and Anglo‐Nubian breeds. More recent introgressions are those from European goats into the native Korean goat population and from Boer goat into Uganda, Kenya, Tanzania, Malawi and Zimbabwe. This study illustrates the power of the Y‐chromosomal variants for reconstructing the history of domestic species with a wide geographical range. [ABSTRACT FROM AUTHOR]
Published: 2022
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32. Analysis of Polycerate Mutants Reveals the Evolutionary Co-option of HOXD1 for Horn Patterning in Bovidae

Author: Allais-Bonnet, Aurélie, Hintermann, Aurélie, Deloche, Marie-Christine, Cornette, Raphaël, Bardou, Philippe, Naval-Sanchez, Marina, Pinton, Alain, Haruda, Ashleigh, Grohs, Cécile, Zakany, Jozsef, Bigi, Daniele, Medugorac, Ivica, Putelat, Olivier, Greyvenstein, Ockert, Hadfield, Tracy, Jemaa, Slim Ben, Bunevski, Gjoko, Menzi, Fiona, Hirter, Nathalie, Paris, Julia M, Hedges, John, Palhiere, Isabelle, Rupp, Rachel, Lenstra, Johannes A, Gidney, Louisa, Lesur, Joséphine, Schafberg, Renate, Stache, Michael, Wandhammer, Marie-Dominique, Arbogast, Rose-Marie, Guintard, Claude, Blin, Amandine, Boukadiri, Abdelhak, Rivière, Julie, Esquerré, Diane, Donnadieu, Cécile, Danchin-Burge, Coralie, Reich, Coralie M, Riley, David G, van Marle-Koster, Este, Cockett, Noelle, Hayes, Benjamin J, Drögemüller, Cord, Kijas, James, Pailhoux, Eric, Tosser-Klopp, Gwenola, Duboule, Denis, Capitan, Aurélien, Allais-Bonnet, Aurélie, Hintermann, Aurélie, Deloche, Marie-Christine, Cornette, Raphaël, Bardou, Philippe, Naval-Sanchez, Marina, Pinton, Alain, Haruda, Ashleigh, Grohs, Cécile, Zakany, Jozsef, Bigi, Daniele, Medugorac, Ivica, Putelat, Olivier, Greyvenstein, Ockert, Hadfield, Tracy, Jemaa, Slim Ben, Bunevski, Gjoko, Menzi, Fiona, Hirter, Nathalie, Paris, Julia M, Hedges, John, Palhiere, Isabelle, Rupp, Rachel, Lenstra, Johannes A, Gidney, Louisa, Lesur, Joséphine, Schafberg, Renate, Stache, Michael, Wandhammer, Marie-Dominique, Arbogast, Rose-Marie, Guintard, Claude, Blin, Amandine, Boukadiri, Abdelhak, Rivière, Julie, Esquerré, Diane, Donnadieu, Cécile, Danchin-Burge, Coralie, Reich, Coralie M, Riley, David G, van Marle-Koster, Este, Cockett, Noelle, Hayes, Benjamin J, Drögemüller, Cord, Kijas, James, Pailhoux, Eric, Tosser-Klopp, Gwenola, Duboule, Denis, and Capitan, Aurélien
Published: 2021

33. VarGoats project: a dataset of 1159 whole-genome sequences to dissect Capra hircus global diversity

Author: Agence Nationale de la Recherche (France), Région Occitanie / Pyrénées-Méditerranée, Ministère de l’Enseignement supérieur et de la Recherche (France), Biotechnology and Biological Sciences Research Council (UK), Bill & Melinda Gates Foundation, Department for International Development (UK), Center for Tropical Studies and Conservation (US), University of Edinburgh, Scottish Government's Rural and Environment Science and Analytical Services, Denoyelle, Laure, Talouarn, Estelle, Bardou, Philippe, Colli, Licia, Alberti, Adriana, Danchin, Coralie, Del Corvo, Marcello, Engelen, Stefan, Orvain, Céline, Palhière, Isabelle, Rupp, Rachel, Sarry, Julien, Salavati, Mazdak, Amills, Marcel, Clark, Emily, Crepaldi, Paola, Faraut, Thomas, Wandui Masiga, Clet, Pompanon, François, Rosen, Benjamin D., Stella, Alessandra, Van Tassell, Curtis P., Tosser-Klopp, Gwenola, VarGoats Consortium, Agence Nationale de la Recherche (France), Région Occitanie / Pyrénées-Méditerranée, Ministère de l’Enseignement supérieur et de la Recherche (France), Biotechnology and Biological Sciences Research Council (UK), Bill & Melinda Gates Foundation, Department for International Development (UK), Center for Tropical Studies and Conservation (US), University of Edinburgh, Scottish Government's Rural and Environment Science and Analytical Services, Denoyelle, Laure, Talouarn, Estelle, Bardou, Philippe, Colli, Licia, Alberti, Adriana, Danchin, Coralie, Del Corvo, Marcello, Engelen, Stefan, Orvain, Céline, Palhière, Isabelle, Rupp, Rachel, Sarry, Julien, Salavati, Mazdak, Amills, Marcel, Clark, Emily, Crepaldi, Paola, Faraut, Thomas, Wandui Masiga, Clet, Pompanon, François, Rosen, Benjamin D., Stella, Alessandra, Van Tassell, Curtis P., Tosser-Klopp, Gwenola, and VarGoats Consortium
Abstract: [Background]: Since their domestication 10,500 years ago, goat populations with distinctive genetic backgrounds have adapted to a broad variety of environments and breeding conditions. The VarGoats project is an international 1000-genome resequencing program designed to understand the consequences of domestication and breeding on the genetic diversity of domestic goats and to elucidate how speciation and hybridization have modeled the genomes of a set of species representative of the genus Capra., [Findings]: A dataset comprising 652 sequenced goats and 507 public goat sequences, including 35 animals representing eight wild species, has been collected worldwide. We identified 74,274,427 single nucleotide polymorphisms (SNPs) and 13,607,850 insertion-deletions (InDels) by aligning these sequences to the latest version of the goat reference genome (ARS1). A Neighbor-joining tree based on Reynolds genetic distances showed that goats from Africa, Asia and Europe tend to group into independent clusters. Because goat breeds from Oceania and Caribbean (Creole) all derive from imported animals, they are distributed along the tree according to their ancestral geographic origin., [Conclusions]: We report on an unprecedented international effort to characterize the genome-wide diversity of domestic goats. This large range of sequenced individuals represents a unique opportunity to ascertain how the demographic and selection processes associated with post-domestication history have shaped the diversity of this species. Data generated for the project will also be extremely useful to identify deleterious mutations and polymorphisms with causal effects on complex traits, and thus will contribute to new knowledge that could be used in genomic prediction and genome-wide association studies.
Published: 2021

34. Analysis of Polycerate Mutants Reveals the Evolutionary Co-option of HOXD1 for Horn Patterning in Bovidae

Author: Allais-Bonnet, Aurélie, primary, Hintermann, Aurélie, additional, Deloche, Marie-Christine, additional, Cornette, Raphaël, additional, Bardou, Philippe, additional, Naval-Sanchez, Marina, additional, Pinton, Alain, additional, Haruda, Ashleigh, additional, Grohs, Cécile, additional, Zakany, Jozsef, additional, Bigi, Daniele, additional, Medugorac, Ivica, additional, Putelat, Olivier, additional, Greyvenstein, Ockert, additional, Hadfield, Tracy, additional, Jemaa, Slim Ben, additional, Bunevski, Gjoko, additional, Menzi, Fiona, additional, Hirter, Nathalie, additional, Paris, Julia M, additional, Hedges, John, additional, Palhiere, Isabelle, additional, Rupp, Rachel, additional, Lenstra, Johannes A, additional, Gidney, Louisa, additional, Lesur, Joséphine, additional, Schafberg, Renate, additional, Stache, Michael, additional, Wandhammer, Marie-Dominique, additional, Arbogast, Rose-Marie, additional, Guintard, Claude, additional, Blin, Amandine, additional, Boukadiri, Abdelhak, additional, Rivière, Julie, additional, Esquerré, Diane, additional, Donnadieu, Cécile, additional, Danchin-Burge, Coralie, additional, Reich, Coralie M, additional, Riley, David G, additional, Marle-Koster, Este van, additional, Cockett, Noelle, additional, Hayes, Benjamin J, additional, Drögemüller, Cord, additional, Kijas, James, additional, Pailhoux, Eric, additional, Tosser-Klopp, Gwenola, additional, Duboule, Denis, additional, and Capitan, Aurélien, additional
Published: 2021
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35. An open-source tool to assess the carbon footprint of research

Author: Mariette, Jérôme, primary, Blanchard, Odile, additional, Berné, Olivier, additional, Aumont, Olivier, additional, Carrey, Julian, additional, Ligozat, Anne Laure, additional, Lellouch, Emmanuel, additional, Roche, Philippe-e, additional, Guennebaud, Gäel, additional, Thanwerdas, Joel, additional, Bardou, Philippe, additional, Salin, Gérald, additional, Maigne, Elise, additional, Servan, Sophie, additional, and Ben-Ari, Tamara, additional
Published: 2021
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36. The Medicago genome provides insight into the evolution of rhizobial symbioses

Author: Young, Nevin D., Debellé, Frédéric, Oldroyd, Giles E. D., Geurts, Rene, Cannon, Steven B., Udvardi, Michael K., Benedito, Vagner A., Mayer, Klaus F. X., Gouzy, Jérôme, Schoof, Heiko, Van de Peer, Yves, Proost, Sebastian, Cook, Douglas R., Meyers, Blake C., Spannagl, Manuel, Cheung, Foo, De Mita, Stéphane, Krishnakumar, Vivek, Gundlach, Heidrun, Zhou, Shiguo, Mudge, Joann, Bharti, Arvind K., Murray, Jeremy D., Naoumkina, Marina A., Rosen, Benjamin, Silverstein, Kevin A. T., Tang, Haibao, Rombauts, Stephane, Zhao, Patrick X., Zhou, Peng, Barbe, Valérie, Bardou, Philippe, Bechner, Michael, Bellec, Arnaud, Berger, Anne, Bergès, Hélène, Bidwell, Shelby, Bisseling, Ton, Choisne, Nathalie, Couloux, Arnaud, Denny, Roxanne, Deshpande, Shweta, Dai, Xinbin, Doyle, Jeff J., Dudez, Anne-Marie, Farmer, Andrew D., Fouteau, Stéphanie, Franken, Carolien, Gibelin, Chrystel, Gish, John, Goldstein, Steven, González, Alvaro J., Green, Pamela J., Hallab, Asis, Hartog, Marijke, Hua, Axin, Humphray, Sean J., Jeong, Dong-Hoon, Jing, Yi, Jöcker, Anika, Kenton, Steve M., Kim, Dong-Jin, Klee, Kathrin, Lai, Hongshing, Lang, Chunting, Lin, Shaoping, Macmil, Simone L., Magdelenat, Ghislaine, Matthews, Lucy, McCorrison, Jamison, Monaghan, Erin L., Mun, Jeong-Hwan, Najar, Fares Z., Nicholson, Christine, Noirot, Céline, O’Bleness, Majesta, Paule, Charles R., Poulain, Julie, Prion, Florent, Qin, Baifang, Qu, Chunmei, Retzel, Ernest F., Riddle, Claire, Sallet, Erika, Samain, Sylvie, Samson, Nicolas, Sanders, Iryna, Saurat, Olivier, Scarpelli, Claude, Schiex, Thomas, Segurens, Béatrice, Severin, Andrew J., Sherrier, Janine D., Shi, Ruihua, Sims, Sarah, Singer, Susan R., Sinharoy, Senjuti, Sterck, Lieven, Viollet, Agnès, Wang, Bing-Bing, Wang, Keqin, Wang, Mingyi, Wang, Xiaohong, Warfsmann, Jens, Weissenbach, Jean, White, Doug D., White, Jim D., Wiley, Graham B., Wincker, Patrick, Xing, Yanbo, Yang, Limei, Yao, Ziyun, Ying, Fu, Zhai, Jixian, Zhou, Liping, Zuber, Antoine, Dénarié, Jean, Dixon, Richard A., May, Gregory D., Schwartz, David C., Rogers, Jane, Quétier, Francis, Town, Christopher D., and Roe, Bruce A.
Published: 2011
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37. Le projet « Mille Génomes Gallus » : partager les données de séquences pour mieux les utiliser

Author: TIXIER-BOICHARD, Michèle, primary, LECERF, Frédéric, additional, HÉRAULT, Frédéric, additional, BARDOU, Philippe, additional, and KLOPP, Christophe, additional
Published: 2020
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38. Analysis of Polycerate Mutants Reveals the Evolutionary Co-option of HOXD1 to Determine the Number and Topology of Horns in Bovidae

Author: Allais-Bonnet, Aurélie, primary, Hintermann, Aurélie, additional, Deloche, Marie-Christine, additional, Cornette, Raphaël, additional, Bardou, Philippe, additional, Naval-Sanchez, Marina, additional, Pinton, Alain, additional, Haruda, Ashleigh, additional, Grohs, Cécile, additional, Zakany, Jozsef, additional, Bigi, Daniele, additional, Medugorac, Ivica, additional, Putelat, Olivier, additional, Greyvenstein, Ockert, additional, Hadfield, Tracy, additional, Ben Jemaa, Slim, additional, Bunevski, Gjoko, additional, Menzi, Fiona, additional, Hirter, Nathalie, additional, Paris, Julia M., additional, Hedges, John, additional, Palhiere, Isabelle, additional, Rupp, Rachel, additional, Lenstra, Johannes A., additional, Gidney, Louisa, additional, Lesur, Joséphine, additional, Schafberg, Renate, additional, Stache, Michael, additional, Wandhammer, Marie-Dominique, additional, Arbogast, Rose-Marie, additional, Guintard, Claude, additional, Blin, Amandine, additional, Boukadiri, Abdelhak, additional, Riviere, Julie, additional, Esquerré, Diane, additional, Donnadieu, Cécile, additional, Danchin-Burge, Coralie, additional, Reich, Coralie M, additional, Riley, David, additional, van Marle-Koster, Este, additional, Cockett, Noelle, additional, Hayes, Benjamin J., additional, Drögemüller, Cord, additional, Kijas, James, additional, Pailhoux, Eric, additional, Tosser-Klopp, Gwenola, additional, Duboule, Denis, additional, and Capitan, Aurélien, additional
Published: 2020
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39. Genome wide association analysis on semen volume and milk yield using different strategies of imputation to whole genome sequence in French dairy goats

Author: Talouarn, Estelle, primary, Bardou, Philippe, additional, Palhière, Isabelle, additional, Oget, Claire, additional, Clément, Virginie, additional, Tosser-Klopp, Gwenola, additional, Rupp, Rachel, additional, and Robert-Granié, Christèle, additional
Published: 2020
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40. Interest of Genotyping-by-Sequencing technologies as an alternative to low density SNP chips for genomic selection in layer chicken

Author: Herry, Florian, Herault, Frédéric, Picard Druet, David, Bardou, Philippe, Eché, Camille, Varenne, Amandine, Burlot, Thierry, Le Roy, Pascale, Allais, Sophie, Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage [Rennes] (PEGASE), AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA), Novogen, 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, GeT PlaGe, Genotoul, Institut National de la Recherche Agronomique (INRA), AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de la Recherche Agronomique (INRA), Génome et Transcriptome - Plateforme Génomique (GeT-PlaGe), Institut National de la Recherche Agronomique (INRA)-Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), 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], Université Toulouse III - Paul Sabatier (UT3), and Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3)
Subjects: Imputation accuracy, génotypage, [SDV]Life Sciences [q-bio], Genotyping-by-Sequencing, Genomic selection, Low density panel, Genomic evaluation accuracy, laying hen, évaluation génomique, sélection génomique, poule pondeuse, précision de sélection, genomic selection
Abstract: To reduce the cost of genomic selection, low density SNP chip can be used in combination with imputation for genotyping the selection candidates instead of using high density (HD) SNP chip. Concurrently, next-generation sequencing (NGS) techniques has been increasingly used in livestock species but remain expensive to be routinely used in selection. An alternative and costefficient solution is the Genotyping by Genome Reducing and Sequencing (GGRS) techniques to sequence only a fraction of the genome by using restriction enzymes. This approach was simulated from sequences of 1027 individuals in a pure layer line, using four enzymes (EcoRI, TaqI, AvaII and PstI). Imputation accuracy on HD genotypes was assessed as the mean correlation between true and imputed genotypes. Egg weight, egg shell color, egg shell strength and albumen height were evaluated with single-step GBLUP methodology. The impact of imputation errors on the genomic estimated breeding values (GEBV) was also investigated.AvaII or PstI led to the detection of more than 10K SNPs in common with the HD SNP chip resulting in imputation accuracy higher than 0.97. The impact of imputation errors on the ranking of the selection candidates was reduced with Spearman correlation (between GEBV calculated on true and imputed genotypes) higher than 0.97 for AvaII and PstI. Finally, the GGRS approach can be an interesting alternative to low density SNP chip for genomic selection. However, with real data, heterogeneity between individuals with missing data has to be taken into account.
Published: 2019

41. Accuracy of whole-genome sequence genotype imputation in a layer line

Author: Allais, Sophie, Herry, Florian, Herault, Frédéric, Picard Druet, David, Bardou, Philippe, Eche, Camille, Varenne, Amandine, Burlot, Thierry, Le Roy, Pascale, Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage [Rennes] (PEGASE), AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA), Novogen, 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, US 1426 Génome et Transcriptome - Plateforme Génomique, Institut National de la Recherche Agronomique (INRA), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, 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], 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), Génome et Transcriptome - Plateforme Génomique (GeT-PlaGe), Institut National de la Recherche Agronomique (INRA)-Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université Toulouse III - Paul Sabatier (UT3), and Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3)
Subjects: Layer line, NGS, [SDV]Life Sciences [q-bio], GWAS, SNP beadchip, Imputation
Abstract: Over the past several years, high-density genotyping has led to major advances in genomic selection and understanding of genomes. This is also the case in laying hens with the availability of the Affymetrix HD 600K chip since 2013. Nowadays, NGS costs are becoming more and more affordable. Based on the HD SNP chip, the use of imputation to go back to the sequence level then makes it possible to obtain information on millions of polymorphisms for a large number of individuals. In this study, we analyzed the quality of the imputation of the HD chip genotypes on sequence genotypes for 90 individuals of a layer line presenting the 2 types of information. After quality control, these individuals presented genotypes for 290K and more than 6 million SNPs respectively with 600K genotyping and 20X sequencing. We carried out a cross-validation with 8 draws of 5 individuals. The correlation between true and imputed genotypes was between 0.96 and 0.99 depending on the individual.Correlations were greater than 0.90 for all chromosomes except chromosomes 16 and 25. After this validation work, we imputed an additional set of 95 individuals to perform GWAS. These analyses confirmed some QTLs of interest as a QTL of egg shell color on chromosome 7 and a QTL of egg shell strength on chromosome 1.
Published: 2019

42. Using sequence data to refine QTL mapping in French dairy goats

Author: Talouarn, Estelle, Bardou, Philippe, Tosser-Klopp, Gwenola, Rupp, Rachel, Robert-Granie, Christele, Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées
Subjects: milk, [SDV.OT]Life Sciences [q-bio]/Other [q-bio.OT], dairy goat, production, genetic
Abstract: International audience; Goats were domesticated 10,500 years ago with the aim of supplying milk, meat and fibres. Since then, breeds have specialized and adapted to their local environment developing specific genetic profiles. The VarGoats project is an international resequencing program, which aims at covering at best the genetic diversity of the Capra species. To date the sequence data 829 Capra hircus of various breeds and geographical origins. Variant calling led to the identification of a total of 110,193,942 variants on the 29 autosomal chromosomes. Quality checks were applied to sequence variants using various indicators: quality, depth, minor allele frequency and position. For French Alpine and Saanen breeds the concordance with 50k genotypes (CaprineSNP50 BeadChip) was checked. Mean concordance rate was 98.22% and ranged from 94.00 to 99.96% among individuals. Imputation was tested on the 23,338,436 filtered variants using FImpute software. Pedigree was provided and imputation was performed in a within-breed leaveone-out scenario. Imputation quality was checked for 4 individuals on all chromosomes and for every sequenced animal on chromosome 29. Mean concordance rate for chromosome 29 ranged from 73.49 to 85.71% and from 72.72 to 79.27% in Alpine and Saanen breeds respectively. On all chromosomes, average correlation between true and imputed sequence were 0.77 and 0.76 in Alpine and Saanen respectively. Imputation was then applied to a population of 1,129 French Alpine and Saanen males with at least 10 daughters phenotypes. Association analysis was performed on production and functional traits using polygenic models with the GCTA software. Using genotype data imputed to sequence level allowed to improve the significance of QTL previously identified with 50k SNP-chip only. In Saanen breed, 1.6 Mb region on chromosome 19 was identified as significantly linked to 4 conformation traits, 3 semen production traits, somatic cell count, milk yield and protein and fat contents. These researches provided insights on how to implement a quality check, imputation that will ensure the quality of subsequent analyses, and on new SNPs to be added to the 50k SNP-chip.
Published: 2019

43. Le projet mille génomes gallus : comment partager les données de séquences pour mieux les utiliser

Author: Tixier-Boichard, Michèle, Lecerf, Frédéric, Bardou, Philippe, Klopp, Christophe, Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage [Rennes] (PEGASE), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Institut 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), SIGENAE, and Institut National de la Recherche Agronomique (INRA)
Subjects: [SDV.GEN]Life Sciences [q-bio]/Genetics, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, [SDV]Life Sciences [q-bio], [INFO]Computer Science [cs]
Abstract: National audience; The Mille Gallus genomes project aims at gathering whole genome sequence data in chicken, produced by research teams as well as breeding companies, on the model of the Mille Bull genomes project. The main interest is to increase the power of analyses by increasing the number of genomes to compare. Applications are to improve the knowledge of the chicken genome, to characterize with a high accuracy the genetic diversity at the species level, to facilitate the identification of causal mutations and to provide support to genomic selection by facilitating imputation of sequence data from SNP data. A pilot project has started in France with the collection of 207 individual genome sequences produced by eight publicly funded projects on a range of chicken populations (fastgrowing and slow-growing broilers, layers, local breeds, wild ancestors). Data sets are described by technical metadata and by metadata on the animal and its population of origin. Phenotypic data are not shared. The SIGENAE team has aligned all sequences on the GalGal5 reference genome and used a common pipeline for SNP calling. More than 42 millions SNP were identified. A structure analysis led to group the 207 individuals in seven genetic clusters. The analysis of SNP in the coding sequence of the MC1R gene showed a selection signature in the brown-egg layers related to red plumage. Other analysis are planned, including detection of structural variants. On-going projects in Europe and feedback from international teams led to think that the target of Mille genomes can be reached quickly. The principles of a future consortium agreement are presented; Le séquençage du génome entier est maintenant utilisé dans de nombreux projets de recherche sur le poulet. Le projet Mille Génomes Gallus s’inspire du projet Mille Génomes Bovins et a pour objectif de rassembler les séquences du génome entier d’animaux du genre Gallus, produites par les équipes de recherche et les entreprises de sélection. L’intérêt est d’augmenter la puissance des analyses en augmentant le nombre de génomes comparés. Les applications concernent l’analyse de la structure du génome, la caractérisation globale de la diversité de l’espèce, l’identification de mutations causales et l’aide à la sélection génomique. Cette synthèse décrit d’abord le contexte de la génomique du poulet avant de développer le concept du projet Mille Génomes, de l’illustrer avec un projet pilote utilisant les données produites par des équipes françaises et de discuter les modalités de son extension. Le projet pilote français regroupe 207 séquences individuelles issues de 8 projets de recherches financés par des fonds publics, sur une large gamme de populations (poulets de chair, poules pondeuses, races locales, ancêtres sauvages). Les jeux de données sont décrits par des métadonnées techniques et des métadonnées liées à l’animal et sa population d’origine. Aucune information phénotypique n’est partagée. L’équipe SIGENAE a aligné l’ensemble des séquences sur la version 5 du génome de référence et a répertorié plus 40 millions de variants SNP. L’analyse de structure des populations regroupe les 207 individus en sept groupes génétiques. L’étude des SNP du gène MC1R montre une signature de sélection chez les pondeuses de plumage rouge. D’autres analyses sont prévues, notamment pour les variants structuraux. Les projets en cours en Europe et les contacts pris avec des équipes étrangères laissent penser que la cible de Mille Génomes peut être atteinte rapidement. Les principes d’un futur accord de consortium sont exposés.
Published: 2019

44. VarGoats project: a dataset of 1159 whole-genome sequences to dissect Capra hircus global diversity.

Author: Denoyelle, Laure, Talouarn, Estelle, Bardou, Philippe, Colli, Licia, Alberti, Adriana, Danchin, Coralie, Del Corvo, Marcello, Engelen, Stéfan, Orvain, Céline, Palhière, Isabelle, Rupp, Rachel, Sarry, Julien, Salavati, Mazdak, Amills, Marcel, Clark, Emily, Crepaldi, Paola, Faraut, Thomas, Masiga, Clet Wandui, Pompanon, François, and Rosen, Benjamin D.
Subjects: GOATS, GENOME-wide association studies, GOAT breeds, GENETIC variation, GENETIC distance, SINGLE nucleotide polymorphisms
Abstract: Background: Since their domestication 10,500 years ago, goat populations with distinctive genetic backgrounds have adapted to a broad variety of environments and breeding conditions. The VarGoats project is an international 1000-genome resequencing program designed to understand the consequences of domestication and breeding on the genetic diversity of domestic goats and to elucidate how speciation and hybridization have modeled the genomes of a set of species representative of the genus Capra. Findings: A dataset comprising 652 sequenced goats and 507 public goat sequences, including 35 animals representing eight wild species, has been collected worldwide. We identified 74,274,427 single nucleotide polymorphisms (SNPs) and 13,607,850 insertion-deletions (InDels) by aligning these sequences to the latest version of the goat reference genome (ARS1). A Neighbor-joining tree based on Reynolds genetic distances showed that goats from Africa, Asia and Europe tend to group into independent clusters. Because goat breeds from Oceania and Caribbean (Creole) all derive from imported animals, they are distributed along the tree according to their ancestral geographic origin. Conclusions: We report on an unprecedented international effort to characterize the genome-wide diversity of domestic goats. This large range of sequenced individuals represents a unique opportunity to ascertain how the demographic and selection processes associated with post-domestication history have shaped the diversity of this species. Data generated for the project will also be extremely useful to identify deleterious mutations and polymorphisms with causal effects on complex traits, and thus will contribute to new knowledge that could be used in genomic prediction and genome-wide association studies. [ABSTRACT FROM AUTHOR]
Published: 2021
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45. Imputation from CaprineSNP50 BeadChip to sequence : a case-study in French Alpine and Saanen data from the VarGoats project

Author: Talouarn, Estelle, Bardou, Philippe, Tosser, Gwenola, Rupp, Rachel, Robert-Granie, Christele, Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées
Subjects: genomic, [SDV.OT]Life Sciences [q-bio]/Other [q-bio.OT], beadchip, saanen, goat, alpine, genetic
Abstract: International audience; Goats were domesticated 10,500 years ago with the aim of supplying milk, meat and fibers. Since then, breeds have specialized and adapted to their local environment developing specific genetic profiles. The VarGoats project is an international resequencing program which aims at covering at best the genetic diversity of the Capra species. To date the sequence data available include 16 wild types and 578 Capra hircus of 65 different breeds. Variant calling led to the identification of a total of 105,772,894 variants on the 29 autosomal chromosomes. For French Alpine and Saanen individuals the concordance with 50k genotypes was checked. Mean concordance rate was 97.74% and ranged from 90.16% to 99.96%. Quality checks were applied to sequence variants using various indicators: QUAL, GQ, DP, MAF and position. Imputation was tested on the 5,926,620 filtered variants using FImpute software. Pedigree was provided and different reference populations were compared in a leave-one-out scenario. Mean concordance rate ranged from 90.6 to 92.5% and from 89.7 to 91.7% in Alpine and Saanen breeds respectively. Correlation between true and imputed sequence ranged from 0.78 to 0.83 and from 0.76 to 0.81 in Alpine and Saanen respectively. Imputation will be applied to a population of 3,618 French Alpine and Saanen goats genotyped with the CaprineSNP50 BeadChip. The next step will be to compare association studies using 50K data or SNPs imputed from the sequence data. This research provides insights on how to implement a solid quality check, and imputation that will ensure the quality of subsequent analyses.
Published: 2019

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

Author: Foissac, Sylvain, Djebali, Sarah, Munyard, Kylie, Vialaneix, Nathalie, Rau, Andrea, Muret, Kevin, Esquerré, Diane, Zytnicki, Matthias, Derrien, Thomas, Bardou, Philippe, Blanc, Fany, Cabau, Cédric, Crisci, Elisa, Dhorne-Pollet, Sophie, Drouet, Françoise, Faraut, Thomas, Gonzalez, Ignacio, Goubil, Adeline, Lacroix-Lamandé, Sonia, Laurent, Fabrice, Marthey, Sylvain, Marti-Marimon, Maria, Raphaelle Momal-Leisenring, Mompart, Florence, Quéré, Pascale, Robelin, David, Cristobal, Magali, Tosser-Klopp, Gwenola, Vincent-Naulleau, Silvia, Fabre, Stéphane, Marie-Hélène Pinard-Van Der Laan, Klopp, Christophe, Tixier-Boichard, Michèle, Acloque, Hervé, Lagarrigue, Sandrine, and Giuffra, Elisabetta
Abstract: Additional file 1 Additional file 1: Supplementary figures (S1-S26) and tables (S1-S15).
Published: 2019
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47. VarGoats: first results of an international 1000-genome project

Author: Tosser-Klopp, Gwenola, Bardou, Philippe, Denoyelle, Laure, Faraut, Thomas, Pompanon, Francois, 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 Université Grenoble Alpes (COMUE) (UGA)
Subjects: [SDV.GEN]Life Sciences [q-bio]/Genetics, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, genone, [SDV]Life Sciences [q-bio], [INFO]Computer Science [cs], ComputingMilieux_MISCELLANEOUS
Abstract: National audience
Published: 2018

48. Analysis of whole genome sequence data on a tropical admixed cattle breed, the Creole cattle of Guadeloupe

Author: Adam, Gabrièle, Esquerré, Diane, Bouchez, Olivier, Bardou, Philippe, Klopp, Christophe, Naves, Michel, Unité de Recherches Zootechniques (URZ), Institut National de la Recherche Agronomique (INRA), Génome et Transcriptome - Plateforme Génomique (GeT-PlaGe), Institut National de la Recherche Agronomique (INRA)-Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), 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), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), and Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse)
Subjects: [SDV.GEN]Life Sciences [q-bio]/Genetics, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, [SDV]Life Sciences [q-bio], [INFO]Computer Science [cs], [MATH]Mathematics [math], ComputingMilieux_MISCELLANEOUS
Abstract: National audience
Published: 2018

49. Présentation et premiers résultats du programme 1000 génomes caprins : VarGoats

Author: Bardou, Philippe, Bourdon, Céline, Denoyelle, Laure, Faraut, Thomas, Talouarn, Estelle, Alberti, Adriana, Boussaha, Mekki, Engelen, Stefan, Palhière, Isabelle, Le Provost, Fabienne, Pompanon, François, Robert-Granié, Christèle, Rupp, Rachel, Tosser-Klopp, Gwenola, Consortium Vargoats, ., Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-École nationale supérieure agronomique de Toulouse (ENSAT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Génétique Animale et Biologie Intégrative (GABI), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire d'Ecologie Alpine (LECA ), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Laboratoire de Biologie Moléculaire pour l’Etude des Génomes [Evry] (LBioMEG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut de biologie François Jacob, Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)
Subjects: [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics
Abstract: International audience
Published: 2018

50. Genome wide association analysis on semen volume and milk yield using different strategies of imputation to whole genome sequence in French dairy goats

Author: Talouarn, Estelle, primary, Bardou, Philippe, additional, Palhière, Isabelle, additional, Oget, Claire, additional, Clément, Virginie, additional, Tosser-Klopp, Gwenola, additional, Rupp, Rachel, additional, and Robert-Granié, Christèle, additional
Published: 2019
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