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1. Design and characterization of a 52K SNP chip for goats

Author

Tosser-Klopp G., Bardou P., Bouchez O., Cabau C., Crooijmans R., Dong Y., Donnadieu-Tonon C., Eggen A., Heuven H.C.M., Jamli S., Jiken A.J., Klopp C., Lawley C.T., McEwan J., Martin P., Moreno C.R., Mulsant P., Nabihoudine I., Pailhoux E., Palhiere I., Rupp R., Sarry J., Sayre B.L., Tircazes A., Wang J., Wang W., Zhang W., Ajmone P., Amills M., Boitard S., Faraut T., San Cristobal M., Servin B., Chen W., Cheng S., Liu X., Pan S., Song C., Xu X., Ye C., Zhang B., Lv J., Li X., Ren L., Shi P., Yu J., Faruque O., Lenstra H., Poli M.A., Zhao J., Rui S., Zhang Y., Stella A., Valentini A., Zhao S., Ecole Nationale Vétérinaire de Toulouse - ENVT (FRANCE), Institut National Polytechnique de Toulouse - INPT (FRANCE), Institut National de la Recherche Agronomique - INRA (FRANCE), Laboratoire de Génétique Cellulaire (LGC), Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Recherche Agronomique (INRA), Animal Breeding and Genomics Centre, Wageningen University and Research Centre [Wageningen] (WUR), Kunming Institute of Zoology, State Key Laboratory of Genetic Resources and Evolution, Chinese Academy of Sciences [Changchun Branch] (CAS), Faculty of Veterinary Medicine, Utrecht University [Utrecht], Strategic Livestock Research Centre, Malaysian Agricultural Research Development Institute, Unité de Biométrie et Intelligence Artificielle (UBIA), Institut National de la Recherche Agronomique (INRA), Invermay Agricultural Center, AgResearch, Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Station d'Amélioration Génétique des Animaux (SAGA), Biologie du Développement et Reproduction (BDR), Department of Biology, Virginia State University, Inner Mongolia Key Laboratory of Animal Genetics, Breeding and Reproduction, Inner Mongolia Agricultural University, ANR-09-GENM-009-03 GENIDOV, ANR CHEST-454, CAPRISNIP programme: UNCEIA, CAPGENES and APIS-GENE French Breeding organizations, Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Wageningen University and Research [Wageningen] (WUR), Biologie du développement et reproduction (BDR), Centre National de la Recherche Scientifique (CNRS)-École nationale vétérinaire d'Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA), Institut National Polytechnique de Toulouse - Toulouse INP (FRANCE), and Amills i Eras, Marcel

Subjects
[SDV.SA]Life Sciences [q-bio]/Agricultural sciences, Gene Identification and Analysis, lcsh:Medicine, Sequence assembly, polledness, Molecular Inversion Probe, Genome, Sequence alignment, generation, single-nucleotide polymorphisms, lcsh:Science, Génétique, Animal Management, Genetics, 0303 health sciences, Multidisciplinary, Goats, Illumina 52K SNP Chip, goat, Agriculture, Genomics, 04 agricultural and veterinary sciences, Tag SNP, SNP genotyping, Grasslands, Research Article, dbSNP, Animal Breeding and Genomics, Biology, Molecular Genetics, 03 medical and health sciences, Genetic Mutation, Biologie animale, Genome-Wide Association Studies, Fokkerij en Genomica, BioNanoTechnology, genome, prp gene, Alleles, 030304 developmental biology, classical scrapie, capra-hircus, lcsh:R, Sequence assembly tools, 0402 animal and dairy science, association, snp, Genome analysis, 040201 dairy & animal science, Sustainable Agriculture, genotyping assay, Genetic Polymorphism, WIAS, lcsh:Q, Veterinary Science, Cattle, Animal Genetics, Population Genetics, Genomic databases, discovery, Reference genome
Abstract

The success of Genome Wide Association Studies in the discovery of sequence variation linked to complex traits in humans has increased interest in high throughput SNP genotyping assays in livestock species. Primary goals are QTL detection and genomic selection. The purpose here was design of a 50-60,000 SNP chip for goats. The success of a moderate density SNP assay depends on reliable bioinformatic SNP detection procedures, the technological success rate of the SNP design, even spacing of SNPs on the genome and selection of Minor Allele Frequencies (MAF) suitable to use in diverse breeds. Through the federation of three SNP discovery projects consolidated as the International Goat Genome Consortium, we have identified approximately twelve million high quality SNP variants in the goat genome stored in a database together with their biological and technical characteristics. These SNPs were identified within and between six breeds (meat, milk and mixed): Alpine, Boer, Creole, Katjang, Saanen and Savanna, comprising a total of 97 animals. Whole genome and Reduced Representation Library sequences were aligned on >10 kb scaffolds of the de novo goat genome assembly. The 60,000 selected SNPs, evenly spaced on the goat genome, were submitted for oligo manufacturing (Illumina, Inc) and published in dbSNP along with flanking sequences and map position on goat assemblies (i.e. scaffolds and pseudo-chromosomes), sheep genome V2 and cattle UMD3.1 assembly. Ten breeds were then used to validate the SNP content and 52,295 loci could be successfully genotyped and used to generate a final cluster file. The combined strategy of using mainly whole genome Next Generation Sequencing and mapping on a contig genome assembly, complemented with Illumina design tools proved to be efficient in producing this GoatSNP50 chip. Advances in use of molecular markers are expected to accelerate goat genomic studies in coming years. Copyright: © 2014 Tosser-Klopp et al.

Published
2014
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2. Genomic analysis of the necrotrophic fungal pathogens Sclerotinia sclerotiorum and Botrytis cinerea

Author

Patrick Wincker, Mathias Choquer, Muriel Viaud, Nicholas J. Talbot, Chinnappa D. Kodira, Amir Sharon, Caroline Levis, Joelle Amselem, Ernesto P. Benito, Evan Mauceli, Julia Schumacher, Béatrice Segurens, Ronald P. de Vries, Pedro M. Coutinho, Sandrine Grossetete, Darren M. Soanes, Cécile Neuvéglise, Jan A. L. van Kan, Jeffrey A. Rollins, Sabine Fillinger, Nicolas Lapalu, Pascale Cotton, Chandri Yandava, Jean-Marc Pradier, Julie Poulain, Etienne Danchin, Celedonio González, Matthias Hahn, Adeline Simon, Hadi Quesneville, Christine Rascle, Nathalie Poussereau, Angélique Gautier, Paul S. Dyer, Tatiana Giraud, Matthias Kretschmer, Jérôme Collemare, Corinne Giraud, Ourdia Bouzid, Qiandong Zeng, Oded Yarden, Arjen ten Have, Rolland Beffa, Baptiste Brault, Elisabeth Fournier, Bernard Henrissat, Catherine Sirven, Ross E. Beever, Isabelle Benoit, Matthew D. Pearson, Matthew D. Templeton, Bettina Tudzynski, Zehua Chen, Evelyn Silva, Birgitt Oeser, Marion Andrew, Marty Dickman, Christina A. Cuomo, Barbara J. Howlett, Paul Tudzynski, Anne Lappartient, Emmanuel Quévillon, Ulrich Güldener, Arnaud Couloux, Marc-Henri Lebrun, Adrienne Sexton, Lilian Gout, Kim M. Plummer, Michaela Leroch, Linda M. Kohn, Véronique Anthouard, Corinne Da Silva, Unité de Recherche Génomique Info (URGI), Institut National de la Recherche Agronomique (INRA), BIOlogie et GEstion des Risques en agriculture (BIOGER), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Broad Institute of MIT and Harvard (BROAD INSTITUTE), Harvard Medical School [Boston] (HMS)-Massachusetts Institute of Technology (MIT)-Massachusetts General Hospital [Boston], Wageningen University and Research [Wageningen] (WUR), Departamento de Microbiología y Genética, Centro Hispano-Luso de Investigaciones Agrarias, Universidad de Salamanca, 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), Architecture et fonction des macromolécules biologiques (AFMB), Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Kluyver Centre for Genomics of Industrial Fermentations, Centraalbureau voor Schimmelcultures Fungal Biodiversity Centre (CBS-KNAW), School of Biology, University of Nottingham, UK (UON), Biologie et Génétique des Interactions Plante-Parasite (UMR BGPI), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Faculty of Biology, University of Kaiserslautern, Biology Department, University of Toronto, Botany Department, La Trobe University [Melbourne], Microbiologie, adaptation et pathogénie (MAP), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Department of Molecular Microbiology and Biotechnology, Tel Aviv University (TAU), Instituto de Investigaciones Biológicas [Mar del Plata] (IIB), Consejo Nacional de Investigaciones Científicas y Técnicas [Buenos Aires] (CONICET)-Facultad de Ciencias Exactas y Naturales [Mar del Plata], Universidad Nacional de Mar del Plata [Mar del Plata] (UNMdP)-Universidad Nacional de Mar del Plata [Mar del Plata] (UNMdP), Molekularbiologie und Biotechnologie der Pilze, Institut für Biologie und Biotechnologie der Pflanzen, Westfälische Wilhelms-Universität Münster = University of Münster (WWU)-Westfälische Wilhelms-Universität Münster = University of Münster (WWU), Manaaki Whenua – Landcare Research [Lincoln], Génomique fonctionnelle des champignons pathogènes des plantes (FungiPath), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Laboratory of Phytopathology, Laboratoire de Génomique Fonctionnelle des Champignons Pathogènes de Plantes, Centre National de la Recherche Scientifique (CNRS), Interactions Biotiques et Santé Végétale, Ecologie Systématique et Evolution (ESE), Université Paris-Sud - Paris 11 (UP11)-AgroParisTech-Centre National de la Recherche Scientifique (CNRS), Departamento de Bioquímica y Biología Molecular, Universidad de La Laguna [Tenerife - SP] (ULL), Helmholtz Zentrum München = German Research Center for Environmental Health, School of Botany [Melbourne], Faculty of Science [Melbourne], University of Melbourne-University of Melbourne, MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), Fundacion Ciencia para la Vida and Facultad de Ciencias Biologicas, Universidad Andrés Bello [Santiago] (UNAB), School of Biosciences, University of Exeter, Plant and Food Research, Mt. Albert Research Centre, Department of Plant Pathology and Microbiology, The Hebrew University of Jerusalem (HUJ), Department of Plant Pathology, University of Florida [Gainesville] (UF), Borlaug Genomics and Bioinformatics Center, Department of Plant Pathology and Microbiology, Institute for Plant Genomics and Biotechnology, ANR-07-BIOE-0006,E-TRICEL,Exploration de la biodiversité enzymatique pour la complémentation du secrétome de Trichoderma reesei afin d'améliorer l'hydrolyse des lignocelluloses(2007), European Project: LSHB-CT-2004-511952, Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Tel Aviv University [Tel Aviv], University of Münster-University of Münster, Helmholtz-Zentrum München (HZM), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Wageningen University and Research Centre [Wageningen] (WUR), 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)-Université Paris-Saclay, Landcare Research, University of Florida [Gainesville], ANR-07-BIOE-0006,BIOE,Exploration de la biodiversité enzymatique pour la complémentation du secrétome de Trichoderma reesei afin d'améliorer l'hydrolyse des lignocelluloses(2007), Amselem, Joelle, Cuomo, Christina A., van Kan, Jan A. L., Viaud, Muriel, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), and Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)

Subjects
Homothallism, Cancer Research, Arabidopsis thaliana, [SDV]Life Sciences [q-bio], genome sequence, Molecular phylogeny, Genome, purl.org/becyt/ford/1 [https], mort cellulaire programmée, Rice blast fungus, Oxalic acid, acide oxalique, Development specific protein, Genome Sequencing, Genome Evolution, Genetics (clinical), Phylogeny, Botrytis cinerea, Programmed cell death, genome analysis, 2. Zero hunger, Genetics, 0303 health sciences, neurospora-crassa, biology, Ascomycota, EPS-2, Sclerotinia sclerotiorum, Development-specific protein, Expressed sequence tags, Programmed cell-death, Mating-type loci, Oxalic-acid, Neurospora-crassa, Arabidopsis-thaliana, Secondary metabolism, Fungal genetics, Genomics, Functional Genomics, white mould, Botrytis, Genome, Fungal, CIENCIAS NATURALES Y EXACTAS, Research Article, mating-type loci, food.ingredient, rice blast fungus, molecular phylogeny, secondary metabolism, arabidopsis thaliana, neurospora crassa, oxalic acid, mating type loci, programmed cell death, expressed sequence tags, development specific protein, lcsh:QH426-470, Genes, Fungal, arabidopsis-thaliana, Mating type loci, Synteny, Ciencias Biológicas, 03 medical and health sciences, food, Biología Celular, Microbiología, Botany, phylogénie moléculaire, étiquette de séquence exprimée, purl.org/becyt/ford/1.6 [https], Molecular Biology, Biology, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, programmed cell-death, Plant Diseases, Neurospora crassa, gray mould, 030306 microbiology, fungi, 15. Life on land, métabolisme secondaire, development-specific protein, Comparative Genomics, biology.organism_classification, oxalic-acid, Laboratorium voor Phytopathologie, lcsh:Genetics, Laboratory of Phytopathology, DNA Transposable Elements, Genome Expression Analysis, Mecondary metabolism
Abstract

Sclerotinia sclerotiorum and Botrytis cinerea are closely related necrotrophic plant pathogenic fungi notable for their wide host ranges and environmental persistence. These attributes have made these species models for understanding the complexity of necrotrophic, broad host-range pathogenicity. Despite their similarities, the two species differ in mating behaviour and the ability to produce asexual spores. We have sequenced the genomes of one strain of S. sclerotiorum and two strains of B. cinerea. The comparative analysis of these genomes relative to one another and to other sequenced fungal genomes is provided here. Their 38–39 Mb genomes include 11,860–14,270 predicted genes, which share 83% amino acid identity on average between the two species. We have mapped the S. sclerotiorum assembly to 16 chromosomes and found large-scale co-linearity with the B. cinerea genomes. Seven percent of the S. sclerotiorum genome comprises transposable elements compared to, Author Summary Sclerotinia sclerotiorum and Botrytis cinerea are notorious plant pathogenic fungi with very wide host ranges. They cause vast economic damage during crop cultivation as well as in harvested produce. These fungi are typical examples of necrotrophs: they first kill host plant cells and then colonize the dead tissue. The genome sequences of the two fungi were determined in order to examine commonalities in structure and content and in order to find unique features that may distinguish them from other pathogenic fungi and from saprotrophic fungi. The genomes show high sequence identity and a similar arrangement of genes. S. sclerotiorum and B. cinerea differ in their regulation of sexual reproduction, and the genetic basis and its evolution could be explained from the genome sequence. The genome sequence revealed a striking difference in the number and diversity of secondary metabolism gene clusters, which may be involved in the adaptation to different ecological niches. Altogether, there were no unique features in the genomes of S. sclerotiorum and B. cinerea that could be identified as “silver bullets,” which distinguish these aggressive pathogens from other pathogenic and non-pathogenic fungi. These findings reinforce the quantitative, multigenic nature of necrotrophic pathogenesis.

Published
2011
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3. Bio-energy retains its mitigation potential under elevated CO2

Author

Nicolas Viovy, Sylvestre Njakou Djomo, Ivan A. Janssens, Martin Lukac, Carlo Calfapietra, Reinhart Ceulemans, Giuseppe Scarascia-Mugnozza, Sebastiaan Luyssaert, Marcel R. Hoosbeek, Marion Liberloo, Valentin Bellassen, Galina Churkina, Department of Biology, University of Antwerp (UA), Laboratoire des Sciences du Climat et de l'Environnement [Gif-sur-Yvette] (LSCE), Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), Natural Environment Research Council (NERC), Centre for Population Biology, Imperial College London, Institute of Agro-Environmental and Forest Biology (IBAF), Consiglio Nazionale delle Ricerche [Roma] (CNR), Department of Environmental Sciences [Wageningen], Wageningen University and Research [Wageningen] (WUR), Modélisation des Surfaces et Interfaces Continentales (MOSAIC), Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), Leibniz-Zentrum für Agrarlandschaftsforschung = Leibniz Centre for Agricultural Landscape Research (ZALF), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), NERC, IBAF, National Research Council [Italy] (CNR), Leibniz-Zentrum für Agrarlandschaftsforschung (ZALF), Leibniz Association, DOFOCO (242654), European Project: 242564,EC:FP7:ERC,ERC-2009-StG,DOFOCO(2010), Systems Ecology, Wageningen University and Research Centre [Wageningen] (WUR), National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), and Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)

Subjects
enrichment, 010504 meteorology & atmospheric sciences, [SDV]Life Sciences [q-bio], Energy balance, 02 engineering and technology, Carbon sequestration, 01 natural sciences, 7. Clean energy, irrigation, Agricultural soil science, Environmental protection, 0202 electrical engineering, electronic engineering, information engineering, SDG 13 - Climate Action, Biomass, rotation poplar plantation, 2. Zero hunger, Multidisciplinary, agricultural irrigation, Chemistry, Agroforestry, Ecology/Plant-Environment Interactions, Carbon sink, Plants, séquestration du carbone, carbon dioxine, Biofuel, Medicine, coniferous forests, Research Article, Ecology/Global Change Ecology, productivity, Science, 020209 energy, Plant Development, poplars, Earth System Science, soil, Bioenergy, biomass production, greenhouse gases, increases, Biology, fossil fuel, 0105 earth and related environmental sciences, WIMEK, business.industry, combustible fossile, Fossil fuel, Carbon Dioxide, 15. Life on land, carbon sequestration, life cycles, biofuels, biocarburant, 13. Climate action, Greenhouse gas, Leerstoelgroep Aardsysteemkunde, carbone, Short rotation coppice, Ecology/Ecosystem Ecology, Energy Metabolism, business
Abstract

Background: If biofuels are to be a viable substitute for fossil fuels, it is essential that they retain their potential to mitigate climate change under future atmospheric conditions. Elevated atmospheric CO2 concentration [CO2] stimulates plant biomass production; However, the beneficial effects of increased production may be offset by higher energy costs in crop management. Methodology/Main Findings: We maintained full size poplar short rotation coppice (SRC) systems under both current ambient and future elevated [CO2] (550 ppm) and estimated their net energy and greenhouse gas balance. We show that a poplar SRC system is energy efficient and produces more energy than required for coppice management. Even more, elevated [CO2] will increase the net energy production and greenhouse gas balance of a SRC system with 18%. Managing the trees in shorter rotation cycles (i.e., 2 year cycles instead of 3 year cycles) will further enhance the benefits from elevated [CO2] on both the net energy and greenhouse gas balance. Conclusions/Significance: Adapting coppice management to the future atmospheric [CO2] is necessary to fully benefit from the climate mitigation potential of bio-energy systems. Further, a future increase in potential biomass production due to elevated [CO2] outweighs the increased production costs resulting in a northward extension of the area where SRC is greenhouse gas neutral. Currently, the main part of the European terrestrial carbon sink is found in forest biomass and attributed to harvesting less than the annual growth in wood. Because SRC is intensively managed, with a higher turnover in wood production than conventional forest, northward expansion of SRC is likely to erode the European terrestrial carbon sink.

Published
2010
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