Design and characterization of a 52K SNP chip for goats
| Autor: | 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. |
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| Přispěvatelé: | 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), Amills i Eras, Marcel |
| Jazyk: | angličtina |
| Rok vydání: | 2014 |
| Předmět: |
[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 |
| Zdroj: | PLoS ONE PLoS ONE, Public Library of Science, 2014, 9, online (1), Non paginé. ⟨10.1371/journal.pone.0086227⟩ PLoS ONE 9 (2014) 1 Plos One 1 (9), e86227. (2014) Recercat. Dipósit de la Recerca de Catalunya instname Dipòsit Digital de Documents de la UAB Universitat Autònoma de Barcelona Recercat: Dipósit de la Recerca de Catalunya Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya) PLoS ONE, Vol 9, Iss 1, p e86227 (2014) PLoS ONE, 9(1) PloS one 9 (2014). doi:10.1371/journal.pone.0086227 info:cnr-pdr/source/autori: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.; Li X.; Valentini A.; Zhao S./titolo:Design and characterization of a 52K SNP chip for goats/doi:10.1371%2Fjournal.pone.0086227/rivista:PloS one/anno:2014/pagina_da:/pagina_a:/intervallo_pagine:/volume:9 |
| ISSN: | 1932-6203 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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