Design and Characterization of a 52K SNP Chip for Goats
Tosser-Klopp, Gwenola (Institut national de la recherche agronomique (França). Laboratoire de Génétique Cellulaire)
Bardou, Philippe (Institut national de la recherche agronomique (França). Laboratoire de Génétique Cellulaire)
Bouchez, Olivier (Institut national de la recherche agronomique (França). Laboratoire de Génétique Cellulaire)
Cabau, Cédric (Institut national de la recherche agronomique (França). Laboratoire de Génétique Cellulaire)
Crooijmans, Richard (Wageningen University. Animal Breeding and Genomics Centre)
Dong, Yang (Chinese Academy of Sciences. Kunming Institute of Zoology)
Donnadieu-Tonon, Cécile (Institut national de la recherche agronomique (França). GeT-PlaGe)
Eggen, André (Illumina Inc. (Hayward, Calif., Estats Units d'Amèrica))
Heuven, Henri C. M. (Utrecht University. Faculty of Veterinary Medicine)
Jamli, Saadiah (Malaysian Agricultural Research and Development Institute)
Johari Jiken, Abdullah (Malaysian Agricultural Research and Development Institute)
Klopp, Christophe (Institut National de la Recherche Agronomique (França))
Lawley, Cynthia T. (Illumina Inc. (Hayward, Calif., Estats Units d'Amèrica))
McEwan, John (Invermay Agricultural Center (Mosgiel, Nova Zelanda))
Martin, Patrice (Institut national de la recherche agronomique (França). Génétique Animale et Biologie Intégrative)
Moreno, Carole R. (Institut national de la recherche agronomique (França). Station d'Amélioration Génétique des Animaux)
Mulsant, Philippe (Institut national de la recherche agronomique (França). Laboratoire de Génétique Cellulaire)
Nabihoudine, Ibouniyamine (Institut national de la recherche agronomique (França). Laboratoire de Génétique Cellulaire)
Pailhoux, Eric (Institut national de la recherche agronomique (França). Biologie du Développement et Reproduction)
Palhière, Isabelle (Institut national de la recherche agronomique (França). Station d'Amélioration Génétique des Animaux)
Rupp, Rachel (Institut national de la recherche agronomique (França). Station d'Amélioration Génétique des Animaux)
Sarry, Julien (Institut national de la recherche agronomique (França). Laboratoire de Génétique Cellulaire)
Sayre, Brian L. (Virginia State University, Department of Biology)
Tircazes, Aurélie (Institut national de la recherche agronomique (França). Station d'Amélioration Génétique des Animaux)
Wang, Jun (Bejing Genome Institute)
Wang, Wen (Bejing Genome Institute)
Zhang, Wenguang (Chinese Academy of Sciences. Kunming Institute of Zoology)
Amills i Eras, Marcel, col. (Universitat Autònoma de Barcelona. Departament de Ciència Animal i dels Aliments)
International Goat Genome Consortium

Fecha:	2014
Resumen:	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.
Derechos:	Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, fins i tot amb finalitats comercials, sempre i quan es reconegui l'autoria de l'obra original.
Lengua:	Anglès
Documento:	Article ; recerca ; Versió publicada
Materia:	Goats ; Genomic databases ; Sequence assembly tools ; Genome analysis ; Alleles ; Cattle ; Grasslands ; Sequence alignment
Publicado en:	PloS one, Vol. 9 Issue 1 (January 2014) , p. e86227, ISSN 1932-6203

DOI: 10.1371/journal.pone.0086227
PMID: 24465974

8 p, 356.0 KB

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