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Design and characterization of a 52K SNP chip for goats

Tosser, Gwenola and Bardou, Philippe and Bouchez, Olivier and Cabau, Cédric and Crooijmans, Richard and Dong, Yang and Donnadieu, Cécile and Eggen, André and Heuven, Henri C. M. and Jamli, Saadiah and Jiken, Abdullah Johari and Klopp, Christophe and Lawley, Cynthia T. and McEwan, John and Martin, Patrice and Moreno, Carole R. and Mulsant, Philippe and Nabihoudine, Ibouniyamine and Pailhoux, Eric and Palhiere, Isabelle and Rupp, Rachel and Sarry, Julien and Sayre, Brian L. and Secula, Aurélie and Wang, Jun and Wang, Wen and Zhang, Wenguang and Zhang, Wenguang and Boitard, Simon and Faraut, Thomas and San Cristobal, Magali and Servin, Bertrand Design and characterization of a 52K SNP chip for goats. (2014) PLoS ONE, 9 (1). 1-8. ISSN 1932-6203

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Official URL: https://doi.org/10.1371/journal.pone.0086227

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.

Item Type:Article
ProdINRA Id:458959
Audience (journal):International peer-reviewed journal
Uncontrolled Keywords:
Institution:Université de Toulouse > Ecole Nationale Vétérinaire de Toulouse - ENVT (FRANCE)
Université de Toulouse > Institut National Polytechnique de Toulouse - INPT (FRANCE)
French research institutions > Institut National de la Recherche Agronomique - INRA (FRANCE)
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Funders:
ANR-09-GENM-009-03 GENIDOV CHEST-454 ; APIS-GENE ; CAPRISNIP programme: UNCEIA ; CAPGENES ; EC's Seventh Framework Programme, 3SR Integrated Project
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Deposited By: INRA INRA
Deposited On:21 Jun 2019 09:39

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