Design and characterization of a 52K SNP chip for goats

Gwenola Tosser-Klopp, Philippe Bardou, Olivier Bouchez, Cédric Cabau, Richard Crooijmans, Yang Dong, Cécile Donnadieu-Tonon, André Eggen, Henri C.M. Heuven, Saadiah Jamli, Abdullah Johari Jiken, Christophe Klopp, Cynthia T. Lawley, John McEwan, Patrice Martin, Carole R. Moreno, Philippe Mulsant, Ibouniyamine Nabihoudine, Eric Pailhoux, Isabelle PalhièreRachel Rupp, Julien Sarry, Brian L. Sayre, Aurélie Tircazes, Jun Wang, Wen Wang, Wenguang Zhang, Paolo Ajmone, Marcel Amills, Simon Boitard, Thomas Faraut, Magali San Cristobal, Bertand Servin, Wenbin Chen, Shifeng Cheng, Xin Liu, Shengkai Pan, Chao Song, Xun Xu, Chen Ye, Bo Zhang, Jun Lv, Xin Li, Lichen Ren, Peng Shi, Jiang Yu, Omar Faruque, Hans Lenstra, Mario A. Poli, Jinshan Zhao, Su Rui, Yanjun Zhang, Alessandra Stella, Xianglong Li, Alessio Valentini, Shuhong Zhao

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109 Citations (Scopus)


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.
Original languageEnglish
Article numbere86227
JournalPLoS ONE
Publication statusPublished - 22 Jan 2014


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