Open AccessDesign and Characterization of a 52K SNP Chip for Goats
Author(s) -
Gwenola TosserKlopp,
Philippe Bardou,
Olivier Bouchez,
Cédric Cabau,
R.P.M.A. Crooijmans,
Yang Dong,
Cécile Donnadieu-To,
Andre A. Eggen,
H.C.M. Heuven,
Saadiah Jamli,
Abdullah Johari Jiken,
Christophe Klopp,
Cindy Lawley,
John McEwan,
Patrice Martin,
Carole Moréno,
Philippe Mulsant,
Ibouniyamine Nabihoudine,
Éric Pailhoux,
Isabelle Palhière,
Rachel Rupp,
Julien Sarry,
Brian Sayre,
Aurélie Tircazes,
Jun Wang,
Wen Wang,
Wenguang Zhang
Publication year - 2014
Publication title -
plos one
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.99
H-Index - 332
ISSN - 1932-6203
DOI - 10.1371/journal.pone.0086227
Subject(s) - snp genotyping , dbsnp , biology , snp , genotyping , genome , single nucleotide polymorphism , genetics , bovine genome , tag snp , molecular inversion probe , snp array , sequence assembly , reference genome , genome wide association study , computational biology , genotype , gene , gene expression , transcriptome
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.