Design and characterization of a 52K SNP chip for goats.
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.
INRA, UMR444, Laboratoire de Génétique Cellulaire, Castanet-Tolosan, France ; ENVT, UMR444, Laboratoire de Génétique Cellulaire, Castanet-Tolosan, France.
Gwenola
G
Tosser-Klopp
INRA, UMR444, Laboratoire de Génétique Cellulaire, Castanet-Tolosan, France ; ENVT, UMR444, Laboratoire de Génétique Cellulaire, Castanet-Tolosan, France ; INRA, Sigenae, Castanet-Tolosan, France.
Philippe
P
Bardou
INRA, UMR444, Laboratoire de Génétique Cellulaire, Castanet-Tolosan, France ; ENVT, UMR444, Laboratoire de Génétique Cellulaire, Castanet-Tolosan, France ; INRA, GeT-PlaGe, Genotoul, Castanet-Tolosan, France.
Olivier
O
Bouchez
INRA, UMR444, Laboratoire de Génétique Cellulaire, Castanet-Tolosan, France ; ENVT, UMR444, Laboratoire de Génétique Cellulaire, Castanet-Tolosan, France ; INRA, Sigenae, Castanet-Tolosan, France.
Cédric
C
Cabau
Wageningen University, Animal Breeding and Genomics Centre, Wageningen, The Netherlands.
Richard
R
Crooijmans
Kunming Institute of Zoology, Chinese Academy of Sciences, State Key Laboratory of Genetic Resources and Evolution, Kunming, China.
Yang
Y
Dong
INRA, UMR444, Laboratoire de Génétique Cellulaire, Castanet-Tolosan, France ; ENVT, UMR444, Laboratoire de Génétique Cellulaire, Castanet-Tolosan, France ; INRA, GeT-PlaGe, Genotoul, Castanet-Tolosan, France.
Cécile
C
Donnadieu-Tonon
Illumina Inc., Hayward, California, United States of America.
André
A
Eggen
Utrecht University, Faculty of Veterinary Medicine, Utrecht, The Netherlands.
Henri C M
HC
Heuven
Malaysian Agricultural Research and Development Institute, Strategic Livestock Research Centre, Kuala Lumpur, Malaysia.
Saadiah
S
Jamli
Malaysian Agricultural Research and Development Institute, Strategic Livestock Research Centre, Kuala Lumpur, Malaysia.
Abdullah Johari
AJ
Jiken
INRA, Sigenae, Castanet-Tolosan, France ; INRA, UR 0875, Mathématiques et Informatique Appliquées Toulouse, Castanet-Tolosan, France.
Christophe
C
Klopp
Illumina Inc., Hayward, California, United States of America.
Cynthia T
CT
Lawley
AgResearch, Invermay Agricultural Center, Mosgiel, New Zealand.
John
J
McEwan
INRA, UMR1313 Génétique Animale et Biologie Intégrative, Jouy en Josas, France ; AgroParisTech, UMR 1313 Génétique Animale et Biologie Intégrative, Jouy en Josas, France.
Patrice
P
Martin
INRA, UPR0631, Station d'Amélioration Génétique des Animaux, Castanet-Tolosan, France.
Carole R
CR
Moreno
INRA, UMR444, Laboratoire de Génétique Cellulaire, Castanet-Tolosan, France ; ENVT, UMR444, Laboratoire de Génétique Cellulaire, Castanet-Tolosan, France.
Philippe
P
Mulsant
INRA, UMR444, Laboratoire de Génétique Cellulaire, Castanet-Tolosan, France ; ENVT, UMR444, Laboratoire de Génétique Cellulaire, Castanet-Tolosan, France ; INRA, Sigenae, Castanet-Tolosan, France.
Ibouniyamine
I
Nabihoudine
INRA, UMR1198 Biologie du Développement et Reproduction, Jouy en Josas, France ; ENVA, UMR1198 Biologie du Développement et Reproduction, Jouy en Josas, France.
Eric
E
Pailhoux
INRA, UPR0631, Station d'Amélioration Génétique des Animaux, Castanet-Tolosan, France.
Isabelle
I
Palhière
INRA, UPR0631, Station d'Amélioration Génétique des Animaux, Castanet-Tolosan, France.
Rachel
R
Rupp
INRA, UMR444, Laboratoire de Génétique Cellulaire, Castanet-Tolosan, France ; ENVT, UMR444, Laboratoire de Génétique Cellulaire, Castanet-Tolosan, France.
Julien
J
Sarry
Virginia State University, Department of Biology, Petersburg, Virginia, United States of America.
Brian L
BL
Sayre
INRA, UPR0631, Station d'Amélioration Génétique des Animaux, Castanet-Tolosan, France.
Aurélie
A
Tircazes
Bejing Genome Institute, BGI-Shenzhen, Shenzhen, China.
Jun Wang
Kunming Institute of Zoology, Chinese Academy of Sciences, State Key Laboratory of Genetic Resources and Evolution, Kunming, China ; Bejing Genome Institute, BGI-Shenzhen, Shenzhen, China.
Wen
W
Wang
Kunming Institute of Zoology, Chinese Academy of Sciences, State Key Laboratory of Genetic Resources and Evolution, Kunming, China ; Inner Mongolia Agricultural University, Inner Mongolia Key Laboratory of Animal Genetics, Breeding and Reproduction, Hohhot, Inner Mongolia, China.
Wenguang
W
Zhang
D000818:Animals; D001947:Breeding; D016678:Genome; D023281:Genomics; D006041:Goats / Q000145:classification / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods; D020641:Polymorphism, Single Nucleotide; D015203:Reproducibility of Results