Cargando…

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...

Descripción completa

Detalles Bibliográficos
Autores principales: Tosser-Klopp, Gwenola, Bardou, Philippe, Bouchez, Olivier, Cabau, Cédric, Crooijmans, Richard, Dong, Yang, Donnadieu-Tonon, Cécile, Eggen, André, Heuven, Henri C. M., Jamli, Saadiah, Jiken, Abdullah Johari, Klopp, Christophe, Lawley, Cynthia T., McEwan, John, Martin, Patrice, Moreno, Carole R., Mulsant, Philippe, Nabihoudine, Ibouniyamine, Pailhoux, Eric, Palhière, Isabelle, Rupp, Rachel, Sarry, Julien, Sayre, Brian L., Tircazes, Aurélie, Jun Wang, Wang, Wen, Zhang, Wenguang
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3899236/
https://www.ncbi.nlm.nih.gov/pubmed/24465974
http://dx.doi.org/10.1371/journal.pone.0086227
_version_ 1782300540562046976
author Tosser-Klopp, Gwenola
Bardou, Philippe
Bouchez, Olivier
Cabau, Cédric
Crooijmans, Richard
Dong, Yang
Donnadieu-Tonon, Cécile
Eggen, André
Heuven, Henri C. M.
Jamli, Saadiah
Jiken, Abdullah Johari
Klopp, Christophe
Lawley, Cynthia T.
McEwan, John
Martin, Patrice
Moreno, Carole R.
Mulsant, Philippe
Nabihoudine, Ibouniyamine
Pailhoux, Eric
Palhière, Isabelle
Rupp, Rachel
Sarry, Julien
Sayre, Brian L.
Tircazes, Aurélie
Jun Wang,
Wang, Wen
Zhang, Wenguang
author_facet Tosser-Klopp, Gwenola
Bardou, Philippe
Bouchez, Olivier
Cabau, Cédric
Crooijmans, Richard
Dong, Yang
Donnadieu-Tonon, Cécile
Eggen, André
Heuven, Henri C. M.
Jamli, Saadiah
Jiken, Abdullah Johari
Klopp, Christophe
Lawley, Cynthia T.
McEwan, John
Martin, Patrice
Moreno, Carole R.
Mulsant, Philippe
Nabihoudine, Ibouniyamine
Pailhoux, Eric
Palhière, Isabelle
Rupp, Rachel
Sarry, Julien
Sayre, Brian L.
Tircazes, Aurélie
Jun Wang,
Wang, Wen
Zhang, Wenguang
author_sort Tosser-Klopp, Gwenola
collection PubMed
description 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.
format Online
Article
Text
id pubmed-3899236
institution National Center for Biotechnology Information
language English
publishDate 2014
publisher Public Library of Science
record_format MEDLINE/PubMed
spelling pubmed-38992362014-01-24 Design and Characterization of a 52K SNP Chip for Goats Tosser-Klopp, Gwenola Bardou, Philippe Bouchez, Olivier Cabau, Cédric Crooijmans, Richard Dong, Yang Donnadieu-Tonon, Cécile Eggen, André Heuven, Henri C. M. Jamli, Saadiah Jiken, Abdullah Johari Klopp, Christophe Lawley, Cynthia T. McEwan, John Martin, Patrice Moreno, Carole R. Mulsant, Philippe Nabihoudine, Ibouniyamine Pailhoux, Eric Palhière, Isabelle Rupp, Rachel Sarry, Julien Sayre, Brian L. Tircazes, Aurélie Jun Wang, Wang, Wen Zhang, Wenguang PLoS One Research Article 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. Public Library of Science 2014-01-22 /pmc/articles/PMC3899236/ /pubmed/24465974 http://dx.doi.org/10.1371/journal.pone.0086227 Text en © 2014 Tosser-Klopp et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Tosser-Klopp, Gwenola
Bardou, Philippe
Bouchez, Olivier
Cabau, Cédric
Crooijmans, Richard
Dong, Yang
Donnadieu-Tonon, Cécile
Eggen, André
Heuven, Henri C. M.
Jamli, Saadiah
Jiken, Abdullah Johari
Klopp, Christophe
Lawley, Cynthia T.
McEwan, John
Martin, Patrice
Moreno, Carole R.
Mulsant, Philippe
Nabihoudine, Ibouniyamine
Pailhoux, Eric
Palhière, Isabelle
Rupp, Rachel
Sarry, Julien
Sayre, Brian L.
Tircazes, Aurélie
Jun Wang,
Wang, Wen
Zhang, Wenguang
Design and Characterization of a 52K SNP Chip for Goats
title Design and Characterization of a 52K SNP Chip for Goats
title_full Design and Characterization of a 52K SNP Chip for Goats
title_fullStr Design and Characterization of a 52K SNP Chip for Goats
title_full_unstemmed Design and Characterization of a 52K SNP Chip for Goats
title_short Design and Characterization of a 52K SNP Chip for Goats
title_sort design and characterization of a 52k snp chip for goats
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3899236/
https://www.ncbi.nlm.nih.gov/pubmed/24465974
http://dx.doi.org/10.1371/journal.pone.0086227
work_keys_str_mv AT tosserkloppgwenola designandcharacterizationofa52ksnpchipforgoats
AT bardouphilippe designandcharacterizationofa52ksnpchipforgoats
AT bouchezolivier designandcharacterizationofa52ksnpchipforgoats
AT cabaucedric designandcharacterizationofa52ksnpchipforgoats
AT crooijmansrichard designandcharacterizationofa52ksnpchipforgoats
AT dongyang designandcharacterizationofa52ksnpchipforgoats
AT donnadieutononcecile designandcharacterizationofa52ksnpchipforgoats
AT eggenandre designandcharacterizationofa52ksnpchipforgoats
AT heuvenhenricm designandcharacterizationofa52ksnpchipforgoats
AT jamlisaadiah designandcharacterizationofa52ksnpchipforgoats
AT jikenabdullahjohari designandcharacterizationofa52ksnpchipforgoats
AT kloppchristophe designandcharacterizationofa52ksnpchipforgoats
AT lawleycynthiat designandcharacterizationofa52ksnpchipforgoats
AT mcewanjohn designandcharacterizationofa52ksnpchipforgoats
AT martinpatrice designandcharacterizationofa52ksnpchipforgoats
AT morenocaroler designandcharacterizationofa52ksnpchipforgoats
AT mulsantphilippe designandcharacterizationofa52ksnpchipforgoats
AT nabihoudineibouniyamine designandcharacterizationofa52ksnpchipforgoats
AT pailhouxeric designandcharacterizationofa52ksnpchipforgoats
AT palhiereisabelle designandcharacterizationofa52ksnpchipforgoats
AT rupprachel designandcharacterizationofa52ksnpchipforgoats
AT sarryjulien designandcharacterizationofa52ksnpchipforgoats
AT sayrebrianl designandcharacterizationofa52ksnpchipforgoats
AT tircazesaurelie designandcharacterizationofa52ksnpchipforgoats
AT junwang designandcharacterizationofa52ksnpchipforgoats
AT wangwen designandcharacterizationofa52ksnpchipforgoats
AT zhangwenguang designandcharacterizationofa52ksnpchipforgoats
AT designandcharacterizationofa52ksnpchipforgoats