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Design and Characterization of a 52K SNP Chip for Goats
文献类型：期刊论文
| 作者 | Tosser-Klopp G[*]1,2; Bardou P1,2,3; Bouchez O1,2,4; Cabau C1,2,3; Crooijmans R5; Dong Y6; Donnadieu-Tonon C1,2,4; Eggen A7; Heuven HCM8; Jamli S9 |
| 刊名 | PLOS ONE
 |
| 出版日期 | 2014 |
| 卷号 | 9期号:1页码:e86227 |
| 通讯作者 | Tosser@toulouse.inra.fr ; atcgnmbi@aliyun.com |
| 合作状况 | 其它 |
| 英文摘要 | 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. |
| 资助信息 | Grants were funded by ANR (http://www.agence-nationale-recherche.fr/), ANR-09-GENM-009-03 GENIDOV, CHEST-454, funded by APIS-GENE; CAPRISNIP programme: UNCEIA, CAPGENES and APIS-GENE French Breeding organizations; and EC’s Seventh Framework Programme, 3SR Integrated Project(Sustainable Solutions for Small Ruminants) http://www.3srbreeding.eu). |
| 收录类别 | SCI |
| 语种 | 英语 |
| WOS记录号 | WOS:000330283100129 |
| 公开日期 | 2014-03-07 ; 2014-03-07 |
| 源URL | [http://159.226.149.42:8088/handle/152453/7810]  |
| 专题 | 昆明动物研究所_基因起源组 昆明动物研究所_遗传资源与进化国家重点实验室 |
| 作者单位 | 1.INRA, UMR444, Laboratoire de Genetique Cellulaire, Castanet-Tolosan, France 2.ENVT, UMR444, Laboratoire de Genetique Cellulaire, Castanet-Tolosan, France 3.INRA, Sigenae, Castanet-Tolosan, France 4.INRA, GeT-PlaGe, Genotoul, Castanet-Tolosan, France 5.Wageningen University, Animal Breeding and Genomics Centre, Wageningen, The Netherlands 6.Kunming Institute of Zoology, Chinese Academy of Sciences, State Key Laboratory of Genetic Resources and Evolution, Kunming, China 7.Illumina Inc., Hayward, California, United States of America 8.Utrecht University, Faculty of Veterinary Medicine, Utrecht, The Netherlands 9.Malaysian Agricultural Research and Development Institute, Strategic Livestock Research Centre, Kuala Lumpur, Malaysia 10.NRA, UR 0875, Mathe ´matiques et Informatique Applique ´es Toulouse, Castanet- Tolosan, France |
| 推荐引用方式 GB/T 7714 | Tosser-Klopp G[*],Bardou P,Bouchez O,et al. Design and Characterization of a 52K SNP Chip for Goats[J]. PLOS ONE,2014,9(1):e86227. |
| APA | Tosser-Klopp G[*].,Bardou P.,Bouchez O.,Cabau C.,Crooijmans R.,...&Zhang WG[*].(2014).Design and Characterization of a 52K SNP Chip for Goats.PLOS ONE,9(1),e86227. |
| MLA | Tosser-Klopp G[*],et al."Design and Characterization of a 52K SNP Chip for Goats".PLOS ONE 9.1(2014):e86227. |
入库方式： OAI收割
来源：昆明动物研究所
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