Journal article
A Global View of 54,001 Single Nucleotide Polymorphisms (SNPs) on the Illumina BovineSNP50 BeadChip and Their Transferability to Water Buffalo
International journal of biological sciences, Vol.7(1), pp.18-27
2011
Handle:
https://hdl.handle.net/2376/109758
PMCID: PMC3014552
PMID: 21209788
Abstract
The Illumina BovineSNP50 BeadChip features 54,001 informative single nucleotide polymorphisms (SNPs) that uniformly span the entire bovine genome. Among them, 52,255 SNPs have locations assigned in the current genome assembly (Btau_4.0), including 19,294 (37%) intragenic SNPs (i.e., located within genes) and 32,961 (63%) intergenic SNPs (i.e., located between genes). While the SNPs represented on the Illumina Bovine50K BeadChip are evenly distributed along each bovine chromosome, there are over 14,000 genes that have no SNPs placed on the current BeadChip. Kernel density estimation, a non-parametric method, was used in the present study to identify SNP-poor and SNP-rich regions on each bovine chromosome. With bandwidth = 0.05 Mb, we observed that most regions have SNP densities within 2 standard deviations of the chromosome SNP density mean. The SNP density on chromosome X was the most dynamic, with more than 30 SNP-rich regions and at least 20 regions with no SNPs. Genotyping ten water buffalo using the Illumina BovineSNP50 BeadChip revealed that 41,870 of the 54,001 SNPs are fully scored on all ten water buffalo, but 6,771 SNPs are partially scored on one to nine animals. Both fully scored and partially/no scored SNPs are clearly clustered with various sizes on each chromosome. However, among 43,687 bovine SNPs that were successfully genotyped on nine and ten water buffalo, only 1,159 were polymorphic in the species. These results indicate that the SNPs sites, but not the polymorphisms, are conserved between two species. Overall, our present study provides a solid foundation to further characterize the SNP evolutionary process, thus improving understanding of within- and between-species biodiversity, phylogenetics and adaption to environmental changes.
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- Title
- A Global View of 54,001 Single Nucleotide Polymorphisms (SNPs) on the Illumina BovineSNP50 BeadChip and Their Transferability to Water Buffalo
- Creators
- Vanessa N Michelizzi - 1. Department of Animal Sciences, Washington State University, Pullman, WA 99164-6351, USAXiaolin Wu - 2. Department of Dairy Science, University of Wisconsin-Madison, Madison, WI 53706-1284, USAMichael V Dodson - 1. Department of Animal Sciences, Washington State University, Pullman, WA 99164-6351, USAJennifer J Michal - 1. Department of Animal Sciences, Washington State University, Pullman, WA 99164-6351, USAJorge Zambrano-Varon - 3. Facultad de Medicina Veterinaria y de Zootecnia, Universidad Nacional de Colombia, Bogotá D.C., ColombiaDerek J McLean - 1. Department of Animal Sciences, Washington State University, Pullman, WA 99164-6351, USAZhihua Jiang - 1. Department of Animal Sciences, Washington State University, Pullman, WA 99164-6351, USA
- Publication Details
- International journal of biological sciences, Vol.7(1), pp.18-27
- Academic Unit
- Animal Sciences, Department of; Center for Reproductive Biology
- Publisher
- Ivyspring International Publisher; Sydney
- Identifiers
- 99900547148401842
- Language
- English
- Resource Type
- Journal article