A global view of 54,001 single nucleotide polymorphisms (SNPs) on the Illumina BovineSNP50 BeadChip and their transferability to water buffalo.

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 st

SUBMITTER: Michelizzi VN 

PROVIDER: S-EPMC3014552 | biostudies-literature | 2010 Dec

REPOSITORIES: biostudies-literature