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United States Department of Agriculture

Agricultural Research Service

Title: In Silico Discovery, Mapping, and Genotyping of 1,039 Cattle Snps on a Panel of Eighteen Breeds

Authors
item Donthu, Ravikiran - UNIV OF ILLINOIS
item Larkin, Denis - UNIV OF ILLINOIS
item Heaton, Michael
item Lewin, Harris - UNIV OF ILLINOIS

Submitted to: Plant and Animal Genome Conference Proceedings
Publication Type: Abstract Only
Publication Acceptance Date: November 1, 2005
Publication Date: January 14, 2006
Citation: Donthu, R., Larkin, D.M., Heaton, M.P., Lewin, H.A. 2006. In silico discovery, mapping, and genotyping of 1,039 cattle SNPs on a panel of eighteen breeds [abstract]. Plant and Animal Genome Conference Proceedings. p. 235.

Technical Abstract: To contribute to cattle haplotype map construction we discovered ~3,000 putative single nucleotide polymorphisms (SNPs) by comparison of repeat-masked BAC-end sequences (BESs) from the cattle RPCI-42 BAC library with the cattle whole-genome shotgun (WGS) contigs. For the sequence alignment, the TimeLogic tera-BLASTn was used with e-value of E-50 as a threshold. Alignments were parsed using Perl scripts for identification of putative SNP positions. Phred scores greater than or equal to 30 were allowed for the SNP base in BESs, and greater than or equal to 60 for the SNP base in the WGS contigs. For SNP-containing sequences COMPASS, an in silico comparative mapping tool, was used to assign SNPs to positions on the cattle chromosomes. In total, 2,031 SNPs were assigned to cattle chromosomes, with 1 SNP every ~1.5 Mbp on average. Genotyping of a set of SNPs was performed using the Illumina platform and a DNA panel containing 188 samples from 18 cattle breeds, including 43 trios. Of 1,039 SNPs, 1,001 were found informative for at least one breed in the panel. Although sample size was limited, minor allele frequency of these SNPs was not less than .25. Frequency of scorable genotypes was 95.5% and heritability in sample trios was 99.5%, thus demonstrating high accuracy of the genotyping. All of SNP sequences positioned to BTAX by COMPASS were assigned to BTAX by the genotyping system. Our set of in silico and confirmed SNPs, thus forms a reliable resource for genetic analysis in cattle breeds and contributes significantly to the achievement of the goal of construction of high-density cattle haplotype map.

Last Modified: 8/22/2014
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