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United States Department of Agriculture

Agricultural Research Service

Title: A Comparison of the Utility of Snps Discovered by Different Methods

Authors
item Grosz, Michael - MONSANTO, ST. LOUIS
item Tao, Nengbing - MONSANTO, ST. LOUIS
item Cao, Yongwei - MONSANTO, ST. LOUIS
item Snelling, Warren
item Rohrer, Gary
item Byatt, John - MONSANTO, ST. LOUIS

Submitted to: Animal Genetics International Conference Proceedings
Publication Type: Abstract Only
Publication Acceptance Date: July 1, 2004
Publication Date: September 11, 2004
Citation: Grosz, M.D., Tao, N., Cao, Y., Snelling, W.M., Rohrer, G.A., Byatt, J.C. 2004. A comparison of the utility of SNPs discovered by different methods. Proc., 29th International Conference on Animal Genetics (ISAG). 9/11-16/2004. Toyko, Japan. Abstract A009. p. 43.

Technical Abstract: One of the obstacles to generating a high density SNP map of the porcine genome is cost associated with SNP discovery and validation. We compared the efficiency of discovery, validation and mapping of SNPs by three methods. Potential porcine SNPs were identified by 1) clustering of 185,000 EST sequences (eSNP), 2) clustering of genomic sequences from a reduced representation library (rrSNP), and 3) PCR re-sequencing of genomic sequences, using template from 12 unrelated animals of the same line (rsSNP). Potential SNP sequences were masked for repetitive elements and primer extension assays were attempted for 76 eSNP, 78 rrSNP and 178 rsSNP. All SNPs with working assays were genotyped on a "diversity" panel of 184 samples representing eight lines from four breeds (Yorkshire, Landrace, Duroc & Pietrain). The assay conversion efficiency (no. working assays/no. attempted assays) for eSNPs was 0.78, vs. 0.55 & 0.65 for rrSNP and rsSNP, respectively. A larger percentage of eSNPs showed no allelic variation (38%) vs. rrSNP (17%) and rsSW (6%) on the diversity panel. In addition, new SNPs have limited value without information on chromosomal location and relative order of markers. The MARC porcine reference panel was also genotyped to assess the efficiency with which SNPs could be mapped. Of the working assays that had >1% minor allele frequency on the diversity panel, the percentage of eSNP, rrSNP and rsSNP that could be assigned to linkage groups was 47, 77 & 76%, respectively. Low mapping efficiency for eSNPs was because a much larger proportion had no informative meioses. Nonetheless, the poor success of mapping eSNP is offset by much lower discovery costs, compared to rrSNP and rsSNP.

Last Modified: 11/1/2014
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