Abstract

SNP discovery using PolyBayes was performed using 810 k EST sequences generated by the Danish-Chinese Pig Genome Sequencing Initiative. While focusing only on high-quality SNP prediction disregards potentially interesting medium-quality SNPs as candidates we show that, by careful inspection of chromatograms, more than 61% of the bi-allelic candidates were valid and not predicted due to sequencing artifacts. Exemplarily, selected candidate SNPs were genotyped on a breed panel and average minor allele frequencies were calculated to show that candidates derived from medium-quality SNP predictions represent an additional resource for SNP maps or genome-wide QTL scans. Additionally, medium-quality SNPs were compared to the Pig EST Data Explorer database as an independent dataset.

F. Panitz, H. Stengaard, A. Hoj, C. Bendixen

Proceedings of the World Congress on Genetics Applied to Livestock Production, Volume , , 23.20, 2006