Development and characterization of in silico SNP map in pigs

Kyungtag Do 1, Sunjin Moon 1, Zhi-Liang Hu 2, Bong-Hwan Choi 1, Byung-Wook Cho 1, Max Rothschild 2, Heebal Kim 1, James Reecy 2 and Kwan-Suk Kim 1

1. Chungbuk National University, Cheongju, South Korea

2. Department of Animal Science, Center for Integrated Animal Genomics, Iowa State University, 2255 Kildee Hall, Ames, Iowa 50011-3150, USA

(Manuscript in preparation)

ABSTRACT: Over 6,600 pig single nucleotide polymorphisms (SNPs) were currently deposited into the NCBI SNP database. Knowing sequence identity, allelic distribution and chromosomal location of these SNPs is critical for positional QTL mining and commercial application of these polymorphisms. To address these points, we retrieved 5,450 pig SNPs submitted by USMARC and performed Blastx to convert SNP containing sequences into protein sequences and compare against the NCBI protein databases. 457 sequences including 1,308 pig SNPs (24%) were matched with human protein genes with identities more than 80%. 430 porcine protein gene sequences were virtually assigned on the pig-human comparative map available on the PigQTLdb. For utilization of these SNPs for linkage and association studies in commercial populations important to pork production, 194 pig genes sequences containing 449 NCBI pig SNPs on chromosomes 1-7 and 13 were re-sequenced with multiple individuals of Duroc, Berkshire, Landrace, Large White and Korean Native pigs. A total of 309 SNPs from 449 NCBI SNPs were segregating in more than one of the five pig breeds. 82 new SNPs were identified and 151 SNPs were likely to be breed-specific SNPs from the comparative re-sequencing of the five pig breeds. These results will be useful for marker-assisted selection using the QTL information in commercial pig populations and help to differentiate commercial pig breeds at DNA level.

Acknowledgement:

This work was supported by a research program of National Livestock Research Institute, a grant from BioGreen 21 program of Korea Rural Administration (Grant no. 20050401034804), and partly by the U.S. NRSP-8 Bioinformatics Coordination Program.

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