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KMID : 1094720070120040424
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Biotechnology and Bioprocess Engineering
2007 Volume.12 No. 4 p.424 ~ p.432
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Discovery of cSNPs in pig using full-length enriched cDNA libraries of the Korean native pig as a source of genetic diversity
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Dirisala Vijaya
Kim Ju-Hyun
Park Kwang-Ha
Lee Hoon-Taek
Park Chan-Kyu
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Abstract
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Clones from full-length enriched cDNA libraries serve as valuable resources for functional genomic studies. We analyzed 3.210 chromatograms obtained from sequencing the 5′-ends of brainstem, liver, neocortex, and spleen clones derived from full-length enriched cDNA libraries of Korean native pigs. In addition, 50,000 pig EST sequence trace files were obtained from Genbank and combined with our sequencing information for SNP identificationin silico. For the SNP analysis, neocortex, and liver libraries were newly constructed, whereas the sequencing results from brainstem and spleen libraries were from previously constructed libraries. The putative SNPs from thein silico analysis were confirmed by genomic PCR from a group of 20 pigs of four different breeds. Using this approach, 86% of cSNPs identifiedin silico were confirmed and the SNP detection frequency was 1 SNP per 338 bp. Interestingly, we found a valine deletion at amino acid position 126 of the neuronal and endocrine protein gene in the Korean native pig. We confirmed that this deletion was caused by alternative splicing at the NAGNAG acceptors. Our study shows that large-scale EST sequencing of Korean native pigs can be effectively employed for natural polymorphism-based pig genome analysis.
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KEYWORD
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SNP, Korean native pig, full-length cDNA libraries, NAGNAG acceptor, alternative spliding
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