Reporting 678 putative cSNPs from full‐length enriched cDNA sequences of the Korean native pig

Abstract

Sequences from the clones of full-length enriched cDNA libraries serve as valuable resources for functional genomic studies. We have analysed 1970 high-quality chromatograms (Phred value >or= 30) that were obtained from sequencing the 5' ends of brainstem, liver, neocortex and spleen clones derived from full-length enriched cDNA libraries from Korean native pigs. In addition, 50,000 pig expressed sequence tag (EST) sequence trace files were obtained from Genbank and combined with our sequencing information to facilitate SNP identification in silico. The process generated 8118 contigs, of which 239 included minimum one sequence from Korean native pig and contained 678 putative coding single nucleotide polymorphisms (cSNPs). Of these, 33 putative cSNPs were randomly selected for confirmatory analysis and validated using 20 pigs from four different breeds (Duroc, Landrace, Yorkshire, Korean native pig). Of the 33 putative cSNPs, 20 were confirmed (61%), which was similar to the frequency reported in other studies. We also identified 15 new cSNPs from the validation process, which were not detected by our in silico analysis. Our study shows that analysing genetically diverse pig breeds including the Korean native pig could serve as a useful strategy for generating a large number of cSNPs.

Simple and comprehensive SLA-DQB1 genotyping using genomic PCR and direct sequencing

“…A total of 350 animals from seven breeds were used, including 106 Korean native (KNP) (38), 64 NIH miniature (39), 112 SNU (Seoul National University) miniature, 20 Duroc, 20 Yorkshire, 20 Landrace, and 8 Berkshire pigs. The SNU miniature pigs (40) were derived from Chicago Medical University miniature pigs which were originated from Minnesota miniature swine (41).…”

Localization of 31 porcine transcripts to the pig genome by SSRH radiation hybrid mapping

“…For sequences either without any available pig sequences (n= 10) or no annotation in the public database, we annotated them by ourselves. Among the 38 transcripts, the polymorphisms of five transcripts including cAMP responsive element binding protein 3 (CREB3), armadillo repeat-containing X-linked protein 1 (ARMCX1), elongation of very long chain fatty acids -like 1 (ELOVL1), pleckstrin homology domain containing, family B member 1 (PLEKHB1) and cold inducible RNA binding protein (CIRBP) were reported from our previous study (Dirisala et al, 2007;Park et al, 2009). The primer sequences and PCR conditions for the mapping of 38 pig transcripts were described in Table 2.…”

“…From the analysis of 1150 pig-genome transcripts which were generated in our previous study (Park et al, 2009) The annotation of sequences for pig transcripts with an asterisk (*) were carried out in this study since either only unannotated sequences or sequences from species other than pig were available in the public database. mapped markers (Farber et al, 2003;Jiang et al, 2003;Cao et al, 2004;Caetano et al, 2005;Cepica et al, 2005;Leeb et al, 2005;Wang et al, 2005;Shimogiri et al, 2006;Yasue et al, 2008;Liu et al, 2008;Ma et al, 2009), designed primers for RH mapping, and performed PCR against the SSRH radiation hybrid cell panel.…”

“…We previously reported the construction of full-length enriched cDNA libraries from Korean native pigs and also reported the discovery of cSNPs (Dirisala et al, 2005;Dirisala et al, 2007;Park et al, 2009). Among the 1150 transcript contigs generated from the previous study, we selected 38 transcripts for mapping based on the confirmation that they have not been mapped by any other Figure 1.…”

Molecular cloning and expression of the IL-10 gene from guinea pigs

“…3). On an average approximately 10 cSNPs per 100 bp of the IL-10 cDNA sequence reported from C4D guinea pigs were identified in comparison with IL-10 sequence from Hartley or Strain 2 which was a much higher rate than those reported from other mammalian species (Kim et al, 2003;Park et al, 2009;The International SNP map Working Group, 2001). Amplification of genomic DNA from C4D, C2D and Hartley generated PCR products of the expected size.…”