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ARS Home » Plains Area » Clay Center, Nebraska » U.S. Meat Animal Research Center » Livestock Bio-Systems » Research » Publications at this Location » Publication #233170

Title: SNP Discovery in Swine by Reduced Representation and High Throughput Pyrosequencing

item Nonneman, Danny - Dan
item Wiedmann, Ralph
item Smith, Timothy - Tim

Submitted to: Plant and Animal Genome Conference Proceedings
Publication Type: Abstract Only
Publication Acceptance Date: 12/1/2008
Publication Date: 1/10/2009
Citation: Nonneman, D.J., Wiedmann, R.T., Smith, T.P. 2009. SNP Discovery in Swine by Reduced Representation and High Throughput Pyrosequencing. Plant and Animal Genome Conference XVII Proceedings. 1/10-14/2009, San Diego, CA. Abstract P531.

Interpretive Summary:

Technical Abstract: Relatively little information is available for sequence variation in the pig. Because reduced representation reduces the complexity of the genome being sampled by orders of magnitude and samples identical regions dispersed across the genome, it is an ideal strategy for SNP discovery in a species without a complete genome sequence. Longer-read pyrosequencing-based technologies can provide sufficient flanking sequence information for assay design. Swine SNP were discovered in this study using a reduced representation of 450 bp porcine genomic fragments (approximately 4% of the swine genome) prepared from a pool of 26 animals relevant to current pork production, and a GS-FLX instrument producing 240 bp reads. Approximately 5 million sequence reads were collected and assembled into contigs having an overall observed depth of 7.65-fold coverage. The approximate minor allele frequency was estimated from the number of observations of alternate alleles. The average coverage at the SNPs was 12.6-fold. This approach identified 115,572 SNPs in 47,830 contigs. Comparison to partial swine genome draft sequence indicated 49,879 SNP (43%) and 22,045 contigs (46%) mapped to a position on a sequenced pig chromosome. A sample of 176 putative SNPs were examined and 168 (95.5%) were confirmed to have segregating alleles; the correlation of the observed minor allele frequency (MAF) to that predicted from the sequence data was 0.58. The process was a highly efficient means to identify a large number of porcine SNP having high validation rate to be used in an ongoing international collaboration to produce a highly parallel genotyping assay for swine.