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Updated: Jun 27, 2026
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Novel Sequence Discovery by Subtractive Genomics
Published on: January 25, 2019
SNP discovery in swine by reduced representation and high throughput pyrosequencing
Ralph T Wiedmann1, Timothy P L Smith, Dan J Nonneman
1USDA, ARS, US Meat Animal Research Center, State Spur 18D, NE 68933-0166, USA. ralph.wiedmann@ars.usda.gov
BMC Genetics
|December 6, 2008
Summary
Researchers identified over 115,000 pig single nucleotide polymorphisms (SNPs) using pyrosequencing. This efficient method provides a high-quality resource for swine genetic research and breeding programs.
Area of Science:
- Genomics
- Animal Genetics
- Bioinformatics
Background:
- Limited sequence variation data available for pigs.
- Previous cattle SNP discovery methods were constrained by incomplete swine genome sequence.
- Longer-read sequencing technologies offer potential for swine SNP discovery.
Purpose of the Study:
- To discover a large number of single nucleotide polymorphisms (SNPs) in pigs.
- To develop a resource for swine genetic research and breeding.
- To validate the efficiency of a specific sequencing approach for SNP discovery.
Main Methods:
- Utilized reduced representation of porcine genomic fragments (450 bp) from a pool of 26 animals.
- Employed GS-FLX instrument for pyrosequencing, generating 240 bp reads.
- Assembled sequence reads into contigs and identified SNPs based on allele frequency.
Main Results:
- Generated approximately 5 million sequence reads, assembled into 47,830 contigs with 7.65-fold coverage.
- Identified 115,572 SNPs, with 43% mapping to known pig chromosomes.
- Validated 95.5% of a sample of 176 putative SNPs, confirming segregating alleles.
Conclusions:
- The pyrosequencing approach proved efficient for discovering numerous porcine SNPs.
- Identified SNPs possess a high validation rate and suitable minor allele frequency for genotyping.
- The discovered SNPs will support an international collaboration for a high-throughput swine genotyping assay.
Related Concept Videos
01:05Single Nucleotide Polymorphisms-SNPs
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