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Updated: May 28, 2026
13:33
Infinium Assay for Large-scale SNP Genotyping Applications
Published on: November 19, 2013
Identification of high utility SNPs for population assignment and traceability purposes in the pig using
A M Ramos1, H J Megens, R P M A Crooijmans
1Animal Breeding and Genomics Centre, Wageningen University, Marijkeweg 40, Wageningen, The Netherlands. marcos.ramos23@gmail.com
Animal Genetics
|November 1, 2011
Summary
Researchers developed breed-specific single nucleotide polymorphisms (SNPs) for pigs using next-generation sequencing. These SNPs accurately identify pig breeds, enhancing traceability for animal products.
Area of Science:
- Animal genetics
- Genomics
- Bioinformatics
Background:
- Accurate breed assignment is crucial for livestock traceability and genetic resource management.
- Developing breed-specific genetic markers aids in distinguishing between closely related breeds.
Purpose of the Study:
- To develop and validate breed-specific single nucleotide polymorphisms (SNPs) in five pig breeds.
- To assess the utility of these SNPs for accurate breed assignment and traceability.
Main Methods:
- Sequencing of 153 animals across five pig breeds (Duroc, Landrace, Large White, Pietrain, Wild Boar).
- Bioinformatic analysis to identify high-confidence and breed-specific SNPs using the pig genome build.
- Genotyping using the PorcineSNP60 beadchip and subsequent breed assignment tests.
Main Results:
- Identification of 313,964 high-confidence SNPs, with 29,146 putative breed-specific SNPs.
- Validation of 193 highly breed-specific SNPs.
- Successful breed assignment for 99% of 490 additional individuals with an average probability of 99.2%.
Conclusions:
- Next-generation sequencing is effective for identifying breed-specific SNPs in pigs.
- The validated breed-specific SNPs are highly effective for accurate breed assignment and traceability of pig breeds and products.
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