Identifying SNPs in Pig Genome Sequences
Author Information
Author(s): Kerstens Hindrik HD, Kollers Sonja, Kommadath Arun, del Rosario Marisol, Dibbits Bert, Kinders Sylvia M, Crooijmans Richard P, Groenen Martien AM
Primary Institution: Wageningen University
Hypothesis
Can we effectively identify single nucleotide polymorphisms (SNPs) in pig genome sequences using publicly available data?
Conclusion
The SNP identification method provides thousands of high-quality SNPs, with over 80% of predicted SNPs representing true genetic variation.
Supporting Evidence
- 4.8 million whole genome shotgun sequences were analyzed for SNPs.
- 98,151 unique SNPs were identified in the pig genome.
- Benchmarking showed that 134 out of 163 tested SNPs were polymorphic.
Takeaway
Scientists found a lot of tiny differences in pig DNA that can help us understand genetics better. They used computer tools to look at DNA data from many pigs.
Methodology
The study used a high throughput genome sequence mining pipeline to analyze whole genome shotgun sequences and identify SNPs.
Potential Biases
There may be risks of bias due to the reliance on publicly available data and the computational methods used for SNP identification.
Limitations
The study's SNP predictions may not represent the entire pig genome due to the lack of a complete genome draft and potential clustering errors.
Participant Demographics
The study involved three purebred boar lines and wild boar.
Digital Object Identifier (DOI)
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