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Infinium Assay for Large-scale SNP Genotyping Applications
Published on: November 19, 2013
Genotyping by genome reducing and sequencing for outbred animals
Qiang Chen1, Yufang Ma, Yumei Yang
1School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China.
Plos One
|July 23, 2013
Summary
Genotyping by genome reducing and sequencing (GGRS) offers a cost-effective solution for single nucleotide polymorphism (SNP) identification in outbred populations. This new method enables high-density SNP discovery and genotyping in species like pigs, overcoming challenges of genetic heterogeneity.
Area of Science:
- Genomics
- Animal Genetics
- Bioinformatics
Background:
- Next-generation sequencing (NGS) is vital for genome-wide genetic marker discovery and genotyping.
- Current NGS methods face challenges in SNP identification for outbred populations due to heterogeneity and phase ambiguity.
- Efficient genotyping of outbred species is crucial for genetic research and breeding programs.
Purpose of the Study:
- To introduce a novel SNP genotyping method, Genotyping by Genome Reducing and Sequencing (GGRS), for outbred species.
- To demonstrate the cost-effectiveness and high reproducibility of the GGRS approach.
- To evaluate GGRS for high-density SNP discovery and genotyping in a large outbred genome.
Main Methods:
- Development of an improved library preparation procedure for GGRS.
- Implementation of a dedicated marker discovery and genotyping pipeline.
- Application and evaluation of GGRS in a large genome pig species (2.8 Gb).
Main Results:
- GGRS successfully genotypes outbred species with high cost-effectiveness and reproducibility.
- The method enabled identification of over 70,000 single nucleotide polymorphisms (SNPs) in pigs.
- SNP discovery and genotyping were achieved at an expenditure of only $80 USD per sample.
Conclusions:
- GGRS provides an efficient and accurate solution for SNP genotyping in genetically diverse outbred populations.
- This method significantly reduces the cost of high-density SNP discovery and genotyping.
- GGRS has broad applicability for genetic studies in various outbred species, including livestock and humans.
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