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Genotyping by multiplexed sequencing (GMS): A customizable platform for genomic selection
Travis M Ruff1,2, Elliott J Marston3, Jonathan D Eagle3
1Department of Crop and Soil Sciences, Washington State University, Pullman, Washington, United States of America.
Plos One
|May 2, 2020
Summary
We developed a new PCR-based genotyping method for high-throughput analysis of thousands of single nucleotide polymorphism (SNP) markers. This genotyping by multiplexed sequencing (GMS) approach offers accurate and reliable results, validated against existing technologies.
Area of Science:
- Genetics
- Molecular Biology
- Bioinformatics
Background:
- Genotyping technologies are advancing in throughput and multiplexing.
- High-throughput genotyping is crucial for genetic studies and breeding programs.
Purpose of the Study:
- To introduce a novel, high-throughput, PCR-based genotyping technology.
- To demonstrate a user-friendly bioinformatic pipeline for interpreting genotyping data.
Main Methods:
- A two-step PCR approach for multiplexing thousands of single nucleotide polymorphism (SNP) markers.
- Genotyping by multiplexed sequencing (GMS) protocol tested on Triticum aestivum L. recombinant inbred line (RIL) populations.
- Sequencing compatibility with Ion Torrent and Illumina next-generation sequencing (NGS) platforms.
Main Results:
- The GMS protocol successfully multiplexed 1,656 wheat SNP markers, 207 barley SNP markers, and 49 informative markers, yielding up to 2,433 data points.
- 100% agreement was observed between GMS data and existing Illumina Infinium assay data for two RIL populations.
- Direct sequencing products offer enhanced reliability compared to scatter plot analysis from other methods.
Conclusions:
- The GMS method provides a reliable, high-throughput, and user-friendly solution for SNP genotyping.
- This technology is adaptable to different NGS platforms, offering flexibility for researchers.
- The accuracy and agreement with existing data validate GMS as a robust genotyping approach.
