High-throughput SNP discovery in common bean
Author Information
Author(s): Hyten David L, Song Qijian, Fickus Edward W, Quigley Charles V, Lim Jong-Sung, Choi Ik-Young, Hwang Eun-Young, Pastor-Corrales Marcial, Cregan Perry B
Primary Institution: U.S. Department of Agriculture, Agricultural Research Service
Hypothesis
Can we develop a method for high-throughput SNP discovery in common bean without a whole genome sequence?
Conclusion
We developed a method that allows high-throughput SNP discovery in common bean using two next generation sequencing techniques.
Supporting Evidence
- A total of 3,487 SNPs were discovered, with 2,795 suitable for assay development.
- 86% of the SNPs validated were likely true SNPs.
- 79% of the designed GoldenGate assays produced working results.
Takeaway
Scientists found a way to quickly identify genetic differences in common beans, which helps improve the plants without needing a complete genetic map.
Methodology
The study used a multi-tier reduced representation library and combined Roche 454-FLX and Illumina GA sequencing for SNP discovery.
Limitations
The method may not be as effective for organisms with more complex genomes or those requiring extensive genomic resources.
Participant Demographics
DNA was isolated from bulk root tissue of 100-150 plants of two common bean genotypes.
Digital Object Identifier (DOI)
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