High-throughput SNP discovery and assay development in common bean

Publication Overview
TitleHigh-throughput SNP discovery and assay development in common bean
AuthorsHyten DL, Song Q, Fickus EW, Quigley CV, Lim JS, Choi IY, Hwang EY, Pastor-Corrales M, Cregan PB
TypeJournal Article
Journal NameBMC genomics
Volume11
Year2010
Page(s)475
CitationHyten DL, Song Q, Fickus EW, Quigley CV, Lim JS, Choi IY, Hwang EY, Pastor-Corrales M, Cregan PB. High-throughput SNP discovery and assay development in common bean. BMC genomics. 2010 Aug 16; 11:475.

Abstract

BACKGROUND
Next generation sequencing has significantly increased the speed at which single nucleotide polymorphisms (SNPs) can be discovered and subsequently used as molecular markers for research. Unfortunately, for species such as common bean (Phaseolus vulgaris L.) which do not have a whole genome sequence available, the use of next generation sequencing for SNP discovery is much more difficult and costly. To this end we developed a method which couples sequences obtained from the Roche 454-FLX system (454) with the Illumina Genome Analyzer (GA) for high-throughput SNP discovery.

RESULTS
Using a multi-tier reduced representation library we discovered a total of 3,487 SNPs of which 2,795 contained sufficient flanking genomic sequence for SNP assay development. Using Sanger sequencing to determine the validation rate of these SNPs, we found that 86% are likely to be true SNPs. Furthermore, we designed a GoldenGate assay which contained 1,050 of the 3,487 predicted SNPs. A total of 827 of the 1,050 SNPs produced a working GoldenGate assay (79%).

CONCLUSIONS
Through combining two next generation sequencing techniques we have developed a method that allows high-throughput SNP discovery in any diploid organism without the need of a whole genome sequence or the creation of normalized cDNA libraries. The need to only perform one 454 run and one GA sequencer run allows high-throughput SNP discovery with sufficient sequence for assay development to be performed in organisms, such as common bean, which have limited genomic resources.

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Properties
Additional details for this publication include:
Property NameValue
Journal AbbreviationBMC Genomics
DOI10.1186/1471-2164-11-475
Elocation10.1186/1471-2164-11-475
Language Abbreng
Publication TypeJournal Article
LanguageEnglish
Publication Date2010 Aug 16
Journal CountryEngland
Publication ModelElectronic
ISSN1471-2164
eISSN1471-2164
Publication TypeResearch Support, U.S. Gov't, Non-P.H.S.