High-resolution genotyping via whole genome hybridizations to microarrays containing long oligonucleotide probes

Yan Fu, Nathan M. Springer, Kai Ying, Cheng Ting Yeh, A. Leonardo Iniguez, Todd Richmond, Wei Wu, Brad Barbazuk, Dan Nettleton, Jeff Jeddeloh, Patrick S. Schnable

Research output: Contribution to journalArticlepeer-review

10 Scopus citations

Abstract

To date, microarray-based genotyping of large, complex plant genomes has been complicated by the need to perform genome complexity reduction to obtain sufficiently strong hybridization signals. Genome complexity reduction techniques are, however, tedious and can introduce unwanted variables into genotyping assays. Here, we report a microarray-based genotyping technology for complex genomes (such as the 2.3 GB maize genome) that does not require genome complexity reduction prior to hybridization. Approximately 200,000 long oligonucleotide probes were identified as being polymorphic between the inbred parents of a mapping population and used to genotype two recombinant inbred lines. While multiple hybridization replicates provided,97% accuracy, even a single replicate provided,95% accuracy. Genotyping accuracy was further increased to.99% by utilizing information from adjacent probes. This microarray-based method provides a simple, high-density genotyping approach for large, complex genomes.

Original languageEnglish (US)
Article numbere14178
JournalPloS one
Volume5
Issue number12
DOIs
StatePublished - 2010

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