High-Resolution Genotyping via Whole Genome Hybridizations to Microarrays Containing Long Oligonucleotide Probes

Date
2010-12-01
Authors
Fu, Yan
Nettleton, Dan
Springer, Nathan
Ying, Kai
Yeh, Cheng-Ting
Iniguez, A. Leonardo
Richmond, Todd
Wu, Wei
Barbazuk, Brad
Nettleton, Dan
Jeddeloh, Jeff
Schnable, Patrick
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Statistics
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Agronomy
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StatisticsAgronomyGenetics, Development and Cell BiologyGenetics and GenomicsCenter for Plant Genomics
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.

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This article is published as Fu Y, Springer NM, Ying K, Yeh C-T, Iniguez AL, Richmond T, et al. (2010) High-Resolution Genotyping via Whole Genome Hybridizations to Microarrays Containing Long Oligonucleotide Probes. PLoS ONE 5(12): e14178. doi: 10.1371/journal.pone.0014178.

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