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.
Highlights
The ability to rapidly determine genotypes at many loci in numerous individuals is critical to furthering our understanding of the inheritance of complex traits and for developing improved strategies for plant breeding
The use of molecular markers based on isozymes, RFLPs, SSRs and CAPS genetic markers allowed for the construction of early genetic maps
There are additional approaches that combine the use of microarrays and restriction digests such as diversity array technology (DArT) [5] and restriction site associated DNA (RAD) tags [6] to assay up to several thousand markers
Summary
The ability to rapidly determine genotypes at many loci in numerous individuals is critical to furthering our understanding of the inheritance of complex traits and for developing improved strategies for plant breeding. The use of molecular markers based on isozymes, RFLPs (restriction fragment length polymorphisms), SSRs (simple sequence repeats) and CAPS (cleaved amplified polymorphic sequences) genetic markers allowed for the construction of early genetic maps These initial genotyping technologies were of relatively low throughput and required significant effort per data point. There are additional approaches that combine the use of microarrays and restriction digests such as diversity array technology (DArT) [5] and restriction site associated DNA (RAD) tags [6] to assay up to several thousand markers These high-throughput approaches vary substantially in number of markers, amount of information required for development, accuracy, ease of application and data analysis. There are limitations on the application of some of these methods to species with large, complex genomes
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