title: High-resolution genotyping via whole genome hybridizations to microarrays containing long oligonucleotide probes.
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.
authors.affiliation: Department of Agronomy, Iowa State University, Ames, Iowa, United States of America.
authors.forename: Yan
authors.initials: Y
authors.lastname: Fu
authors.forename: Nathan M
authors.initials: NM
authors.lastname: Springer
authors.forename: Kai
authors.initials: K
authors.lastname: Ying
authors.forename: Cheng-Ting
authors.initials: CT
authors.lastname: Yeh
authors.forename: A Leonardo
authors.initials: AL
authors.lastname: Iniguez
authors.forename: Todd
authors.initials: T
authors.lastname: Richmond
authors.forename: Wei
authors.initials: W
authors.lastname: Wu
authors.forename: Brad
authors.initials: B
authors.lastname: Barbazuk
authors.forename: Dan
authors.initials: D
authors.lastname: Nettleton
authors.forename: Jeff
authors.initials: J
authors.lastname: Jeddeloh
authors.forename: Patrick S
authors.initials: PS
authors.lastname: Schnable
mesh_terms: D002874:Chromosome Mapping / Q000379:methods; D032461:Chromosomes, Plant; D017343:Genes, Plant; D016678:Genome; D005838:Genotype; D006824:Hybridization, Genetic; D009693:Nucleic Acid Hybridization; D015345:Oligonucleotide Probes / Q000235:genetics*; D009841:Oligonucleotides / Q000235:genetics; D011110:Polymorphism, Genetic; D015203:Reproducibility of Results; D003313:Zea mays / Q000235:genetics*
chemical_list: D015345:Oligonucleotide Probes; D009841:Oligonucleotides