Abstract
BackgroundWe report the development of a microarray platform for rapid and cost-effective genetic mapping, and its evaluation using rice as a model. In contrast to methods employing whole-genome tiling microarrays for genotyping, our method is based on low-cost spotted microarray production, focusing only on known polymorphic features.ResultsWe have produced a genotyping microarray for rice, comprising 880 single feature polymorphism (SFP) elements derived from insertions/deletions identified by aligning genomic sequences of the japonica cultivar Nipponbare and the indica cultivar 93-11. The SFPs were experimentally verified by hybridization with labeled genomic DNA prepared from the two cultivars. Using the genotyping microarrays, we found high levels of polymorphism across diverse rice accessions, and were able to classify all five subpopulations of rice with high bootstrap support. The microarrays were used for mapping of a gene conferring resistance to Magnaporthe grisea, the causative organism of rice blast disease, by quantitative genotyping of samples from a recombinant inbred line population pooled by phenotype.ConclusionWe anticipate this microarray-based genotyping platform, based on its low cost-per-sample, to be particularly useful in applications requiring whole-genome molecular marker coverage across large numbers of individuals.
Highlights
We report the development of a microarray platform for rapid and cost-effective genetic mapping, and its evaluation using rice as a model
Nipponbare and cv. 93-11 genomic sequences revealed 880 indel loci where oligonucleotide probes could be designed with specifications suitable for hybridization (Additional File 1)
The order and positions of the resulting single feature polymorphism (SFP) markers was determined based their positions in the cv
Summary
We report the development of a microarray platform for rapid and cost-effective genetic mapping, and its evaluation using rice as a model. In contrast to methods employing wholegenome tiling microarrays for genotyping, our method is based on low-cost spotted microarray production, focusing only on known polymorphic features. Considerable interest exists in the ability to determine genotypes within species in a cost-effective manner. Costeffectiveness is principally determined by desired outcome: when the outcome is a complete genotypic description of a single individual (for example a human patient), the cost is largely defined by healthcare economics, and is the driving force behind initiatives to minimize the whole genome costs of sequencing [1]. For outcomes in the agricultural sector, for example ones leading to identification of genes responsible for desired agronomic traits, genotyping is applied to large populations rather than single (page number not for citation purposes)
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