Development and evaluation of a high-throughput, low-cost genotyping platform based on oligonucleotide microarrays in rice.

ABSTRACT:

Background

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 whole-genome tiling microarrays for genotyping, our method is based on low-cost spotted microarray production, focusing only on known polymorphic features.

Results

We 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 acr

SUBMITTER: Edwards JD 

PROVIDER: S-EPMC2435114 | biostudies-literature | 2008 May

REPOSITORIES: biostudies-literature