Arabidopsis 2010: Array-Based Genotyping: An Affordable Alternative

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An array-based genotyping method will be developed as a tool for Arabidopsis researchers. The current rate-limiting step or mapping mutations in F2 populations and for creating genetic maps of recombinant inbred line populations is that large numbers of individual plants need to be genotyped using several hundred genetic markers. Array-based genotyping permits the simultaneous assessment of many molecular markers, suggesting this approach as a rapid and cost-effective genotyping method. Spotted oligonucleotide glass slide microarrays that can be used to detect approximately 500 insertion/deletion differences (InDel) between the Columbia and Landsberg erecta Arabidopsis accessions will be produced. Once they have been developed, printed oligonucleotide arrays will be made available to the Arabidopsis research community at cost. The DNA sequences of the informative oligonucleotides, marker data for recombinant inbred lines used to test the arrays, and information for ordering printed arrays will be published on the project web site (http://bti.cornell.edu/jander/mapping_array). Publicly available genotyping arrays will promote the goals of the Arabidopsis 2010 program by facilitating the rapid identification of genes based on mutant phenotypes. Student education is an important aspect of this project, and well-defined array experiments will provide excellent undergraduate research opportunities. In addition, this novel genotyping approach can be applied to other organisms with genomes that are too complex for efficient genotyping using currently available array-based methods.