Queitsch Lab




Department of Genome Sciences
University of Washington
1705 NE Pacific St
Seattle, WA 98195-5065

The Arabidopsis Indel Array

ABSTRACT

Natural variation and induced mutations are important resources for gene discovery and the elucidation of genetic circuits. Mapping such polymorphisms requires rapid and cost-efficient methods for genotyping diverse sets of recombinant inbred lines (RILs) and F2 populations. Here we report the development of a microarray-based method that assesses 240 unique markers in a single hybridization experiment at a cost of less than $50 in materials per line. Our genotyping array is built with 70-mer oligonucleotide elements representing insertion/deletion (indel) polymorphisms between the Arabidopsis thaliana accessions Columbia-0 (Col) and Landsberg erecta (Ler). These indel polymorphisms are recognized with great precision by competitive genomic hybridization, eliminating the need for array replicates and complex statistical analysis. Markers are present genome-wide with an average spacing of ~500kb. PCR primer information is provided for all array indels, allowing for rapid single-locus inquiries. Multi-well chips allow groups of 16 lines to be genotyped in a single experiment. We demonstrate the utility of the array for accurate mapping of recessive mutations, RIL populations, and mixed genetic backgrounds from accessions other than Col and Ler. Given the ease of using shotgun sequencing to generate partial genomic sequences of unsequenced species, this approach is readily transferable to non-model organisms. This work was funded by the NSF Arabidopsis 2010 Project, award number 0313473.

HOW TO ORDER

Printed microarray slides (AL and MPX) are available at cost. Contact cqueitsch@cgr.harvard.edu with "Indel Array" in the subject line.

PROTOCOLS

I. Printing and blocking slides II. DNA purification III. DNA labeling IV. Data analysis