Plant & Animal Genomes XIV Conference

January 14-18, 2006
Town & Country Convention Center
San Diego, CA

Gene Expression Markers: Using Transcript Levels Obtained From Microarrays To Genotype A Segregating Population

Marilyn A.L. West¹ , Hans van Leeuwen¹ , Alexander Kozik¹ , Daniel J. Kliebenstein¹ , Richard W. Michelmore¹ , R.W. Doerge² , Dina A. St.Clair¹

¹  University of California, Department of Plant Sciences, One Shields Ave., Davis, CA 95616, USA

²  Purdue University, Department of Statistics, West Lafayette, IN 47907, USA

As part of our project on expression QTL mapping in Arabidopsis, we used Affymetrix ATH1 ‘whole genome’ microarrays to measure transcriptional responses in 148 recombinant inbred lines (RILs) derived from a cross between Bayreuth-0 and Shahdara. This population was created and genotyped previously with 38 SSR markers by Loudet et al. (2002). To supplement the existing genotypic data for this population, we obtained expression-based markers from replicated microarrays, which were then used to develop detailed haplotypes for the RILs. These Gene Expression Markers (GEMs) allowed the construction of a high density genetic map of the Bay-0 X Sha RIL population that was directly comparable to the previous map constructed with 38 SSR markers. GEMs capitalize on differences in transcript levels, which can be measured on microarray platforms that are based on either short or long oligonucleotides, or on spotted cDNAs. Since GEMs rely on differences in expression levels, and are not specific to a single type of microarray platform, they are applicable to species for which there are limited genomics resources. We demonstrate that data from the same set of microarrays measured in a segregating population can be used simultaneously to analyze gene expression across the genome, obtain molecular markers, produce dense haplotypes and create a detailed linkage map.