Plant & Animal Genomes XIV Conference

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

High-Density Haplotyping With Microarray-Based Single Feature Polymorphism Markers In Arabidopsis

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

¹  University of California-Davis, Department of Plant Sciences, Mail Stop 3, One Shields Ave, Davis, CA 95616, USA

²  Purdue University, Department of Statistics, Mathematical Sciences Building, 150 North University Street, West Lafayette, IN 47907, USA

High-density haplotypes and dense linkage maps for a segregating population can be obtained from gene expression microarrays. RNA samples from 148 Arabidopsis thaliana recombinant inbred lines (RILs) derived from accessions Bayreuth-0 and Shahdara grown in a replicated experiment were hybridized to Affymetrix ATH1 GeneChips, each representing 22,810 genes. The ATH1 GeneChip contains 11 perfect match (PM) oligonucleotides per gene. The PM oligonucleotides were used to detect single feature polymorphisms (SFPs) that rely on differences in hybridization to individual oligonucleotides. We developed a statistic to describe each probe in relation to the other 10 probes within the probe set, which minimizes variation due to differential gene expression that impacts the probe set as a whole. We used two novel approaches to identify SFPs and assign the alleles in the RILs. Capitalizing on the microarray data obtained from biological replicates of inbred parental lines and their respective RILs, our approach identified robust SFP markers in hundreds of genes dispersed throughout the genome. These markers exhibited a low percentage of missing genotype scores and a high concordance between genetic linkage and physical position in the genomic sequence of Col-0. The number of markers that can be identified by this technology allowed identification of the majority of recombination breakpoints in the 148 RILs. The resulting dense haplotypes and high-density linkage map demonstrate that gene expression microarrays on a segregating population can be used to obtain both phenotypic and genotypic information simultaneously.