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Abstract:
We have previously surveyed Arabidopsis accessions for variation in hypocotyl length light response (Maloof et al, 2001) and performed Quantitative Trait Locus (QTL) analysis in the Cvi/Ler RILs (Borevitz et al, 2002). Major QTL include a novel locus LIGHT1, and a locus where PHYTOCHROME B (PHYB) is a candidate gene. Sequence variation at PHYB revealed several candidate amino acid changes however less than would be expected had PHYB been evolving neutrally (McDonald-Kreitman: p=0.027). Two nonsynonymous changes in PHYB are significantly associated with hypocotyl length across accessions. A survey of 163 genome wide SNPs provided no evidence of long range linkage disequilibrium (LD) nor of population structure among 73 accessions, indicating that LD mapping could be used to fine map QTL (Nordborg et al, 2002). In addition SNP108 was significantly associated with hypocotyl length and mapped to LIGHT1. Results from a high resolution LD mapping study at LIGHT1 will be presented. If QTL are determined by gene expression variation, this could be detected using global transcription analysis. We profiled three day old seedlings of the LIGHT1 NIL and parental Ler and Cvi lines. Significant transcription variation, mapping to the LIGHT1 interval, was identified. In order to identify thousands of markers for genome wide LD and traditional mapping and to remove hybridization noise from transcription analysis across accessions we developed a genotyping method using Affymetrix GeneChips. Nearly 4000 Single Feature Polymorphisms (SFPs) were identified between Col and Ler at a 5% false positive rate. Bulk segregant analysis with chip genotyping was used to map a known mutation. 105 potential gene deletions were identified, including transposons, disease resistance genes (R genes), genes involved in secondary metabolism, and other potential QTL candidate genes. Linkage Disequilibrium mapping, transcription profiling, and chip genotyping techniques are being used to identify QTL.
