| Plants have evolved an elaborate signaling network to sense and respond to their light environment. The photoreceptors trigger downstream events to coordinate developmental responses with daily and seasonal light cues. Plants native to different light environments may have adapted creating a natural diversity that can be exploited to discover new genes involved in light signaling and to learn about the molecular basis of evolution. A survey of the light response trait, hypocotyl length, in seven light and hormone environments across 140 accessions of Arabidopsis thaliana was conducted. Variation exists within and among known photoreceptor pathways as well as in the PHYTOCHROME A photoreceptor itself. Twelve Quantitative Trait Loci (QTL) across seven environments were mapped between two accessions. Some QTL act broadly across light environments where as some act in specific light conditions. Epistatic interactions were also identified. Most QTL define new light response loci while one QTL maps to be the PHYTOCHROME B photoreceptor. Linkage disequilibrium (LD) mapping uses historical recombination events and may allow fine mapping of QTL. The extent of LD in Arabidopsis was found to be variable across the genome in the range of approximately 1cM (50–250kb). In order to develop a fine scale LD map for Arabidopsis a high resolution genotyping method has been developed based on DNA hybridization to expression based oligo-nucleotide arrays. Greater than 14,000 single feature polymorphisms (SFPs) have been identified among 5 accessions. Applications of this approach can be extended to improve candidate gene selection, assist in mapping mutations, and control for background differences in expression analysis. |
