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Abstract

LIGHT1 is a major effect quantitative trait locus (QTL) detected in all light environments controlling hypocotyl elongation in Arabidopsis. In white light, it explains 21 percent of the phenotypic variance between the Landsberg errecta (Ler) and Cape Verde Island (Cvi) accessions. It is inherited semi-dominantly with the Cvi allele conferring elongated hypocotyls under all light conditions tested. Fine mapping of LIGHT1 with near isogenic lines (NILs) reduced the candidate region to about 135 kb comprising 34 genes. We confirmed that there was only this region from Cvi present in the Ler background of NIL189 using DNA hybridization to Affymetrix ATH1 arrays. In this interval there are no known light signaling, or previously characterized genes. To identify candidate genes, we extracted triplicate RNA samples at midday from 5 day-old seedlings of either Ler or NIL189, and hybridized them to ATH1 arrays. Of the 67 genes that were significantly differentially expressed between NIL189 and Ler, one gene fell in the LIGHT1 interval. We named this gene UNCHARACTERIZED LIGHT SIGNALING (ULS) since this single copy gene, which is conserved in other plant species, encodes an uncharacterized molecular function. Expression of ULS decreased in NIL189 compared to Ler. ULS is also the only gene in the LIGHT1 interval that is circadian regulated. Among the other 66 genes, the gene encoding the DET1 interactor DDB1B is the gene with the strongest change in expression, suggesting LIGHT1 may play a role in the DET1 pathway. We also tested homozygous T-DNA insertions of 22/34 genes in the LIGHT1 interval, and coincidently uls was the only mutant to display an interesting light-related phenotype. There is only a single nucleotide difference in the coding sequence of ULS between Ler and Cvi, causing a non-synonymous amino acid substitution, with the Cvi sequence at this position being the same as that of the Columbia (Col) reference strain. The Col and Cvi amino acid is conserved in both tomato and potato, while the Ler amino acid change is found as a medium frequency allele in Arabidopsis thaliana accessions (10/96). Multiple lines of evidence thus suggest that ULS is responsible for the LIGHT1 QTL. Quantitative complementation experiments for further confirmation are in progress.