URGI IWGSC Sequence Repository as a Tool for Addressing and Solving Specific Molecular Issues: The DRF1 Gene Promoter in Durum Wheat

A drought related gene belonging to the DREB gene family was isolated in durum wheat. The characterization included the expression of its transcripts, the evaluation of polymorphisms in a large number of durum wheat varieties, phylogenetic studies involving ancestors and related species, a possible relationship between an identified transposon encompassing the coding sequence and the gene evolution.

Studies are in progress to use the gene sequence for developing a marker related to agronomical traits. During the marker characterization, the sequence of the upstream 5' region became necessary for understanding some molecular data. Because the molecular strategy for genome walking is expensive and time consuming, a bioinformatic approach was used, based on IWGSC Sequence Repository at URGI (http://urgi.versailles.inra.fr/Platform).

Using the URGI BLAST tool, it was found that the DRF1 gene was located on Chromosome 1. When relevant contig sequences became available, it was possible to analyze the region located upstream 5’UTR. The various specific signals suggesting a promoter were identified and the sequences in the three genomes were compared and differences identified.

Using above sequence information, ad hoc primers were designed and the corresponding portion of the promoters were quickly cloned and sequenced in our durum wheat variety. In conclusion, the knowledge of the complete DRF1 gene structure has been improved, allowing the identification of the two corresponding copies in the two genomes (A and B) and their chromosome location. Furthermore, it was possible to describe a coherent frame accounting for the previous confounding molecular data.