BIOINFORMATIC ANALYSIS OF CDNAS POTENTIALLY INVOLVED IN THORN DEVELOPMENT

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This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. Many plants use thorns as an initial line of defense to prevent consumption by herbivores. Surprisingly little is known about the molecular signals that control prickle development, although it is known that they are composed of a single proliferating outer cell type called the epidermis. It has been suggested that the proliferation of this cell type is controlled by a molecular signaling pathway between the epidermal cells and the underlying cambial tissue. In an interesting contrast, cancer growth is the opposite - an uncontrolled proliferation of cells. If the mechanism underlying thorn growth could be identified by directly comparing gene expression between prickled and prickleless varieties of plants, the mechanisms underlying cancer may be better understood. I propose to use raspberries and blackberries (genus Rubus) as a model system to study the genes implicated in prickle development. These plants are ideal because both produce prickled and prickleless varieties, allowing precise genetic comparisons to be made. Moreover, compounds that prevent cancer tumor growth have already been isolated from Rubus although very little molecular research has been done to date. We are currently preparing and sequencing a subtractive cDNA library contrasting prickled and prickleless Rubus plants. In an effort to elucidate candidate genes, we intend to use a bioinformatic approach which will involve comparing and organizing these ESTs to allow us to identify potential gene candidates that will be subjected to further analysis. The potential gene candidates identified in the analysis will be further tested in subsequent experiments that will provide further evidence as to their role in thorn development and may ultimately help identify gene candidates that control cancer tumor growth. The gene candidates identified will be used as preliminary data to strengthen a proposal for federal funding.