• Name: Allan Caplan, Ph.D.
  • Institution: University of Idaho
  • Department: Plant, Soil, and Entomological Sciences
  • Phone: 208-885-9441
  • Email: acaplan@uidaho.edu

Summary: Solanum sisymbriifolium, more commonly called sticky nightshade (SNS) or litchi tomato, is naturally resistant to the nematode species, Globodera pallida, that parasitizes potatoes and a few other crops. The goal of this research is to characterize this process of resistance and to clone some of the genes responsible for it. The underlying hope is that introducing these genes into potatoes, or modifying the potato’s own genes to act like those of SNS, could shape an equally effective pathway in this economically pivotal crop. However, not only is little known about the biology of SNS, but very few SNS genes have been cloned or characterized at all. Instead of sequencing the entire nuclear genome, which we have estimated is as large as that of tetraploid potatoes, and therefore capable of encoding twice as many proteins as the human genome, we have sequenced normalized cDNA collections generated from RNA from the major organs of the plant. This database serves as a “reference library” of commonly expressed sequences.  We then compared the expression of these genes in nematode-infected roots with the expression of those same genes in our reference library.  Even after setting very stringent statistical criteria for which of the observed changes was most likely to matter, we were left with 277 candidate genes.  One approach for distinguishing primary determinants of resistance from secondary ones requires us to be able to knockdown expression of identified candidates in SNS. For this reason, we are trying to adapt Agrobacterium-mediated gene transfer techniques to SNS so that CRISPR, antisense or RNAi-generating constructs can be introduced. In parallel, we also want to clone these candidates and express them in potatoes so their effects on pathogen resistance can be tested.

Minimum Classes: Familiarity with some of the most basic principles of bioinformatics or computer science is desirable, but not necessary. In addition, some familiarity with sterile technique, and/or plant tissue culture, and/or a lecture course on genetics or genomics would be beneficial, but again, not required.  An enthusiasm for research into eukaryotic Molecular Biology would be greatly appreciated.

Projects: A majority of the time will be spent cloning genes from cDNA preparations, analyzing genes using simple computer software, and using Agrobacterium tumefasciens to introduce the cloned genes into plants.  The tools and aims of this work are commonly used in all eukaryotic molecular research.

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