• 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 begun to sequence normalized cDNA populations generated from RNA from the major organs of the plant. This database will serve as a “reference library” of commonly expressed sequences that will be compared with the expression profiles of nematode-infected roots using a survey technique called RNAseq. We anticipate that nematode infection will change the expression of hundreds, and perhaps thousands of genes. Our future task will be determining which of these changes contributes to resistance. One approach for distinguishing primary determinants of resistance from secondary ones requires us to be able to knockdown expression in SNS of identified candidates. For this reason, we seek to adapt Agrobacterium-mediated gene transfer techniques to SNS so that CRISPR, antisense or RNAi-generating constructs can be introduced. The transgenic plants will then be tested in laboratory or growth chamber conditions for changes in nematode sensitivity.

Minimum Classes: Familiarity with some of the principles of bioinformatics or computer science is desirable, but not necessary. In addition, some familiarity with sterile technique, and/or plant plant tissue culture, and/or a lecture course on genetics or genomics would be beneficial, but again, not required.

Projects: This work will be carried out under the joint guidance of Joe Kuhl (PSES) and myself. We anticipate a part of the student’s time will be spent analyzing new datasets of sequences expressed in uninfected and infected plants in an attempt to identify genes that change expression in response to nematodes.  A majority of the time will be spent assisting on-going efforts to transform SNS both transiently (short-term analysis of transgene expression) and stably (incorporation of transgenes to create heritable changes in metabolic pathways).  This would involve some work with gene cloning, bacteria, and sterile plant tissue culture.

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