Identification of genes differentially expressed in sugar beet roots in response to challenge by polymyxa graminis

Representational difference analysis (RDA) was used to identify expressed sequence tags (ESTs) differentially expressed in sugar beet roots in response to challenge by the ‘non-host’ parasite Polymyxa graminis. Sequence analysis using BLASTX against the GenBank sequence database of the RDA ESTs identified 43 unigene sequences of which 27 were homologous to plant genes, including 14 with roles in defence, and 16 sequences had unknown functions. PCR analysis confirmed that all of the uni-gene sequences were derived from sugar beet except EST BvNH1E4 which was specific to P. graminis. Semi-quantitative RT-PCR analysis of six of the ESTs (three with putative functions implicated in defence and three with no matches to the GenBank database) demonstrated up-regulation during the first hour in response to the non-host parasite. Results from these experiments, including details of in silico analysis of the ESTs of unknown function, are discussed