The Smut-sugarcane Interaction as a Model System for the Integration of Marker Discovery and Gene Isolation

Genes that are differentially expressed by resistant sugarcane varieties in response to challenge by pathogens or pests have the potential to be useful in Marker Assisted Selection (MAS) once a link with resistance has been confirmed. Methodologies and resources designed to maximise the discovery of genetic markers and to facilitate the isolation of full-length coding sequences of resistance genes are described. To test the potential of the authors’ approach, the smut-sugarcane interaction was chosen for a preliminary study. Sequence analysis of genes differentially expressed in response to challenge by smut has identified putative receptors involved in the signalling of resistance mechanisms, transcription factors, and enzymes involved in phenylpropanoid-flavonoid metabolism. Fragments having homology with flavonoid pathway transcription factors X1 and P1 were utilised as RFLP probes in a marker discovery effort. A resultant multiple linear regression model included two polymorphisms and explained 26% of the variation in smut resistance ratings within a set of 78 phenotypically well-characterised sugarcane clones. The full-length coding sequence for transcription factor X1 is in the process of being isolated from a PCR amplified cDNA pool using a ‘capture-enrichment’ methodology. Two full-length thaumatin (PR5) antifungal proteincoding sequences have already been isolated and are available for use as transgenes.