Application of gene discovery to varietal improvement in sugarcane

Abstract

Recent work has shown that differentially expressed cDNA fragments identified during biotic challenge have great potential as genetic markers for pest and disease resistance in sugarcane. Responses to the smut fungus ( Ustilago scitaminea ), the stalk borer eldana ( Eldana saccharina ) and Sugarcane Mosaic Virus (SCMV) have been the main functional targets to date. Potentially useful cDNAs were identified using SSH and cDNA-AFLP differential display. These were isolated, sequenced and assigned putative functions by comparison with international databases. Using an RFLP approach, fragments with identities suggesting a role in resistance mechanisms were used as probes on a population of 78 sugarcane genotypes used in the breeding programme and well characterised for the traits of interest. Polymorphic markers were scored, and association with phenotype analysed using statistical methods developed in house. A set of 51 probes used for RFLP analysis has yielded 275 polymorphisms to date. Preliminary analyses of the data have identified 69 polymorphisms showing correlation with eldana resistance, 59 with smut, and 35 with SCMV. Most of the probes (76%) yielded at least one RFLP marker associated with smut, eldana or SCMV resistance, illustrating the efficiency of this marker generating strategy. Groups of uncorrelated markers have been found to be associated with each of the resistance traits under investigation, indicating the likelihood that each one represents a different aspect or mechanism of resistance. Markers identified in this project are already being used to devise crosses for the coordinated assembly of resistance factors in progeny. A subset of the most significant markers has been screened against a further collection of 53 varieties in order to extend the capacity of marker-assisted breeding. In addition, newly identified cDNAs are continually being investigated via RFLP screening.