Identification and implementation of markers for smut resistance in sugarcane breeding

Sugarcane smut is arguably the most important sugarcane disease. It is present worldwide, complex and, despite extensive study, it is still little understood. Caused by the fungus Sporisorium scitamineum, in a severe epidemic combined with either a susceptible or intermediate variety up to 62% yield loss can occur. Recent studies have shown that resistance is controlled by two major mechanisms, an external resistance probably due to the thickness of bud scale and an internal resistance due to a cascade or defence mechanism that includes the induction of R genes, anti-microbial compounds and increase in lignin at point of pathogen entry. Understanding what triggers this cascade of defence mechanisms and determining how we harness its power to generate resistance in a variety has been a major study area worldwide. The development of the Affymetrix Axiom sugarcane SNP array has enabled whole-genome searches to identify smut resistance regions that can be interrogated for useful markers which can then be implemented into the sugarcane breeding program for selection for resistance. The methods used to date to identify these resistant and susceptible regions of the genome and how we are working to identify the most efficient method to incorporate them into the Australian breeding program are discussed.