Expression profiling of transcripts associated with defense responses during pathogenesis of red rot pathogen Colletotrichum falcatum in sugarcane using Affymetrix GeneChip Sugarcane Genome Array

Abstract

Sugarcane is an economically important crop cultivated widely in tropical and sub-tropical regions of the world for sugar and energy. Besides being a rich source of sugar, in recent years it also serves as a valuable source of biomass, bioelectricity, biofuel and bioplastic. In India, the crop is cultivated in more than 4.5 M ha however its cultivation of sugarcane is threatened by many biotic and abiotic constraint. Among the biotic constraints, red rot caused by the fungal pathogen Colletotrichum falcatum is a serious disease affecting cane production and its quality. Resistance to red rot is an important trait for the release and cultivation of sugarcane varieties in the country. However, due to its genetic complexity in sugarcane, genetics of inheritance to the disease is poorly understood. In the recent years genomics approach to identify red rot resistance has been studied at the institute. Further to understand the defense mechanisms in sugarcane in response to C. falcatum infection, a total of 8236 genes were profiled using Affymetrix GeneChip Sugarcane Genome Array. A number of transcripts belonging to functional categories pertaining to signal transduction, defense, secondary metabolite biosynthesis and oxidative stress were up-regulated in sugarcane in response to C. falcatum. The transcripts involved in plant – pathogen interaction namely calcium-dependent protein kinase, respiratory burst oxidase, cyclic nucleotide gated channel and jasmonate ZIM domain – containing protein were up-regulated in incompatible interaction but down-regulated in compatible interaction. The other transcripts involved in secondary metabolite biosynthesis namely cinnamyl alcohol dehydrogenase, shikimate O-hydroxy cinnamoyl transferase, chalcone synthase and flavonoid 3’-monooxygenase, the transcripts involved in defense namely chitinase, glucanase and peroxidase were up-regulated in incompatible interaction and down-regulated in compatible interaction. This study concludes that in the incompatible interaction between sugarcane and C. falcatum, the transcripts involved in defense responses are rapid to arrest the pathogen entry whereas the defense responses are weak or down-regulated in the compatible interaction