Transcriptome profiling reveals genetic basis of disease resistance against Corynespora cassiicola in rubber tree (Hevea brasiliensis)

Abstract

Corynespora leaf disease caused by Corynespora cassiicola (Berk. & Curt.) is one of the major diseases responsible for significant yield loss in rubber trees (Hevea brasiliensis). Next-generation sequencing based transcriptomic study of two rubber clones: RRII 105 (susceptible) and GT 1 (moderately resistant) were performed to understand the molecular basis of host tolerance to fungal diseases. Genes encoding disease resistance proteins, leucine-rich repeat proteins and genes involved in carbohydrate metabolic processes were significantly up-regulated in GT 1 upon infection, but were either completely suppressed or down-regulated in RRII 105. Transcription factor activity was a major molecular function triggered in both inoculated clones. Gene Ontology analysis revealed that majority of the transcripts was enriched for defense response, response to stimulus and stress. Higher expression of 118 transcripts with complete ORFs was identified in inoculated GT 1, indicating their possible role in disease resistance. In addition, both unique and common simple sequence repeats (SSRs) were identified. In silico analysis revealed 191 informative SSRs differentiating the two clones. Variant calling in control and disease GT 1 transcriptomes with reference to RRII 105 revealed over one lakh putative base substitutions. Microarray was used to validate the results obtained on transcriptional responses. Biotic stress overview from MapMan analysis revealed stronger activation of defense-related genes, receptor-like kinases and transcription factors. This study presents the first comprehensive transcriptome of resistant and susceptible rubber clones in response to C. cassiicola. The newly identified differentially regulated genes and sequence variation provide critical knowledge for understanding the genetic basis of disease resistance and marker development.