Time-series expression profiling of sugarcane leaves infected with Puccinia kuehnii reveals an ineffective defense system leading to susceptibility

Abstract

Puccinia kuehnii is an obligate biotrophic fungus that infects sugarcane leaves causing a disease called orange rust. It spread out to other countries resulting in reduction of crop yield since its first outbreak in Australia. One of the knowledge gaps of that pathosystem is to understand the molecular mechanisms altered in susceptible plants by the stress induced by P. kuehnii. Here we investigated changes in temporal expression of transcripts in pathways associated with the immune system. To achieve this purpose, we used RNA-Seq to analyze infected leaf samples collected at 0, 12, 24, 48 hours after inoculation (hai), 5 and 12 days after inoculation (dai). A de novo transcriptome was assembled with preprocessed reads, filtering out potential fungal sequences to focus on plant transcripts. Differential expression analyses of adjacent time points revealed substantial changes at 12, 48 hai and 12 dai, coinciding with the events of spore germination, haustoria post-penetration and post-sporulation. During the first 24 hours, a lack of transcripts involved with resistance mechanisms was revealed by underrepresentation of hypersensitive and defense responses. However, two days after inoculation, upregulation of genes involved with immune response regulation provided evidence of some potential defense response. Events related to biotic stress and phenylpropanoid biosynthesis pathways were predominantly downregulated in the initial time points, but expression was later restored to basal levels. Similar waves of expression were apparent for sets of genes in photosynthesis and oxidative processes, whose initial repression could avoid production of signaling molecules. Their subsequent upregulation possibly restored carbohydrate metabolism, ensuring pathogen nutritional requirements were met. Our results support the hypothesis that P. kuehnii initially suppressed sugarcane genes involved in plant defense systems. Late overexpression of specific regulatory pathways also suggests the possibility of an inefficient recognition system by a susceptible sugarcane genotype.