Transcriptome Profiling of Rust Resistance in Switchgrass Using RNA-Seq Analysis

Switchgrass rust (SGR) caused by Puccinia emaculata is a major limiting factor for switchgrass production, especially in monoculture. Natural populations of switchgrass displayed diverse reactions to P. emaculata when evaluated in an Ardmore, Oklahoma, field. To identify the differentially expressed genes during the rust infection process and the mechanisms of SGR resistance, transcriptome analysis using RNA-Seq was conducted in two pseudo-F1 parents (PV281 and NFGA472), and three moderately resistant and three susceptible progenies selected from a three-generation, four-founder switchgrass population (K5/A4)//(AP13/VS16). On average, 23.5 M reads per sample (leaf tissue collected at 0, 24 and 60 hours post-inoculation (hpi)) were obtained from paired-end (2x100 bp) sequencing on the Illumina HiSeq2000 platform. Mapping of the RNA-Seq reads to the switchgrass reference genome (AP13 v1.1 assembly) constructed a total of 84,209 transcripts from 98,007 gene loci among all of the samples. Further analysis revealed that host defense-related genes, including the NBS-LRR domain containing disease resistance gene analogs (RGA), play an important role in resistance to rust infection. Rust-induced gene (RIG) transcripts inherited across generations were identified. The rust-resistant gene transcripts can be a valuable resource for developing molecular markers for rust resistance. Furthermore, the rust-resistant genotypes and gene transcripts identified in this study can expedite rust-resistant cultivar development in switchgrass.