Transcriptome Analysis Using RNA-Seq for Rust Resistance in Switchgrass

The advancement of DNA sequencing technology coupled with reducing price promoted transcriptome analysis in non-model organisms. Switchgrass rust, Puccinia emaculata, is expected to be the major limiting factor to biomass yield and quality in switchgrass production for bioenergy. To identify the differentially expressed genes during rust infection process, transcriptome analysis using RNA-seq was initiated on four founders, two parents, and three moderately resistant and three susceptible progeny of a switchgrass mapping population. The plants were inoculated in a growth chamber with rust spore collected from Ardmore, Oklahoma over 2007 to 2011. RNA was extracted from leaf tissue samples collected at three time points: 0, 24, and 60h after rust inoculation. The RNA-sequencing was conducted using Illumina TruSeq™ technology. A range of 24-68 million reads (46m average) per sample was obtained from paired-end (2x100) sequencing.  Assembly to the switchgrass reference genome (release v0.0) showed an average of 50x coverage. There were a total of 149,441 transcripts from 97,732 gene loci identified among all of the samples. Data analysis is in progress and the result will be presented.