Identification, Characterization, and Gene Expression Analysis of NB-LRR Encoding Resistance Genes in the Bioenergy Plant Switchgrass (Panicum virgatum L.)

Switchgrass has received attention for its potential use as a second generation biofuel feedstock. Sustainable switchgrass biomass production could be negatively impacted by the epidemics of various disease problems, such as rust. Therefore, the molecular mechanisms underlying disease tolerance must be elucidated. The majority of plant disease resistance (R) genes belong to a large family of nucleotide binding - leucine rich repeat (NB-LRR) genes. In this study, we used a homology-based computational method to identify 610 putative NB-containing R genes in the switchgrass genome (v 0.0). The results of this search identified 28 potential NB-containing R proteins with novel domains such as jacalin, WRKY, B3, WD40, and zinc-finger binding domains. In order to validate putative R gene expression, RNA-sequencing of leaf-tissue from Dacotah, a rust-susceptible switchgrass cultivar, and Alamo, a rust-resistant switchgrass cultivar, was performed. Approximately 6,148 genes were differentially regulated (>2 fold change) between these cultivars. Interestingly, 166 (2.7%) of these genes are predicted to be NB-containing genes. Of the 610 previously identified NB-containing R genes, 451 were found to have expression evidence in Alamo, 402 were found to have expression evidence in Dacotah, and 357 of these genes were expressed in both cultivars. Variant detection within the 610 NB-containing genes identified 1,425 homozygous SNPs between Alamo and Dacotah. qPCR and PCR were used to validate differential gene expression and SNP detection. The results of this study will aid in understanding the genetic mechanisms that control disease resistance in switchgrass and may produce switchgrass cultivars with improved disease tolerance.