Identification, characterization, and gene expression analysis of nucleotide binding site (NB)-type resistance gene homologues in switchgrass.
Switchgrass (Panicum virgatum L.) is a warm-season perennial grass that can be used as a second generation bioenergy crop. However, foliar fungal pathogens, like switchgrass rust, have the potential to significantly reduce switchgrass biomass yield. Despite its importance as a prominent bioenergy crop, a genome-wide comprehensive analysis of NB-LRR disease resistance genes has yet to be performed in switchgrass.



In this study, we used a homology-based computational approach to identify 1011 potential NB-LRR resistance gene homologs (RGHs) in the switchgrass genome (v 1.1). In addition, we identified 40 RGHs that potentially contain unique domains including major sperm protein domain, jacalin-like binding domain, calmodulin-like binding, and thioredoxin. RNA-sequencing analysis of leaf tissue from 'Alamo', a rust-resistant switchgrass cultivar, and 'Dacotah', a rust-susceptible switchgrass cultivar, identified 2634 high quality variants in the RGHs between the two cultivars. RNA-sequencing data from field-grown cultivar 'Summer' plants indicated that the expression of some of these RGHs was developmentally regulated.



Our results provide useful insight into the molecular structure, distribution, and expression patterns of members of the NB-LRR gene family in switchgrass. These results also provide a foundation for future work aimed at elucidating the molecular mechanisms underlying disease resistance in this important bioenergy crop.
Department of Horticulture, Virginia Tech, Blacksburg, VA, 24061, USA.
Taylor P
TP
Frazier
Grain, Forage and Bioenergy Research Unit, USDA-ARS, Lincoln, NE, 68583-0937, USA.
Nathan A
NA
Palmer
Department of Biology, East Carolina University, Greenville, NC, 27858, USA.
Fuliang
F
Xie
Crop Improvement and Genetics Research, USDA-ARS, Albany, CA, 94710, USA.
Christian M
CM
Tobias
Department of Biology, West Chester University of Pennsylvania, Wester Chester, PA, 19382, USA.
Teresa J
TJ
Donze-Reiner
Department of Horticulture, Virginia Tech, Blacksburg, VA, 24061, USA.
Aureliano
A
Bombarely
Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA.
Kevin L
KL
Childs
Department of Energy Joint Genome Institute, Walnut Creek, CA, 94595, USA.
Shengqiang
S
Shu
HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA.
Jerry W
JW
Jenkins
Department of Energy Joint Genome Institute, Walnut Creek, CA, 94595, USA.|HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA.
Jeremy
J
Schmutz
Department of Biology, East Carolina University, Greenville, NC, 27858, USA.
Baohong
B
Zhang
Grain, Forage and Bioenergy Research Unit, USDA-ARS, Lincoln, NE, 68583-0937, USA.
Gautam
G
Sarath
Department of Horticulture, Virginia Tech, Blacksburg, VA, 24061, USA. bzhao07@vt.edu.|, 407 Latham Hall, 220 Ag Quad Lane, Blacksburg, VA, 24061, USA. bzhao07@vt.edu.
Bingyu
B
Zhao
D000483:Alleles; D000595:Amino Acid Sequence; D019295:Computational Biology / Q000379:methods; D030561:Databases, Nucleic Acid; D060467:Disease Resistance / Q000235:genetics*; D020869:Gene Expression Profiling; D017343:Genes, Plant; D056726:Genetic Association Studies; D020022:Genetic Predisposition to Disease; D018745:Genome, Plant; D023281:Genomics / Q000379:methods; D008897:Panicum / Q000145:classification / Q000235:genetics*; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D056510:Position-Specific Scoring Matrices; D054730:Protein Interaction Domains and Motifs / Q000235:genetics; D015203:Reproducibility of Results
Biofuel; Disease resistance; Gene expression; NB-LRR; Panicum virgatum (switchgrass); RNA-seq; SNP