Identification, characterization, and gene expression analysis of nucleotide binding site (NB)-type resistance gene homologues in switchgrass

BMC Genomics

Research Article

Christian M. Tobias¹  Fuliang Xie²  Baohong Zhang²  Teresa J. Donze-Reiner³  Shengqiang Shu⁴  Jeremy Schmutz⁵  Aureliano Bombarely⁶  Taylor P. Frazier⁶  Bingyu Zhao⁷  Kevin L. Childs⁸  Gautam Sarath⁹  Nathan A. Palmer⁹  Jerry W. Jenkins^1,10 

[1] Crop Improvement and Genetics Research, USDA-ARS, 94710, Albany, CA, USA;Department of Biology, East Carolina University, 27858, Greenville, NC, USA;Department of Biology, West Chester University of Pennsylvania, 19382, Wester Chester, PA, USA;Department of Energy Joint Genome Institute, 94595, Walnut Creek, CA, USA;Department of Energy Joint Genome Institute, 94595, Walnut Creek, CA, USA;HudsonAlpha Institute for Biotechnology, 35806, Huntsville, AL, USA;Department of Horticulture, Virginia Tech, 24061, Blacksburg, VA, USA;Department of Horticulture, Virginia Tech, 24061, Blacksburg, VA, USA;407 Latham Hall, 220 Ag Quad Lane, 24061, Blacksburg, VA, USA;Department of Plant Biology, Michigan State University, 48824, East Lansing, MI, USA;Grain, Forage and Bioenergy Research Unit, USDA-ARS, 68583-0937, Lincoln, NE, USA;HudsonAlpha Institute for Biotechnology, 35806, Huntsville, AL, USA;

关键词: Biofuel;    Disease resistance;    Gene expression;    NB-LRR;    Panicum virgatum;    RNA-seq;    SNP;   

DOI  :  10.1186/s12864-016-3201-5

 received in 2016-03-16, accepted in 2016-10-25,  发布年份 2016

来源: Springer

【 摘 要 】

BackgroundSwitchgrass (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.ResultsIn 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.ConclusionsOur 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.

【 授权许可】

CC BY   
© The Author(s). 2016