skip to main content
OSTI.GOV title logo U.S. Department of Energy
Office of Scientific and Technical Information

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

Abstract

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.

Authors:
 [1];  [2];  [3];  [4];  [5];  [1];  [6];  [7];  [8];  [9];  [3];  [2];  [1]
  1. Virginia Polytechnic Inst. and State Univ. (Virginia Tech), Blacksburg, VA (United States)
  2. USDA-ARS, Lincoln, NE (United States)
  3. East Carolina Univ., Greenville, NC (United States)
  4. USDA-ARS, Albany, CA (United States)
  5. Univ. of Pennsylvania, Philadelphia, PA (United States)
  6. Michigan State Univ., East Lansing, MI (United States)
  7. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  8. HudsonAlpha Institute for Biotechnology, Huntsville, AL (United States)
  9. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); HudsonAlpha Institute for Biotechnology, Huntsville, AL (United States)
Publication Date:
Research Org.:
Argonne National Lab. (ANL), Argonne, IL (United States). Advanced Photon Source (APS)
Sponsoring Org.:
USDOE
OSTI Identifier:
1373292
Grant/Contract Number:  
2011-67009-30133; AI02-09ER64829; 2011-67009-30096; 3042-21000-030-00D; AC02-05CH11231
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
BMC Genomics
Additional Journal Information:
Journal Volume: 17; Journal Issue: 1; Journal ID: ISSN 1471-2164
Publisher:
Springer
Country of Publication:
United States
Language:
English
Subject:
09 BIOMASS FUELS; biofuel; disease resistance; gene expression; NB-LRR; Panicum virgatum (switchgrass); RNA-seq; SNP

Citation Formats

Frazier, Taylor P., Palmer, Nathan A., Xie, Fuliang, Tobias, Christian M., Donze-Reiner, Teresa J., Bombarely, Aureliano, Childs, Kevin L., Shu, Shengqiang, Jenkins, Jerry W., Schmutz, Jeremy, Zhang, Baohong, Sarath, Gautam, and Zhao, Bingyu. Identification, characterization, and gene expression analysis of nucleotide binding site (NB)-type resistance gene homologues in switchgrass. United States: N. p., 2016. Web. doi:10.1186/s12864-016-3201-5.
Frazier, Taylor P., Palmer, Nathan A., Xie, Fuliang, Tobias, Christian M., Donze-Reiner, Teresa J., Bombarely, Aureliano, Childs, Kevin L., Shu, Shengqiang, Jenkins, Jerry W., Schmutz, Jeremy, Zhang, Baohong, Sarath, Gautam, & Zhao, Bingyu. Identification, characterization, and gene expression analysis of nucleotide binding site (NB)-type resistance gene homologues in switchgrass. United States. doi:10.1186/s12864-016-3201-5.
Frazier, Taylor P., Palmer, Nathan A., Xie, Fuliang, Tobias, Christian M., Donze-Reiner, Teresa J., Bombarely, Aureliano, Childs, Kevin L., Shu, Shengqiang, Jenkins, Jerry W., Schmutz, Jeremy, Zhang, Baohong, Sarath, Gautam, and Zhao, Bingyu. Tue . "Identification, characterization, and gene expression analysis of nucleotide binding site (NB)-type resistance gene homologues in switchgrass". United States. doi:10.1186/s12864-016-3201-5. https://www.osti.gov/servlets/purl/1373292.
@article{osti_1373292,
title = {Identification, characterization, and gene expression analysis of nucleotide binding site (NB)-type resistance gene homologues in switchgrass},
author = {Frazier, Taylor P. and Palmer, Nathan A. and Xie, Fuliang and Tobias, Christian M. and Donze-Reiner, Teresa J. and Bombarely, Aureliano and Childs, Kevin L. and Shu, Shengqiang and Jenkins, Jerry W. and Schmutz, Jeremy and Zhang, Baohong and Sarath, Gautam and Zhao, Bingyu},
abstractNote = {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.},
doi = {10.1186/s12864-016-3201-5},
journal = {BMC Genomics},
number = 1,
volume = 17,
place = {United States},
year = {Tue Nov 08 00:00:00 EST 2016},
month = {Tue Nov 08 00:00:00 EST 2016}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record

Citation Metrics:
Cited by: 1 work
Citation information provided by
Web of Science

Save / Share:

Works referenced in this record:

Predicting coiled coils from protein sequences
journal, May 1991