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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:
; ; ; ; ; ; ; ; ; ; ; ;
Publication Date:
Research Org.:
Argonne National Laboratory (ANL), Argonne, IL (United States). Advanced Photon Source (APS); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER); USDA
OSTI Identifier:
1618558
Alternate Identifier(s):
OSTI ID: 1373292; OSTI ID: 1616051
Grant/Contract Number:  
AI02-09ER64829; SC0001490; 2011-67009-30133; 2011-67009-30096; 3042-21000-030-00D; AC02-05CH11231
Resource Type:
Published Article
Journal Name:
BMC Genomics
Additional Journal Information:
Journal Name: BMC Genomics Journal Volume: 17 Journal Issue: 1; Journal ID: ISSN 1471-2164
Publisher:
Springer
Country of Publication:
United Kingdom
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 Kingdom: 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 Kingdom. https://doi.org/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 Kingdom. https://doi.org/10.1186/s12864-016-3201-5.
@article{osti_1618558,
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 Kingdom},
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
https://doi.org/10.1186/s12864-016-3201-5

Citation Metrics:
Cited by: 12 works
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Figures / Tables:

Fig. 1 Fig. 1: Numerical and structural representation of the 1011 switchgrass RGHs identified in this study. Four different protein structures were found for the 1011 switchgrass RGHs identified in this study. The coiled-coil (CC) domain is depicted in purple, the nucleotide binding (NB) domain in green, and the leucine rich repeatmore » (LRR) region in yellow. The placement of the domains below does not reflect accurate molecular distances« less

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