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

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

doi:10.1186/s12864-016-3201-5

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

Journal Article · Tue Nov 08 00:00:00 EST 2016 · BMC Genomics

DOI:https://doi.org/10.1186/s12864-016-3201-5· OSTI ID:1618558

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

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.

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Research Organization:: Argonne National Laboratory (ANL), Argonne, IL (United States). Advanced Photon Source (APS); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER); USDA

Grant/Contract Number:: AI02-09ER64829; SC0001490; 2011-67009-30133; 2011-67009-30096; 3042-21000-030-00D; AC02-05CH11231

OSTI ID:: 1618558

Alternate ID(s):: OSTI ID: 1373292; OSTI ID: 1616051

Journal Information:: BMC Genomics, Journal Name: BMC Genomics Vol. 17 Journal Issue: 1; ISSN 1471-2164

Publisher:: SpringerCopyright Statement

Country of Publication:: United Kingdom

Language:: English

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Cited by: 12 works

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