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

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dc.contributor.authorFrazier, Taylor Price
dc.contributor.authorPalmer, Nathan A.
dc.contributor.authorXie, Fuliang
dc.contributor.authorTobias, Christian M.
dc.contributor.authorDonze-Reiner, Teresa J.
dc.contributor.authorBombarely, Aureliano
dc.contributor.authorChilds, Kevin L.
dc.contributor.authorShu, Shengqiang
dc.contributor.authorJenkins, Jerry W.
dc.contributor.authorSchmutz, Jeremy
dc.contributor.authorZhang, Baohong
dc.contributor.authorSarath, Gautam
dc.contributor.authorZhao, Bingyu
dc.date.accessioned2016-11-29T14:02:43Z
dc.date.available2016-11-29T14:02:43Z
dc.date.issued2016-11-08
dc.date.updated2016-11-08T07:03:15Z
dc.description.abstractAbstract Background 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. Results 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. Conclusions 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.en_US
dc.identifier.citationBMC Genomics. 2016 Nov 08;17(1):892en_US
dc.identifier.urihttp://dx.doi.org/10.1186/s12864-016-3201-5
dc.identifier.urihttp://hdl.handle.net/10342/5984
dc.language.isoen_USen_US
dc.language.rfc3066en
dc.relation.urihttp://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-016-3201-5en_US
dc.rights.holderThe Author(s).
dc.subjectBiofuelen_US
dc.subjectDisease resistanceen_US
dc.subjectGene expressionen_US
dc.subjectNB-LRR geneen_US
dc.subjectPanicum virgatumen_US
dc.subjectSwitchgrassen_US
dc.subjectRNA sequencingen_US
dc.subjectSingle nucleotide polymorphismsen_US
dc.titleIdentification, characterization, and gene expression analysis of nucleotide binding site (NB)-type resistance gene homologues in switchgrassen_US
dc.typeArticleen_US
ecu.journal.issue1en_US
ecu.journal.nameBMC Genomicsen_US
ecu.journal.pages892en_US
ecu.journal.volume17en_US

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