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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 P.en
dc.contributor.authorPalmer, Nathan A.en
dc.contributor.authorXie, Fuliangen
dc.contributor.authorTobias, Christian M.en
dc.contributor.authorDonze-Reiner, Teresa J.en
dc.contributor.authorBombarely, Aurelianoen
dc.contributor.authorChilds, Kevin L.en
dc.contributor.authorShu, Shengqiangen
dc.contributor.authorJenkins, Jerry W.en
dc.contributor.authorSchmutz, Jeremyen
dc.contributor.authorZhang, Baohongen
dc.contributor.authorSarath, Gautamen
dc.contributor.authorZhao, Bingyu Y.en
dc.contributor.departmentSchool of Plant and Environmental Sciencesen
dc.date.accessioned2017-01-17T04:34:40Zen
dc.date.available2017-01-17T04:34:40Zen
dc.date.issued2016-11-08en
dc.description.abstractBACKGROUND: 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
dc.description.versionPublished versionen
dc.format.mimetypeapplication/pdfen
dc.identifier.doihttps://doi.org/10.1186/s12864-016-3201-5en
dc.identifier.eissn1471-2164en
dc.identifier.issue1en
dc.identifier.urihttp://hdl.handle.net/10919/74355en
dc.identifier.volume17en
dc.language.isoenen
dc.relation.urihttp://www.ncbi.nlm.nih.gov/pubmed/27821048en
dc.rightsCreative Commons Attribution 4.0 Internationalen
dc.rights.holderThe Author(s)en
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en
dc.subjectBiofuelen
dc.subjectDisease resistanceen
dc.subjectGene expressionen
dc.subjectNB-LRRen
dc.subjectPanicum virgatum (switchgrass)en
dc.subjectRNA-seqen
dc.subjectSNPen
dc.titleIdentification, characterization, and gene expression analysis of nucleotide binding site (NB)-type resistance gene homologues in switchgrassen
dc.title.serialBMC Genomicsen
dc.typeArticle - Refereeden
dc.type.dcmitypeTexten
pubs.organisational-group/Virginia Techen
pubs.organisational-group/Virginia Tech/Agriculture & Life Sciencesen
pubs.organisational-group/Virginia Tech/Agriculture & Life Sciences/CALS T&R Facultyen
pubs.organisational-group/Virginia Tech/Agriculture & Life Sciences/Horticultureen
pubs.organisational-group/Virginia Tech/All T&R Facultyen

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