title: The WRKY transcription factor family and senescence in switchgrass.
abstract: BACKGROUND
  Early aerial senescence in switchgrass (Panicum virgatum) can significantly limit biomass yields. WRKY transcription factors that can regulate senescence could be used to reprogram senescence and enhance biomass yields.
  
  
  METHODS
  All potential WRKY genes present in the version 1.0 of the switchgrass genome were identified and curated using manual and bioinformatic methods. Expression profiles of WRKY genes in switchgrass flag leaf RNA-Seq datasets were analyzed using clustering and network analyses tools to identify both WRKY and WRKY-associated gene co-expression networks during leaf development and senescence onset.
  
  
  RESULTS
  We identified 240 switchgrass WRKY genes including members of the RW5 and RW6 families of resistance proteins. Weighted gene co-expression network analysis of the flag leaf transcriptomes across development readily separated clusters of co-expressed genes into thirteen modules. A visualization highlighted separation of modules associated with the early and senescence-onset phases of flag leaf growth. The senescence-associated module contained 3000 genes including 23 WRKYs. Putative promoter regions of senescence-associated WRKY genes contained several cis-element-like sequences suggestive of responsiveness to both senescence and stress signaling pathways. A phylogenetic comparison of senescence-associated WRKY genes from switchgrass flag leaf with senescence-associated WRKY genes from other plants revealed notable hotspots in Group I, IIb, and IIe of the phylogenetic tree.
  
  
  CONCLUSIONS
  We have identified and named 240 WRKY genes in the switchgrass genome. Twenty three of these genes show elevated mRNA levels during the onset of flag leaf senescence. Eleven of the WRKY genes were found in hotspots of related senescence-associated genes from multiple species and thus represent promising targets for future switchgrass genetic improvement. Overall, individual WRKY gene expression profiles could be readily linked to developmental stages of flag leaves.
authors.affiliation: Texas A&M AgriLife Research and Extension Center, Dallas, TX, 75252, USA. crinerson@gmail.com.
authors.forename: Charles I
authors.initials: CI
authors.lastname: Rinerson
authors.affiliation: Grain, Forage and Bioenergy Research Unit USDA-ARS UNL, Lincoln, NE, 68583-0937, USA. Erin.Scully@ars.usda.gov.
authors.forename: Erin D
authors.initials: ED
authors.lastname: Scully
authors.affiliation: Grain, Forage and Bioenergy Research Unit USDA-ARS UNL, Lincoln, NE, 68583-0937, USA. nathan.palmer@ars.usda.gov.
authors.forename: Nathan A
authors.initials: NA
authors.lastname: Palmer
authors.affiliation: Department of Biology, West Chester University of Pennsylvania, West Chester, PA, 19382, USA. TDonze-Reiner@wcupa.edu.
authors.forename: Teresa
authors.initials: T
authors.lastname: Donze-Reiner
authors.affiliation: Texas A&M AgriLife Research and Extension Center, Dallas, TX, 75252, USA. roel.rabara@tamu.edu.
authors.forename: Roel C
authors.initials: RC
authors.lastname: Rabara
authors.affiliation: Molecular and Computational Biology Section, Dana & David Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, CA, USA. tprateek@dornsife.usc.edu.
authors.forename: Prateek
authors.initials: P
authors.lastname: Tripathi
authors.affiliation: School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, 89154, USA. jeffery.shen@unlv.edu.
authors.forename: Qingxi J
authors.initials: QJ
authors.lastname: Shen
authors.affiliation: Grain, Forage and Bioenergy Research Unit USDA-ARS UNL, Lincoln, NE, 68583-0937, USA. Scott.Sattler@ars.usda.gov.
authors.forename: Scott E
authors.initials: SE
authors.lastname: Sattler
authors.affiliation: Department of Biology and Microbiology, South Dakota State University, Brookings, SD, 57007, USA. jai.rohila@sdstate.edu.
authors.forename: Jai S
authors.initials: JS
authors.lastname: Rohila
authors.affiliation: Grain, Forage and Bioenergy Research Unit USDA-ARS UNL, Lincoln, NE, 68583-0937, USA. Gautam.Sarath@ars.usda.gov.
authors.forename: Gautam
authors.initials: G
authors.lastname: Sarath
authors.affiliation: Texas A&M AgriLife Research and Extension Center, Dallas, TX, 75252, USA. prushton@xxiicentury.com.|Current address: 22nd Century Group Inc., Clarence, 14031, New York. prushton@xxiicentury.com.
authors.forename: Paul J
authors.initials: PJ
authors.lastname: Rushton
mesh_terms: D018506:Gene Expression Regulation, Plant / Q000235:genetics; D017343:Genes, Plant / Q000235:genetics; D008897:Panicum / Q000235:genetics*; D010802:Phylogeny; D018515:Plant Leaves / Q000235:genetics; D014157:Transcription Factors / Q000235:genetics*
chemical_list: D014157:Transcription Factors