Location: Wheat, Sorghum and Forage ResearchTitle: The WRKY transcription factor family and senescence in switchgrass Author
|Rinerson, Charles - Texas A&m University|
|Palmer, Nathan - Nate|
|Donze-reiner, Teresa - University Of Nebraska|
|Rabara, Role - Texas A&m University|
|Tripathi, Prateek - University Of Southern California|
|Shen, Qingxi - University Of Nevada|
|Rohila, Jai - South Dakota State University|
|Rushton, Paul - Texas A&m University|
Submitted to: Biomed Central (BMC) Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/13/2015
Publication Date: 11/9/2015
Publication URL: http://handle.nal.usda.gov/10113/62190
Citation: Rinerson, C.I., Scully, E.D., Palmer, N.A., Donze-Reiner, T., Rabara, R.C., Tripathi, P., Shen, Q.J., Sattler, S.E., Rohila, J.S., Sarath, G., Rushton, P.J. 2015. The WRKY transcription factor family and senescence in switchgrass. Biomed Central (BMC) Genomics. 16:912. doi: 10.1186/s12864-015-2057-4.
Interpretive Summary: Switchgrass is a promising biofuel crop. Biomass yields can be compromised by early leaf senescence during a growing season. If senescence can be delayed, it could result in increasing harvestable biomass yields. Plant senescence is a complex process that is governed by a number of cellular factors. Many of these cellular factors are proteins known as transcription factors that can directly bind to the DNA and either increase or decrease gene expression. One major class of plant transcription factors is called WRKY transcription factors. The specific expression of certain WRKY genes is known to hasten or delay leaf senescence in other model plants. Unfortunately almost nothing is known about these WRKY factors in switchgrass. Using tools in bioinformatics all of the potential WRKY genes in the switchgrass genome were identified. Next using previously collected data on the global gene expression in switchgrass flag leaf over its natural development, it was possible to assign specific WRKY factors to specific periods of leaf development. These analyses resulted in the identification of 23 WRKY genes that were highly correlated to the onset of leaf senescence in field-grown switchgrass plants. Identification of these specific WRKYs now provides tools to better understand the senescence process in switchgrass and utilize these genes as markers within breeding programs.
Technical 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 RNASeq datasets were analyzed using clustering and network analyses tools to identify both WRKY and WRKYassociated 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.