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ARS Home » Plains Area » Lincoln, Nebraska » Wheat, Sorghum and Forage Research » Research » Publications at this Location » Publication #323749
Title: Identification, characterization, and gene expression analysis of nucleotide binding site (NB)-type resistance gene homologues in switchgrass

Author
item FRAZIER, TAYLOR - Virginia Tech
item XIE, FULIANG - East Carolina University
item Palmer, Nathan - Nate
item Tobias, Christian
item DONZE-REINER, TERESA - West Chester State University
item BOMBARELY, AURELIANO - Virginia Tech
item CHILDS, KEVIN - Michigan State University
item ZHANG, BAOHONG - East Carolina University
item Sarath, Gautam
item ZHAO, BINGYU - Virginia Tech

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/25/2016
Publication Date: 11/8/2016
Publication URL: https://handle.nal.usda.gov/10113/5763068
Citation: Frazier, T.P., Xie, F., Palmer, N.A., Tobias, C.M., Donze-Reiner, T., Bombarely, A., Childs, K., Zhang, B., Sarath, G., Zhao, B. 2016. Identification, characterization, and gene expression analysis of nucleotide binding site (NB)-type resistance gene homologues in switchgrass. Biomed Central (BMC) Genomics. 17(1):892. doi:10.1186/s12864-016-3201-5.

Interpretive Summary: All plants have genes that control their ability to detect and ward off pests and diseases, and are part of their innate immunity. All of these genes are part of the disease resistance network of plants and are collectively termed resistance gene homologs (RGHs). There is limited understanding of these RGHs in switchgrass, although they can be expected to have a key role in defending the plant from fungal, viral and other pests. Switchgrass plants are susceptible to attack by a fungal pathogen that causes rust. Switchgrass rust can significantly reduce biomass yields Finding adequate sources of resistance that can be incorporated into switchgrass breeding programs remains a priority, especially in areas where rust is a problem. In the current study all of the RGHs in the switchgrass genome were detected and classified using bioinformatics. Other techniques were then used to discover and quantify unique genetic variation that might exist in some of these RGHs in rust-resistant versus rust-susceptible switchgrass cultivars. Lastly a profile of RGH expression in field-grown switchgrass plants was developed. As a result of this study potential DNA markers have been identified that can be used to discover new sources of rust resistance in switchgrass.

Technical Abstract: 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 theseRGHs 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.