Identification, characterization, and gene expression analysis of nucleotide binding site NB-type resistance gene homologues in switchgrassReport as inadecuate




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BMC Genomics

, 17:892

Plant genomics

Abstract

BackgroundSwitchgrass 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.

ResultsIn 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.

ConclusionsOur 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.

KeywordsBiofuel Disease resistance Gene expression NB-LRR Panicum virgatum switchgrass RNA-seq SNP AbbreviationsbpBase pair

CCCoiled-coil domain

EDGE testEmpirical analysis of differential gene expression test

FDRFalse discovery rate

indelsInsertions and deletions

LRRLeucine rich repeat

MEModule Eigengene

MNPsMultiple nucleotide polymorphisms

NBNucleotide binding site

NB-ARCProteins containing a nucleotide binding site and domains homologous to human APAF-1, plant disease resistance proteins, and C. elegans CED-4 protein

NB-LRRNucleotide binding site- Leucine rich repeat genes-proteins

NLSNuclear localization signal

Q-scoreQuality score

R genesPlant disease resistance genes

RGHResistance gene homolog

RNA-seqRNA-sequencing

RPKMReads per kilobase of transcript per million mapped reads

SMARTSimple modular architecture research tool

SNPSingle nucleotide polymorphism

TIRDomain homologous to Drosophila Toll and mammalian Interleukin 1 Receptors

WGCNAWeighted gene co-expression network analysis

Electronic supplementary materialThe online version of this article doi:10.1186-s12864-016-3201-5 contains supplementary material, which is available to authorized users.

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Author: Taylor P. Frazier - Nathan A. Palmer - Fuliang Xie - Christian M. Tobias - Teresa J. Donze-Reiner - Aureliano Bombarely

Source: https://link.springer.com/







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