Document Type

Dissertation - Open Access

Award Date


Degree Name

Doctor of Philosophy (PhD)

Department / School

Biology and Microbiology

First Advisor

Madhav P. Nepal


Defense Response, Disease Resistance, Grasses, NLR, Phylogenetics, Phytopathology


Plants have evolved a complex defense system against pests and pathogens utilizing many types of receptors, signaling factors, and defense compounds to detect pathogen presence and respond effectively. Since many pathogens have evolved immunesuppressing effectors used to reduce plant resistance, plants have evolved a family of receptors that detect pathogenic effectors as a result of an evolutionary arms race. These receptors contain Nucleotide-Binding Site and Leucine-Rich Repeat domains and are called NBS-LRR or NLR proteins. Many grasses possess huge genomes with hundreds of NLR-encoding genes, often found in clusters at the extra-pericentromeric regions of chromosomes, where unequal crossing over causes tandem duplication and a mechanism for resistance (R) gene diversification. R genes also possess domains associated with signaling factors that either serve as baits for pathogen effectors or as active signaling components to initiate defense responses. The objectives of this dissertation project were to: 1) identify R genes in wheat and some of its relatives; 2) assess how they may have evolved in grasses with available genomes, such as wheat, barley, foxtail millet, and rice; 3) investigate integrated domains found in wheat NLRs; and 4) assess differences in gene expression between tan spot resistant and susceptible wheat when exposed to Pyrenophora tritici-repentis (Ptr), a pathogen that uses wheat R gene Tsn1 as a susceptibility gene to facilitate infection. Genomic data was analyzed by the construction of Hidden Markov Model profiles and sequence annotation using programs such as InterProScan and MEME (Multiple Expectation maximization for Motif Elicitation). R genes were used to construct phylogenetic trees, chromosomal maps, exon-intron diagrams, and syntenic maps. The interaction between wheat and Ptr was investigated through a greenhouse experiment, where resistant and susceptible wheat was inoculated with Ptr spores or directly infiltrated with the Ptr ToxA protein. Genome-wide identification of R genes revealed that Hordeum vulgare, Setaria italica, Aegilops tauschii, and Triticum aestivum had 175, 202, 402, and 802 NLRs with N-terminal Coiled-Coil domains (CNLs), respectively. In each species studied, R genes formed clusters, many containing highly similar genes, providing evidence of tandem duplication. CNLs in wheat and wheat relatives formed an expansion of the CNL-C clade that showed evidence of purifying selection. R gene sequences necessary for effector detection diversified, while domains necessary for signaling remained conserved. Wheat NLRs contained integrated domains (IDs) associated with kinase, transcription factor, and other signaling mechanisms. Wheat NLR-ID genes encoded multiple transcripts, indicating that wheat is able to include or exclude IDs through alternative splicing. Greenhouse experiments revealed several groups of genes that differed in expression between tan spot resistant and susceptible cultivars. Wheat resistant to Ptr showed increased expression of genes associated with resistance: chitinases, signaling factors (i.e. transcription factors and kinases), resistance receptors, and enzymes associated with phytoalexin production. These results all showed that resistance in wheat and its relatives relies on a complex network of factors, and that NLRs have diversified to be a variable family of components that initiate defense responses when triggered by pathogenic effectors.

Library of Congress Subject Headings

Wheat -- Disease and pest resistance -- Genetic aspects.
Grasses -- Disease and pest resistance -- Genetic aspects.



Number of Pages



South Dakota State University



Rights Statement

In Copyright