Roger P Wise

USDA-Agricultural Research Service / Iowa State University · Corn Insects & Crop Genetics Research Unit / Dept of Plant Pathology & Microbiology

Mildew locus a (Mla ) from the Triticeae grain crop barley ( Hordeum vulgare L.) encodes a multi-allelic series of nucleotide-binding leucine-rich repeat (NLR) immune receptors. These variable NLRs recognize complementary secreted effectors from the powdery mildew fungus, Blumeria hordei ( Bh ), to block disease progression. We used a dynamic time-...

Yeast two-hybrid next-generation interaction screening (Y2H-NGIS) uses the output of next-generation sequencing to mine for novel protein-protein interactions. Here, we outline the analytics underlying Y2H-NGIS datasets. Different systems, libraries, and experimental designs comprise Y2H-NGIS methodologies. We summarize the analysis in several laye...

Yeast two-hybrid is a powerful approach to discover new protein-protein interactions. Traditional methods involve screening a target protein against a cDNA expression library and assaying individual positive colonies to identify interacting partners. Here we describe a simple approach to perform yeast two-hybrid screens of a cDNA expression library...

Plant disease resistance often occurs upon direct or indirect recognition of pathogen effectors by host nucleotide-binding leucine-rich-repeat (NLR) receptors. The barley powdery mildew fungus, Blumeria graminis f. sp. hordei ( Bgh ), secretes hundreds of candidate secreted effector proteins (CSEPs) to facilitate pathogen infection and colonization...

The barley MLA nucleotide-binding leucine-rich-repeat (NLR) receptor and its orthologs confer recognition specificity to many fungal diseases, including powdery mildew, stem- and stripe rust. We used interolog inference to construct a barley protein interactome (HvInt) comprising 66133 edges and 7181 nodes, as a foundation to explore signaling netw...

The Mla (Mildew resistance locus a) of barley (Hordeum vulgare L.) is an effective model for cereal immunity against fungal pathogens. Like many resistance proteins, variants of the MLA coiled-coil nucleotide-binding leucine-rich repeat (CC-NLR) receptor often require the HRS complex (HSP90, RAR1, and SGT1) to function. However, functional analysis...

The barley MLA nucleotide-binding, leucine-rich-repeat (NLR) receptor and its orthologs confer recognition specificity to many cereal diseases, including powdery mildew, stem and stripe rust, Victoria blight, and rice blast. We used interolog inference to construct a barley protein interactome (HvInt) comprising 66133 edges and 7181 nodes, as a fou...

Background Gene annotation in eukaryotes is a non-trivial task that requires meticulous analysis of accumulated transcript data. Challenges include transcriptionally active regions of the genome that contain overlapping genes, genes that produce numerous transcripts, transposable elements and numerous diverse sequence repeats. Currently available g...

Protein-protein interaction networks are one of the most effective representations of cellular behavior. In order to build these models, high-throughput techniques are required. Next-generation interaction screening (NGIS) protocols that combine yeast two-hybrid (Y2H) with deep sequencing are promising approaches to generate interactome networks in...

Barley (Hordeum vulgare L.) Mla (Mildew resistance locus a) and its nucleotide-binding, leucine-rich-repeat receptor (NLR) orthologs protect many cereal crops from diseases caused by fungal pathogens. However, large segments of the Mla pathway and its mechanisms remain unknown. To further characterize the molecular interactions required for NLR-bas...

Background Gene annotation in eukaryotes is a non-trivial task that requires meticulous analysis of accumulated transcript data. Challenges include transcriptionally active regions of the genome that contain overlapping genes, genes that produce numerous transcripts, transposable elements and numerous diverse sequence repeats. Currently available g...

Mapping protein-protein interactions at a proteome scale is critical to understanding how cellular signaling networks respond to stimuli. Since eukaryotic genomes encode thousands of proteins, testing their interactions one-by-one is a challenging prospect. High-throughput yeast-two hybrid (Y2H) assays that employ next-generation sequencing to inte...

Interactomes embody one of the most effective representations of cellular behavior by revealing function through protein associations. In order to build these models at the organism scale, high-throughput techniques are required to identify interacting pairs of proteins. Next-generation interaction screening (NGIS) protocols that combine yeast two-...

Mapping protein-protein interactions at a proteome scale is critical to understanding how cellular signaling networks respond to stimuli. Since eukaryotic genomes encode thousands of proteins, testing their interactions one-by-one is a challenging prospect. High-throughput yeast-two hybrid (Y2H) assays that employ next-generation sequencing to inte...

Following the publication of the original article [1], the authors noted several typesetting errors which are noted in this Correction article.

Background: Plants encounter pathogenic and non-pathogenic microorganisms on a nearly constant basis. Small RNAs such as siRNAs and miRNAs/milRNAs influence pathogen virulence and host defense responses. We exploited the biotrophic interaction between the powdery mildew fungus, Blumeria graminis f. sp. hordei (Bgh), and its diploid host plant, bar...

Pathogen effectors are excellent tools to explore dynamic regulation of plant resistance and susceptibility. To discover novel mechanisms of effector action, we exploited the biotrophic powdery mildew fungus, Blumeria graminis f. sp. hordei (Bgh), and its host, barley (Hordeum vulgare). We used next-generation sequencing to identify interacting par...

The PCA locus was mapped between two RFLP markers. Earlier work mapped it to the distal end of a linkage group. The flanking markers will enable breeders to introgress the locus into cultivated oat.

The Pseudomonas syringae cysteine protease AvrPphB activates the Arabidopsis resistance protein RPS5 by cleaving a second host protein, PBS1. AvrPphB induces defense responses in other plant species, but the genes and mechanisms mediating AvrPphB recognition in those species have not been defined. Here, we show that AvrPphB induces defense response...

Over the last 100 years, research in barley disease resistance has progressed from classical genetic approaches up to molecular genetics and genome-wide functional profiling. Along the way, a multitude of well-characterized genetic resources have paved the way for mechanistic investigations into barley immunity. Seminal discoveries in barley have b...

The Pseudomonas syringae cysteine protease AvrPphB activates the Arabidopsis resistance protein RPS5 by cleaving a second host protein, PBS1. AvrPphB induces defense responses in other plant species, but the genes and mechanisms mediating AvrPphB recognition in those species have not been defined. Here, we show that AvrPphB induces defense response...

This letter describes a newly discovered confounding effect of bacterial titer in a previously published type III delivery-based assay of the fungal effector BEC1019. The original publication has been retracted as a consequence of this discovery. The letter tabulates the affected and unaffected figures and conclusions in the original publication, a...

Identification of central genes and proteins in biomolecular networks provides credible candidates for pathway analysis, functional analysis, and essentiality prediction. The DiffSLC centrality measure predicts central and essential genes and proteins using a protein-protein interaction network. Network centrality measures prioritize nodes and edge...

Difference in top ranked proteins between NT3 and NF3 networks. DiffSLC ranked proteins based on using two different expression data sets. The results from each ranking are compared to find the differences in DiffSLC detected essential proteins. (XLSX)

AUC of the ROC based on choices of ω and β. This table shows impact of various ω and β value choices on the AUC of the ROC for DiffSLC applied to NT1, NT2, NT3, and NF1, NF2, NF3 networks. (XLSX)

Powdery mildew pathogens colonize over 9,500 plant species, causing critical yield loss. The Ascomycete fungus, Blumeria graminis f. sp. hordei (Bgh), causes powdery mildew disease in barley (Hordeum vulgare L.). Successful infection begins with penetration of host epidermal cells, culminating in haustorial feeding structures, facilitating delivery...

Significance Gene-for-gene immunity is frequently found in interactions between plants and host-adapted pathogens and reflects population-level diversification of immune receptors detecting matching pathogen effectors. We identified effector genes of a pathogenic powdery mildew fungus that are recognized by allelic variants of barley intracellular...

Copy-number alterations are widespread in animal and plant genomes, but their immediate impact on gene expression is still unclear. In animals, copy-number alterations usually exhibit dosage effects, except for sex chromosomes that tend to be dosage compensated. In plants, genes within small duplications (<100 kb) often exhibit dosage-dependent exp...

Barley (Hordeum vulgare L.) possesses a large and highly repetitive genome of 5.1 Gb that has hindered the development of a complete sequence. In 2012, the International Barley Sequencing Consortium released a resource integrating whole-genome shotgun sequences with a physical and genetic framework. However, because only 6,278 BACs in the physical...

Plants have evolved complex regulatory mechanisms to control a multi-layered defense response to microbial attack. Both temporal and spatial gene expression are tightly regulated in response to pathogen ingress, modulating both positive and negative control of defense. BLUFENSINs, small knottin-like peptides in barley, wheat, and rice, are highly i...

The interaction of barley, Hordeum vulgare L., with the powdery mildew fungus, Blumeria graminis f. sp. hordei, is a well-developed model to investigate resistance and susceptibility to obligate biotrophic pathogens. The 130-Mb Blumeria genome encodes ca. 540 predicted effectors, which are hypothesized to suppress or induce host processes to promot...

Barley (Hordeum vulgare L.) Mla alleles encode coiled-coil (CC), nucleotide binding, leucine-rich repeat (NB-LRR) receptors that trigger isolate-specific immune responses against the powdery mildew fungus, Blumeria graminis f. sp. hordei (Bgh). How Mla or NB-LRR genes in grass species are regulated at post-transcriptional level is not clear. The mi...

##Assembly-Data-START## Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##

Genes encoding early signaling events in pathogen defense often are identified only by their phenotype. Such genes involved in barley-powdery mildew interactions include Mla, specifying race-specific resistance; Rar1 (Required for Mla12-specified resistance1), and Rom1 (Restoration of Mla-specified resistance1). The HSP90-SGT1-RAR1 complex appears...

Bacterial leaf streak of rice, caused by Xanthomonas oryzae pv. oryzicola (Xoc) is an increasingly important yield constraint in this staple crop. A mesophyll colonizer, Xoc differs from X. oryzae pv. oryzae (Xoo), which invades xylem to cause bacterial blight of rice. Both produce multiple distinct TAL effectors, type III-delivered proteins that t...

Barley ( Hordeum vulgare L.) M ildew resistance locus a ( M la ) confers allele‐specific interactions with natural variants of the ascomycete fungus B lumeria graminis f. sp. hordei ( B gh ), the causal agent of powdery mildew disease. Significant reprogramming of M la ‐mediated gene expression occurs upon infection by this obligate biotrophic path...

Figure S1. Distribution of the number of successful genotype calls at variant positions detected in the whole data of the Morex x Barke and OWB populations.

Appendix S1. Applications of a POPSEQ assembly for comparative genomics, reference-based genetic mapping and gene isolation.

Figure S2. Observed and expected sequence coverage according to the model of Lander and Waterman (1988).

Figure S3. Potential uses for an assembly ordered by POPSEQ.

Table S1. The percentage of WGS contigs pairs assigned to the same BAC that are positioned farther apart than the specified distance.

Methods S1. Experimental procedures for Appendix S1.

Next-generation, whole genome shotgun (WGS) assemblies of complex genomes are highly enabling, but fail to link nearby sequence contigs with each other or provide a linear order of contigs along individual chromosomes. Here, we introduce a strategy based on sequencing progeny of a segregating population that allows the de novo production of a genet...

Grass genomes harbor a diverse and complex content of repeated sequences. Most of these repeats occur as abundant transposable elements (TEs), which present unique challenges to sequence, assemble, and annotate genomes. Multiple copies of Long Terminal Repeat (LTR) retrotransposons can hinder sequence assembly and also cause problems with gene anno...

Rusts are one of the most severe threats to cereal crops because new pathogen races emerge regularly, resulting in infestations that lead to large yield losses. In 1999, a new race of stem rust, Puccinia graminis f. sp. tritici (Pgt TTKSK or Ug99), was discovered in Uganda. Most of the wheat and barley cultivars grown currently worldwide are suscep...

Obligate biotrophic pathogens of plants must circumvent or counteract defences to guarantee accommodation inside the host. To do so, they secrete a variety of effectors, which regulate host immunity and facilitate the establishment of pathogen feeding structures called haustoria. The barley powdery mildew fungus, Blumeria graminis f. sp. hordei, pr...

WRKY proteins represent a large family of transcription factors (TF), involved in plant development and defense. In all, 60 unique barley TF have been annotated that contain the WRKY domain; 26 of these are represented on the Barley1 GeneChip. Time-course expression profiles of these 26 HvWRKY TF were analyzed to investigate their role in mildew lo...

The use of DNA markers in public sector plant breeding is now the norm. Such markers are common across breeding programs and this commonality enables and enhances collaboration. Therefore, large collaborative research projects that measure several phenotypes across multiple environments coupled wiThthe expanding amount of genotype data attainable w...

Plant pathogens elicit dramatic changes in the expression of host genes during both compatible and incompatible interactions. Gene expression profiling studies of plant-pathogen interactions have only considered messenger RNAs (mRNAs) present in total RNA, which contains subpopulations of actively translated mRNAs associated with polyribosomes (pol...