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United States Department of Agriculture

Agricultural Research Service


Location: Corn Insects and Crop Genetics Research

2012 Annual Report

1a.Objectives (from AD-416):
Objective 1: Apply functional genomics tools and resources available to barley, rice, and the model dicot Arabidopsis thaliana, to accelerate comparative analysis of cereal disease defense pathways and associate newly discovered genes with biological function. Objective 2: Characterize diversity of global gene expression in cereal crops as a baseline to determine effects of transgene insertion and assess risk of developing improved crop products by bioengineering or marker-assisted breeding approaches.

1b.Approach (from AD-416):
Objective 1: Utilize allelic variability inherent to barley Mla, Rar1, and Rom1 as a switch to discover new pathways involved in both Rar1-dependent and Rar1-independent plant disease resistance. High-throughput barley dsRNAi and Arabidopsis T-DNA reverse genetic systems will be used to functionally validate candidate genes in resistance pathways of both monocot and dicot plants. Objective 2: Determine the global transcript profiles of a diverse set of barley germplasm and specific sets of transgenic lines and their progenitors. Integrative computational approaches will be used to establish whether or not differences in gene expression can be used as a predictor for genetic anomalies associated with transgenic crops.

3.Progress Report:
As one of our most important food sources, cereal crops are the nutritional foundation of humans and domesticated animals world-wide. So, successfully controlling existing and emerging cereal crop diseases is vital to food security. In recent years, large-scale DNA sequencing of plant and plant-pathogen genomes has provided unprecedented access to the genes and gene networks that underlie host-pathogen interactions. In FY 2012, we continued to investigate barley responses to powdery mildew, to develop biological and molecular assays to help locate and characterize the hundreds of host genes that respond to pathogen attack. Our primary entry point has been to determine function of genes that are uniquely activated in resistant barley plants, as compared to powdery mildew susceptible plants via genome-wide transcript profiling. This enables us to use computational and bioinformatic methods to sharpen our focus on the most critical genes and gene pathways that are causal to resistance to devastating fungal pathogens. A greater understanding of the molecular interchange and signaling that takes place during the development of barley powdery mildew will facilitate new control strategies and provide insight into the interactions of fungal pathogens with their crop plant hosts. Identification and characterization of specific powdery mildew proteins, termed effectors, that enable the pathogen to colonize the host, is a critical step. The obligate biotrophic lifestyle of powdery mildew, however, hinders genetic studies. Our approach is to leverage the recently completed powdery mildew genome sequence ( combined with several gene silencing and overexpression systems to identify these pathogen proteins. Our approach is to examine effector function in barley, maize, and rice using these different systems that enable us to screen for defense eliciting, defense suppressive, and susceptibility enhancing effects. We expect this approach ultimately to enable us to discover and compare important corresponding plant targets that promote or suppress defense in host and nonhost, cereal crop-fungal pathogen interactions. Regulatory focal points critical to these interactions are being investigated. Determination of these focal points will provide the molecular foundation necessary to dissect important disease resistance pathways, as well as the creation of a molecular toolbox from which to apply modern plant breeding methodologies.

1. Barley genome sequenced by International Barley Genome Sequencing Consortium. ARS researchers at Ames, IA contributed to the International Barley Genome Sequencing Consortium, a collaborative effort by researchers from Germany, Scotland, Japan, Finland, Australia, China, and the U.S. ( This integrated, multi-layered informational resource provides researchers with access to nearly all barley genes in a structured physical and genetic framework, thus, promoting new approaches to broaden the germplasm base, facilitate new breeding strategies and accelerate rates of genetic gain. This is significant because barley grain is particularly high in soluble dietary fiber, which significantly reduces the risk of human diseases, including type II diabetes, cardiovascular disease and colorectal cancer. The completed barley genome, also supported by USDA-National Research Initiative, USDA-Agriculture and Food Research Initiative, and the National Science Foundation-Plant Genome Research Program, provides new knowledge of broad significance to plant scientists and breeders, enabling growers to produce nourishing, disease resistant, and higher yielding crops.

Review Publications
Moeller, J.R., Moscou, M.J., Bancroft, T., Skadsen, R.W., Wise, R.P., Whitham, S.A. 2012. Differential regulation of host mRNA translation during obligate pathogen-plant interactions. Molecular Biosystems. 8:2153-2165.

Meyer, J.M., Pei, D., Wise, R.P. 2011. Rf8-mediated T-urf13 transcript accumulation coincides with a pentatricopeptide repeat cluster on maize chromosome 2L. The Plant Genome. 4(3):283-299.

Dash, S., Van Hemert, J., Hong, L., Wise, R.P., Dickerson, J.A. 2011. PLEXdb: Gene expression resources for plants and plant pathogens. Nucleic Acids Research. 40(D1):D1194-D1201.

Blake, V.C., Kling, J.G., Hayes, P.M., Jannink, J., Jillella, S.R., Lee, J., Matthews, D.E., Chao, S., Close, T.J., Muehlbauer, G.J., Smith, K.P., Wise, R.P., Dickerson, J.A. 2012. The hordeum toolbox - the barley CAP genotype and phenotype resource. The Plant Genome. DOI: 10.385/plantgenome2012.03.0002.

Brown, A.N., Lauter, N.C., Vera, D.L., McLaughlin-Large, K.A., Steele, T.M., Fredette, N.C., Bass, H.W. 2011. QTL mapping and candidate gene analysis of telomere length control factors in maize (Zea mays L.). Genes, Genomes, Genetics. 1(6):437-450.

Meng, Y., Wise, R.P. 2012. HvWRKY10, HvWRKY19, and HvWRKY28 positively regulate Mla-triggered immunity and basal defense to barley powdery mildew. Molecular Plant-Microbe Interactions. DOI:10.1094/MPMI-04-12-0082-R.

Last Modified: 4/19/2014
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