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United States Department of Agriculture

Agricultural Research Service

Research Project: FUNCTIONAL GENOMICS OF CEREAL DISEASE DEFENSE
2013 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:
The overall theme for this project has been to uncover regulatory mechanisms that govern the interactions between plants and their pathogens. Crop loss caused by disease remains one of the greatest challenges in agriculture in both developed and developing countries. Likewise, cereal crops are one of the most important nutritional foundations of humans and domesticated animals world-wide. Hence, controlling existing and emerging cereal crop diseases is vital to food security. Rusts and mildews, major diseases caused by obligate fungal pathogens, are a significant threat to cereal grain production worldwide. In addition to their economic importance, cereal hosts to obligate biotrophs also present unique models for cellular biology. Effector proteins are secreted by these pathogens, which co-opt, modulate, inhibit or accelerate host processes to augment the cellular environment to enable the pathogen to acquire nutrients and colonize the host. As such, pathogen effectors are change agents that influence host immunity and are optimal molecular probes to tease apart important agronomic signaling pathways in plant biology. The overall objective was to investigate barley responses to important fungal diseases and 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 susceptible plants via genome-wide transcript profiling. This enabled 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. In the barley host, we took a systems-wide-approach by using loss-of-function resistance signaling mutants to identify genes that are uniquely activated in resistant vs. susceptible plants via Barley1 GeneChip transcript profiling, where 22,000 genes can be investigated simultaneously. The most significant and interesting of these genes were then confirmed with various molecular assays, confirming their role in disease resistance. In the powdery mildew pathogen, we showed that a broadly conserved effector functions to suppress defense and enhance virulence during the development of disease in barley. Similar copies of this effector were found in ~90 other diverse fungi, including obligate plant pathogens, necrotrophic animal pathogens, and free-living non-pathogens. The copy from the human pathogen Candida albicans, also suppresses cell death in barley, suggesting that this effector represents a large and ancient family of conserved fungal virulence factors. Functional identification of their precise regulatory roles is a key step toward understanding how to achieve resistance to a broad spectrum of fungal diseases in barley, wheat, corn, and soybean.


4.Accomplishments
1. ARS researchers collaborate with international team to defeat plant-pathogenic microbes. Crop loss caused by disease remains one of the greatest challenges in agriculture in both developed and developing countries. Rusts and mildews, caused by obligate fungal pathogens, are a major threat to cereal grain production worldwide. Effector proteins secreted by these pathogens take over host processes to enable their colonization. As such, effectors are optimal probes to help understand host pathways, particularly disease resistance. ARS researchers collaborated with an international team from the United Kingdom and Germany to identify a novel class of pathogen effectors from the barley powdery mildew pathogen. This finding, like similar discoveries in human medicine, will be used to develop new ways to combat diseases of crop plants, most notable cereal grains, which are our most important food sources. Because common themes govern all plant-pathogen interactions, this finding provides new knowledge of broad significance to plant scientists, and to growers who utilize disease resistance to protect their crops. This discovery, also supported by the National Science Foundation-Plant Genome Research Program, establishes a previously unrecognized role for this new class of disease causing proteins.


Review Publications
Mayer, K., Waugh, R., Langridge, P., Close, T.J., Wise, R.P., Graner, A., Matsumoto, T., Sato, K., Schulman, A., Muehlbaueer, G.J., Stein, N., Ariyadasa, R., Schulte, D., Poursarebani, N., Zhou, R., Steuernagel, B., Mascher, M., Scholz, U., Shi, B., Madishetty, K., Svensson, J.T., Bhat, P., Moscou, M., Resnik, J., Hedley, P., Liu, H., Morris, J., Frenkel, Z., Korol, A., Berges, H., Taudien, S., Felder, M., Groth, M., Platzer, M., Himmelbach, A., Lonardi, S., Duma, D., Alpert, M., Cordero, F., Beccuti, M., Ciardo, G., Ma, Y., Wanamaker, S., Cattonaro, F., Vendramin, V., Scalabrin, S., Radovic, S., Wing, R., Morgante, M., Nussbaumer, T., Gundlach, H., Martis, M., Poland, J.A., Spannagl, M., Pfeifer, M., Moisy, C., Tanskanen, J., Zuccolo, A., Russell, J., Druka, A., Marshall, D., Bayer, M., Sampath, D., Febrer, M., Caccamo, M., Tanaka, T., Platzer, M., Fincher, G., Schmutzer, T. 2012. A physical, genetic and functional sequence assembly of the barley genome. Nature. 491:711-716.

Jansen, C., De Leon, N., Lauter, N.C., Hirsch, C., Ruff, L., Luebberstedt, T. 2013. Genetic and morphometric analysis of cob architecture and biomass related traits in the intermated B73xMo17 recombinant inbred lines of maize. BioEnergy Research. 6(3):903-916.

Ballini, E., Lauter, N.C., Wise, R.P. 2013. Prospects for advancing defense to cereal rusts through genetical genomics. Frontiers in Plant Science. 4:117.

Pliego, C., Nowara, D., Bonciani, G., Gheorghe, D., Xu, R., Surana, P., Whigham, E., Nettleton, D., Bogdanove, A., Wise, R.P., Schweizer, P., Bindschedler, L., Spanu, P. 2013. Host-Induced gene silencing in barley powdery mildew reveals a class of ribonuclease-like effectors. Molecular Plant-Microbe Interactions. 26(6):633-642.

Maffin, L., Hall, G., Hubbard, T., Whigham, E., Wise, R.P. 2012. iTAG Barley: A 9-12 classroom module to explore gene expression and segregation using Oregon Wolfe Barley. American Society of Plant Biologists. http://c.ymcdn.com/sites/my.aspb.org/resource/group/a9372bf4-9ae4-4d0b-ad0c-595c9dfc3543/itag_v20_march_2013.pdf.

King, K.E., Lauter, N.C., Lin, S., Scott, M.P., Shoemaker, R.C. 2013. Evaluation and QTL mapping of phosphorous concentration in soybean seed. Euphytica. 189(2):261-269.

Last Modified: 10/24/2014
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