2011 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 Successfully controlling existing and emerging cereal crop diseases is vital to food security because cereals form the foundation of human and domesticated animal diets world-wide. To mitigate the emerging disease threat to wheat and barley Ug99 stem rust, we have employed genetical genomics, which surveys 22,000 barley genes at the same time. By performing genome-wide expression profiling on an entire segregating population under multiple conditions, we discovered a master switch that regulates the expression of over 350 Ug99-responsive defense genes and co-localizes with an Adult Plant Resistance Quantitative Trait Loci (QTL). Since Ug99 can devastate yields among nearly all wheat and barley varieties grown worldwide, genetic manipulation of the switch could be used to enhance resistance to Ug99. A better understanding of the molecular signaling that takes place during the development of barley powdery mildew will facilitate new control strategies and provide useful insight into interactions of obligate fungal biotrophs with their plant hosts. Thus, a third approach utilizes pathogen-derived information to identify plant targets. Identification and characterization of powdery mildew effector proteins 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 (http://www.blugen.org/) combined with several gene silencing and overexpression systems to identify pathogen effectors. 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. 4.Accomplishments 1. Master regulator of enhanced Ug99 stem rust resistance discovered in barley. The identification of molecular events directly involved in conferring resistance to pathogens is critical to 21st century strategies for plant disease resistance. ARS researchers at Ames, Iowa used a combination of genomic and bioinformatic tools to investigate resistance to Ug99 stem rust, a devastating fungal pathogen of wheat and barley. They identified a master switch that controls hundreds of genes in response to this disease. In collaboration with U.S. and Kenyan partners, they showed that enhanced adult plant resistance to Ug99 is associated with the switch. Ug99 can devastate yields among nearly all wheat and barley varieties grown worldwide, thus characterization of the master switch and development of molecular markers for plant breeding can be used to mitigate the threat of Ug99. This discovery, also supported by the National Science Foundation-Plant Genome Research Program, provides new knowledge of broad significance to plant scientists, and to growers who utilize disease resistance to protect their crops. Review Publications Moscou, M.J., Lauter, N.C., Caldo, R.A., Nettleton, D., Wise, R.P. 2011. Quantitative and temporal definition of the Mla transcriptional regulon during barley-powdery mildew interactions. Molecular Plant-Microbe Interactions. 24(6):694-705. Moscou, M.J., Lauter, N.C., Steffenson, B., Wise, R.P. 2011. Quantitative and qualitative stem rust resistance factors in barley are associated with transcriptional suppression of defense regulons. PLoS Genetics. 7(7):DOI: 10.1371/journal.pgen.1002208.