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United States Department of Agriculture

Agricultural Research Service

2010 Annual Report

1a.Objectives (from AD-416)
Obj. 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.

Obj. 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)
Obj. 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.

Obj. 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
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. We continued to investigate barley responses to two important fungal pathogens, stem rust and powdery mildew, to develop biological and molecular assays to help locate and characterize the hundreds of barley genes that respond to pathogen attack. Our primary entry point has been to determine function of genes that are uniquely activated in resistant vs. susceptible plants via Barley1 GeneChip transcript profiling. We discovered the novel blufensin family of cereal-specific peptides, and demonstrated that Blufensin1 is a negative regulator of plant defense. Further investigations identified genes involved in nuclear import and the secretory pathway as being regulated by Blufensin1, plant processes that are critical to the genetic brigade that is activated when fungal pathogens establish their feeding structures in the host. Conserved mechanisms have been shown to govern most plant-pathogen interactions, thus, these discoveries should extend to other cereal grains, such as wheat, rice, and maize. To mitigate the emerging disease threat to Ug99 stem rust, we have employed genetical genomics, in which genome-wide expression profiling is performed on entire segregating populations. With this approach, we have discovered a master switch that regulates the expression of over 500 Ug99 responsive defense genes and co-localizes with an Adult Plant Resistance Quantitative Trait Loci (QTL) or region of DNA associated with resistance to Ug99. 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.

1. Exosome complex potentiates cell survival in barley. Cell death is a key component of plant development and disease resistance. Hence, investigations into the molecular mechanisms of cell death provide insight into diverse cellular processes. Utilizing a combined strategy of high-throughput transcript profiling with classical genetic analysis of cell death mutants, ARS researchers at Ames, Iowa, isolated the ribosomal RNA (rRNA)-processing protein 46 (RRP46) gene from barley. RRP46 is one of eight core components of the exosome, a conserved complex involved in rRNA maturation, RNA degradation, and messenger RNA (mRNA) quality control. RRP46 appears to be a master regulator that controls the expression of dozens of other genes, which are necessary for plant survival, stature, and yield. 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
Wise, R.P., Lauter, N.C., Szabo, L.J., Schweizer, P. 2009. Genomics of Biotic Interactions in the Triticeae. In: Feuillet, C., Muehlbauer, G., editors. Genetics and Genomics of the Triticeae. New York, NY: Springer. p. 559-589.

Wang, K., Frame, B., Xu, X., Moeller, L., Lamkey, K., Wise, R.P. 2009. Strategies for the Production of Maize-derived Pharmaceuticals using Cytoplasmic Male Sterile Lines: in vitro Tissue Culture/Transformation and Field Breeding Approaches. Maydica. 54(1):199-210.

Zhou, S., Wei, F., Nguyen, J., Bechner, M., Potamousis, K., Goldstein, S., Pape, L., Mehan, M.R., Churas, C., Pasternak, S., Forrest, D.K., Wise, R.P., Ware, D., Wing, R., Waterman, M., Livny, M., Schwartz, D.C. 2009. A Single Molecule Scaffold for the Maize Genome. PLoS Genetics. 5(11):1-14.

Abebe, T., Wise, R.P., Skadsen, R.W. 2009. Comparative Transcriptional Profiling Established the Awn as the Major Photosynthetic Organ of the Barley Spike while the Lemma and the Palea Primarily Protect the Seed. The Plant Genome. 2(3):247-259.

Wise, R.P., Meng, Y., Moscou, M.J., Xu, W. 2010. Regulators of Innate Immunity in Cereal-fungal Interactions. In: Antoun, H., Avis, T., Brisson, L., Prevost, D., Trepanier, M., editors. Biology of Plant-Microbe Interactions. St. Paul, MN: International Society for Molecular Plant-Microbe Interactions. p. 1-7.

Xi, L., Moscou, M.J., Meng, Y., Xu, W., Caldo, R.A., Shaver, M., Nettleton, D., Wise, R.P. 2009. Transcript-based Cloning of RRP46, a Regulator of rRNA Processing and R-Gene-Independent Cell Death in Barley–Powdery Mildew Interactions. The Plant Cell. 21(10):3280-3295.

Kronmiller, B.A., Wise, R.P. 2009. Computational Finishing of Large Sequence Contigs Reveals Interspersed Nested Repeats and Gene Islands in the rf1-associated Region of Maize. Plant Physiology. doi: 10.1104. p. 109.143370. 151(2):483-495.

Crossett, A., Lauter, N.C., Love, T.M. 2010. An Empirical Method for Establishing Positional Confidence Intervals Tailored for Composite Interval Mapping of QTL. PLoS One. 5:e9039.

Abebe, T., Melmaiee, K., Berg, V., Wise, R.P. 2009. Drought Response in the Spikes of Barley: Gene Expression in the Lemma, Palea, Awn, and Seed. Functional and Integrative Genomics. 10(2):191-205.

Last Modified: 8/31/2015
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