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United States Department of Agriculture

Agricultural Research Service

2006 Annual Report

1.What major problem or issue is being resolved and how are you resolving it (summarize project aims and objectives)? How serious is the problem? Why does it matter?
This research is aligned with NP302, Plant Biological and Molecular Processes - Component 1. Functional Utilization of Plant Genomes: Translating Plant Genomics into Crop Improvement.

Fungal pathogens are perhaps the greatest impediment to production of grain cereal plants worldwide. When environmental conditions are opportune for pathogen growth, between 30 and 50% of potential yield can be lost. To offset crop losses from pathogens, plant breeders have turned to genetic varieties that help crops resist these diseases. We are using barley powdery mildew as our model system. The disease is caused by the obligate fungal pathogen, Blumeria graminis, and is widely distributed throughout the world. It is most damaging in cool, wet climates such as northern Europe and the winter growing season in the mid-Atlantic and southeastern U.S. Powdery mildew disease causes reduced grain yield, kernel weight, and grain protein. Excellent genetic materials and availability of cloned genes specifying resistance to this disease make this system ideal for basic studies relating to recognition and active defense.

Two interlinked objectives will drive our investigations: The first is to dissect the transcriptional control of disease defense in cereals and identify key pathways and regulators. Such detailed knowledge will provide target genes to enhance disease resistance, one of the most effective ways to protect crops. The second is to develop reliable methods to evaluate the effects of novel transgenes on recipient genomes, thus providing molecular indicators of new transgenic varieties. To accomplish the first objective, we will exploit the detailed molecular genetics of Mla-specified, barley-powdery mildew interactions as a launching point to investigate defense gene function across wide taxonomic boundaries. We will take advantage of the publicly available Barley1 GeneChip, a uniform RNA profiling platform that allows the investigation of 22,000 cereal genes in a single experiment. Near-isogenic barley lines that possess various Mla resistance alleles and associated mutants will be utilized to identify significant new genes in disease resistance networks. Project data will be integrated into BarleyBase/PLEXdb (, our MIAME-compliant and Plant Ontology enhanced plant expression database, to facilitate the bioinformatic and statistical analysis of co-regulated genes. High-throughput reverse genetic systems in barley and Arabidopsis will be used to functionally validate candidate genes in resistance pathways of both monocot and dicot plants. To achieve the second objective, global gene expression profiling will be used to assess the gene expression consequences of crop improvement strategies such as hybridization, marker assisted selection, and transgenesis. Within a unifying context, comparisons will be made between hybrid and inbred lines, MAS lines and their recurrent parents, and transgenic lines and their progenitors. Differences that are discovered will be used to focus improvements in transgenic technologies.

2.List by year the currently approved milestones (indicators of research progress)
FY 2006 Identify genes involved in plant disease defense from analysis of microarray analysis of rapid acting Mla alleles

Four new gene candidates from Obj. 1 tested via single-cell RNA interference (dsRNAi)

Genes identified for DIStilling

Homozygous T-DNA knockout mutations for Arabidopsis candidate orthologs obtained

Enhance Rice-Triticeae linkages from Gramene and PlantGDB

Design overgo probes and identify BAC clones

Evaluate maize inbreds, transgenic lines, and marker-assisted selection lines via global gene expression profiling

FY 2007 Identify genes involved in plant disease defense from analysis of microarray analysis of delayed acting Mla alleles

Twenty new gene candidates from Obj. 1 tested via dsRNAi

Comparison of resistance responses mediated TIR-NBS-LRR and CC-NBS-LRR R proteins examined

Direct links to Triticeae map positions in Graingenes and Gramene databases completed

Expand BarleyBase platform to rice, wheat, maize, sugarcane, and other important crop chips

Design overgo probes and identify BAC clones

Evaluate maize inbreds, transgenic lines, and marker-assisted selection lines via global gene expression profiling

FY 2008 Twenty new gene candidates from Obj. 1 tested for overexpression

DIStilling mutants identified; crosses made

Time-course query experiments to look for causal relationships between significant genes

Direct links to map positions and in MaizeGDB completed

Promoter regions sequenced; rice orthologs identified

Complete data analysis of expression profiling experiments

FY 2009 Forty new gene candidates from Obj. 1 tested via dsRNAi

Heterologous expression used to establish gene function

Comparative synteny browser completed

Identify motifs in 5’ and 3’ regions of co-regulated genes

Complete assessment of aberrant gene expression in wildtype, transgenic, and mutant barley lines

4a.List the single most significant research accomplishment during FY 2006.
This accomplishment is aligned with NP302, Plant Biological and Molecular Processes - Component 1. Functional Utilization of Plant Genomes: Translating Plant Genomics into Crop Improvement

Gene Expression Research Provides Important Information on Growth of Cereal Crops

We worked with an international team of cereal scientists from five U.S. universities, in addition to institutions from five countries on four continents to evaluate the expression of 22,000 genes in fifteen tissues from seed-to-seed in barley development. The "Barley Gene Atlas" is the first map of the barley transcriptome for nearly all of these stages, and provides a unique opportunity to integrate detailed information on individual genes into a unified developmental framework. It is available to the worldwide research community as a comparative dataset for those investigating genes or regulatory networks in other plant species. The Barley1 GeneChip contains probe sets corresponding to approximately 22,000 barley genes. The ability to survey the mRNA expression of 22,000 genes in a single experiment has promoted a high-throughput approach to investigate a wide range of developmental, physiological, or biochemical processes in this large-genome cereal crop. Thus, the information derived from these studies will advance new methods for disease resistance, yield, and nutrition for all cereal crops, which are among the world’s most important food sources.

4b.List other significant research accomplishment(s), if any.

4c.List significant activities that support special target populations.

5.Describe the major accomplishments to date and their predicted or actual impact.

6.What science and/or technologies have been transferred and to whom? When is the science and/or technology likely to become available to the end-user (industry, farmer, other scientists)? What are the constraints, if known, to the adoption and durability of the technology products?
Information on the Barley Gene Atlas has been communicated to other scientists and breeders through publication in peer-reviewed journals and by presentation at invited seminars at universities, and national and international meetings. The Barley Gene Atlas was also selected for a USDA-CSREES Research Highlight.

7.List your most important publications in the popular press and presentations to organizations and articles written about your work. (NOTE: List your peer reviewed publications below).
Three invited lectures at NOVA Ph.D. course in Genomics and Plant Breeding in Mustiala, Finland, June 3-9, 2006.

Lauter, N.C., Moose, S.P. 2006. Functional and positional dissection of a novel QTL affecting the duration of juvenility in maize. 42nd Annual Illinois Corn Breeders School Proceedings. 42:64-82.

USDA Awards $5 Million for Barley Applied Genome Research, Education and Extension

National Barley Project Involves Iowa State Researchers

Review Publications
Druka, A., Muehlbauer, G., Druka, I., Caldo, R., Baumann, U., Rostoks, N., Schreiber, A., Wise, R.P., Close, T., Kleinhofs, A. 2006. An atlas of gene expression from seed to seed through barley development. Functional and Integrative Genomics. 6(3):202-211.

Last Modified: 9/3/2015
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