FY2010 Oat Research Priorities
Enhancement of USDA-ARS Regional Small Grains Molecular Genotyping Laboratories
Fargo, ND Raleigh, NC Manhattan, KS Pullman, WA
Request: Additional Funding of $1,200,000
The USDA-ARS Regional Molecular Genotyping Laboratories are a critical resource to facilitate application of genomics information and DNA molecular marker technologies in improvement and breeding of wheat, barley and oats. Regional genotyping laboratories overcome barriers to practical use of markers through application of automated DNA extraction, and high-throughput marker screening procedures. These USDA-ARS labs support most plant breeding and variety development programs across the US by providing essential molecular marker and genomics assistance to university and private plant breeders.
The application of molecular-based selection strategies (marker-assisted and genome wide selection) and improved knowledge of genes and gene interactions will contribute directly to the improvement of oat and benefit producers, processors and consumers. Critical for this to occur is marker development and finding associations between the markers and important traits. In addition, development of a high throughput, breeder-friendly assay will allow direct application of the developed technologies by plant breeders. A replicated multi-location study across N. America will be needed for development of a predictive model to aid breeders in selection of lines to improve targeted traits.
(See below for details)
Oat Virus Research
USDA-ARS, West Lafayette, IN and the University of Illinois, Urbana, IL
Request: Additional Funding of $100,000
Barley Yellow Dwarf Virus (BYDV) is one of the most economically important diseases of oats in North America. Support for a research specialist at Urbana, IL will enhance the capacity to evaluate breeding lines from many different breeding programs for resistance to BYDV. There will be a new effort directed to fall-sown oats similar to that in place for spring-sown oats. The program has a national focus and assists numerous oat breeding programs. (See below for details)
Please see the following pages for rationale and justification for these programs.
Enhancement of USDA-ARS Regional Small Grains Molecular Genotyping Laboratories
Fargo, ND Raleigh, NC Manhattan, KS Pullman, WA
Recommendation: The National Barley, Oat and Wheat Improvement Committees express their appreciation to Congress for providing funding to establish four Regional Small Grains Molecular Genotyping Laboratories in Fargo, ND; Manhattan, KS; Raleigh, NC; and Pullman, WA. We are requesting additional funds for these laboratories to enable them to more fully meet their missions and expand capacity.
The four genotyping labs provide molecular marker and genotyping support to plant breeding and variety development programs carried out by seven private companies and by public breeding programs in 26 states across the US. Additional states are impacted because they produce and process varieties developed by these breeding programs.
| USDA-ARS Salaries and Expenses | FY2010 Request |
| Fargo, ND (Northern Plains) | $ 200,000 |
| Manhattan, KS (Central) | $ 200,000 |
| Pullman, WA (West) | $ 400,000* |
| Raleigh, NC (East) | $ 400,000 ** |
| $1,200,000 |
* The Pullman, WA laboratory is funded at only $350,000, with minimum funding of $750,000 per laboratory required to be functional and additional funding above that level needed to meet the rapidly increasing demands for genomic research.
** Part of this allocation would be used to fund oat-specific molecular marker research as described below. Several other laboratories will collaborate with the primary location including the USDA-ARS Small Grains and Potato Research Unit in Aberdeen, ID; USDA Regional Small Grains Molecular Genotyping Labs at Fargo, North Dakota, Raleigh, North Carolina; and the Genomics and Gene Discovery Lab at Albany, California.
Justification: The USDA-ARS Regional Molecular Genotyping Laboratories are a critical resource to facilitate application of genomics information and DNA molecular marker technologies in improvement and breeding of wheat, barley and oats. Molecular information for small grains is being compiled daily through the International Triticeae expressed sequence tag (EST) consortium (ITEC), the USDA-ARS Wheat Endosperm sequencing project, the NSF Wheat Genome project, the US Barley Genome Project, the USDA-NRI-CGP funded barley EST project and the CSREES NRI CAP grants for Wheat and Barley Applied Genomics.
A major gap remains between the discovery of molecular information and the use of that information in practical wheat, barley, and oat improvement programs. In order to counter threats to the nation’s crops from natural or maliciously introduced pests and maintain our position in the world marketplace, plant breeders must be equipped with gene-specific markers that give them rapid access to traits of value.
Regional genotyping laboratories overcome barriers to practical use of markers through application of automated DNA extraction, and high-throughput marker screening procedures but they are already operating at capacity. They provide a bio-informatics interface between rapidly expanding molecular genetic data and practical public and private breeding programs. With regional focus and responsibilities, the laboratories can more effectively address priority traits and constraints for specific production areas, market classes, and breeding programs.
The application of molecular-based selection strategies (marker-assisted and genome wide selection) and improved knowledge of genes and gene interactions will contribute directly to the improvement of oats and benefit both producers and consumers. A corporate stakeholder has pledged to fund a collaborative group of North American researchers to develop essential oat genetic information and new molecular markers. This effort will lay the groundwork for utilization of molecular technologies for oat improvement, but will require additional research to i) identify associations between molecular markers and important traits, ii) establish high throughput assays based on those markers so that breeders can effectively apply them, and iii) calculate a predictive model for N. American breeders to select the best lines to improve a particular trait such as soluble fiber content. Investment in genetic information and marker technology is critical if we are to develop new oat varieties with better nutritional characteristics and production stability in the face of disease and insect attack. Research support for oats and other under-funded specialty crops will enhance the diversity and strength of our agricultural economy, and consumer health.
The primary goal for oats is the identification and implementation of molecular markers to significantly improve the capacity and rate of selecting key traits during oat breeding. This will be accomplished by the development of oat gene-based, user-friendly markers similar to those developed in other grass species including wheat, barley and fescue, some of which will be adaptable and useful in oats. Comparative and integrative mapping of these sequences with gene structure, function and regulation information generated in other species will be used to identify oat genes and DNA markers targeted for oat improvement. The ability to identify oat genes that are turned on or off during infection by a pathogen or during adverse growing conditions will improve our ability and efficiency to breed oat cultivars with more effective disease resistance and stress tolerance. For nutritionally important traits that are specifically important in oat (e.g., heart-healthy b-glucan or endosperm oil content), identifying genes that differ in expression between good and poor quality varieties will greatly enhance breeders’ ability to manipulate these traits.
These USDA-ARS locations and their affiliated Land-Grant Universities have well established genomics research programs and consequently are positioned to make excellent progress in comparative oat genomics and oat nutritional quality.
Objectives:
- Identify new DNA markers associated with resistance to important production risks like cereal rusts, Fusarium head blight, powdery mildew, wheat streak mosaic virus, and cold or heat injury. Identify new DNA markers associated with enhanced end-use quality.
- Create marker profiles of cultivars and breeding lines cross-linked to other genetic information currently available; including cooperative regional nurseries, USDA-ARS National Small Grains Germplasm Center, and USDA-NAL crop databases.
- Develop and deploy breeder-friendly markers for important genes derived from wild relatives and other exotic germplasm resources.
- Develop and deploy new high throughput technology for marker assisted selection in breeding programs.
- yield and disease resistance in barley, while maintaining malting quality
- grain protein content in wheat using genes from Triticum diccocoides
- resistance to Fusarium head blight (scab) in wheat and barley.
- resistance to Hessian fly, greenbug, barley yellow dwarf and wheat streak mosaic viruses, aluminum toxicity and preharvest sprouting in wheat.
- durable resistance to stem, stripe, leaf and crown rust and powdery mildew
- winter survival in winter wheat, barley and oats.
Additional Location Updates and Budget Justifications for USDA-ARS Regional Small Grains Molecular Genotyping Laboratories are available.
Oat Virus Research
USDA-ARS, West Lafayette, IN and the University of Illinois, Urbana, IL
Recommendation: The National Oat Improvement Committee and the North American Millers’ Association request that Congress support research to combat oat viruses at the USDA-ARS Crop Production and Pest Control Research Unit at West Lafayette IN, and the University of Illinois, Urbana, IL. Barley Yellow Dwarf Virus (BYDV) is one of the most economically important diseases of oats in North America. Chronic BYDV problems have contributed substantially to the decline in US oat acreage, yet there is no full-time position, either in USDA-ARS or state agricultural experiment stations, devoted exclusively to this problem. BYDV has been an increasing problem in the southeastern and midwestern United States in recent years. In the midwest this may due to fewer late spring frosts which have killed early virus-infected aphid populations migrating from the South. Economic losses due to BYDV are significant. We request additional funding of $100,000 per year ($50,000 to support a Research Specialist position at Urbana, IL and $50,000 for research support at West Lafayette, IN). This position will support university oat breeding programs across the US by providing information of genetic resistance of breeding lines to this important pest.
Justification: Plant breeders, using conventional phenotypic selection methods, along with controlled inoculation with the virus, have made substantial progress in reducing susceptibility to this disease in spring sown oats. However, additional research is needed on evaluation of breeding lines of both fall and spring-sown oats and on the mechanisms involved in resistance. The situation is complicated by the existence of several strains of the virus. Research is required on how plants resist infection with several virus strains. Research to identify molecular markers associated with genes for resistance to BYDV would be very beneficial, and would allow oat breeders to more efficiently select for BYDV resistance.
Approach: Support for a research specialist at Urbana, IL will enhance the capacity to evaluate breeding lines from many different oat breeding programs for resistance to BYDV. There will be a new effort directed to fall-sown germplasm similar to that in place on spring-sown germplasm. This will improve selection for resistance to BYDV and benefit oat breeders and oat producers in many regions. It is our expectation that an ARS scientist at West Lafayette, IN would collaborate with oat breeders at Purdue University, the University of Illinois, and other locations to enhance the understanding of this important disease and accelerate the capability to develop BYDV resistant oat varieties. Because BYDV is also an important disease of wheat and barley, this research will likely provide new knowledge with application to the development of BYDV resistant wheat and barley varieties.
Last update February 6, 2009
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