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United States Department of Agriculture

Agricultural Research Service

Research Project: Oat SNP Development and Identification of Loci Affecting Key Traits in North American Oat Germplasm Using Association Genetics
2011 Annual Report


1a.Objectives (from AD-416)
1) Develop genetic marker resources for MAB of traits impacting human health, agronomics, milling quality, and disease resistance,.
2)Conduct a two year multi-location association mapping study to develop marker-trait associations to facilitate the development of new oat varieties with superior health benefits and improved agronomics, milling quality, and disease resistance,.
3)Partner with the barley CAP portal to effectively utilize and disseminate the information generated by the project, and.
4)To convert OOPA SNP and DArT markers to TaqMan® real-time PCR-based assays for immediate use in marker-assisted breeding (MAB).


1b.Approach (from AD-416)
The OOPA-MAB and DArT-MAB platforms will be developed by selecting SNPs or DArTs from pilot arrays based on assay robustness, chromosome position, and minor allele frequency. Association mapping studies will be done using a population of 592 oat lines selected by collaborating breeders. The spring, winter, and validation lines will be grown in separate trials with appropriate checks. Agronomic traits will be collected by breeders in at least four locations. Seed will be harvested from these locations and shipped to Aberdeen for milling quality analysis and seed will be process and shipped to Madison for avenanthramide, a-tocotrienol, and a-tocopherol analysis and Winnipeg for ß-glucan analysis. Disease data (Crown rust, Stem rust, and BYDV) will be collected in eight locations, while freeze tolerance data will be collected in NC. Genotypic and phenotypic data will be uploaded to the project database at the GrainGenes website enabling easy access for downstream statistical analyses. Appropriate analyses will be done in TASSEL. DArT P/L will provide complementary statistical analysis using its proprietary data mining software based on Statistical Machine Learning. OOPA SNP and DArT markers linked to targeted QTL will be converted to TaqMan-based assays for use in practical MAB efforts.


3.Progress Report

Over the past 48 years world-wide oat production has declined 58%, while production of crops like corn and soybean have drastically increased. Research groups in North America actively working on oat have also declined from 28 (1998) to 11 (2008). The Collaborative Oat Research Enterprise was recently established by the USDA-ARS in Aberdeen, Idaho as an international scientific collaboration to reverse these trends. As part of the project, ARS scientists at Aberdeen, ID, enlisted the help of scientists at the Texas A & M breeding program to evaluate 685 oat lines for photoperiod sensitivity and disease resistance including crown and stem rust. Over the last year (2010 – 2011), field evaluations have yielded key information enabling the development of genetic “signpost” for resistance to these diseases. To date, several signpost have been developed and are being used by North American breeding programs as a genetic “GPS” to expedite the development of oat varieties with crown and stem rust resistance. This work will allow target development of high beta glucan lines possible in oat. This work directly relates to objective 3 of the current ARS Aberdeen project plan (5366-21000-024-00D) “Develop improved barley and oat cultivars meeting the needs of conventional and specialty markets for both dryland and irrigated production systems.” Monitoring of the project is accomplished via site visits, phone conversations, e-mail and written reports.


Last Modified: 10/31/2014
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