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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
2010 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. Documents Reimbursable with AFRI. Log 38795.


3.Progress Report

A population of 685 oat lines was selected by ten North American breeding programs containing lines expressing valuable traits like high soluble fiber and resistance to particular diseases. Seed for each line was purified in Aberdeen, ID and increase over the winter in New Zealand. Seed for the population was shipped to over 15 locations across the globe and agronomic traits like heading date and lodging were evaluated. In addition, disease reactions to barley yellow dwarf virus, crown rust, and stem rust were recorded for the population in select locations. Based on sequence information from the General Mills Trust project number 5366-21000-028-07T, 700 new oat genetic markers were developed. Additionally, a new database called The Avena Toolbox (TAT) has been established. Communication and exchange of work has taken place via meetings, and conference calls


Last Modified: 10/21/2014
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