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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

Location: Small Grains and Potato Germplasm Research

2012 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:

Progress was made on the objective, which fall under National Program 301, Component 2, Crop Informatics, Genomics, and Genetic Analyses. Progress on this project focuses on problem of expanding the DArT markers pools in oat by adding the marker detection in tetraploid oat species. Collaboration with Diversity Arrays Technology Pty Ltd Canberra, Australia – we expanded the existing DArT marker array and developed a new DArT marker array based on tetraploid oat species. These results support Objective 1 in the parent project, development of molecular tools for oat. Currently, we are awaiting approval from NIFA for a one year no-cost extension.


Last Modified: 4/17/2014
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