2007 Annual Report 1a.Objectives (from AD-416) The purpose of this project is to characterize small grains germplasm using molecular and other methods to better understand diversity within the National Small Grains Collection. Information generated will help guide future evaluation, maintenance, and acquisition work and will benefit ARS breeding research. 1b.Approach (from AD-416) An important activity within the National Small Grains Collection is the evaluation of germplasm in the collection. In the past this evaluation was focused on agronomic, quality, and disease resistance traits. Future evaluations will also include molecular characterization of germplasm resources and the research proposed here is part of this theme. Core subsets of various collections have been designated based on geographic origin of accessions. The first step in the proposed research will be to evaluate genetic diversity of the core subsets based on molecular data and to determine their validity and usefulness based on comparisons to other available descriptor data using established statistical techniques. The work will also seek to identify and evaluate new molecular techniques (e.g., bioinformatics, cell and tissue culture) that can be applied to germplasm characterization work. Information generated will be then applied to small grains improvement programs within the Aberdeen Unit. Documents SCA with Alabama A & M. 3.Progress Report This report serves to document research conducted under a specific cooperative agreement between ARS and the Alabama A&M College , Normal. Additional details of research can be found in the report for the parent project, 5366-21000-024-00D, “Barley and Oat Germplasm Evaluation and Enhancement”. This report includes the progress made by the graduate student, Ms. Chaitanya Vemulapalli, who was initiated in the Project in the Year 2005. Ms Chaitanya finished the project entitled ‘Assessment of genetic variation in Avena fatua by DNA marker profiling’. She graduated with a M.S. in Plant Science from the Department of Plant & Soil Science at Alabama A&M University during Fall 2006. She is currently working with Operon Biotechnologies in Huntsville, AL. During the Masters’ study, Ms. Vemulapalli’s objectives were i) to characterize a core subset of wild oat collection within the national small grains germplasm resource using molecular markers and ii) to determine their validity and usefulness based on comparisons to agronomic, morphological and genetic descriptors. Sixty four accessions of A. fatua and four cultivated oat varieties were grown in greenhouse and leaf tissue was collected at 3 weeks old stage for DNA isolation. Leaf tissue samples of 15 cultivated oat genotypes were obtained from Aberdeen. DNA was extracted using the sodium bisulfate DNA extraction procedure used for cereals. DNA quality was estimated by running the DNA samples in 0.8 % Agarose gel @ 40 V for 4 hours and quantified using Fluorometer. A total of 143 primer pairs including 22 RFLP-PCR, 114 SSR, and 7 Intron based primer pairs were identified through literature search. Optimization of PCR conditions for primer pairs was performed using the cultivated oat genotypes, Kanota, TAMO-301 and Ogle. Amplified PCR products were screened for polymorphism using both 4% Metaphor Agarose gel electrophoresis and 6% Polyacrylamide gel electrophoresis (PAGE). Over 40 markers showed polymorphism between each of the two mapping parental combinations used for generating Oat genetic maps. There was considerable variation among the Oat accessions tested. However all cultivated oats were clustered in a group separate from the phylogenetic group composed wild oat accessions. The marker profiling data is being analyzed along with the morphological and agronomic trait data in order to find markers associated with important traits. Monitoring activities by email and phone calls.