Plant & Animal Genomes XIV Conference

January 14-18, 2006
Town & Country Convention Center
San Diego, CA

Estimation Of Population Structure In The Douglas-Fir Association Mapping Study

Konstantin V. Krutovsky¹ , John Bradley St. Clair² , Robert Saich³ , Valerie D. Hipkins³ , David B. Neale⁴

¹  Department of Forest Science, Texas A&M University, College Station, TX 77843-2135, USA

²  Pacific Northwest Research Station, USDA Forest Service, Corvallis, Oregon 97331-4401, USA

³  National Forest Genetics Laboratory, Pacific Southwest Research Station, USDA Forest Service, Placerville, California 95667, USA

⁴  Department of Plant Sciences, University of California, Davis, California 95616, USA

To avoid false associations between phenotypes and genotypes for pooled samples in association mapping due to the demographic or population structure the population differentiation should be carefully estimated using preferably neutral markers. The population structure has been studied in a range-wide sample of ~1300 Douglas-fir trees from Washington and Oregon that are used for association mapping between cold-hardiness and phenology related phenotypes and SNPs in the adaptive trait related candidate genes. All trees have been genotyped for 25 isozyme and 6 SSR markers using individual megagametophytes. Population structure analysis has been done separately for isozyme and SSR markers, as well as for both data sets combined. Results based on isozyme and SSR data sets have been compared and discussed. We also discuss how population structure should be taken into account in the association mapping.