Plant & Animal Genomes XV Conference

January 13-17, 2007
Town & Country Convention Center
San Diego, CA

Candidate Gene-Based Association Genetics In Douglas-Fir

Barnaly Pande¹ , Konstantin, V. Krutovsky² , Kathleen, D. Jermstad³ , Glenn, T. Howe⁴ , J. Bradley St. Clair⁵ , Nicholas, C. Wheeler⁶ , David, B. Neale¹

¹  Department of Plant Sciences, University of California, Davis, CA, USA

²  Department of Forest Science, Texas A&M University, 2135 TAMU, College Station, TX

³  USDA Forest Service, Pacific Southwest Research Station, Institute of Forest Genetics, Davis / Placerville, CA, USA

⁴  Department of Forest Science, Oregon State University, Corvallis, OR , USA

⁵  USDA Forest Service, Pacific Northwest Research Station, Corvallis, OR, USA

⁶  Molecular Tree Breeding Services LLC, Centralia, WA, USA

Adaptation is critical to plant survival and growth in a changing environment. The genetics of plant response to cold and drought stress, and to changing photoperiod is well understood and recent microarray studies in model organisms are beginning to elucidate putative candidate genes for the control of these responses. In trees, size and complexity of the genome precludes any attempt at positional cloning and yet, understanding the molecular basis of adaptation is in these long-lived species is critical to improving tree-breeding and conservation efforts, and to understand the impact of global warming on forests in the US. We are using candidate gene-based association mapping to identify the loci and alleles responsible for phenotypic variation among conifers. We have already successfully demonstrated this approach and identified SNPs associated with variation in wood quality and response to drought stress in loblolly pine (Pinus taeda L.). Our research in Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco) aims to identify variation in candidate gene homologs for cold tolerance and test these for association with collected phenotypic data in a population of c.900 trees which have been tested for evidence of population structure using both isozyme and SSR markers. The extensive range of this species across the heterogenous environments of the western US demonstrates its remarkable capacity for adaptation. We report the analysis of sequences representing 150 candidate gene homologs for low temperature tolerance based on a modest EST collection, and the success and efficacy of automated primer design, sequence validation and SNP identification within these sequences.