Plant & Animal Genomes XIII Conference

January 15-19, 2005
Town & Country Convention Center
San Diego, CA

Nucleotide Diversity And Linkage Disequilibrium In Adaptive Trait Related Candidate Genes In Douglas-Fir

Konstantin V. Krutovsky¹ , Barnaly Pande² , Kathleen D. Jermstad³ , Glenn T. Howe⁴ , John Bradley St. Clair⁵ , Nicholas C. Wheeler⁶ , David B. Neale^1,2

¹  Institute of Forest Genetics, Pacific Southwest Research Station, USDA Forest Service, Davis, California 95616, USA

²  Department of Plant Sciences, University of California, Davis, California 95616, USA

³  Institute of Forest Genetics, Pacific Southwest Research Station, USDA Forest Service, Placerville, California 95667, USA

⁴  Department of Forest Science, Oregon State University, Corvallis, Oregon 97331-5752, USA

⁵  Pacific Northwest Research Station, USDA Forest Service, Corvallis, OR 97331-4401, USA

⁶  Molecular Tree Breeding Services, LLC, Centralia, Washington 98531, USA

This study provided the results from the survey of nuclear sequence variation and linkage disequilibrium in cold-hardiness and wood quality related candidate genes in Douglas-fir. The set of genes has been selected based on their collocation with cold-hardiness related QTLs found in the previous studies, and published expressional and/or physiological data for close homologs studied in other plant species that support their potential involvement in the low temperature response or wood development. The SNP discovery panel represented 24 different trees from six regions in the Washington and Oregon states plus parents of the segregation population used in the QTL study. The SNPs were relatively frequent with one SNP per every 46 bp. Haplotype and nucleotide diversities were also relatively high with Θ_W = 0.00702 and π = 0.00655 on average. The substitutions were almost five times less frequent in nonsynonymous sites than in synonymous and noncoding sites with Θ_W = 0.00261 vs. 0.01132 and π = 0.00210 vs. 0.01055 for nonsynonymous vs. silent (synonymous plus noncoding) substitutions, respectively. Linkage disequilibrium decayed relatively slow within genes and often extended beyond 500 bp. Haploblock analysis was used to define haplotype tagged SNPs. Several likelihood-based methods were used for estimating the rates of nonsynonymous and synonymous substitutions at each site along the phylogeny in order to identify SNPs under positive or negative selection. Obtained data helped to select SNPs for association mapping in progress.