Plant & Animal Genomes XI Conference

January 11-15, 2003
Town & Country Convention Center
San Diego, CA

Workshop: Forest Trees
            

NUCLEOTIDE DIVERSITY IN LOBLOLLY PINE (Pinus taeda L.)

¹ Environmental Horticulture, University of California, Davis CA USA

² Weyerhaeuser Company, Weyerhaeuser Technical Center, Tacoma WA USA

³ Forest Biotechnology Group, North Carolina State University, Raleigh NC USA

⁴ Institute of Forest Genetics, USDA Forest Service, Davis CA USA

There exists a large body of experimental data describing sequence diversity in plants and animals at individual nuclear loci. Genome-wide levels of nucleotide diversity and linkage disequilibrium (LD) have been estimated in only a few species, primarily human, Drosophila, Arabidopsis, and maize; these studies have contributed significant insights into the evolutionary forces shaping patterns of single nucleotide polymorphism and to theoretical and practical approaches to associating genotypes with phenotypes. We report nucleotide diversity and the extent of linkage disequilibrium in the gymnosperm loblolly pine (Pinus taeda L.). A common sample of alleles drawn from the haploid megagametophyte tissue of 32 unrelated individuals selected from the geographic range of loblolly pine was used. Approximately 460 kilobases representing 16 loci were sequenced and more than 14,000 bases were aligned over all loci. The distribution and frequency of single nucleotide polymorphisms, estimates of the population-recombination parameter (4Nc), and tests of neutrality will be presented. The extent of intralocus LD, and LD between linked loci, will be discussed in the context of future association mapping to identify genes that may contribute to phenotypic variation in loblolly pine.