Plant & Animal Genomes XV Conference

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

ADEPT2 – Re-Sequencing And SNP Discovery In Loblolly Pine

Jennifer M Lee¹ , Jill L Wegrzyn¹ , Kristian Stevens¹ , Andrew J Eckert¹ , Charles H. Langley¹ , David B Neale²

¹  University of California at Davis Deptartment of Evolution and Ecology Davis, CA 95616

²  University of California at Davis Deptartment of Plant Sciences Davis, CA 95616

The ADEPT2 project is aimed at determining the associations between natural genetic variation and complex traits (http://dendrome.ucdavis.edu/adept2). This is a collaborative project between UC Davis, North Carolina State University, University of Florida and Texas A&M University. Each partner is taking the lead on a part of the overall project and UC Davis is conducting all SNP discovery and genotyping. This will then be combined with the phenotyping being done at the partner institutes for analysis. The re-sequencing of 10,000 genes in loblolly pine in a diversity panel of 18 individuals is underway. Primers have been designed by Agencourt Biosciences for all EST clusters identified from the University of Georgia loblolly EST libraries and are in the process of being validated. Haploid megagametophyte tissue is being used for the re-sequencing and has been extracted and sent to Agencourt. Re-sequencing has begun and as sequences are received from Agencourt they are sent through a SNP discovery pipeline developed at UC Davis that is based on the polybayes SNP identification program. All information about the DNA extractions, trees, ESTs, primers, validation, sequences and SNPs are being entered into the TreeGenes database to ensure data integrity and allow users to track data. This information will be available through a series of interfaces developed at UC Davis. SNPs will then be evaluated and a subset used to genotype three loblolly pine populations for which phenotype data is available or is being collected from five phenotypic groups, wood properties (UF), disease resistance (UF), drought resistance (NCSU), gene expression (TAMU) and metabolomics (UCD). From here we will have the foundation for looking into the diversity of the loblolly pine genome and dissecting association between genotypes and phenotypes. At UC Davis we will develop the tools to give the community access to the data required for more detailed analysis.