Plant & Animal Genomes XIV Conference

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

Towards Physical Mapping And Genome Sequencing Of Loblolly Pine

Daniel G. Peterson^1,2 , C. Dana Nelson^2,3 , M. Nurul Islam-Faridi^3,4 , Doreen S. Main^5,6 , Jeffrey P. Tomkins⁵ , Annita Avery⁷ , John E. Carlson⁸ , Philippe Chouvarine^1,2 , Zenaida V. Magbanua^1,2 , Dipaloke Mukherjee^1,2 , LaShonda Robertson⁷ , Surya Saha¹ , Supaphan Thummasuwan^1,2

¹  Mississippi Genome Exploration Laboratory, Mississippi State University, 117 Dorman Hall, Mississippi State, MS, 39762, USA

²  Department of Plant and Soil Sciences, Mississippi State University, 117 Dorman Hall, Mississippi State, MS, 39762, USA

³  USDA Forest Service, Southern Institute of Forest Genetics, Saucier, MS, 39564, USA

⁴  Department of Forest Science, 305 Forest Science Bldg., Texas A&M University, College Station, TX, 77843, USA

⁵  Clemson University Genomics Institute, 51 New Cherry St, 304 Biosystems Research Complex, Clemson University, Clemson, SC, 29634, USA

⁶  Department of Horticulture & Landscape Architecture, Washington State University, P.O. Box 646414, Pullman, WA, 99164, USA

⁷  Department of Biology, Tougaloo College, 500 West County Line Road, Tougaloo, MS, 39174, USA

⁸  School of Forest Resources, Pennsylvania State University, 405C Life Sciences Building, University Park, PA, 16802, USA

We are working to establish a better understanding of the genome of loblolly pine, Pinus taeda L., the most economically important tree in the U.S. Deliverables of this project, now starting its second year, include a 10X BAC library for the loblolly genotype "7-56," characterization of the pine genome via Cot analysis, sequencing of random genomic and Cot-filtered sequences, and study of the organization of repetitive and low-copy sequences by fluorescence in situ hybridization (FISH) and macroarray analysis. Collectively, the data generated in this study will provide considerable insight into the structure of the pine genome which in turn will help guide efficient physical mapping and sequencing of pine. To date, high-throughput archival of BAC clones is well underway, Cot analysis has been completed, and Cot-filtered libraries are under construction. With regard to sequencing, a new partnership with John Carlson (Pennsylvania State University) and minor re-budgeting has provided us with an opportunity to utilize a 454 Genome Sequencer 20 (www.454.com) to produce > 20 times the sequence data slated for generation in the original funded proposal. The 454 sequence data will be compared with genomic and Cot-filtered sequences elucidated using standard capillary sequencing techniques. The > 60 Mb of sequence data produced to date and the growing BAC library have set the stage for the FISH- and macroarray-based physical mapping of the pine genome slated to begin in Year 2. Additional information on this project is available at www.mgel.msstate.edu.