Plant & Animal Genomes XVI Conference

January 12-16, 2008
Town & Country Convention Center
San Diego, CA

Pine Physical Mapping And Genome Sequencing

C. Dana Nelson¹ , Daniel G. Peterson² , Craig S. Echt¹ , Ross Whetten³ , Kostya Krutovsky⁴ , Cetin Yuceer⁵ , Jeffrey Dean⁶

¹  Southern Institute of Forest Genetics, Southern Research Station, USDA Forest Service, Saucier, Mississippi, 39574, USA

²  Department of Plant and Soil Sciences, Mississippi State University, Mississippi State, Mississippi, USA

³  Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, North Carolina, USA

⁴  Department of Ecosystem Science and Management, Texas A&M University, College Station, Texas, USA

⁵  Department of Forestry, Mississippi State University, Mississippi State, Mississippi, USA

⁶  Daniel B. Warnell School of Forestry and Natural Resources, University of Georgia, Athens, Georgia, USA

Within the pine genomics community there is an emerging consensus that physical mapping and sequencing of a reference genome is the most logical means of rapidly advancing genomic research on this key plant taxon and that such an endeavor is now technically and fiscally feasible. For these reasons we believe that it should be pursued forthwith. A promising physical mapping and sequencing strategy involves isolation and shearing of individually-archived BAC clones, labeling of each BAC with a unique oligonucleotide “bar code,” and pooling and sequencing groups of fragmented, differentially bar-coded BACs using an ultra-throughput sequencer. In theory, the 1 Gb/run capability of an Illumina/Solexa sequencer would permit simultaneous sequencing of 1000 bar-coded BACs at 10X coverage per BAC (assuming 100 kb BAC inserts). Deconvolution of the pooled reads should allow BAC-specific sequence assembly while integration of data from multiple sequencer runs should enable construction of BAC contigs encompassing whole chromosomes. We propose that the loblolly pine genotype 7-56 is the most logical reference genome due, in part, to its available BAC and EST resources. We see a significant need for a purpose-built, high resolution genetic map to assist in genome physical mapping and sequence assembly. A haploid mapping population of megagametophytes collected from 7-56 female strobili would be specifically tailored for efficient mapping of 7-56 SNPs and STSs. Subsequent ordering of physical sequences could then use the resulting genetic map as a guide.