Accelerating Pine Genomics Mississippi Genome Exploration Laboratory

APG Only
Pinus taeda
Loblolly pine (Pinus taeda L.)

Our research mission can be divided into long-term, mid-range, and project-specific goals.

Our research mission can be divided into long-term, mid-range, and project-specific goals.

Long-term goals
The long-term goal of our research is to understand the complex molecular genetic interactions that are responsible for the evolutionary success and socioeconomic importance of pines and other conifers.  Such understanding is critical to (1) protecting America's trees and forests from pests, pathogens, and environmental stresses, (2) developing safe and effective means of improving plantation trees, (3) realizing the tremendous potential of conifers as bioenergy feedstocks, (4) curbing global warming through carbon sequestration.

Mid-range goals (5-10 yrs)
Complete sequencing of the pine genome is a goal that we share with many members of the conifer genomics community.  APG represents a major step towards this goal.

Project-specific goals

  complete   (1) Construction of a pine bacterial artificial chromosome (BAC) library that will serve as an essential resource for physical mapping, gene discovery, and eventual genome sequencing (see BAC Library).  In fall 2008 the BAC library was completed.  It is composed of 1,797,504 individually archived clones and affords roughly 8X coverage of the enormous (21.7 Gb) pine genome.  This BAC library is the largest resource of its kind.  A manuscript on the BAC library has been submitted (see Publications).  
  complete   (2) Generation of a Cot curve for loblolly pine.  This goal has been completed.  A manuscript on the Cot curve is in preparation.  A manuscript describing a new algorithm/program for analyzing Cot data has been submitted (see Publications).  
  complete   (3) Isolation of gene- and repeat-enriched DNA components (via Cot filtration) and sample sequencing of components and unbiased genomic DNA.  Sequences are available through GenBank (see DNA Sequence for additional information).  
  complete   (4) Determination of how repeats are spatially organized within chromosomes and BACs via filter- and chromosome-based DNA hybridization.  A manuscript describing a novel retrotransposon family in pine has been published (see Publications), and additional research is in progress.  
  In progress   (4) Association of pine linkage groups with their cytologically-defined chromosomes.  A karyotype of pine has been published (see Publications).  Cytomolecular mapping is in progress.  
  complete   (5) Physical mapping of select gene and single-copy sequence probes onto pine BACs.  Initial work on this topic will be found in the pine BAC library manuscript (see Publications).  
  complete   (5) Education and training of students at graduate, undergraduate, and K-12 levels (see Education) with emphasis on engaging individuals from groups traditionally under-represented in the sciences (see Promoting Diversity).  

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*This material is based upon work supported by the National Science Foundation under Grant No. DBI-0421717.  Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.