Diane Jofuku Okamuro
IOS Division of Integrative Organismal Systems
BIO Directorate for Biological Sciences
Start Date:
September 1, 2004
Expires:
August 31, 2010 (Estimated)
Awarded Amount to Date:
$1668611
Investigator(s):
Daniel Peterson dpeterson@pss.msstate.edu (Principal Investigator)
Islam-Faridi (Co-Principal Investigator) Doreen Main (Co-Principal Investigator) C. Dana Nelson (Co-Principal Investigator) Christopher Saski (Co-Principal Investigator)
Jeffrey Tomkins (Former Co-Principal Investigator)
Sponsor:
Mississippi State University
PO Box 6156
MISSISSIPPI STATE, MS 39762 662/325-7404
NSF Program(s):
PLANT GENOME RESEARCH RESOURCE, PLANT GENOME RESEARCH PROJECT
Field Application(s):
Program Reference Code(s):
BIOT, 9251, 9232, 9150, 9109, 2886, 1228
Program Element Code(s):
7577, 1329
ABSTRACT
Loblolly pine (Pinus taeda) is the primary source of pulpwood for the U.S. paper industry and the most economically important crop of any kind in the southeastern states. Isolation, sequencing, and characterization of the genes of loblolly pine represents a means to better understand the evolutionary success of pine, to develop environmentally sound strategies for dealing with pine diseases and pests, to effectively manipulate genes responsible for pine's many economic traits, and to maximize yield per acre. However, the loblolly pine genome, like other gymnosperm genomes, is exceedingly large and is composed primarily of non-genic repetitive elements, making characterization of the parts of the pine genome containing the genes (the "gene space") difficult. In addition, many of the genetic, molecular, and cytogenetic resources enjoyed by other crop species are lacking or underdeveloped for pine. We will generate important molecular and cytogenetic resources for pine and utilize these resources to provide insight into the structure and evolution of the loblolly genome. The information generated in this study and the molecular resources themselves will accelerate physical mapping and sequencing of pine's gene space and advance pine genome research.
Specific project objectives include:
(1) construction of a pine 10X Bacterial Artificial Chromosome (BAC) library that will serve as an essential resource for physical mapping, gene discovery, and eventual genome sequencing,
(2) production of gene- and repeat-enriched DNA libraries (via Cot-Based Cloning and Sequencing or CBCS) that will be used to explore genomic sequence diversity in pine, acquire critical information on pine genes including regulatory sequences, and characterize the repeats that comprise most of the pine DNA,
(3) determination of how repeats and low-copy sequences are spatially organized within chromosomes and BACs via filter- and chromosome-based DNA hybridization,
(4) association of pine linkage groups with their cytologically-defined chromosomes as a means of studying relationships between genetic linkage, chromosome structure, and physical (DNA) distances, and
(5) education and training of students at graduate, undergraduate, and K-12 levels with emphasis on engaging individuals from groups traditionally under-represented in the sciences.
Access to project outcomes
Biological resources resulting from this project (e.g., DNA libraries and filters) will be made available to the public through the Clemson University Genomics Institute (http://www.genome.clemson.edu). Raw DNA sequence data (i.e., trace, quality, and flat files) will be deposited in the NCBI Trace Repository within one week of generation (as per the Bermuda/Ft. Lauderdale agreements; http://www.genome.gov/10506537) while annotated sequence data will be archived in the GenBank GSS database.
PUBLICATIONS PRODUCED AS A RESULT OF THIS RESEARCH
Blakey CA, Costich D, Sokolov V, Islam-Faridi MN. "Tripsacum Genetics: From observation along a river to molecular genomics," Maydica, v.52, 2007, p. 81.
Bunge J, Epstein SS, Peterson DG. "Comment on "Computational Improvements Reveal Great Bacterial Diversity and High Metal Toxicity in Soil"," Science, v.313, 2006, p. 918.
Bunge, J; Epstein, SS; Peterson, DG. "Comment on "Computational improvements reveal great bacterial diversity and high metal toxicity in soil"," SCIENCE, v.313, 2006.
Chouvarine P, Saha S, Peterson DG. "An automated, high-throughput sequence read classification pipeline for preliminary genome characterization," Analytical Biochemistry, v.373, 2008, p. 78.
Dennis JH, Fan H-Y, Reynolds S, Yuan G, Jim Meldrim4, Peterson DG, Richter D, Noble W, Kingston R. "Novel independent and complimentary methods for the analysis of mammalian chromatin structure," Genome Research, v.17, 2007.
Islam-Faridi MN, Nelson CD, Kubisiak TL. "A standard karyotype for loblolly pine (Pinus taeda) using FISH and AT-rich banding," Genome, v.50, 2007.
Lamoureux D, Peterson DG, Li W, Fellers JP, Gill BS. "The efficacy of Cot-based gene enrichment in wheat," Genome, v.48, 2005, p. 1120.
Lamoureux, D; Peterson, DG; Li, WL; Fellers, JP; Gill, BS. "The efficacy of Cot-based gene enrichment in wheat (Triticum aestivum L.)," GENOME, v.48, 2005, p. 1120-1126.
Saha S, Bridges S, Magbanua ZV, Peterson DG. "Computational approaches and tools used in identification of dispersed repetitive DNA sequences," Tropical Plant Biology, v.1, 2008, p. 85.
Saha S, Bridges S, Magbanua ZV, Peterson DG. "Discovering relationships among dispersed repeats using spatial association rule mining," BMC Bioinformatics, v.9, 2008, p. O4.
Saha S, Bridges S, Magbanua ZVM, Peterson DG. "Empirical comparison of ab initio repeat finding programs," Nucleic Acids Res., v.36, 2008, p. 2284.
