Diane Jofuku Okamuro
DBI Division of Biological Infrastructure
BIO Directorate for Biological Sciences
Start Date:
July 1, 2005
Expires:
June 30, 2010 (Estimated)
Awarded Amount to Date:
$4619563
Investigator(s):
Scott Jackson sjackson@purdue.edu (Principal Investigator)
Gary Stacey (Co-Principal Investigator) Jeffrey Doyle (Co-Principal Investigator) Gregory May (Co-Principal Investigator) Randy Shoemaker (Co-Principal Investigator)
William Beavis (Former Co-Principal Investigator)
Sponsor:
Purdue University
Young Hall
West Lafayette, IN 47907 765/494-4600
NSF Program(s):
PLANT GENOME RESEARCH RESOURCE, PLANT GENOME RESEARCH PROJECT
Field Application(s):
Program Reference Code(s):
BIOT, 9150, 9109, 1228
Program Element Code(s):
7577, 1329
ABSTRACT
The long-term goals of this award are to use genomic tools in soybean to decipher the genetic/genomic effects of multiple rounds of polyploidization followed by diploidization, a poorly understood phenomenon, and develop a BAC-based, sequence ready map for the public. To begin to address the goals, the team will create a physical map integrated with the available genetic map. A physical map is the basic building block used to clone important agricultural genes and to sequence segments of genomes or entire genomes. In addition to development of an integrated genetic-physical map, DNA sequencing will be done to assess the microstructure of the soybean genome at several locations. The soybean genome is highly duplicated; that is, any particular region may be present multiple times, which complicates genome mapping and sequencing. The team will target and sequence the duplicated regions to ascertain the level of conservation between duplicated regions and to determine how to overcome the difficulty posed by duplications within the genome. Integrated into the project are opportunities for faculty and students from Primarily Undergraduate Institutions to participate each summer in the project at each of the involved institutions.
Access to project outcomes
All DNA sequences will be deposited in GenBank and trace files in the trace file repository as soon as the qualities are checked. Integrated physical and genetic map data will be made available through the Legume Information System (LIS: http://www.comparative-legumes.org/).
PUBLICATIONS PRODUCED AS A RESULT OF THIS RESEARCH
Hass-Jacobus BL, Futrell-Griggs M, Abernathy B, Westerman R, Goicoechea JL, Stein J, Klein P, Hurwitz B, Zhou B, Rakhshan F, Sanyal A, Gill N, Lin JY, Walling JG, Luo MZ, Ammiraju JS, Kudrna D, Kim HR, Ware D, Wing RA, SanMiguel P, Jackson SA. "Integration of hybridization-based markers (overgos) into physical maps for comparative and evolutionary explorations in the genus Oryza and in Sorghum.," BMC Genomics, 2006.
Innes, RW; Ameline-Torregrosa, C; Ashfield, T; Cannon, E; Cannon, SB; Chacko, B; Chen, NWG; Couloux, A; Dalwani, A; Denny, R; Deshpande, S; Egan, AN; Glover, N; Hans, CS; Howell, S; Ilut, D; Jackson, S; Lai, HS; Mammadov, J; del Campo, SM; Metcalf, M; Ngu. "Differential Accumulation of Retroelements and Diversification of NB-LRR Disease Resistance Genes in Duplicated Regions following Polyploidy in the Ancestor of Soybean," PLANT PHYSIOLOGY, v.148, 2008, p. 1740-1759.
Jackson SA, Rokhsar D, Stacey G, Shoemaker RC, Schmutz J, Grimwood J. "Toward a Reference Sequence of the Soybean Genome: A Multiagency Effort.," The Plant Genome, 2006.
Jackson SA, Rounsley S, Purugganan M. "Comparative sequencing of plant genomes: choices to make.," Plant Cell, 2006.
Jackson, S.A., D. Rokhsar, G. Stacey, R. Shoemaker, J. Schmutz and J. Grimwood.. "Toward a reference sequence of the soybean genome: a multi-agency effort.," The Plant Genome; Crop Science
, v.46, 2006, p. 55.
Ma J, Wing RA, Bennetzen JL, Jackson SA. "Plant centromere organization: a dynamic structure with conserved functions.," Trends in genetics, 2007.
Schlueter J, Goicoechea JL, Collura K, Gill N, Lin JY, Yu Y, Kudrna D, Zuccolo A, Vallejos CE, Munoz-Torres M, Blair MW, Tohme J, Tomkins J, McClean P, Wing RA, Jackson S. "BAC-end sequence analysis and a draft physical map of the common bean (Phaseolus vulgaris L.) genome.," Tropical Plant Biology, 2008.
Schlueter JA, Lin JY, Schlueter SD, Vasylenko-Sanders IF, Deshpande S, Yi J, O'Bleness M, Roe BA, Nelson RT, Scheffler BE, Jackson SA, Shoemaker RC. "Gene duplication and paleopolyploidy in soybean and the implications for whole genome sequencing.," BMC Genomics, 2007.
Shoemaker RC, Grant D, Olson T, Warren WC, Wing R, Yu Y, Kim H, Cregan P, Joseph B, Futrell-Griggs M, Nelson W, Davito J, Walker J, Wallis J, Kremitski C, Scheer D, Clifton SW, Graves T, Nguyen H, Wu X, Luo M, Dvorak J, Nelson R, Cannon S, Tomkins J, Schm. "Microsatellite discovery from BAC end sequences and genetic mapping to anchor the soybean physical and genetic maps.," Genome, 2008.
Walling JG, Shoemaker RC, Young ND, Mudge J, Jackson SA. "Chromosome level homeology in paleopolyploid soybean (Glycine max) revealed through integration of genetic and chromosome maps.," Genetics, 2005.
Walling, J.G., R.C. Shoemaker, N.D. Young, J. Mudge and S.A. Jackson. "Chromosome
level homeology in paleopolyploid soybean (Glycine max) revealed through
integration of genetic and chromosome maps.," Genetics, v.172, 2006, p. 1893.
Wu X, Zhong G, Findley SD, Cregan P, Stacey G, Nguyen HT. "Genetic marker anchoring by six-dimensional pools for development of a soybean physical map.," BMC Genomics, 2008.
