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Award Abstract #0227414
YIA-PGR: Comparative Genomics of Rice: reconstructing rice chromosome 1 in related species.
| NSF Org: |
IOS
Division of Integrative Organismal Systems
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| Initial Amendment Date: |
September 17, 2002 |
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| Latest Amendment Date: |
August 2, 2006 |
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| Award Number: |
0227414 |
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| Award Instrument: |
Continuing grant |
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| Program Manager: |
Diane Jofuku Okamuro
IOS Division of Integrative Organismal Systems
BIO Directorate for Biological Sciences
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| Start Date: |
October 1, 2002 |
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| Expires: |
March 31, 2009 (Estimated) |
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| Awarded Amount to Date: |
$1740516 |
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| Investigator(s): |
Scott Jackson sjackson@purdue.edu (Principal Investigator)
Phillip SanMiguel (Co-Principal Investigator)
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| Sponsor: |
Purdue University
Young Hall
West Lafayette, IN 47907 765/494-4600
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| NSF Program(s): |
PLANT GENOME RESEARCH PROJECT
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| Field Application(s): |
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| Program Reference Code(s): |
BIOT, 9297, 9251, 9232, 9184, 9109
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| Program Element Code(s): |
1329
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ABSTRACT
Encoded in units called "genes" on linear structures known as "chromosomes" present in essentially every cell of every organism is the instruction set for that organism. The purpose of a genome project, such as the nearly complete Rice Genome Project, is to precisely locate and describe each gene. This is not the end of the story however. For the description generated may only hint at the function of a gene and gives little indication as to the interacting role any gene or group of genes plays in the overall functioning of the organism. At this point enters the discipline of genetic mapping-whereby traits may be localized to specific positions on a chromosome. To this end, in genomes related to rice, we will construct physical maps of regions homologous to rice chromosome 1. Libraries of genomes, called BAC libraries, which consist of bacteria containing large pieces of DNA from the genome of interest, will have been constructed for many of the species in the same genus as rice (Oryza). These BAC libraries are the substrate for genome sequencing and, in this case, building sequence-ready comparative maps to compare genomes. Approximately three-quarters of the nearly 5,000 predicted genes on chromosome 1 will be used to isolate and build comparative maps across this group of species. The end result will be the reconstruction of rice chromosome 1 in a group of related species. This will help us to better understand chromosome evolution and more efficiently utilize the rice sequence data for comparative mapping in more distantly related species, such as maize, sorghum and oat. In addition, by using the natural variation that occurs in this group of species, we will be able to begin assigning biological functions to many of the genes predicted to exist in rice based on the sequence data.
Deliverables:
All information on Overgo sequences, physical location, analysis and
reconstruction of chromosome 1 will be available at:
http://rice.genomics.purdue.edu
Much of the marked up information will be migrated to:
http://www.gramene.org.
Information on the computational pipeline is also available at:
http://rice.genomics.purdue.edu.
PUBLICATIONS PRODUCED AS A RESULT OF THIS RESEARCH
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(Showing: 1 - 10 of 13)
(Showing: 1 - 13 of 13)
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Gill, N, C. Hans and S.A. Jackson. "An overview of plant chromosome structure.," Cytogenetic and Genome Research, v.120, 2008, p. 194.
Hass, B.L., J.C. Pires, R. Porter, R.L. Phillips and S.A. Jackson. "Comparative genetics at the gene and chromosome levels between rice (Oryza sativa) and wildrice (Zizania palustris)," Theor. Appl. Genet., v.107, 2003, p. 773.
Hass-Jacobus, B.L., M. Futrell-Griggs, B. Abernathy, R. Westerman, J.-L. Goicoechea, J. Stein, P. Klein, B. Hurwitz, B. Zhou, F. Rakhshan, A. Sanyal, N. Gill, J.-Y. Lin, J.G. Walling, M.Z. Luo, J.S.S. Ammiraju, D. Kudrna, H.R. Kim, D. Ware, et al.. "Integration of hybridization-based markers (overgos) into physical maps for comparative and evolutionary explorations in the genus Oryza and in Sorghum," BMC Genomics, 2006, p. 199.
Jetty, S.S.A., F. Lu, A. Sanyal, Y. Yu, X. Song, N. Jiang, A. Clara Pontaroli, T. Rambo, J. Currie, K. Collura, J. Talag, C. Fan, J-L. Goicoechea, A. Zuccolo, J.L. Bennetzen, M. Chen, S.A. Jackson, and R.A. Wing. "Dynamic Evolution of Oryza Genomes Revealed by Comparative Genomic Analysis of a Genus-wide Vertical Dataset," The Plant Cell, 2008.
Kim, H.K, B. Hurwitz, Y. Yu, K. Collura, N. Gill, P. SanMiguel, J.C. Mullikin, C. Maher, W. Nelson, M. Soderlund and R.A. Wing. Wissotski, M. Braidotti, D. Kudrna, J.L. Goigochia, L. Stein, D. Ware, S.A. Jackson, C.. "Construction, alignment and analysis of 12 framework physical maps that represent the 10 genome types of the genus Oryza.," Genome Biology, v.9, 2008, p. R45.
Lu, F, J.S.S. Ammiraju, A. Sanyal, S. Zhang, R. Song, J. Chen, G. Li, Y. Sui, Z. Cheng, A. Costa de Oliveira, J.L. Bennetzen, S.A. Jackson, R.A. Wing, M. Chen.. "Comparative Sequence Analysis of the MONOCULM1 Orthologous Regions in 14 Oryza Genomes.," Proceedings of the National Academy of Sciences, 2009.
Ma, J. and S.A. Jackson. "Retrotransposon accumulation and satellite amplification mediated by segmental duplication facilitate centromere expansion in rice," Genome Research, v.16, 2006, p. 251.
Ma, J., J. Bennetzen and S.A. Jackson. "Plant Centromere Organization: conserved functions within a dynamic structure," Trends in genetics, v.23, 2006, p. 134.
Ma, J., and S.A. Jackson. "Retrotransposon accumulation and satellite amplification mediated by segmental duplication facilitate centromere expansion in rice.," Genome Research, v.16, 2006, p. 251.
Piegu, B., R. Guyot, N. Picault, A. Roulin, A. Sanyal, HR. Kim, K. Collura, D.S. Brar, S.A.Jackson, R.A. Wing and O. Panaud.. "Doubling genome size without polyploidization : dynamics of retrotransposition-driven genomic expansions in Oryza australiensis, a wild relative of rice.," Genome Research, v.16, 2006, p. 1262.
Sanyal, A and S.A. Jackson. "Comparative genomics in the genus Arabidopsis of a 789-kilobase region surrounding the FLC locus.," Molecular Genetics and Genomics, v.275, 2006, p. 26.
Wing, R.A., J.S.S. Ammiraju, M. Luo, H.R. Kim, Y. Yu, D. Kudrna, J.L. Goicoechea, W. Wang, W. Nelson, K. Rao, D. Brar, D.J. Mackill, B. Han, C. Soderlund, L. Stein, P. SanMiguel, and S.A. Jackson. "The Oryza Map Alignment Project: The golden path to unlocking the genetic potential of wild rice species," Plant Molecular Biology, v.59, 2005, p. 53.
Zuccolo, A., J.S.S. Ammiraju, H-Y. Kim, A. Sanyal, S.A. Jackson, and R.A. Wing. "Rapid and differential proliferation of the Ty3-gypsy LTR-retrotransposon Atlantys in the genus Oryza.," Rice, 2008.
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