Source: UNIVERSITY OF ARIZONA submitted to NRP
SEQUENCING RICE CHROMOSOMES 3 AND 10
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
COMPLETE
Funding Source
NRI COMPETITIVE GRANT
Reporting Frequency
Annual
Accession No.
0193374
Grant No.
2002-35317-12414
Cumulative Award Amt.
(N/A)
Proposal No.
2002-04206
Multistate No.
(N/A)
Project Start Date
Sep 15, 2002
Project End Date
Sep 14, 2004
Grant Year
2002
Program Code
[52.3]- (N/A)
Recipient Organization
UNIVERSITY OF ARIZONA
888 N EUCLID AVE
TUCSON,AZ 85719-4824
Performing Department
PLANT SCIENCE
Non Technical Summary
Rice is the most important food crop in the world and feeds over half the population. Its compact genome and evolutionary relationship to the other cereals, such as corn and wheat, make rice an ideal target for whole genome sequencing. As part of the International Rice Genome Sequencing Project (IRGSP), ACWW (University of Arizona, Cold Spring Harbor Laboratory, Washington University Genome Sequencing Center, University of Wisconsin), has been assigned to completely sequence and annotate the short arm of chromosome 3 which is the topic of this proposal. Specifically we will production sequence, finish and annotate approximately 44 rice BAC clones (~5.1 Mb) that have been physically mapped to the short arm of chromosome 3. Sequencing will occur in two stages. Stage one will be to production sequence and order all 44 BACs by December 2002 to coincide with the planned IRGSP release of a public phase II high-quality 10X draft of the rice genome. Stage 2 will be to finish and annotate the 44 BACs and combine our data with our previous work and TIGR's chromosome 3 work to produce a finished rice chromosome 3 by September 2003.
Animal Health Component
33%
Research Effort Categories
Basic
34%
Applied
33%
Developmental
33%
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
20115301080100%
Knowledge Area
201 - Plant Genome, Genetics, and Genetic Mechanisms;

Subject Of Investigation
1530 - Rice;

Field Of Science
1080 - Genetics;
Goals / Objectives
The long term objective of this 1 year supplement is to finish the sequence of rice chromosome 3. Specifically we will: 1) 44 ~143kb O. sativa ssp. japonica cv. Nipponbare BAC clones (CUGI/Monsanto) anchored to the short arm of chromosome 3 will be validated for insert integrity and chromosome location; 2) shotgun libraries for the 44 BACs will be constructed followed by production sequencing to 8 fold coverage and additional sequencing to finish the BACs to the IRGSP sequencing standards; 3) WU-GSC will lead a group in finishing technology development aimed at establishing robust chemistries and protocols that can be used by the IRGSP to finish difficult regions of the rice genome; 4) all 44 BAC sequences will be phase I annotated and released to Genbank.
Project Methods
1) 44 ~143kb O. sativa ssp. japonica cv. Nipponbare BAC clones (CUGI/Monsanto) anchored to the short arm of chromosome 3 will be validated for insert integrity and chromosome location; 2) shotgun libraries for the 44 BACs will be constructed followed by production sequencing to 8 fold coverage and additional sequencing to finish the BACs to the IRGSP sequencing standards; 3) WU-GSC will lead a group in finishing technology development aimed at establishing robust chemistries and protocols that can be used by the IRGSP to finish difficult regions of the rice genome; 4) all 44 BAC sequences will be phase I annotated and released to Genbank.

Progress 09/15/02 to 09/14/04

Outputs
The goal of the Arizona, Cold Spring Harbor, Washington University and University of Wisconsin Rice Genome Sequencing Consortia was to completely sequence the short arm of rice chromosome 3. We completed this task and sequenced and finished a total of 121 BACs for a total of 17.13 Mb of rice genome sequence. This sequence was combined with TIGR's long arm data to generated a complete sequence of rice chromosome 3 with only 5 gaps. The sequence was submitted to Genbank on a regular basis. The sequence was also annotated and published in Genome Research as a single article and also later combined with the whole genome sequence in rice in a Nature article in 2005.

Impacts
This project significantly contributed to the generation of the first genome sequence of any crop plant in the world. The sequence is now a fundamental tools for basic and applied research in plant biology and agriculture.

Publications

  • Yang, T.-J., Y. Yu, S.-B. Chang, H.d. Jong, C.-S. Oh, S.-N. Ahn, E. Fang, and R.A. Wing. (2005). Toward closing rice telomere gaps: mapping and sequence characterization of rice subtelomere regions. Theor Appl Genet.
  • The Rice Chromosome 3 Sequencing Consortium (2005). Sequence, Annotation, and Analysis of Synteny Between Rice Chromosome 3 and Diverged Grass Species. Genome Res 15:1-10.
  • The International Rice Genome Sequencing Project Project. (2005). The Map Based Sequence of the Rice Genome. Nature 436:793-800.
  • Zhang, Y., Y. Huang, L. Zhang, Y.L., T. Lu, Y. Lu, Q. Feng, Q. Zhao, Z. Cheng, Y. Xue, R.A. Wing, and B. Han. (2004). Structural features of the rice chromosome 4 centromere. Nucl. Acids Res. 32:2023-2030.
  • The Rice Chromosome 10 Sequencing Consortium (2003). In-depth view of structure, activity, and evolution of rice chromosome 10. Science 300:1566-1569.
  • Yang, T.J., Y. Yu, K. Nah, M. Atkins, S. Lee, D. Frisch, R.A. Wing. (2003). Construction and utility of 10-kb libraries for efficient clone-gap closure of rice genome sequencing. Theor Appl Genet 107:652-660.