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Investigators:
David W. Galbraith, University of Arizona (galbraith@arizona.edu).
Hei Leung, IRRI, Los Banos, The Philippines (h.leung@cgiar.org).
Project Personnel:
Project ObjectivesPostdoctoral Associates
Jeremy Darwin EdwardsGraduate Students
Ambika Gaikwad
Jaroslav Janda
Chanqing Zhang
Stefan Schwab
Technical Support
Georgina Lambert
The ultimate goal of this three-year project is the development and use of microarray platforms for efficient and cost-effective Quantitative Trait Locus (QTL) mapping in rice. To achieve this goal, we propose the development of a microarray platform for rapid and cost-effective mapping of different rice genotypes, the use of available rice long oligo (70-mer) oligonucleotide microarrays for expression profiling, and the application of these two microarray platforms for the analysis of specific recombinant inbred lines. This project involves the following specific objectives: (a) production and utilization of mapping microarrays. (b) use of the genotyping microarrays for a core set of validation and biological experiments including analyses of QTLs relating to specific phenotypes, (c) data archiving and analysis, and (d) training.
Project Approach
To define Single Feature Polymorphisms between the parental rice lines, experiments will be done using a variety of different microarray formats, and in silico methods to identify gene sequences that are present/absent between the genomes of the parental lines. Experimental designs will be defined for expression profiling of rice mapping populations using microarrays that provide sufficient statistical power for uncovering QTLs. Segregating rice populations will be grown under defined conditions for extraction of RNA, for microarray hybridization, scanning, and data extraction. Data analysis will be done to extract statistically significant alterations in gene expression and to correlate these with genotypes defined using the mapping microarrays. These alterations in gene expression profiles will be examined to determine whether they correlate with alterations in “classical” phenotypes. We will use the SFPs to fine-map the locations of the previously located QTLs for important agronomic traits. We will provide putative QTL assignments to the international rice community for confirmation and follow-up experiments, and for identification of candidate genes underlying the QTLs. We will establish a convenient searchable database for storing microarray information and metadata, a web interface for global access and query and for collaborator access, and for searching and presenting the indel maps with other genetic marker maps, and will produce tools for facile analysis of microarray data, including indel search, gene ontology search and pathway query. We propose to establish a program of training for the reliable and sensible use of microarray-based approaches to QTL mapping, and to establish web-based training programs in the use of the derived tools.
This work will be divided between the University of Arizona, which will act as the location for microarray platform development and for high throughput genotyping and expression profiling experiments, and the International Rice Research Institute (IRRI), which will act as the location at which DNA and RNA samples will be extracted from segregating populations for the proposed analyses. A program of exchange visits will efficiently allow technology and biomaterials transfer between the project sites.
Acknowledgement and Disclaimer:
This material is based upon work supported by the USDA under Grant No. 2005-35604-15327. 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 US Department of Agriculture.
Questions or
comments should be addressed to:David Galbraith
Page last
updated May 31, 2005