Introduction
Rice DNA sequences represent an enormous pool of markers and genes for rice improvement through marker-aided selection or transformation. Yet, a full exploitation of this wealth of information will not be possible until we understand the biological functions encoded by the sequenced DNA. A concerted effort is needed to produce a large collection of mutants through which biological functions can be assigned to the DNA sequences.
As an initiative in functional genomics at the International Rice Research Institute, we have begun a systematic production of mutants with the goal of assigning available sequenced DNA to biological variation revealed by these mutations. We focus on the production of deletion lines that would allow us to physically detect mutations in the genome using available ESTs and high-throughput screening techniques
Why IR64?
We have chosen IR64 for large-scale mutagenesis because it is the most widely grown rice variety in the tropics. IR64 carries many valuable agronomic traits related to yield, plant architecture, grain quality, and tolerance to biotic and abiotic stresses. Thus, creating mutations in such an elite genetic background can facilitate the detection of phenotypic changes in important agronomic traits.
Mutagenesis and Mutant Propagation
We treated IR64 breeder seed with three mutagens: diepoxybutane (DEB, 0.006%), fast neutron (FN, 33 Gy), and gamma ray (GR, 250 Gy). Drs. P. Donini and F. Zapata at the International Atomic Energy Commission, Vienna, Austria, did the FN and GR treatments. Their generous assistance is greatly appreciated.
In the first stage of population development, we propagated about 4-6 M3 families derived from each M1 plant to examine the amount of variability in the mutant population. Maintaining the family structure also has enabled us to infer readily the genetic basis of mutations. So far, we have obtained ~40,000 M3 families derived from 10,000 independent M1 plants from treatment with DEB (~3000 M1), FN (~3,000), and GR (~5,000). In the second stage, we accelerate the production by using single seed descent to advance ~7000 lines mutagenized by FN and GR. As of January 2001, we have ~47,000 M3 or M4 lines derived from ~17,000 independent M1 mutants.
We will continue the mutant production until we reach the target of 40,000 independent lines by mid-2002. We expect the IR64 mutants to complement the various insertion mutant stocks being developed around the world.
Use of the Database
This database presents description of mutants identified from visual inspection of the M3 lines planted in the field and from disease screen. We are systematically evaluating these mutants for altered response to an array of biotic (pathogens and insects) and abiotic stresses (drought, submergence, salinity, mineral deficiency). The phenotypic description will be included in the database as soon the data are reviewed for accuracy and completeness. We will also systematically isolate DNA from individual or pools of mutants for reverse genetics.
In partnership with the National Institute of Agrobiological Sciences in Japan (Hirochika and Miyao), we have normalized the list of phenotype descriptions into a fixed list indexed against TOS17 phenotypes. We have also indexed the phenotypes against the Gramene trait ontology (TO) and now, a prototype "Phenotype and Trait Ontology" (PATO) "experiment (observable) attribute value" (EAV) scheme using plant ontology (PO; www.plantontology.org) and PATO attributes (obo.sourceforge.net).
We plan to integrate this phenotype database with public genomic databases as more functional and molecular data are available in these mutants.
We welcome users to use the database to identify mutants of interest. Small amount of seeds will be made available under a Material Transfer Agreement. We also welcome users' comments and suggestions to improve the utility of this database.
Download the Database
A Java/MySQL standalone version of the database is available for downloading here.
We've mainly focused on making it easy to run the application as a standalone under MS Windows (using a batch file) but it is a
Java application proven to work under Unix platforms (i.e. MacOSX), so with a modest effort, a clever bioinformatician can probably configure the
application to run on such platforms. Contact Richard Bruskiewich for assistance with this latter task, if needed.
Project Team
Mutant Stocks: Hei Leung, Mayette Baraoidan, Alice Bordeos
Database: Richard Bruskiewich, Ramil Mauleon, Victor Ulat, Arllet Portugal, Ma. Teresa Ulat, Clarissa Pimentel, Sergio Gregorio
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