A hormone (GA) biosynthesis gene-knockout mutant showing acute dwarf phenotype.

Rice Functional Genomics Project

The Plant Industry Rice Functional Genomics Project was initiated in 1998 and scaled down in 2006, but the results achieved are still of interest to the scientific community. Here, researchers can find out more details about the project and access the results obtained.

• 22 December 2009 | Updated 21 February 2013

Project details

• Background
• Status
• Achievements

Background

A major challenge in the post genomic era is to identify the function of each of the predicted 50 000 plant genes.

For this, a multi-pronged approach is required, using studies on structural similarities, expression profiles (microarrays and DNA chips), and mutant phenotype.

Mutants offer one way to relate a gene to its function. T-DNA, transposable elements and retrotransposons can be effectively used to produce insertional knockout mutants. Researchers are using the two component Ac/Ds transposon gene or enhancer trap system (initially delivered through T-DNA) to generate libraries of T-DNA and/or transposon insertion mutants (knockout populations) in rice.

Rice is used as a model cereal because of its small genome, ease of transformation and because it is the focus of international genome studies.

Genes can be identified using insertional mutants in rice. This approach can also uncover regions of the genome controlling or enhancing the expression of classes of genes or determining developmental processes, which affect productivity and quality.

The discoveries achieved in rice will allow scientist to define targets that can be studied further in major crops (such as wheat) because of the existence of synteny among cereals.  

Status

The Plant Industry Rice Functional Genomics project was initiated in 1998 as one of the components of a special CSIRO research initiative Genomics and Gene Discovery for Australia.

This project was also a component of  Genomics program (1999-2002) of GrainGene (a joint venture between AWB Ltd, CSIRO and the Grains Research and Development Corporation).

Rural Industries Research and Development Corporation (RIRDC), 2001-04, and the New South Wales Agricultural Genomics Centre (2001-06) have funded this project.

This project activity has been scaled down since July 2006. However, this website is being maintained as an access point for information about our gene constructs, mutant lines and other resources.

Achievements

Researchers have shown that Ac/Ds based gene and enhancer trap systems are suitable for generating insertion mutants in rice. The systems involved the following steps:

1. production of immobile Ac (iAc) and Ds (enhancer or gene trap) transgenic lines by Agrobacterium-mediated transformation
2. genetic crossing to produce mutagenic populations containing both iAc and Ds
3. screening of plants from subsequent generations for stable (devoid of iAc) Ds insertions in new genomic locations and for any phenotypes associated with these insertions.
4. cloning and sequencing of regions flanking the Ds element, to create a database of flanking sequences that represent disrupted genes which are BLAST searchable. 

Scientists have also explored the possibility of inducing transposition in callus cultures of proven Ds lines with an excision marker. This is achievable by transiently expressing transposase (TET) after co-cultivation with Agrobacterium harbouring an iAc construct containing gfp as a visual reporter gene. Then, GFP- Ds+ regenerants are selected and tested for Ds excision. It was shown that this transiently expressed transposase could induce Ds transposition.

New generation Gene trapping constructs have been developed for TET system. T-DNA/Ds launch pads mapping to different chromomosomal regions have also been produced which should facilitate chromosomal region-directed insertional mutagenesis.

To manage data generated in this project, scientists developed RGMIMS (Rice Gene Machine Information Management System). RGMIMS automates and integrates multi-step experimental processes using a Web user interface. Built in barcoding utilities, the system enables rapid data capture and tracking of biological resources. 

Ontologies from Gramene and Plant Ontology consortium have been used to describe mutant phenotypes. RGMIMS supports generic research processes in plant mutagenesis and could readily be adapted to general high throughput plant research.

CSIRO’s efforts in hosting an international workshop Towards Building a Global Rice Gene Machine in 2002 have led to the formation of the International Rice Functional Genomics Consortium [external link].

CSIRO is one among 18 institutions (from 10 countries and two international agricultural research centres) represented on the Interim Steering Committee. The mandate of the IRFGC is to coordinate international rice functional genomics research and to build common strategies.

CSIRO is contributing to this global initiative by fostering international collaboration and providing insertion mutants and gene tagging constructs to the scientific community.