Blacksburg, Virgiania
March 4, 2009
Scientists across the world are
building an extensive repository of genetically modified rice
plants in the hope of understanding the function of the
approximately 57,000 genes that make up the genome of Oryza
sativa. The International Rice
Functional Genomics Consortium recently announced the public
availability of more than 200,000 rice mutant lines, which
represent mutations in about half of the known functional genes
mapped for rice to date. *
Researchers have estimated the number of different rice mutants
needed to have a mutant for every gene as somewhere between
180,698 and 460,000. Two hundred thousand rice mutants are now
available and have been mapped by the insertion of what are
known as flanking sequence tags – small pieces of DNA or
molecular tags that integrate into the rice genome. This
approach is useful because it allows scientists to link a
physical location on the genome to a specific gene and its
visible feature or phenotype.
Arjun Krishnan, first author on the paper and a graduate student
in Andy Pereira's laboratory at the
Virginia Bioinformatics
Institute, stated: "Bioinformatics is making it possible to
visualize the vast amounts of sequence information available to
researchers. The resources described in this paper, which are
the combined output of many leading international rice research
laboratories, mean that researchers can see and explore on their
computers the precise positions of mutations in the rice genome
sequence, for each rice mutant plant. About 50 percent of the
protein-coding genes have knockout mutations, which probably
abolish their expression and can provide valuable information on
the genes by virtue of their loss of function. This is a
significant milestone for the project and the availability of
these rice plants represents a powerful resource for the rice
genomics community."
More than 2 million rice mutants were generated in this project
and the diversity of the available plants suits many of the
experimental objectives of researchers looking at rice and other
commercially important grasses. Mapping of the remaining genes
from this population will be required to complete the resource.
Many of them will be smaller genes less amenable to mutation
that will pose significant challenges for researchers as they
continue their work.
Dr. Andy Pereira, Professor at the Virginia Bioinformatics
Institute, stated: "The Oryza sativa genome was sequenced in
2002 and researchers have come a long way since. Advances in
technologies such as high-throughput sequencing and RNA
interference gene silencing methods should help to accelerate
the process of identifying the functions of the remaining genes
in the rice genome." He added: "The availability of the rice
mutant resource is already helping researchers in their quest to
gain insights into the biology of this commercially important
crop. These efforts are critical to understand gene function
and, ultimately, the many biological processes that take place
in rice and other grasses, including maize and wheat, which
collectively produce our staple food."
* Krishnan A, Guiderdoni E, An G, Hsing YI, Han CD, Lee MC, Yu
SM, Upadhyaya N, Ramachandran S, Zhang Q, Sundaresan V,
Hirochika H, Leung H, Pereira A (2009) Plant Physiology 149(1):
165-170.
The Virginia Bioinformatics
Institute (VBI) at Virginia Tech has a research platform
centered on understanding the "disease triangle" of
host-pathogen-environment interactions in plants, humans and
other animals. By successfully channeling innovation into
transdisciplinary approaches that combine information technology
and biology, researchers at VBI are addressing some of today's
key challenges in the biomedical, environmental and plant
sciences. |
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