Rice
is consumed by nearly half of the world's population and it is
the staple food for the largest number of people on the earth
thereby providing one quarter of global per capita energy. It
is grown on 125 million hectares world-wide and rice production
was 600 million tons in 2000. The 2.3 folds increase in rice production
over the last 40 years has been largely contributed by intensive
research leading to better varieties able to grow in shorter period
and showing higher yield potential as well as resistance/tolerance
to various pests, disease
and abiotic stresses.
In India, rice is grown in 44 million
hectares which is 28% of total arable land. About 74 kg of milled
rice per capita was consumed in 1999 in India providing about
30% of total calories/capita/day. The demand of rice in India
is expected to increase from 84 million tons in 2000 to 114 million
tons in 203
0--
an increase of about 35%. This increase in production is to be
achieved without major increase in arable land and with rapidly
degrading ecosystem. Such a challenge requires deployment of all
possible means of higher production, which to large extent involves
development of better varieties and efficient agricultural management
(Khush, G.S. 1999. Genome 42: 646).
To produce high yielding varieties of
rice suited to specific locations, it is imperative to
understand intrinsic yield-limiting factors at molecular level
to help deployment of natural and engineered genetic variability
most effectively. It is also necessary to understand survival
strategy for rice under adverse conditions and innovate means
for rapid integration of the same in genetic improvement programs.
Advent of molecular biotechnology in seventies opened a new possibility
for genetic improvement of rice. Genes associated with specific
traits could be mapped and introgressed leading to molecular breeding
and genetic engineering which allowed movement of genes across
the incompatibility barriers (Tyagi et al. 1999. Critical Reviews
in Biotechnology 19:41). Simultaneously, availability of efficient
gene tagging systems led to application of the concepts of functional
genomics in rice (Tyagi, A.K. & Mohanty, A. 2000. Plant Science
158:1, Rice Genetics IV. 2001. IRRI, Manila). In 1998, an International
Rice Genome Sequencing Program (IRGSP) was initiated to sequence
the entire genome of rice, estimated to be about 430 Mb, drawing
upon the information already available on rice genetics and generated
by the Rice Genome Program (RGP) in Japan. The components of IRGSP
have developed an integrated physical and genetic map as well
as a comprehensive transcript map of rice (Chen M et al. 2
002.
Plant Cell 14: 537, Wu et al. 2002. Plant Cell 14: 525). The high
quality (>lOX) sequence of rice has already been declared in
December 2004. India is actively participating in this public
sector
international venture. Monsanto and Syngenta from private sector
have also produced a draft sequence of the variety bejng investigated
by IRGSP and made available their data to IRGSP (Barry, G.F. 2001.
Plant Physiol.125:
1164, Goff S.A. et al. 2002. Science 296: 92). An indica variety
genome has been sequenced in China (Yu, J. et al. 2002. Science
296: 79). Notwithstanding the enormous value of these reports
as a significant step in sequencing complete rice genome, the
lower sequence reads in any particular area and loose relationship
of the genes to each other and to the genetic map, as reported,
makes the application of information cumbersome and required consistent
efforts by IRGSP to produce highly accurate sequence to serve
as golden standard (International Rice Genome Sequencing Project
2005.Nature 436:793). It is estimated that the rice genome may'
contain 37,544 genes. Functional analysis of these genes and their
useful alleles would be a challenge for rice scientists in near
future and
require global attention and initiatives by various countries.
India, being a major rice producer and consumer, obviously need
to take a lead in the functional genomics of rice.
Success in genome sequencing and transgenics is paving the way
for preparing a road map of functional genomics
which is expected to correlate action of a gene to a trait in
cellular and organismal context. Realizing the immense potential,
various nations have provided huge in-put to researchers to initiate
investigation on functional genomics of plants. Prominent among
these are Plant Genomics Programs supported by the National Science
Foundation USA, European Functional Genomics Program, Australian
Centre for Plant Functional Genomics, Rice Simulator Program of
Japan and Chinese Program on Functional Genomics
of rice. The International Rice Research Institute (IRRI) has
helped form an International Rice Functional Genomics Working
Group. Most of these programs concern with development and application
of tools and resources for genome-wide understanding of gene functions.
This includes analysis of expression
profiles,
generation of mutants and tagged lines or target-specific silencing
of genes, functional validation in transgenics, allele mining,
comparative genomics and virtual plant concept (Ausubel,
F. & Benfy, P. 2002. Plant Physiol. 129: 393, Harris, S.B.
2002. EMBO Rep. 3: 511). The initiation point of these investigations
is either selected traits or a group of genes and in certain cases
the whole transcriptome. Most of these approaches ultimately aim
at providing input for marker-assisted breeding or genetic engineering
of new crop varieties (Ronald, P. & Leung, H. 2002. 10 Science
296: 58). In appreciation of the potential and need of India,
a meeting of Indian Rice Scientists and Scientists from IRRI was
organized in New Delhi in May 2002. Deliberations of two days
led to crystalization of the idea of forming a National Consortium
for Functional Genomics of Rice (NCFGR). It was also decided to
develop programs on the functional genomics of indica rice in
selected areas.
In parallel with 'Impact Research
and Delivery' approach and the 'Strategic Research' approach are
expected to unravel the function of most crucial group of genes
from rice, i.e. signal transduction and transcription components.
The analysis of the rice genome reveals
that such genes might be represented by as much as 8000 genes.
Their activity is responsible for perceiving environmental (abiotic
and biotic) and intrinsic (developmental and hormonal) signals
and prepare the plant to respond to adverse environment to survive
and follow a set pattern of life-cycle. The program, therefore,
starts with
analysis of expression and data mining to select useful genes
which would be target for functional validation.
The
"Strategic
Research" area project involves five institutions and thirteen
scientists having prior experience in rice genetics, transgenics
and genomics. At least four scientists from Delhi University South
Campus (UDSC) and Indian Institute of Science (IISc) would work
together to procure/design/develop a microarray system to analyze
signal transduction ( e.g. kinases, receptors) and transcription
factor genes. This would require in silico analysis of
the whole genome and transcriptome-related
information to be undertaken
by UDSC and IISc. The selection of target genes will be based
on their expression pattern during critical developmental windows
of the rice plant (including seed development, meristem determination,
floral initiation and reproductive organ development). For this,
existing germplasm as well
as germplasm developed by other network programs will be utilized
and useful alleles will be identified. Selected crucial genes
will be functionally validated in transgenics by over-expression
and functional knockout approaches, to be-taken at UDSC, IISc,
Madurai Kamraj University (MKU), Osmania University (OU) and the
Directorate of Rice Research (DRR). Simultaneously, vectors for
artificial target-specific gene silencing will also be developed
and utilized. Specific
technology development for functional genomics, viz, (a) targeted
gene integration by homologous recombination (MKU), (b) efficient
transformation
of Indian genotypes (OU), and (c) germplasm
resource, diversification and trials (DRR) would also be undertaken.
It is expected that microarray analysis would narrow down to about
50 genes for functional analysis. For each gene, one over-expression
and one knockout (antisense or RNAi) construct is to be made.
In addition, there would be at least 50 constructs for stage-specific
promoters. Thus, each group at UDSC and groups at DRR, IISc, MKU
and OU would work with about 20 constructs to generate at least
10-20 independent
transgenic lines for each and analyze them in network mode at
To and TI generations. It is expected that 'Strategic Research'
program would identify several useful genes for improvement of
rice and related crops as well as validate their function for
crop improvement.
The
IRRI platform would help development of international collaboration
for functional validation and go on to resource and information
sharing. Agreement of Scientists from Japan to be advisors and
contributors of genomics resources has also been obtained. It
may also be mentioned that functional genomics is a frontier area
undergoing rapid development and would require regular moderation
and flexibility to achieve the goals most rapidly. The 'Strategic
Research' program would also share microarray platform and bioinformatics
logistics with other areas of NCFGR. Looking at the potential
of groups involved and a minimum need to achieve the objectives,
a budget of Rs 670 millions has been approved. The present proposal
has been developed by in-puts from participating labs which can
take shape of a virtual institution in the area of 'Strategic
Research' for gene discovery in rice. It is expected that in-put
from IRRI, Phillipines, and NIAS, Japan, would greatly supplement
our initiative, while efforts would be made to take advantage
of other international programmes as well.
Donor
varieties for important traits in rice
