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. 2002. 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

What's New
Physical Mapping
Sequencing Status
General Objectives