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Scope of Rice Genome Project

INTRODUCTION

Rice has been cultivated for more than 9,000 years. Rice is a largest staple food crop worldwide that is an important food for half the world population providing 20% of calorific content. According to IRRI, World rice production in 2007 was approximately 645 million tons. At least 114 countries grow rice. Asian farmers produce about 90% of the total, with two countries, China and India, growing more than half the total crop. It is expected that the population in Asia will increase by 1.5 times or more in the next 10-20 years. The current production of major food crops is not sufficient to meet the growing demand so that millions of people all over the world are not getting sufficient meals every day. The world rice production must increase by 30% to keep pace with the growing population. However, decrease in farming land, reduction in the level of ground water, change in climate and global warming are resulting in the decreased yield of rice. Rice is also grain is fermented into wine, its straw makes cattle feed, paper, and ropes. Rice oil is used in soap and cosmetics, and seed hulls are used as a fuel. Rice consumes lot of water when compared to other crops. It typically uses up to three times more water than other food crops such as maize or wheat and consumes around 30 percent of the fresh water used for crops worldwide. In conditions where water is scarce, it is important to have crops that can give more yield using limited amounts of water.

Rice has the smallest genome size of all cereals, of around 430 million base pairs of DNA. Rice is considered a model system for plant biology largely due to its compact genome (430 million base pairs on its 12 chromosomes) and evolutionary relationships with other large-genome cereals, such as sorghum (750 Mb), maize (2,500 Mb), barley (5,000 Mb) and wheat (15,000 Mb). Rice is the first plant to be mapped in a working draft form. Rice is a model species for learning about traits such as yield, hybrid vigor, and single and multi-genic disease resistance of all monocots including wheat and corn. Studying the genes of rice is will help us to develop new varieties of rice that will produce greater yields, be more resistant to pests and disease, and grow in different types of climates and soils.

 

Rice Genome Project

Science and technology has taken a new turn in the field of agriculture especially in the case of cereal crops. Recent research works have paved a way for the production of more yields while the land available for cultivation is constantly decreasing. The sequencing of the rice genome is the greatest milestone, science has taken us to. Researchers are able to develop new variety of rice that is better in quality and more in yield. The rice researchers are also focusing on the developing rice varieties that are having better taste, aroma and high nutrition. This will also fetch good revenue to the farmers.

Genetic research on rice was started in 1990’s. The Rice Genome Research Program (RGP) was started in October 1991 and is an integral part of the Japanese Ministry of Agriculture, Forestry and Fisheries (MAFF) Genome Research Project with the aim of finding the structure and function of the genome of the rice. It is jointly coordinated by the National Institute of Agro biological Sciences (NIAS), a government research institute under MAFF and the Society for Techno-innovation of Agriculture, Forestry and Fisheries (STAFF), a semi-private research organization managed and supported by MAFF and a consortium of some twenty Japanese companies. The research is funded with yearly grants from MAFF and additional funds from the Japan Racing Association (JRA).The first phase of RGP continued till 1997. It was reorganized into a national project in 1998. The research was to analyze all the expressed genes in rice, construction of a genetic map and establishment of a physical map of the genome. Research activities were conducted at the STAFF Institute located in Tsukuba City, Ibaraki Prefecture, Japan, about 50 km northeast of Tokyo. During the first phase of the project from 1991 to 1997, STAFF successfully found nucleotide sequences of about 20,000 genes that were expressed in rice and they also established a high-density linkage map of rice with more than 3000 DNA markers accurately positioned in the genome. They reproduced more than 60% of the genome by using these markers to align DNA fragments cloned in yeast artificial chromosome (YAC). With the success of the first phase of the RGP, the MAFF planned for two large-scale projects from 1998 with the aim of completely sequencing rice genome. These projects focused on rice genome sequencing and functional characterization of the genome which later focused on mutant panel project and full-length cDNA project.

 The International Rice Genome Sequencing Project (IRGSP), a consortium of publicly funded laboratories, began in September 1997, at a workshop held in conjunction with the International Symposium on Plant Molecular Biology in Singapore, to obtain a high quality, map-based sequence of the rice genome using the cultivar Nipponbare of Oryza sativa ssp. japonica. IRGSP is comprised of ten members: Japan, India, United States of America, China, Taiwan, Korea, Thailand, France, Brazil, and the United Kingdom. The IRGSP adopts the clone-by-clone shotgun sequencing strategy so that each sequenced clone can be associated with a specific position on the genetic map and adheres to the policy of immediate release of the sequence data to the public domain. The largest IRGSP meeting was held on September 19 and 20, 2000 at Clemson University in South Carolina. Meeting was attended by more than 70 scientists and administrators from Japan, Taiwan, Thailand, Korea, China, India, Brazil, France, Canada, and the United States. The meeting was organized by Rod Wing, U.S. IRGSP Representative (Clem-son University), and chaired by Ben Burr, IRGSP Coordinator (Brookhaven National Laboratory, New York), and Takuji Sasaki, Program Director of the Rice Genome Research Program (RGP) in Japan.

Two complementary approaches were used, for construction of sequence-ready physical maps. The Rice Genome Research Program (RGP) used the genomic clones using expressed sequence tags/sequence-tagged sites (EST/STS) and genetic markers from the genetic and transcript maps of rice. The Clemson University Genomics Institute, the Arizona Genomics Institute, and the Arizona Genomics Computational Laboratory used a high-throughput bacterial artificial chromosome (BAC) fingerprint and automatic BAC contig assembly system using FPC software, and anchored the assembled contigs on the rice genome by hybridization-based screening. The rice genome project was completed in 2005. The completion of the rice genome sequence will be very helpful in the field of genetics and to combat most of the disease of the mostly consumed crop and also to differentiate between different rice varieties and also for the study of the other monocot crops.

 

The major events of rice genome project are:-

1991 – Rice genome Project started.

September 1997 - The International Rice Genome Sequencing Project (IRGSP) was formed.

4th April 2000 - Monsanto announced that the company had completed a working draft of the rice genome, which would be made     available to the IRGSP.

September 19 and 20, 2000 – The largest IRGSP meeting to date was held at Clemson University in South Carolina.

9th April 2000 - The University of Washington and China Released Genome Sequence of Rice.

The University of Washington (UW) rice genome project was directed by Dr. Leroy Hood and managed by Dr. Gregory G. Mahairas. The lab included 80 high-throughput DNA sequencers, robotic machines and powerful data processing computers. Monsanto Company financed the research project.

April 1, 2003 - The NIAS has established the Rice Genome Resource Center (RGRC).

December 2004 - The genome sequence of the japonica cultivar Nipponbare was completed by the IRGSP.

August 10, 2005 - On 10th August 2005 Rice Genome Project was completed. Researchers with the International Rice Genome Sequencing Project (IRGSP) published the "finished" DNA blueprint. It was published in Journal Nature on 11th August. It included the location and sequence of over 37,500 protein-encoding genes in 389 million bases of DNA. Rice is the first crop whose genome has been sequenced. Rice genome Project will give valuable information for all scientists worldwide. It will pave a new way for the production of rice resistant variety, more yielding variety. It will also be helpful for the scientists to study other crops that are closely related with the rice such as barley, corn, wheat etc.  After making the draft sequence of the japonica in 2002, the IRGSP scientists have increased the quality of the sequence to 95 percent complete at greater than 99 percent accuracy. By comparison, the 3 billion-base-pair human genome, with its 25,000 genes, reached that quality level in 2004, some 3 years after its draft sequence was completed.

 

August 11, 2005 - The results of Rice Genome Project were published in the issue of Nature.

 

Major Works:-

July 2002 - the genome of rice blast disease was sequenced. Rice blast disease destroys enough rice to feed 60 million people worldwide. This finding will help in understanding the nature of the disease and will take us to a solution for the rice blast disease so that we can stop the destruction of rice by rice blast disease.

Jan 2003   - Research found that about 40% of rice genome comprises repetitive DNA, known as Junk DNA, similar to that of MITEs. A 430 bp sequence was found to be identical to that of MITE in size and other characteristics. It was named as mPing or miniature ping.  japonica rice contains about 70copies of mping while indica rice about 14 copies.

June 2003 - Scientists Buell, Wing and their colleagues compared the proteins of the chromosome 10 with Arabidopsis. Chromosome 10 is the smallest chromosome in rice. They found that about two-third of proteins were similar between both the plants. This similarity was with respect to the long arm of chromosome 10, the short arm being little or no matching. These proteins were produced to bind nucleic acid, cell growth and maintenance, immunity against pathogens and for other biological processes. Researchers also found that on Chromosome 10, 43 different genes were clustered in groups of three. These genes will help the rice to fight against pathogens.

March 2007 - Meyer and his colleagues examined the normal gene expression as well as small ribonucleic acids in rice. They studied gene sequences that represented nearly 47 million mRNA molecules and 3 million small RNA. They found that small RNA plays an important role in gene regulation. "Small RNAs also have been associated with other important biological processes, such as responses to stress," Meyers said. "Many of small RNAs in rice have related sequences in the many important cereal crop plants, including maize and wheat."

October 2007 - Already around 1 billion people have no access to drinking water. It is expected that the demand for rice will increase by 40% by 2040 causing severe water crisis problem study was conducted to grow rice with less water. The study found that the system of rice intensification (SRI) method has helped increase yields by over 30% — four to five tonnes per hectare instead of three tonnes per hectare, while using 40% less water than conventional methods. Another advantage is SRI fields do not emit methane as is the case with the more conventional system of growing rice. Conventional method of rice cultivation uses 60-70 kilos of seeds per hectare; SRI requires just five kilos per hectare. The SRI was based on eight principles which are different to conventional rice cultivation. They include developing nutrient-rich and un-flooded nurseries instead of flooded ones; ensuring wider spacing between rice seedlings; preferring composts or manure to synthetic fertilizers; and managing water carefully to avoid that the plants’ roots are not saturated. If the SRI method was applied to 20 million hectares of land under rice cultivation in India, the country could meet its food grain objectives of 220 million tonnes of grain by 2012 instead of 2050. A conference was held from 3-5 October in Tripura. The conference was jointly organized by the Department of Agriculture of the Government of Tripura, the Directorate of Rice Research (DRR), the Central Rice Research Institute (CRRI), the Directorate of Rice Development (DRD), the Acharya NG Ranga Agriculture University (ANGRAU), the National Bank for Agriculture and Rural Development (NABARD), Sir Dorabji Tata Trust (SDTT) Mumbai and World Wide Fund for Nature (WWF)-ICRISAT Dialogue Project based at ICRISAT, Patancheru.  Professor Andy Pereira at the Virginia Bioinformatics Institute (VBI) also worked with colleagues in India, Indonesia, Israel, Italy, Mexico and The Netherlands to identify, characterize and make use of a gene known as HARDY that improves key features of this important grain crop. The research shows that HARDY contributes to more efficient water use in rice, a primary source of food for more than half of the world's population.

August 2007 - Cell and molecular biology major Tameka Bailey’s studied certain type of proteins and the molecular mechanisms that trigger rice’s response to stressful conditions, such as drought, high salinity and also to rice blast.  “The proteins have so much power in the cell, it’s amazing,” Bailey said. “They can change the whole fate of the plant.” Bailey also studied proteins called mitogen-activated protein kinases. These proteins regulate the plants’ response to external stimuli, such as drought or disease. The particular type of kinase Bailey studied is the last one in a cascade of kinases that convert signals from receptors into responses from the plant. She found that these proteins regulate the plants’ production of an acid called abscisic acid, which led to stress tolerance in drought and high salinity conditions, a trait that appears to be conserved in other types of plants. Bailey isolated and characterized these proteins, which are responsible for activating the plant’s response to stress. To give rice plants a boost in their ability to tolerate stressful conditions, Bailey used genetic engineering to create plants that would express a great deal of the protein. To do this, she inserted extra copies of the protein kinase DNA into the DNA of a rice plant. The transgenic rice plant then expressed an abundance of that particular protein. In contrast, Bailey produced transgenic plants where the protein kinase was suppressed to see how the plants responded to stress in the absence of the protein of interest. Her studies showed that the extra boost of protein kinases led to increased drought tolerance. “Those traits are really important to rice farmers,” Bailey said. “Making a direct contribution to this is really a plus to my work.”

 

CONCLUSION

Rice genome Project which was completed in 2005 has paved a way for new research. It is a model plant for cereal crops. Sequencing of its genome has opened a way for developing new varieties of rice to combat the pests and also to grow with less water. RGP will also help to produce more proteins in rice that can be beneficial to mankind (ex. golden rice). Finding of new proteins and the genes for blast disease will help to produce more yields by manipulating the gene responsible for blast disease.

About the Author

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