Rice genome information.

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Dear Editor,

Thanks for the reply. It will be very informative to know all about rice Genome. Is it possible to know how laboratory samples were obtained for testing?

Regards,
Abdul Rauf

Dear Rauf Ji

We shall try to find out. This can only be verified by the scientists who carried out the testing. We hope to raise this issue in our bulletin and will contact a few researchers to find out.

Best regards
Editor

By editor on Thursday, June 19, 2003 - 09:22 am:

Here you find some vital information on Rice Genome and also some points cleared by the Commercial research corporations and their strategies. We produce this information to inform our readers:


Rice Genome

1. What is the Rice Genome ?

The Rice Genome is the world’s first complete genome of a crop plant, rice. The sequence contains all of the genetic information that determines the makeup of rice. This includes the DNA sequence of every gene, the regulatory DNA sequences that surround the genes, the linear order of the genes along every chromosome, and the correspondence between the genome map and the plant breeder’s map of inherited traits. The DNA sequence is 99.9% accurate.


2. Why to sequence the Rice Genome?

Rice is the largest commercial crop in the world, nourishing over half of the World’s population. There is tremendous potential to improve the world’s ability to feed its people through improving yields and reducing the rice plant’s dependence upon fertilizer and pesticides. Rice is also a key to knowledge of other cereal crops such as corn and wheat.


3. How long did it take to complete the rice genome sequence?

The rice sequence was completed to better than 6x coverage in approximately 14 months. Although enhancements to the system mean that it runs faster all the time, it was running at approximately 12 million base pairs of DNA per day as the genome was completed. 6x coverage means that the genome was sequenced the equivalent of six times over, or approximately 2.6 billion base pairs in total.

4. How will the sequence be used?

The Rice Genome Map will be used by plant breeders to precisely select the best progeny from breeding crosses. This will accelerate the improvement of rice varieties. The map will also be used by biotechnologists to snip out and transfer single genes from one rice variety to another, so that discrete improvements can be made without mixing together all of the genes from both varieties. The Rice Genome Map will be useful as a research tool to understand how crops resist stress, or how they confer health benefits to food. Because of the considerable genetic similarity between rice and other cereals such as wheat and maize, the Rice Genome Map is a virtual map of all cereal species. Therefore, the Rice Genome Map could accelerate the improvement of all cereal species.

5. How was rice sequenced?

The Rice Genome Map was made using a “shotgun” sequencing strategy. This is the same strategy that revolutionized the Human Genome Project. Shotgun sequencing enables full coverage of the genome in a fraction of the time required for the alternative BAC sequencing approach. Other groups such as the International Rice Genome Sequencing Project and Monsanto have used the BAC (Bacterial Artificial Chromosome) sequencing strategy. The IRGSP plans to complete the sequence of rice in 2003.

6. How does the Rice Genome compare with the recently announced genome of Arabidopsis?

Arabidopsis is a small member of the mustard family. It is frequently used for research because of the ease with which it can be grown and studied. Flowering plants are divided in two major groups: the dicots which include Arabidopsis and most fruits and vegetables; and the monocots which include species like rice, wheat, maize, barley, sorghum, millet, and sugarcane. The Rice Genome will provide insight and tools for improving monocots whereas Arabidopsis will be more useful for dicots. The rice genome is three times larger than that of Arabidopsis. The DNA sequence and order of the genes are very different between rice and Arabidopsis.

7. How does the Rice Genome compare with the working draft that was announced by Monsanto?

Monsanto describes their DNA sequence as a working draft. Myriad’s sequence is 99.5% complete or more. The two versions are somewhat like an outline for a book and the finished manuscript.


Access to Information

1. Who will have access to the Rice Genome?

Myriad and Syngenta make the rice genome publicly available through collaboration agreements. Application information is available on the Syngenta website, www.nadii.com. Collaboration proposals are evaluated bimonthly. Criteria for evaluation include scientific significance and potential for social benefit.

2. Who will own the genes that are discovered by this project?

Myriad and TMRI will seek patent protection for inventions relating to specific gene uses that result from this project. In some cases, these inventions will include the composition of a gene.

3. Will the sequence be accessible to academic researchers?

The sequence generated by this project will be made available to researchers via a genome technology access agreement.

4. Will Myriad or Syngenta patent the rice genome?

No. Myriad and Syngenta will seek patent protection for particular uses of selected genes. Neither Myriad or Syngenta will seek a patent on the rice genome.


Benefits and Implications

1. How can this information be used to improve agriculture?

Understanding cereal genomes and proteins will accelerate scientists ability to breed crops with stable yields by improving seed quality, resistance to pests and diseases and plant hardiness. Crop plants could also be made more nutritious or safer. For example, many cereal grains are contaminated by natural mycotoxins that are a potential threat to humans and livestock. Understanding cereal genomes, genes, and proteins will accelerate the ability to breed crops that prevent mycotoxin contamination. A third benefit could be increased environmental protection. The greatest threat to the environment in many areas is the excessive use of land and water for agriculture. Understanding cereal genomes will accelerate the ability to breed crops with increased yield and hardiness, thus reducing the agricultural need for land and water.

2. What does this mean for developing countries?

Agricultural research in developing countries is often focused on rice. The rice genome may create opportunities for the improvement of rice. Torrey Mesa Research Institute will seek to bring those opportunities to rice researchers through collaborations or, in conjunction with Myriad Genetics, through commercial access to the cereal genome database. Research on rice may also lead to the improvement of other cereals.

3. Have any U.S. government or public funds been used in this research project?

No. Syngenta has funded this project entirely independent of public funds.


Genomics

1. What is genomics?

The genome of a plant, animal or microbe is the totality of its genetic information including all the genes as well as the non-transcribed sections of the DNA. In summary, all the genes that a certain organism has.Genomics is the study of this complete genetic content within an organism.

2. What is proteomics?

Proteomics is the study of proteins, their location and their function within the genome.


3. How can researchers use information produced by DNA sequencing, etc.?

Once the gene sequence of an individual rice cell has been established, functional genomics can be used to ascertain the function and inter-relationship of the sequenced genes.

4. How big is the rice genome?

The rice genome is three times larger than that of Arabidopsis, which was recently sequenced. The rice genome has 12 chromosomes containing 430 million base pairs of DNA, and we expect that it has about 50,000 genes.


Who’s who

1. What is the relationship between TMRI and Myriad?

Myriad used its ultra high-throughput DNA sequencing capability to sequence the rice genome. The agreement with Myriad Genetics is a research collaboration that is extended into other areas of interest to the partners.

2. What is the Torrey Mesa Research Institute?

The Torrey Mesa Research Institute (TMRI) is a subsidiary of Syngenta. Syngenta is the world’s leading agribusiness. The company ranks first in crop protection, and third in the high-value commercial seeds market. Pro forma sales in 1999 were approximately US $7 billion. Syngenta employs more than 20,000 people in over 50 countries. The company is committed to sustainable agriculture through innovative Research and Technology. Formed in November 2000 by the merger of Novartis Agribusiness and Zeneca Agrochemicals, Syngenta is listed on the Swiss stock exchange, and in London, New York and Stockholm. Further information is available at www.syngenta.com.


3. What is Myriad Genetics Inc.?

Myriad Genetics is a biopharmaceutical company and a leading gene sequencing organization. The Company's new ultra high-throughput facility, based upon the latest generation of capillary DNA sequencing instruments can routinely produce large quantities of high quality DNA information. Myriad is using its ultra high-throughput DNA sequencing capability to pursue the discovery of animal, microbial and plant genomes of all sizes.

By editor on Thursday, June 19, 2003 - 09:09 am:

http://rgp.dna.affrc.go.jp/

Introduction to Rice Genome Research Program (RGP) at STAFF Institute in Tsukuba, Japan.

INTRODUCTION
The Rice Genome Research Program (RGP) is an integral part of the Japanese Ministry of Agriculture, Forestry and Fisheries (MAFF) Genome Research Project. It is jointly coordinated by the National Institute of Agrobiological 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 program started in October 1991 and the first phase continued through 1997 resulting in the establishment of some of the basic tools of rice genome analysis. Reorganized into a national project in 1998, RGP now aims to completely sequence the entire rice genome and subsequently to pursue integrated goals in functional genomics, genome informatics and applied genomics. It is now the leading member of the International Rice Genome Sequencing Project (IRGSP), a consortium of ten countries sharing the sequencing of the 12 rice chromosomes.

Research activities are principally conducted at the STAFF Institute located in Tsukuba City, Ibaraki Prefecture, Japan, about 50 km northeast of Tokyo. The STAFF Institute is a biotechnology research center operating in a five-story building with the second and third floors devoted to RGP staff comprising of nearly 80 researchers and technicians. We can be reached at the following address:

Rice Genome Research Program (RGP)
STAFF Institute
446-1, Ippaizuka, Kamiyokoba
Tsukuba-shi, Ibaraki-ken 305-0854
Japan

By editor on Thursday, June 19, 2003 - 09:16 am:

Dear Readers Please find some links to some ongoing research programmes in different countries of the world:


RICE GENOME RESEARCH PROGRAM (RGP)

Part of the Japanese MAFF Genome Research Project. It is a joint plant genome research program

rgp.dna.affrc.go.jp/

US Rice Genome
Information generated from a rice genome project could be utilized to increase the quality and quantity of rice production. ...

www.usricegenome.org/


Rice-Research
Monsanto launched the rice-research.org public database in June of 2000 to provide access to the Monsanto draft rice genome sequences to publicly funded ...

www.rice-research.org/


Academia Sinica Plant Genome Center
has finished rice chromosome 5 sequencing.

http://genome.sinica.edu.tw/

The Korea Rice Genome Database. The Korea Rice ... STEPI). Current Status of Rice Genome Sequencing by Internation Consortium Rice

bioserver.myongji.ac.kr/ricemac.html


Current Status of Rice Genomic Sequence. ... Blast Search. Search your sequence for
similarity against our database of rice genomic sequence. Retrieve Sequences. ...

http://nucleus.cshl.org/riceweb/


University of Wisconsin Madison Rice Genome Project
www.gcow.wisc.edu/Rice/

The TIGR Rice Genome Project
Rice Genome Facts, Rice GenBank Entries.
Rice Genome Project has submitted a total of 46.36 MB of DNA to GenBank. ...

http://www.tigr.org/tdb/e2k1/osa1/


Rice GD
Rice Genome Sequencing - the Science, the International Effort, and the Chinese Contribution If a single plant species is crowned ...

http://btn.genomics.org.cn/rice/


TORREY MESA RESEARCH INSTITUTE (TMRI) - The Rice Genome Project.
the access to rice genome sequence

portal.tmri.org/rice/RiceDescription.html

By Abdul on Friday, June 13, 2003 - 06:41 pm:

Dear Editor,

There is a new in Oryza daily report about Basmati rice genome information availability. Can I have the contact from were I can obtain this information.

Regards,
Abdul Rauf

Dear Mr. Rauf

We shall soon post detailed info on Rice Genome.
We keep posting the recent news on discussions and on various pages of oryza.

Ed.