Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

Going with the grain: A tale of rice’s smallest chromosome

06.06.2003


’Finished’ sequence reveals twice as many genes, cereal similarity



Behold a grain of rice. Inside are thousands of cells; within each cell are 12 chromosomes; and on rice’s smallest chromosome, No. 10, are about 3,500 genes and more than 22 million base pairs, the links in the chain of DNA.
So, what’s the big deal about rice’s smallest chromosome?

There are several, according to a report in the June 6 issue of the journal Science. Upon close examination, chromosome 10 has about twice as many genes as were predicted when an international consortium announced draft genome sequence in the same journal last December. An organism’s genome consists of the entire genetic code held in its DNA.



Of potentially greater significance, a detailed look at chromosome 10 shows that the genome map of rice is similar to other grains, particularly sorghum and maize.

The project, led by Rod A. Wing of the University of Arizona and C. Robin Buell of The Institute for Genomic Research (TIGR), was funded by the U.S. Department of Agriculture, National Science Foundation, National Institutes of Health, and the Department of Energy. A portion of chromosome 10 was also sequenced by the Plant Genome Initiative at Rutgers.

The work demonstrates the value of pursuing the full sequence in detail, said Judith Plesset, a program director in NSF’s Directorate for Biological Sciences, which supported the project. "One of the lessons here is, ’Don’t think you know everything simply because you’ve done the draft,’" she said.

According to TIGR’s Buell, getting from the draft to the finished version is painstaking and costly because the process "is not automated to any large extent" and it requires considerable lab work by an extended team of research associates.

The resulting view, however, is immensely clearer. "Like looking at the cosmos through a regular telescope, and then looking at it through the Hubble telescope," Buell said.

Focusing on rice matters because, according to the report, rice (Oryza sativa) has been cultivated for more than 9,000 years and remains a major food staple for more than half the human population.

While rice feeds half the world, its relatively simple genome helps scientists understand the genetics of other plants. According to the Science report, "Rice is considered a model system for plant biology largely due to its compact genome (430 million base pairs, or Mb, 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)."

Added NSF’s Plesset, "We can use rice as a reference for understanding the organization, structure and function of much larger genomes such as maize and wheat. Scientists can use a rice gene to find its counterpart in any of the cereal genomes."

Seeking to identify the roles of the chromosome’s genes by combing through molecular databases, Buell, Wing and their colleagues compared chromosome 10’s proteins with those of another model plant, Arabidopsis, a member of the mustard family whose genome has been completely sequenced and extensively documented. Matches were found for about two-thirds of the proteins, indicating some of the specific genes responsible for enzyme production, binding of nucleic acids, cell growth and maintenance, cell communication, immunity, development and other functions and processes.

On the chromosome’s "short arm," however, they found very little that matched Arabidopsis. Instead, there they found an abundance of heterochromatin, a stretch of highly compacted DNA with few genes among it, a chromosomal substance for which the biological function is unknown.

Though much more detailed than the draft, this version is not completely finished and has seven gaps, representing about 4 percent of the total sequence.

"This," Plesset said, "is a result of the limitation of sequencing technology. As new technologies become available, these gaps will be filled."

The work reported in Science is a part of the international collaboration to sequence the entire rice genome completely. Two of the other 12 rice chromosomes, numbers 1 and 4, have also been essentially "finished," and published by the Japanese and the Chinese groups, respectively. A full sequence for chromosome 3 is expected to be announced by the end of 2003.

Sean Kearns | NSF
Further information:
http://www.nsf.gov
http://www.nsf.gov/od/lpa

More articles from Life Sciences:

nachricht Designed proteins to treat muscular dystrophy
29.06.2017 | Universität Basel

nachricht Funding of Collaborative Research Center developing nanomaterials for cancer immunotherapy extended
28.06.2017 | Johannes Gutenberg-Universität Mainz

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

Die letzten 5 Focus-News des innovations-reports im Überblick:

Im Focus: Can we see monkeys from space? Emerging technologies to map biodiversity

An international team of scientists has proposed a new multi-disciplinary approach in which an array of new technologies will allow us to map biodiversity and the risks that wildlife is facing at the scale of whole landscapes. The findings are published in Nature Ecology and Evolution. This international research is led by the Kunming Institute of Zoology from China, University of East Anglia, University of Leicester and the Leibniz Institute for Zoo and Wildlife Research.

Using a combination of satellite and ground data, the team proposes that it is now possible to map biodiversity with an accuracy that has not been previously...

Im Focus: Climate satellite: Tracking methane with robust laser technology

Heatwaves in the Arctic, longer periods of vegetation in Europe, severe floods in West Africa – starting in 2021, scientists want to explore the emissions of the greenhouse gas methane with the German-French satellite MERLIN. This is made possible by a new robust laser system of the Fraunhofer Institute for Laser Technology ILT in Aachen, which achieves unprecedented measurement accuracy.

Methane is primarily the result of the decomposition of organic matter. The gas has a 25 times greater warming potential than carbon dioxide, but is not as...

Im Focus: How protons move through a fuel cell

Hydrogen is regarded as the energy source of the future: It is produced with solar power and can be used to generate heat and electricity in fuel cells. Empa researchers have now succeeded in decoding the movement of hydrogen ions in crystals – a key step towards more efficient energy conversion in the hydrogen industry of tomorrow.

As charge carriers, electrons and ions play the leading role in electrochemical energy storage devices and converters such as batteries and fuel cells. Proton...

Im Focus: A unique data centre for cosmological simulations

Scientists from the Excellence Cluster Universe at the Ludwig-Maximilians-Universität Munich have establised "Cosmowebportal", a unique data centre for cosmological simulations located at the Leibniz Supercomputing Centre (LRZ) of the Bavarian Academy of Sciences. The complete results of a series of large hydrodynamical cosmological simulations are available, with data volumes typically exceeding several hundred terabytes. Scientists worldwide can interactively explore these complex simulations via a web interface and directly access the results.

With current telescopes, scientists can observe our Universe’s galaxies and galaxy clusters and their distribution along an invisible cosmic web. From the...

Im Focus: Scientists develop molecular thermometer for contactless measurement using infrared light

Temperature measurements possible even on the smallest scale / Molecular ruby for use in material sciences, biology, and medicine

Chemists at Johannes Gutenberg University Mainz (JGU) in cooperation with researchers of the German Federal Institute for Materials Research and Testing (BAM)...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

Plants are networkers

19.06.2017 | Event News

Digital Survival Training for Executives

13.06.2017 | Event News

Global Learning Council Summit 2017

13.06.2017 | Event News

 
Latest News

High conductive foils enabling large area lighting

29.06.2017 | Power and Electrical Engineering

Designed proteins to treat muscular dystrophy

29.06.2017 | Life Sciences

Climate Fluctuations & Non-equilibrium Statistical Mechanics: An Interdisciplinary Dialog

29.06.2017 | Seminars Workshops

VideoLinks
B2B-VideoLinks
More VideoLinks >>>