Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:


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


’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:

More articles from Life Sciences:

nachricht Biologists unravel another mystery of what makes DNA go 'loopy'
16.03.2018 | Emory Health Sciences

nachricht Scientists map the portal to the cell's nucleus
16.03.2018 | Rockefeller University

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

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

Im Focus: Locomotion control with photopigments

Researchers from Göttingen University discover additional function of opsins

Animal photoreceptors capture light with photopigments. Researchers from the University of Göttingen have now discovered that these photopigments fulfill an...

Im Focus: Surveying the Arctic: Tracking down carbon particles

Researchers embark on aerial campaign over Northeast Greenland

On 15 March, the AWI research aeroplane Polar 5 will depart for Greenland. Concentrating on the furthest northeast region of the island, an international team...

Im Focus: Unique Insights into the Antarctic Ice Shelf System

Data collected on ocean-ice interactions in the little-researched regions of the far south

The world’s second-largest ice shelf was the destination for a Polarstern expedition that ended in Punta Arenas, Chile on 14th March 2018. Oceanographers from...

Im Focus: ILA 2018: Laser alternative to hexavalent chromium coating

At the 2018 ILA Berlin Air Show from April 25–29, the Fraunhofer Institute for Laser Technology ILT is showcasing extreme high-speed Laser Material Deposition (EHLA): A video documents how for metal components that are highly loaded, EHLA has already proved itself as an alternative to hard chrome plating, which is now allowed only under special conditions.

When the EU restricted the use of hexavalent chromium compounds to special applications requiring authorization, the move prompted a rethink in the surface...

Im Focus: Radar for navigation support from autonomous flying drones

At the ILA Berlin, hall 4, booth 202, Fraunhofer FHR will present two radar sensors for navigation support of drones. The sensors are valuable components in the implementation of autonomous flying drones: they function as obstacle detectors to prevent collisions. Radar sensors also operate reliably in restricted visibility, e.g. in foggy or dusty conditions. Due to their ability to measure distances with high precision, the radar sensors can also be used as altimeters when other sources of information such as barometers or GPS are not available or cannot operate optimally.

Drones play an increasingly important role in the area of logistics and services. Well-known logistic companies place great hope in these compact, aerial...

All Focus news of the innovation-report >>>



Industry & Economy
Event News

Ultrafast Wireless and Chip Design at the DATE Conference in Dresden

16.03.2018 | Event News

International Tinnitus Conference of the Tinnitus Research Initiative in Regensburg

13.03.2018 | Event News

International Virtual Reality Conference “IEEE VR 2018” comes to Reutlingen, Germany

08.03.2018 | Event News

Latest News

Wandering greenhouse gas

16.03.2018 | Earth Sciences

'Frequency combs' ID chemicals within the mid-infrared spectral region

16.03.2018 | Physics and Astronomy

Biologists unravel another mystery of what makes DNA go 'loopy'

16.03.2018 | Life Sciences

Science & Research
Overview of more VideoLinks >>>