Featured Research

from universities, journals, and other organizations

Genome-scale network of rice genes to speed the development of biofuel crops

Date:
November 28, 2011
Source:
DOE/Lawrence Berkeley National Laboratory
Summary:
Researchers have developed the first genome-scale model for predicting the functions of genes and gene networks in a grass species. Called RiceNet, this systems-level model of rice gene interactions should help speed the development of new crops for the production of advanced biofuels, as well as help boost the production and improve the quality of one of the world's most important food staples.

This graphic is a full-size view of a RiceNet layout, color-coded to indicate the likelihood of network links; red for higher and blue for lower likelihood scores.
Credit: Image from Ronald, et al

The first genome-scale model for predicting the functions of genes and gene networks in a grass species has been developed by an international team of researches that includes scientists with the U.S. Department of Energy (DOE)'s Joint BioEnergy Institute (JBEI), a multi-institutional partnership led by Lawrence Berkeley National Laboratory (Berkeley Lab). Called RiceNet, this systems-level model of rice gene interactions should help speed the development of new crops for the production of advanced biofuels, as well as help boost the production and improve the quality of one of the world's most important food staples.

Related Articles


"With RiceNet, instead of working on one gene at a time based on data from a single experimental set, we can predict the function of entire networks of genes, as well as entire genetic pathways that regulate a particular biological process," says Pamela Ronald, a plant geneticist who holds joint appointments with JBEI, where she directs the grass genetics program, and with the University of California (UC) Davis, where she is a professor in the Department of Plant Pathology and at The Genome Center. "RiceNet represents a systems biology approach that draws from diverse and large datasets for rice and other organisms."

Rice is a staple food for half the world's population and a model for monocotyledonous species -- one of the two major groups of flowering plants. Rice is especially useful as a model for the perennial grasses, such as Miscanthus and switchgrass, that have emerged as prime feedstock candidates for the production of clean, green and renewable cellulosic biofuels.

Given the worldwide importance of rice, a network modeling platform that can predict the function of rice genes has been sorely needed. However, until now the high number of rice genes- in excess of 41,000 compared to about 27,000 for Arabidopsis, a model for the other major group of flowering plants -- along with several other important factors, has proven to be too great a challenge.

Ronald is the corresponding author of a paper in the Proceedings of the National Academy of Sciences (PNAS) that describes how JBEI researchers, working with researchers at the University of Texas in Austin, and Yonsei University in Seoul, Korea, overcame the challenge and developed a network that encompasses nearly half of all rice genes. The paper is titled "Genetic dissection of the biotic stress response using a genome-scale gene network for rice."

"RiceNet builds upon 24 publicly available data sets from five species as well as an earlier mid-sized network of 100 rice stress response proteins that my group constructed through protein interaction mapping," Ronald says. "We have conducted experiments that validated RiceNet's predictive power for genes involved in the rice innate immune response."

Ronald and her team also showed that RiceNet can accurately predict gene functions in another important monocotyledonous crop species, maize.

A RiceNet Website is now available that allows researchers from all over the world to use it. At JBEI, RiceNet will be used to identify genes that have not previously been known to be involved in cell wall synthesis and modification. JBEI researchers are looking for ways to increase the accessibility of fermentable sugars in the cell walls of feedstock plants.

"The ability to identify key genes that control simple or complex traits in rice has important biological, agricultural, and economic consequences," Ronald says. "RiceNet offers an attractive and potentially rapid route for focusing crop engineering efforts on the small sets of genes that are deemed most likely to affect the traits of interest."

Co-authoring the PNAS paper with Ronald were Insuk Lee, Young-Su Seo, Dusica Coltrane, Sohyun Hwang, Taeyun Oh and Edward Marcotte.

This research was supported in part by JBEI through the DOE Office of Science.


Story Source:

The above story is based on materials provided by DOE/Lawrence Berkeley National Laboratory. Note: Materials may be edited for content and length.


Journal Reference:

  1. I. Lee, Y.-S. Seo, D. Coltrane, S. Hwang, T. Oh, E. M. Marcotte, P. C. Ronald. Genetic dissection of the biotic stress response using a genome-scale gene network for rice. Proceedings of the National Academy of Sciences, 2011; DOI: 10.1073/pnas.1110384108

Cite This Page:

DOE/Lawrence Berkeley National Laboratory. "Genome-scale network of rice genes to speed the development of biofuel crops." ScienceDaily. ScienceDaily, 28 November 2011. <www.sciencedaily.com/releases/2011/11/111102125652.htm>.
DOE/Lawrence Berkeley National Laboratory. (2011, November 28). Genome-scale network of rice genes to speed the development of biofuel crops. ScienceDaily. Retrieved March 5, 2015 from www.sciencedaily.com/releases/2011/11/111102125652.htm
DOE/Lawrence Berkeley National Laboratory. "Genome-scale network of rice genes to speed the development of biofuel crops." ScienceDaily. www.sciencedaily.com/releases/2011/11/111102125652.htm (accessed March 5, 2015).

Share This


More From ScienceDaily



More Plants & Animals News

Thursday, March 5, 2015

Featured Research

from universities, journals, and other organizations


Featured Videos

from AP, Reuters, AFP, and other news services

Praying Mantis Looks Long Before It Leaps

Praying Mantis Looks Long Before It Leaps

Reuters - Innovations Video Online (Mar. 5, 2015) — Slowed-down footage of the leaps of praying mantises show the insect&apos;s extraordinary precision, say researchers. Video provided by Reuters
Powered by NewsLook.com
Octopus Grabs Camera and Turns It Around On Photographer

Octopus Grabs Camera and Turns It Around On Photographer

Buzz60 (Mar. 5, 2015) — A photographer got the shot of a lifetime, or rather an octopus did, when it grabbed the camera and turned it around to take an amazing picture of the photographer. Jen Markham (@jenmarkham) has the story. Video provided by Buzz60
Powered by NewsLook.com
Ringling Bros. Eliminating Elephant Acts

Ringling Bros. Eliminating Elephant Acts

AP (Mar. 5, 2015) — The Ringling Bros. and Barnum & Bailey Circus is ending its iconic elephant acts. The circus&apos; parent company, Feld Entertainment, told the AP exclusively that the acts will be phased out by 2018 over growing public concern about the animals. (March 5) Video provided by AP
Powered by NewsLook.com
Raw: Tourists Visit Rare Grey Whales in Mexico

Raw: Tourists Visit Rare Grey Whales in Mexico

AP (Mar. 4, 2015) — Once nearly extinct, grey whales now migrate in their thousands to Mexico&apos;s Vizcaino reserve in Baja California, in search of warmer waters to mate and give birth. Tourists flock to the reserve to see the whales, measuring up to 49 feet long. (March 4) Video provided by AP
Powered by NewsLook.com

Search ScienceDaily

Number of stories in archives: 140,361

Find with keyword(s):
 
Enter a keyword or phrase to search ScienceDaily for related topics and research stories.

Save/Print:
Share:  

Breaking News:

Strange & Offbeat Stories

 

Plants & Animals

Earth & Climate

Fossils & Ruins

In Other News

... from NewsDaily.com

Science News

Health News

Environment News

Technology News



Save/Print:
Share:  

Free Subscriptions


Get the latest science news with ScienceDaily's free email newsletters, updated daily and weekly. Or view hourly updated newsfeeds in your RSS reader:

Get Social & Mobile


Keep up to date with the latest news from ScienceDaily via social networks and mobile apps:

Have Feedback?


Tell us what you think of ScienceDaily -- we welcome both positive and negative comments. Have any problems using the site? Questions?
Mobile iPhone Android Web
Follow Facebook Twitter Google+
Subscribe RSS Feeds Email Newsletters
Latest Headlines Health & Medicine Mind & Brain Space & Time Matter & Energy Computers & Math Plants & Animals Earth & Climate Fossils & Ruins