Seeking a splice for better rice

Jul 13, 2012
Figure 1: Rice is a core component of the diet of billions of people. Identification of the genetic factors that make the plant more robust, or nutritionally beneficial, may further boost the usefulness of this crop. Credit: iStockphoto/hanhanpeggy

Every organism produces a staggering variety of molecules, each with its own particular biological function. Complex interplay between genetic and environmental factors determines the production levels for each compound. By deciphering these factors, plant geneticists can use the information to derive organisms with useful properties, such as crops that are more resistant to pathogens.

A research team led by Kazuki Saito and Fumio Matsuda of the RIKEN Plant Science Center in Yokohama has begun to unravel how genetic variations affect production in rice, a core dietary staple around the world1 (Fig 1). Saito’s group, which has acquired considerable expertise in characterizing the chemical contents of plants, partnered with agricultural specialists at Japan’s National Institute of Agrobiological Science (NIAS) in Tsukuba. “NIAS is the leading research center for rice breeding in Japan and has developed useful experimental lines for genetic analysis of rice qualitative traits,” says Saito.

Saito, Matsuda and their colleagues examined 85 different lines generated via crosses between cultivars representing two different types of rice, known as Indica and Japonica. “Indica rice is fluffy and used for curry dishes, while Japonica short-grain rice is the moist, sticky, bright white rice used in sushi or risotto,” explains Matsuda. From these various lines, the researchers collected data describing 759 different metabolites. Then they determined the extent to which genetic variations associated with Indica or Japonica genomes correlate with differences in the levels of these compounds.

Although many metabolites appeared to be primarily modulated by non-genetic factors, Saito, Matsuda and their colleagues identified several molecules whose production is strongly affected by differences at particular genomic loci. The researchers even identified a ‘hotspot’—a cluster of loci on chromosome 3 that coordinates production of a number of different amino acids and fatty acids. 

Rice plants produce known as flavone glycosides, which protect them from consumption by herbivores but also exhibit antioxidants and anti-inflammatory properties in humans. These could therefore represent promising targets for crop engineering. The research team found clear evidence for heritable factors that affect production, including an Indica-specific variant that is associated with greatly elevated levels of one particular flavone glycoside.

Finer mapping will be needed to pinpoint pertinent genetic alterations, as a possible prelude to targeted modification and optimization. However, this work also reinforces the value of ‘old-fashioned’ genetic engineering techniques. “Our study demonstrates that the metabolic composition in rice grains can be improved by traditional breeding programs, using natural genetic variations in the rice population,” says Saito.

Explore further: Study on pesticides in lab rat feed causes a stir

More information: Matsuda, F., et al. Dissection of genotype-phenotype associations in rice grains using metabolome quantitative trait loci analysis. The Plant Journal 70, 624–636 (2012).

Related Stories

New study sheds light on genetics of rice metabolism

Feb 08, 2012

A large-scale study analyzing metabolic compounds in rice grains conducted by researchers at the RIKEN Plant Science Center (PSC) and their collaborators has identified 131 rice metabolites and clarified the ...

Early agricultural piracy informs the domestication of rice

Jun 09, 2011

The origins of rice have been cast in a new light by research publishing in the open-access journal PLoS Genetics on June 9, 2011. By reconciling two theories, the authors show that the domestication of rice occurred at lea ...

Researchers uncover genetic origins of rice fragrance

Sep 02, 2009

( -- A new Cornell study reports that the gene that gives rice its highly valued fragrance stems from an ancestor of basmati rice and dispels other long-held assumptions about the origins of basmati. ...

Know your tomatoes

May 13, 2011

Genetically modified (GM) tomatoes look much the same as traditional varieties (Fig. 1). But are they? By comparing the chemical diversity of strains of GM tomatoes with a control strain and traditional reference ...

Plant enzymes reveal complex secrets

Mar 09, 2012

The enzymes needed for producing and chemically modifying functionally important plant molecules called anthocyanins have been identified by a research team led by Kazuki Saito of the RIKEN Plant Science Center, ...

Whole genome fine map of rice completed

Feb 21, 2005

Rice is a staple crop for more than half of the world's population, and it was hoped that the availability of its genome sequence might enable scientists to develop more productive and environment friendly rice ...

Recommended for you

Study on pesticides in lab rat feed causes a stir

5 hours ago

French scientists published evidence Thursday of pesticide contamination of lab rat feed which they said discredited historic toxicity studies, though commentators questioned the analysis.

International consortium to study plant fertility evolution

9 hours ago

Mark Johnson, associate professor of biology, has joined a consortium of seven other researchers in four European countries to develop the fullest understanding yet of how fertilization evolved in flowering plants. The research, ...

Making the biofuels process safer for microbes

11 hours ago

A team of investigators at the University of Wisconsin-Madison and Michigan State University have created a process for making the work environment less toxic—literally—for the organisms that do the heavy ...

Why GM food is so hard to sell to a wary public

12 hours ago

Whether commanding the attention of rock star Neil Young or apparently being supported by the former head of Greenpeace, genetically modified food is almost always in the news – and often in a negative ...

The hidden treasure in RNA-seq

Jul 01, 2015

Michael Stadler and his team at the Friedrich Miescher institute for Biomedical Research (FMI) have developed a novel computational approach to analyze RNA-seq data. By comparing intronic and exonic RNA reads, ...

User comments : 0

Please sign in to add a comment. Registration is free, and takes less than a minute. Read more

Click here to reset your password.
Sign in to get notified via email when new comments are made.