Largest rice genetics study finds vast differences in rice

September 15, 2011 By Krishna Ramanujan
Morphological diversity in seeds and whole grains of rice. This image illustrates the diversity of color, size and shape of rice seeds (with hulls intact) and corresponding grains (edible portion of the seed visible only after removal of the hull) in the rice diversity panel used for genome wide association studies. (Raluka Iorga, McCouch lab)

The largest publicly available genomewide association mapping study in rice to date has found that although the five subpopulations of Asian rice -- indica, aus, temperate japonica, aromatic and tropical japonica -- all belong to one species (Oryza sativa), their genetic structures are so different that, genetically speaking, they are almost like different species.

An international team led by Cornell researchers and published Sept. 13 in Nature Communications conducted the study based on genotyping (identifying ) more than 44,000 single (SNPs) across 413 diverse O. sativa varieties from 82 countries. SNPs refer to on the DNA level -- points in the genome where a base pair change makes one individual within a species different from another.

The researchers also phenotyped (measured the observable characteristics) for 34 traits related to size, shape, plant development and agronomic performance. Finally, the researchers analyzed the data to determine which particular traits are associated with which SNPs.

"Unlike maize, tomato and many other , Asian is highly differentiated into five distinct subpopulations or ecotypes," said Susan McCouch, professor of and the paper's senior author. The genetic differences among these five rice subpopulations are greater than the differences between many cultivated crops and their wild ancestors, she added.

That's because ancient rice subpopulations have evolved separately for thousands of years as farmers migrated and selectively bred them in a wide range of different ecological and that collectively altered their genetic makeups, McCouch said.

Also, rice mostly self-pollinates or inbreeds, with plants recycling their own genes, while such crops as maize and potato freely cross-pollinate, so they continuously exchange genes within their species and with their wild ancestors. And other crops such as tomatoes, for example, were domesticated only once, narrowing the gene pool, while rice was domesticated multiple times in different places.

"You have to take all this into account when you evaluate the genetics of rice," McCouch said.

For example, when the researchers analyzed a trait such as the size of rice panicles (the branched structure holding clusters of flowers or grains), they found variation is highly partitioned by subpopulation, such that the genes that determine panicle length in each subpopulation are entirely different, providing an example of convergent evolution, where very different genetic architecture underlies the same phenotype.

Also, the group demonstrated that the same trait may be governed by different genes in different environments, as in the case of flowering time evaluated in Arkansas, Bangladesh and the United Kingdom.

By understanding which different SNPs confer specific traits, breeders can start to understand and predict how crossing between subpopulations can give rise to offspring that outperform their parents in such desired traits as yield, grain size or drought tolerance.

All the genotypic and phenotypic data and the seeds for the 413 lines of rice are publicly available, allowing geneticists and breeders to build on this work, selecting subsets of for use in local rice populations, using phenotypic data to identify lines with desired traits to cross with local varieties, and leveraging genotypic data to better understand the genetics of complex trait variation in natural populations of rice and other plant species.

"On the science side, we are taking complex traits and breaking them down into their genetic components," and then using SNP variation to begin to predict phenotypic variation, McCouch said.

Co-authors for the Nature Communications paper include researchers from Stanford University; the U.S. Department of Agriculture's Dale Bumpers National Rice Research Center in Stuttgart, Ark.; the University of Arkansas; the University of Aberdeen in the United Kingdom (UK); and the Bangladesh Agricultural University in Mymensingh, Bangladesh.

Explore further: Research identifies wild ancestor genes for crop improvement

Related Stories

Research identifies wild ancestor genes for crop improvement

February 22, 2011

Using the genetic variation found in wild and exotic rice species, researchers are providing breeders with genomics tools and knowledge to develop higher yielding, stress-tolerant varieties, a Cornell researcher reported ...

Gene's past could improve the future of rice

January 23, 2009

( -- In an effort to improve rice varieties, a Purdue University researcher was part of a team that traced the evolutionary history of domesticated rice by using a process that focuses on one gene.

Researchers uncover genetic origins of rice fragrance

September 2, 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.

Genomic tools can help researchers develop crops quickly

February 22, 2011

( -- Using powerful genome sequencing tools created for human genetics, researchers can now exploit the genetic diversity of crops to improve productivity, sustainability and nutrition, a Cornell researcher reported ...

Early agricultural piracy informs the domestication of rice

June 9, 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 least ...

Recommended for you

New discovery: Common jellyfish is actually two species

November 21, 2017

University of Delaware professor Patrick Gaffney and alumnus Keith Bayha, a research associate with the Smithsonian's National Museum of Natural History, have determined that a common sea nettle jellyfish is actually two ...


Adjust slider to filter visible comments by rank

Display comments: newest first

not rated yet Sep 15, 2011
the five subpopulations of Asian rice -- indica, aus, temperate japonica, aromatic and tropical japonica -- all belong to one species (Oryza sativa)

Rice? Indica? Sativa?

Ok, botany boy, explain thyself.
not rated yet Sep 15, 2011
Based on the most recent study: "Molecular evidence for a single evolutionary origin of domesticated rice" PNAS May 17, 2011 vol. 108 no. 20 8351-8356, this story contains a false statement. The above study concludes that there was a single domestication of wild rice.

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.