Geneticists Study Origin, Evolution of "Sticky" Rice

A study by two North Carolina State University geneticists traces the origin and evolution of a genetic mutation that long ago led to the creation of a type of rice known as glutinous, or "sticky," rice.

The molecular genetic research leads researchers to believe that glutinous rice - which differs from non-glutinous, or common, rice on account of a mutation in its Waxy gene that suppresses the formation of a starch called amylose - most likely originated a single time in Southeast Asia. Further, DNA evidence - namely the lower-than-expected genetic variability in the Waxy gene - suggests that early domesticators of glutinous rice liked its adhesive quality and wanted to preserve that particular trait.

Dr. Michael Purugganan, associate professor of genetics, and Dr. Kenneth Olsen, post-doctoral research associate in genetics, publish their findings in the Oct. 23 edition of Genetics.

To learn more about the origin and evolution of sticky rice, the researchers studied 105 glutinous and non-glutinous samples of rice donated from the multitudinous stock kept by the International Rice Research Institute in Los Banos, Philippines.

Rice contains two starches: amylose and amylopectin. Glutinous rice lacks amylose; in fact, it is the lack of amylose that gives it its sticky composition. Non-glutinous rice - what you'd find if you cooked up a name-brand package of rice from the grocery store, for example - contains up to 30 percent amylose; the result is rice with grains that separate.

Glutinous rice is the staple food in some areas in Southeast Asia, including parts of Laos, Thailand and Cambodia, the researchers say. Sticky rice has also migrated north to become an important part of the diet in places like China and Japan. Used primarily in a number of desserts - rice cakes, for example - sticky rice has achieved important cultural standing in East and Southeast Asia.

But Asian folklore diverges on the origin of glutinous rice, Purugganan says. He found both a Laotian Buddhist legend charting the existence of glutinous rice to about 1,100 years ago and Chinese folklore that indicated the existence of glutinous rice more than 2,000 years ago.

"Since no one really knows where glutinous rice came from, we wanted to find its origin using molecular means," Purugganan says. "We also wanted to find out the number of times the mutation in the Waxy gene that suppresses amylose, which produces glutinous rice, arose during rice domestication. And, we wanted to see if the Waxy gene showed evidence of selection by early Asian farmers."

Performing genetic sequencing of these samples at NC State's Genome Research Laboratory, Purugganan and Olsen assembled a "gene tree," or network that represents patterns of genetic differences among the DNA sequences, Olsen explains.

Using the gene tree, the researchers found that sticky rice's genetic mutation maps to a single mutation on the gene tree, suggesting that the mutation occurred a single time rather than more than once, Olsen says. Looking at the geographic locations of the rice DNA sequences that are direct ancestors of the mutation, the researchers found fairly strong evidence that Southeast Asia was the geographic origin of sticky rice. This squares with the fact that sticky rice is a staple in some parts of Southeast Asia.

"This type of research really opens up the window of not only how crops originate, but also how specific features evolve," Purugganan says. Olsen adds, "This is one of the first times that anyone has looked within a crop species at the evolutionary and geographical origins of important domestication traits in crops."

Purugganan and Olsen now plan to study other genes involved in starch synthesis in rice.

Research funding for the study of the origin and evolution of glutinous rice was provided by the Alfred P. Sloan Foundation.

Note to editors: An abstract of the paper follows.

"Molecular Evidence on the Origin and Evolution of Glutinous Rice"Authors: Kenneth M. Olsen and Michael D. Purugganan, North Carolina State UniversityPublished: Oct. 23, 2002, in Genetics Abstract: Glutinous rice is a major type of cultivated rice with longstanding cultural importance in Asia. A mutation in an intron 1 splice donor site of the Waxy gene is responsible for the change in endosperm starch leading to the glutinous phenotype. Here we examine an allele genealogy of the Waxy locus to trace the evolutionary and geographical origins of this phenotype. Based on 105 glutinous and non-glutinous landraces from across Asia, we find evidence that the splice donor mutation has a single evolutionary origin, and that it probably arose in Southeast Asia. Nucleotide diversity measures indicate that the origin of glutinous rice is associated with reduced genetic variation characteristic of selection at the Waxy locus; comparison with an unlinked locus, RGRC2, confirms that this pattern is specific to Waxy. In addition, we find that many non-glutinous varieties in Northeast Asia also carry the splice donor site mutation, suggesting that partial suppression of this mutation may have played an important role in the development of Northeast Asia non-glutinous rice. This study demonstrates the utility of phylogeographic approaches for understanding trait diversification in crops, and it contributes to growing evidence on the importance of modifier loci in the evolution of domestication traits.