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UGA researcher comments on her team's discovery of the first 'jumping genes' in rice

University of Georgia

University of Georgia researchers studying rice genomes, under a National Science Foundation Plant Genome award, have identified the species' first active DNA transposons or "jumping genes."

Dr. Susan Wessler, who headed the research team that published the findings in the journal Nature, made the following statements regarding the discovery:

"This is of particular interest at this time because rice is in the news with recent reports of two draft genome sequences by public and private projects and with 40 percent of these sequences derived from transposable elements. Rice is also the most important crop for human nutrition. As such, any discoveries in this plant are of international interest.

"Although genome sequences are available, rice lacks some critical resources that other organisms with sequenced genomes have. One of these is active transposable elements. Active TEs can be exploited and used to generate so-called "knock-out populations"; that is, ones in which the TE has jumped into a gene and inactivated it. This is an important resource, because it creates tagged mutations that can be used to link genes with phenotype, thus giving meaning and revealing function to the genomic sequence.

"We report the first active miniature inverted repeat transposable elements (or "MITEs") from any organism. Since their discovery in my lab more than 10 years ago, MITEs have been shown to comprise a significant fraction of the genomes of many plants, especially the grasses (rice, maize, wheat, sorghum and barley) and have been found in animal genomes including humans, zebrafish, mosquitoes and the worm (C. elegans).

"Of interest is that they are frequently associated with genes, where they are found in the non-coding regions and where they may play a role in diversifying the expression of genes. Changes in patterns of gene expression as opposed to changes in protein coding regions is thought to provide the raw material for the subtle changes that lead to evolutionary change. Despite the identifications of hundreds of thousands of MITEs in a variety of organisms, mPing was the first active MITE identified. The study also reported the first autonomous (transposase encoding) element in rice (called "Pong") and the first autonomous element associated with the movement of MITEs.

"We also report the first use of computational analysis of raw genomic sequence to identify candidate active elements. Prior to our studies, active DNA elements were isolated from mutant alleles when they inserted into a gene and created a mutant phenotype. This is how pioneering geneticist Barbara McClintock discovered TEs - through their effect on maize genes; however, most organisms have not been characterized genetically, and mutations are not available.

"We now know that the vast majority of the genomic DNA from higher organisms is derived from TEs (more than 45 percent of the human genome and up to 95 percent of the genomes of some plants like Iris). Our study requires the availability of genomic sequence from an organism (something that is becoming increasingly available for more and more organisms) to identify candidate active elements. These elements can then be tested for activity in cells where host regulation of TE expression has been compromised as in cell culture. It is not difficult to culture the cells of many types of plants and animals and provide material to test for the activity of candidates.

"Finally, we report the first activation of a transposable element family since domestication. In our case, mPing elements have amplified in temperate japonica rice cultivars (from the cooler climates like Korea and Japan) but not in tropical japonicas (cultivars from such areas as India and the Philippines) where rice originated.

"One hypothesis is that the stress of cultivating a tropical plant in temperate environments may have activated the elements (just like the stress of cell culture has led to their activation) leading to the insertion of the small mPing elements into or near rice genes. This may have led to the creation of genetic diversity thus enriching the gene pool of the temperate varieties."

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