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DNA data can accelerate rice variety development

CROWLEY, La. — Lab work with DNA is doing more than helping to solve crimes. It also is being used to determine if new experimental rice varieties being developed by LSU AgCenter researchers will meet farmers’ needs.

Using the DNA fingerprinting, otherwise known as genetic markers, can save considerable time in developing new rice varieties, according to Herry Utomo, assistant professor at the Rice Research Station near Crowley, La.

In a project funded by the Louisiana Rice Research Board, Utomo is trying to develop a simple and economical “genetic marker detection system” to aid in plant breeding. Such a system is critical for more successful and widespread application of newer technology that can enhance speed and efficiency in rice breeding programs, he said.

“A non-automated marker detection protocol, which is fast, reliable, and cost-effective, is being developed here at the station that will require minimal, standard molecular laboratory equipment,” Utomo said.

Genetic research has come a long way in the past decade, according to Utomo, who said getting genetic marker data 10 years ago would have taken more than a week. Now it can be done in a day.

To extract DNA from rice plants, small bits of plant tissue are placed in formulated solution in plastic vials containing small metal beads. The tray of vials is placed in a machine that rapidly shakes the beads, pulverizing the tissue so that DNA can be removed.

“That way we can process 96 samples in one minute,” the LSU AgCenter scientist said. “We have spent the past six months to figure out a way to extract the DNA easily, fast and economical. We have reached that point, but we need to do a little bit more to perfect the method.”

Before developing this method, sample preparation and DNA extraction caused a bottleneck in the process, taking up to 60 percent of the time required to generate marker data, Utomo said.

The extracted DNA undergoes a process called electrophoresis that enables Utomo to see if the genes of interest are found among the pool of genes in the 12 chromosomes of a rice plant. Electrophoresis is a technique that separates nucleic acids according to size by subjecting them to an electric current in a gel.

That way, instead of waiting to select rice lines based on the expression of a particular trait in the field, Utomo can directly select lines in the laboratory by looking at the results of electrophoresis.

“Selection done this way is more straightforward and can eliminate environmental effects that sometimes mask the presence of certain genes,” he said. “Also, selection can be done at a very early stage of plant growth.”

That saves considerable time in developing a new variety of rice by eliminating candidates that are genetically unsuitable for a breeder’s plans.

Utomo is applying markers in his selection for a number of simple traits, such as plant height, aroma, amylose content, grain elongation and blast resistance. He also has initiated genetic marker work for complex traits such as yield potential.

“It may take several years to be able to come up with markers for these complex traits,” he said.

Another complex trait, resistance or susceptibility to sheath blight, is determined by more than one gene, Utomo explained, but the correct combination of genes has yet to be found.

The LSU AgCenter is working with researchers in several other rice-growing states to obtain a U.S. Department of Agriculture grant to fund mapping the sheath blight genetic composition, Utomo said.

“It’s going to be quite a challenge. The trait is highly affected by environmental effects,” he said. “Thousands of different markers need to be evaluated. At the end, we should be able to come up with a few that can be used to assist us in the breeding process.”

A number of rice scientists from several different disciplines are cooperating in development of marker assisted breeding technology. In addition to Utomo, several rice breeders, a geneticist and two rice pathologists are working to perfect the system.

Don Groth, an LSU AgCenter plant pathologist at the Rice Research Station, eagerly awaits the sheath blight mapping project. It will mean learning early in a plant’s life if it has sheath blight resistance.

“Right now we have to almost wait until the end of the growing season,” he said.

Currently, it takes eight to 10 years to develop and release a new variety of sheath blight-resistant rice, but with DNA marker-assisted breeding, that cycle can be reduced by two to three years, Groth said.

“It’s going to have an efficiency effect,” Groth said. “Once we have it, that’s when the savings comes around. Ultimately, it’s going to greatly benefit the farmer.”

Utomo also is using the technology to assist with an LSU AgCenter project to restore coastal vegetation to maintain the state’s coastal marshlands. Identifying variations of some of the plants, such as smooth cordgrass, can become difficult, but DNA fingerprinting is being used to accomplish that.

“Molecular technology will be a part of regular field work in genetic improvement of many crops including rice,” Utomo said.

Bruce Schultz writes for the LSU AgCenter. e-mail:

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