It's not cloning, and it's not genetic modification. But new research by the Texas Agricultural Experiment Station uses biotechnology to diagnose desired traits in rice so plant breeders can be sure new varieties have those components at the DNA level.
So far the technology has found the DNA markers for starch quality and for resistance to blast, a fungal plant disease that takes its toll on rice yields throughout the U.S. growing regions and much of the world.
“It's faster, cheaper and better to use this technology in breeding new varieties,” said Dr. Bill Park, Experiment Station biochemist and project collaborator. “And it is being put to use in the field more quickly than research findings often are.”
Two new varieties, Cadet and Jacinto, already have been released and are growing in Europe, noted Park, who worked with Dr. Anna M. McClung, head of the U.S. Department of Agriculture-Agricultural Research Service Rice Research Unit in Beaumont.
The technology comes at a good time for the rice industry, which has struggled to remain viable in Texas. In January, private companies announced that rice had been genetically mapped making it the first crop plant to have its genome completed. With the DNA sequence of every gene known, researchers now are trying to delve further into the code to “mark” what each gene expresses in the plant.
That's where the work of Park's team plays a role. The first marker they found regulates amylose, a component of starch.
“In rice, high amylose means that the grains are firm and separate, and low starch means you can eat it with chopsticks because it sticks together,” Park said.
The problem for breeding new varieties, he explained, is that the amount of amylose produced in the plant also is influenced by air temperature while rice is growing in the field.
Standard methods for determining the amount of amylose produced among different rice breeding lines can be misleading because amount produced is so sensitive to the field conditions where the rice is grown. Therefore, if a plant breeder crosses two varieties with the intention of getting high amylose, but unusually cold or hot temperatures occur during the growing season, the breeder would not know whether the amylose level of the rice line was due to genetics or a false reading due to the weather.
Park said it's like eating a cheeseburger before getting a cholesterol check — a person would not know whether the cholesterol is really high or merely reflective of that day's diet.
By diagnosing rice in breeding programs with DNA markers, however, scientists can accurately decide whether to keep a cross in development or remove it from future selection.
“Breeders don't have to worry about unusual weather giving false reads on a potentially good variety,” Park explained.
With the findings on amylose verified, the team tackled another problem for the rice industry — blast disease.
Each year breeding programs put a tremendous amount of effort in evaluating breeding lines for resistance to this pathogen. Breeders try to use natural resistance genes that are available in the rice gene pool so that fewer pesticides are needed to protect farmers yields, thus decreasing production costs and protecting the environment.
Because this fungus is continually evolving, new genes for resistance need to be constantly added to new varieties to maintain the resistance.
Connie Bormans, biochemistry doctoral student who worked on Park's team, said a major problem with stacking multiple genes for blast resistance is that some tend to mask others. In other words, researchers want multiple layers of resistance but cannot tell if there is one layer or multiple layers of resistance with traditional methods.
DNA markers help overcome the problem. “Breeders tend to use very similar strains of rice plants as parents for new crosses in trying to create better varieties,” Bormans said.
“Because the rice plants are closely related, that makes it hard to find the differences in DNA.”
Bormans' six-year effort has found markers for four major blast genes, however, and all have been put to work screening plants in the rice breeding program of the U.S. Department of Agriculture/Texas Agricultural Experiment Station in Beaumont.
The lab annually screens about 3,000 rice strains for blast resistance for U.S. breeding programs, according to the USDA-Agricultural Research Service. In June, the team plans to host a workshop to show other public breeding programs how to use these markers to augment conventional breeding programs.
“It is a system that actually works in the real world,” Park added.
The team is proud not only of the findings but the collaboration that took the work from College Station to Beaumont and into the field in a relatively short period of time. Park said the DNA diagnostics can shave as much as half the time of breeding a new variety to five to seven years compared to the 10 years normally required in traditional breeding program.
The team and others plan to use the marker-assisted technology to help find resistance to other serious rice diseases, milling quality, height and various quality traits associated with specialty rices, according to the USDA.