New DNA analysis speeds up variety development

Frances Gould, Schultz, Bruce  |  1/24/2017 8:49:46 PM

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Research associates Carl Dischler, left, and graduate student Jacob Matson, far right, transplant rice seedlings that have been culled by rice breeder Adam Famoso, center, from lines raised in a greenhouse and tested for disease resistance using robotic technology that reveals genetic characteristics from just a leaf sample of a seedling.

AgCenter rice breeder Adam Famoso, left, collects rice in a bag from lines of rice harvested at the Rice Research Station. Famoso is using DNA technology to screen lines of rice for disease resistance, decreasing the number of test plots that have to be grown in the field.

The H. Rouse Caffey Rice Research Station has acquired new technology to help rice breeders identify lines of rice with desirable traits.

LSU AgCenter rice breeder Adam Famoso said the system can process up to 40,000 samples in a day and have the DNA analyses completed for making selections at a fraction of the cost of other methods.

Plants from segregating populations can be started in the greenhouse, and tissue samples are taken when the plants are only an inch tall. The DNA is analyzed to indicate which plants should be kept to be grown for seed.

“In half a day, we can do thousands of DNA extractions,” Famoso said.

The process uses a series of robotic devices that prepare the samples to be read with cameras that use fluorescent lights to analyze the genetic makeup, which is displayed on a computer screen.

Growing the lines in the field would take up more space and can only be done during warm months. But working in the greenhouse allows plants to be grown year-round to produce seed that can be grown at the Rice Research Station or at the winter nursery in Puerto Rico.

Trying to develop a disease-resistant line can be difficult in years when diseases are not widespread because plants will not show signs of infection, Famoso said. But the DNA testing will reveal whether a plant has the genetic disposition towards resistance or susceptibility.

Famoso said the breeding process will not rely on just the new equipment to indicate if a line has good traits. “It’s not going to replace what we do in the field,” he said. “The final decisions are always going to be made on how plants behave in the field.”

The process also can be used for the foundation seed program. Before headrows are planted, seed can be analyzed for purity, and any seed showing unwanted traits can be discarded before planting. “It will allow us to identify off-types before we ever plant them in the field,” Famoso said.

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