Chris Hernandez is working at Cornell University in Ithaca, New York, to develop a computer program enabling rice breeders to predict the outcome of crosses of different lines of rice. Photo by Kyle LaPlant.

An ongoing research project has the potential to dramatically accelerate the breeding program at the H. Rouse Caffey Rice Research Station.

The two-year program began in June 2019 with support from Horizon Ag Products.

Post-doctorate researcher Chris Hernandez is working at Cornell University in Ithaca, New York, with faculty members Kelly Robbin and Susan McCouch to develop a system that allows rice breeders to predict the result of crossing different lines of rice.

“He is working to develop and optimize methodologies to do genetic predictions with our breeding program,” said Adam Famoso, LSU AgCenter rice breeder.

He said Hernandez is using statistical methodologies to enable genomic predictions of a line’s performance. This will allow breeders to predict the performance of a line for complex traits, including yield and grain quality, before testing it in the field, he said.

Famoso said that traits with simple genetics, such as amylose content, blast resistance and aroma are determined by a single gene and direct marker assisted selection for the target gene is very effective. But this project will focus on complex traits, such as yield potential, sheath blight resistance, milling quality and chalk, all involving several genes, he said.

Since 2017, leaf tissue from each entry tested in yield trials at the rice research station has been collected and frozen. Those samples have been phenotyped as part of the regular breeding activities. Recently, 2,000 of these lines have been sent for genotyping with 1,000 DNA markers. This year, Famoso said, Hernandez will use this initial data set to optimize the methods and the number of markers necessary so that future applications will be as cost-effective as possible.

Hernandez has a unique skill set that combines the computational skills with the practical experience in the field with applied plant breeding, Famoso said.

Hernandez is working alongside geneticists also focused on genomic selection at Cornell, a world-class center of genetic research.

“He is working with leaders in this field to best develop and optimize the methods for application in our specific rice breeding program,” Famoso said.

Hernandez visits the rice research station a few times a year, and he details his progress in regular phone meetings.

Famoso said this system Hernandez is developing will allow the selection of lines for crosses with a highly improved chance of obtaining desired outcomes, improving efficiency and use of space.

He said the breeding project will start using Hernandez’s work in 2020. “We’ll start predicting all the lines in our tests,” Famoso said.

“We’re now choosing lines from a field of 8,000 to 10,000 rather than the current 2,000,” he said. “It’s not a replacement for field testing, but an additional level of selection to determine what should we should test in the field in the first place.”

Hernandez said his work should make variety development more efficient.

“A lot of work goes into developing new rice varieties — a line needs to be evaluated across multiple years and at many locations throughout the state to determine its true potential,” he said. “With genomic prediction we are using DNA markers to share information across related lines in a way that allows us to make more accurate or earlier selections without increasing the number of evaluations in the field. The end result should be even better varieties for rice farmers delivered in a way that makes the most efficient use of breeding resources.”