Genetic markers crucial to rice breeding program

Johnny Morgan, Angira, Brijesh

A man wearing gloves sitting at a desk in a lab puts liquid into a scientific dish.

Brijesh Angira adds reagent to extract DNA from rice leaves and runs molecular markers to select desirable rice plants. Photo by Madeline Fruge


Creating a successful rice variety is a delicate art that requires time, expertise and a substantial dose of science. The molecular breeding lab at the H. Rouse Caffey Rice Research Station in Crowley, established in 2016 with the support of the Louisiana Rice Research Board, is at the forefront of this intricate process.

Brijesh Angira, a rice researcher at the LSU AgCenter, is dedicated to integrating DNA marker technologies into the AgCenter’s applied rice variety development program. Leading a team that includes AgCenter rice breeder Adam Famoso and AgCenter pathologist Jonathan Richards, Angira is the principal investigator in this research.

The methodology involves collecting leaves from rice plants, conducting DNA extractions, running markers and performing data analysis. This DNA marker lab plays a pivotal role in every phase of the breeding cycle, spanning initial crosses, marker-assisted selection, line advancement and foundation seed purification.

Angira said that DNA marker technologies serve as powerful tools that enhance the efficiency of traditional breeding and significantly raise the likelihood of identifying a breeding line that could eventually become a new rice variety.

Over the past six years, Angira and his team have developed and deployed numerous native trait and informative genome-wide markers, significantly enhancing the efficiency and accuracy of the rice breeding program.

“Traditionally, we made crosses and advanced lines, subsequently testing them in the field for desired qualitative and quantitative traits. However, this approach had limitations based on available space and the number of lines that could be tested for advancement,” Angira said. “Now, we can analyze a small portion of a plant leaf to determine its resistance or susceptibility to diseases such as blast, and even predict its performance for more complex traits.”

DNA markers are particularly effective in improving traits controlled by large effect genes, offering higher success rates and lower costs.

“It costs approximately 3 cents per data point in the marker lab, a significant reduction from when these technologies were newer and less practical,” Angira said.

In marker-assisted selection, Angira can identify plants with desirable traits before they undergo field evaluation for other agronomic characteristics. For instance, if one parent is blast disease-resistant while the other is susceptible, he can select the resistant plants before advancing them to the field.

In the U.S., long-grain rice possesses only one major blast resistance gene, while medium-grain germplasm lacks any major blast resistance gene. In Angira's program, a marker-assisted backcross breeding approach has yielded 40 blast-resistant lines containing exotic blast resistance genes. These lines are well-suited to the southern U.S. environment, exhibit strong agronomics and quality, and offer robust blast resistance. They are continually evaluated in the field and employed in crossing blocks to increase the frequency of new blast resistance genes.

In another objective, the AgCenter’s rice breeding program has developed a panel of 550 informative molecular markers for use in LSU's rice breeding program for genomic selection. This objective facilitates sampling, tracking and deployment of genomic selection in rice breeding.

In addition to marker research, the lab receives samples from Louisiana rice farmers to assess herbicide resistance traits and identify weedy rice. Angira emphasized how this service directly benefits farmers, helping them understand and manage weed problems in their fields and plan for future variety planting.

“Our research goals remain steadfast. The lab's primary focus will continue to be supporting applied breeding activities to develop improved rice varieties,” Angira said.

Purifying new varieties before release will be a major undertaking, with an emphasis on the new Clearfield line, as well as potential long- and medium-grain lines slated for release in the near future.

The lab will also maintain its commitment to assisting Louisiana rice farmers in identifying herbicide resistance traits and weedy rice in their fields using molecular markers. This vital service empowers farmers to effectively manage weeds and maintain the cleanliness of their fields.

Angira stressed the pivotal role DNA markers play in enhancing the efficiency and precision of the breeding program, ultimately saving both time and resources. The overarching goal for LSU AgCenter scientists at research stations like the H. Rouse Caffey Rice Research Station remains unwavering: to boost yields and improve the quality of rice varieties for the benefit of producers.

11/21/2023 9:15:00 PM
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