Genome assembly of rice stink bug offers new data-informed tool in fight against costly pest

Download PHOTOS of the researchers and rice stink bugs

FAYETTEVILLE, Ark. — Scientists are getting a leg up on the rice stink bug, one of the most significant threats to rice, a staple food for nearly half of the world’s population and a major crop in Arkansas.

A reference genome of the rice stink bug, generated by Arkansas Agricultural Experiment Station researchers, will help scientists better understand how the insect feeds, adapts to host plants and potentially develops resistance to insecticides. (Photo by Russ Ottens/University of Georgia)

With funding support from the Arkansas Biosciences Institute, researchers with the Arkansas Agricultural Experiment Station, the University of Arkansas Division of Agriculture's research arm, generated the first high-quality, chromosome-scale reference genome for the rice stink bug, Oebalus pugnax, identifying more than 13,000 genes with broad biological and agricultural relevance.

The development created a foundational resource to help scientists better understand how the insect feeds, adapts to host plants and potentially develops resistance to insecticides. The study, published in the Journal of Heredity, provides the most detailed genomic analysis to date of the rice stink bug, which feeds on more than 15 host plant species, including grain sorghum, and has shown resistance to pyrethroid insecticides in some populations.

“This gives us our first chromosome-scale view of the rice stink bug genome,” said Rich Adams, an assistant professor of agricultural statistics for the experiment station and corresponding author of the study. “We were able to assemble much of the nuclear genome, identify more than 13,000 genes and uncover genetic features involved in the insect’s biology and interactions with agricultural systems. It creates a foundation and hypothesis for future studies of rice stink bug biology and management.”

Adams is also a teaching faculty member with department of entomology and plant pathology in the Dale Bumpers College of Agricultural, Food and Life Sciences at the University of Arkansas and the experiment station’s Center for Agricultural Data Analytics.

The genome assembly provided researchers with the first predicted chromosomes and their gene content. It also revealed evidence of roughly 21,000 non-coding RNAs, Adams said. The analysis identified genes with predicted roles in plant digestion, including carbohydrate-active enzymes, and uncovered expansions and contractions in gene families associated with key life history traits and agricultural impact.

Using advanced sequencing technologies, researchers reconstructed the rice stink bug's 826-million-base-pair genome with unprecedented resolution. The work identified gene families associated with feeding, host adaptation and detoxification, as well as genes that may play roles in insecticide resistance.

“This genome provides a foundation for studying genome structure, gene family evolution, plant feeding, host adaptation, detoxification and potential insecticide resistance,” said Allen Szalanski, a professor of entomology and plant pathology for the experiment station and a co-author of the study.

The new research builds on findings from a previous study by Szalanski, Adams and colleagues with UADA and Florida A&M University that examined genetic variation among rice stink bug populations across Arkansas, Mississippi, Florida and Cuba.

In that earlier study, published in Florida Entomologist, researchers analyzed a mitochondrial DNA marker and found high genetic diversity within O. pugnax populations. The results pointed to movement of rice stink bugs among southeastern states and suggested that two invasive Oebalus species found in Florida may have originated in Cuba.

“The first study helped us understand how rice stink bug populations vary genetically and move across regions,” Szalanski said. “This new genome gives us the tools to investigate the biological mechanisms behind those differences and how this pest adapts to rice production systems.”

Adams noted that a genome assembly represents a scientific starting point rather than a final product. As additional data become available, researchers can refine the assembly and use it to test new hypotheses about the evolution, behavior and management of rice stink bugs.

“Knowing more about the genetic basis of these traits can ultimately help researchers develop better monitoring and management strategies for rice producers,” Szalanski said.

Rice stink bugs cost Arkansas rice growers more than $16 million in 2017 alone, with similar costs estimated in 2018 and 2019, the first study noted.