Rice Research Takes Important Step in Solving the High Nighttime Temp Problem
HYR gene hub focus of research to improve rice quality and yield
By John Lovett – Nov. 20, 2025
FAYETTEVILLE, Ark. — Researchers with the Arkansas Agricultural Experiment Station have identified genetic mechanisms in rice that can help counteract the negative effects of higher nighttime temperatures.
Drastic yield losses of up to 90 percent and severe declines in grain quality can occur when nighttime temperatures rise above 82.4 Fahrenheit for just two to three consecutive nights, especially during the flowering and grain-filling stages. This deterioration in grain quality appears as “chalkiness,” an undesirable trait that affects milling efficiency, cooking quality and overall palatability.
Professor Andy Pereira, recently retired, and Research Scientist Julie Thomas in the crop, soil and environmental sciences department, have been investigating a genetic regulation hub in rice that functions as a “master regulator” of the plant’s growth and stress response. Dubbed HYR for “Higher Rice Yield,” the gene hub connects the plant’s genetic makeup with its ability to adapt to environmental changes.
Originally discovered and published by Pereira and his research team in 2014 through a genome-wide regulatory association study in rice, HYR helps rice cope with high nighttime temperatures by switching on other genes that maintain photosynthesis, energy production and proper grain filling — processes that are normally disrupted by heat.
Pereira’s team demonstrated that when HYR is “switched on,” it significantly enhances grain yield under both well-watered and drought-stress environments. The research involved collaborators from Virginia Tech, the Louisiana State University AgCenter and the Arkansas Agricultural Experiment Station, the research arm of the University of Arkansas System Division of Agriculture.
“HYR functions like a master switch,” Pereira said. “It coordinates how rice plants respond to environmental stress while maintaining photosynthetic efficiency and grain quality. Understanding this gene gives us a powerful tool for developing climate-resilient rice varieties.”
Pereira’s more recent work in Arkansas with Thomas has expanded on earlier findings to explore another key function of HYR — its role in reducing grain chalkiness caused by high nighttime temperatures. Their research has further revealed how HYR regulates downstream gene networks involved in photosynthesis and carbon metabolism to help maintain the steady expression of critical genes during the grain-filling stage under high night temperature stress.
How it works
HYR supports cell wall integrity, stabilizes starch granule structure and improves photosynthetic efficiency, or the process of moving the plant’s energy from the leaf to the growing grain. All this collectively contributes to improved yield and grain quality even under stressful environmental conditions, Thomas explained.
Pereira and Thomas have shown that even in a widely cultivated rice variety that typically has high levels of grain chalkiness, overexpression of HYR led to a significant reduction in chalk formation. When geneticists “overexpress” a genetic mechanism, it produces more of its product than it normally would.
The decreased chalkiness from overexpression of HYR was accompanied with enhanced photosynthetic efficiency, even under extended exposure to 88-degree Fahrenheit night temperatures in greenhouse conditions. These results translated directly into improved grain quality and higher yield.
TEMP TOLERANT — Activating HYR in a widely cultivated rice variety, which typically has high levels of grain chalkiness, showed tolerance to high nighttime temperatures, as seen on the left with normal grain filling and seed set. Sterility, as seen on the right, from high nighttime temperatures results in unfilled florets that lack grain development due to disrupted pollen viability and fertilization. (U of A System Division of Agriculture photo by Paden Johnson)
Rice resilience
Expanding on the work, Thomas and Awais Riaz, a Fulbright graduate student, identified a distinct group of genetic markers called haplotypes associated with HYR in multiple rice cultivars from around the world. The haplotypes are correlated with key traits related to how well the plant makes and uses energy, and grain quality.
In addition to its work on HYR, Pereira’s lab has also identified several new gene regulators that play key roles in helping rice plants tolerate drought, heat and disease. Like HYR, these newly identified transcription factors are also involved in controlling photosynthesis and carbon metabolism, as well as water balance and hormone signaling, to form a coordinated genetic network that connects molecular regulation with the plant’s ability to adapt to stress.
“The research highlights HYR as a master regulatory transcription factor orchestrating cascading effects across a broad network of downstream genes involved in photosynthesis, carbon metabolism and stress adaptation,” Pereira said. “It serves as a promising target for breeders to improve rice grain quality, yield stability and stress resilience.”
To learn more about the Division of Agriculture research, visit the Arkansas Agricultural Experiment Station website. Follow us on 𝕏 at @ArkAgResearch, subscribe to the Food, Farms and Forests podcast and sign up for our monthly newsletter, the Arkansas Agricultural Research Report. To learn more about the Division of Agriculture, visit uada.edu. Follow us on 𝕏 at @AgInArk. To learn about extension programs in Arkansas, contact your local Cooperative Extension Service agent or visit uaex.uada.edu.
About the Division of Agriculture
The University of Arkansas System Division of Agriculture’s mission is to strengthen agriculture, communities, and families by connecting trusted research to the adoption of best practices. Through the Agricultural Experiment Station and the Cooperative Extension Service, the Division of Agriculture conducts research and extension work within the nation’s historic land grant education system.
The Division of Agriculture is one of 20 entities within the University of Arkansas System. It has offices in all 75 counties in Arkansas and faculty on three campuses.
Pursuant to 7 CFR § 15.3, the University of Arkansas System Division of Agriculture offers all its Extension and Research programs and services (including employment) without regard to race, color, sex, national origin, religion, age, disability, marital or veteran status, genetic information, sexual preference, pregnancy or any other legally protected status, and is an equal opportunity institution.
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