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ARS Home » Southeast Area » Stuttgart, Arkansas » Dale Bumpers National Rice Research Center » Research » Publications at this Location » Publication #428676
Research Project: Broadening and Strengthening the Genetic Base of Rice for Adaptation to a Changing Climate, Crop Production Systems, and Markets

Location: Dale Bumpers National Rice Research Center

Title: High Nighttime Temperature (HNT)-responsive MicroRNA profiles in developing Caryopses and flag leaves of 13 rice varieties

Author
item PAYNE, DAVID - Oklahoma State University
item LI, YONGFANG - Oklahoma State University
item KUMAR, ANUJ - University Of Arkansas
item THOMAS, JULIE - University Of Arkansas
item Rohila, Jai
item PEREIRA, ANDY - University Of Arkansas
item RAMANJULU, SUNKAR - Oklahoma State University
item GOVINDAN, GANESAN - Oklahoma State University
item NG, PAI - Oklahoma State University

Submitted to: Plant Stress
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/24/2026
Publication Date: 2/28/2026
Citation: Payne, D., Li, Y., Kumar, A., Thomas, J., Rohila, J.S., Pereira, A., Ramanjulu, S., Govindan, G., Ng, P.J. 2026. High Nighttime Temperature (HNT)-responsive MicroRNA profiles in developing Caryopses and flag leaves of 13 rice varieties. Plant Stress. https://doi.org/10.1016/j.stress.2026.101320.
DOI: https://doi.org/10.1016/j.stress.2026.101320

Interpretive Summary: Grain quality of rice including grain chalkiness has been one of the significant constraints of the US rice industry. Developing kernel and flag leaf have an impact on grain chalkiness. Higher nighttime temperature (HNT) during rice growing season, especially at grain filling stages, has been reported to increase grain chalkiness and reduce head rice yields. MicroRNAs (miRNAs) are short, non-coding RNA molecules that play roles in regulating some biological processes, including grain development and maturation, but their role towards rice grain chalkiness under high nighttime temperature (HNT) is poorly understood. Thus, a panel of 13 rice varieties with varying levels of grain chalkiness was used to investigate HNT-responsive miRNAs under controlled environmental conditions. The study identified 787 distinct differentially regulated miRNAs, including 5 novel miRNAs for their potential roles in chalkiness via altering the expression of starch biosynthesis genes under HNT stress. Further, the study revealed a number of differentially regulated miRNAs for their potential roles towards alterations of grain chalkiness in rice under HNT stress. These miRNAs are potential candidates for future analyses for improving rice grain quality and head rice yield under HNT-stress conditions in field settings.

Technical Abstract: Higher ambient temperatures during cropping season, especially during nighttime, causes reductions in rice grain quality by increasing chalkiness, primarily defined by altered starch metabolism in rice plants. MicroRNAs (miRNAs) regulate various biological processes, including grain development and maturation, but their role towards rice grain chalkiness under high nighttime temperature (HNT) is poorly understood. To address this, a study was conducted to identify HNT-responsive miRNAs in developing caryopsis and flag leaves. The miRNA expressions between several high chalky (HC) and low chalky (LC) varieties were investigated and potential microRNAs involved in impacting grain chalkiness traits were identified. 138 small RNA-seq libraries were generated from the R6-stage caryopses and flag leaves from a panel of 13 rice varieties with varying chalkiness under HNT. Genetic variation among rice varieties for miRNAs expression was found. A comparison of miRNAs for differential regulation patterns between genetically closely related HC and LC cultivars revealed specific miRNAs with expression levels consistently associated with either the HC or LC phenotype. Notably, some of these miRNAs have been predicted or had confirmed effects in regulating grain quality and HNT responses. Further, a degradome analysis of mRNA in caryopsis and flag leaf tissues revealed several novel miRNA-mRNA target pairs, with some targets possibly involved in starch metabolism in rice. This study revealed a number of differentially regulated miRNAs for their potential roles towards alterations of grain chalkiness in rice under HNT stress. These miRNAs are good potential candidates for future analyses and to investigate their effects on improving rice grain quality and head rice yield under HNT-stress conditions in field settings.