AUTHOR=Wang Hao , Jia Yan , Bai Xu , Wang Jin , Liu Ge , Wang Haixing , Wu Yulong , Xin Junying , Ma Huimiao , Liu Zhenyu , Zou Detang , Zhao Hongwei 

TITLE=Whole-transcriptome profiling and identification of cold tolerance-related ceRNA networks in japonica rice varieties

JOURNAL=Frontiers in Plant Science

VOLUME=15

YEAR=2024

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2024.1260591

DOI=10.3389/fpls.2024.1260591

ISSN=1664-462X

ABSTRACT=<sec><title>Introduction</title><p>Low-temperature stress negatively impacts rice yield, posing a significant risk to food security. While previous studies have explored the physiological and linear gene expression alterations in rice under low-temperature conditions, the changes in competing endogenous RNA (ceRNA) networks remain largely unexamined.</p></sec><sec><title>Methods</title><p>We conducted RNA sequencing on two <italic>japonica</italic> rice varieties with differing cold-tolerance capabilities to establish ceRNA networks. This enabled us to investigate the transcriptional regulatory network and molecular mechanisms that rice employs in response to low-temperature stress.</p></sec><sec><title>Results</title><p>We identified 364 differentially expressed circular RNAs (circRNAs), 224 differentially expressed microRNAs (miRNAs), and 12,183 differentially expressed messenger RNAs (mRNAs). <italic>WRKY</italic> family was the most prominent transcription factor family involved in cold tolerance. Based on the expression patterns and targeted relationships of these differentially expressed RNAs, we discerned five potential ceRNA networks related to low-temperature stress in rice: osa-miR166j-5p from the miR166 family was associated with cold tolerance; osa-miR528-3p and osa-miR156j-3p were linked to stress response; and osa-miR156j-3p was involved in the antioxidant system. In addition, <italic>Os03g0152000</italic> in the antioxidant system, as well as <italic>Os12g0491800</italic> and <italic>Os05g0381400</italic>, correlated with the corresponding stress response and circRNAs in the network. A gene sequence difference analysis and phenotypic validation of <italic>Os11g0685700</italic> (<italic>OsWRKY61</italic>) within the <italic>WRKY</italic> family suggested its potential role in regulating cold tolerance in rice.</p></sec><sec><title>Discussion and conclusion</title><p>We identified <italic>Os11g0685700</italic> (<italic>OsWRKY61</italic>) as a promising candidate gene for enhancing cold tolerance in <italic>japonica</italic> rice. The candidate miRNAs, mRNAs, and circRNAs uncovered in this study are valuable targets for researchers and breeders. Our findings will facilitate the development of cold-tolerant rice varieties from multiple angles and provide critical directions for future research into the functions of cold-tolerance-related miRNAs, mRNAs, and circRNAs in rice.</p></sec>