The Methylation Patterns and Transcriptional Responses to Chilling Stress at the Seedling Stage in Rice

Abstract

Chilling stress is considered the major abiotic stress affecting the growth, development, and yield of rice. To understand the transcriptomic responses and methylation regulation of rice in response to chilling stress, we analyzed a cold-tolerant variety of rice (Oryza sativa L. cv. P427). The physiological properties, transcriptome, and methylation of cold-tolerant P427 seedlings under low-temperature stress (2–3 °C) were investigated. We found that P427 exhibited enhanced tolerance to low temperature, likely via increasing antioxidant enzyme activity and promoting the accumulation of abscisic acid (ABA). The Methylated DNA Immunoprecipitation Sequencing (MeDIP-seq) data showed that the number of methylation-altered genes was highest in P427 (5496) and slightly lower in Nipponbare (Nip) and 9311 (4528 and 3341, respectively), and only 2.7% (292) of methylation genes were detected as common differentially methylated genes (DMGs) related to cold tolerance in the three varieties. Transcriptome analyses revealed that 1654 genes had specifically altered expression in P427 under cold stress. These genes mainly belonged to transcription factor families, such as Myeloblastosis (MYB), APETALA2/ethylene-responsive element binding proteins (AP2-EREBP), NAM-ATAF-CUC (NAC) and WRKY. Fifty-one genes showed simultaneous methylation and expression level changes. Quantitative RT-PCR (qRT-PCR) results showed that genes involved in the ICE (inducer of CBF expression)-CBF (C-repeat binding factor)—COR (cold-regulated) pathway were highly expressed under cold stress, including the WRKY genes. The homologous gene Os03g0610900 of the open stomatal 1 (OST1) in rice was obtained by evolutionary tree analysis. Methylation in Os03g0610900 gene promoter region decreased, and the expression level of Os03g0610900 increased, suggesting that cold stress may lead to demethylation and increased gene expression of Os03g0610900. The ICE-CBF-COR pathway plays a vital role in the cold tolerance of the rice cultivar P427. Overall, this study demonstrates the differences in methylation and gene expression levels of P427 in response to low-temperature stress, providing a foundation for further investigations of the relationship between environmental stress, DNA methylation, and gene expression in rice.

Alterations of Rice (Oryza sativa L.) DNA Methylation Patterns Associated with Gene Expression in Response to Rice Black Streaked Dwarf Virus

“…Although overall genomic cytosine methylation levels of the RBSDV-infected and RBSDV-free rice plants are similar, we discovered local variations for the density profile at CG, CHG and CHH sites. Genomes of NIP infected by RBSDV undergo a global increase in DNA methylation, which is consistent with changes induced by pesticide atrazine and low-temperature [ 35 , 42 ], but is contrary to NIP exposed to Cd [ 27 ]. The CG, CHG and CHH contexts in TRV-infected Arabidopsis were slightly hypomethylated compared to mock-inoculated controls [ 16 ].…”

“…RBSDV is a member of the genus Fijivirus with dsRNA as genome for replication, its infection results in severe yield losses in rice [ 40 ]. Most of the work on DNA methylation of rice under stress conditions mainly focused on chilling, pesticide, drought and salinity stresses [ 35 , 41 , 42 ]. However, analysis of DNA methylation changes of rice in response to viruses, such as RBSDV, has not been reported.…”

Acceleration of Carbon Fixation in Chilling-Sensitive Banana under Mild and Moderate Chilling Stresses

“…Omics technologies have brought about a significant breakthrough in the knowledge about plant responses to LTs [3][4][5][6][7]. In the present study, global differences in mRNAs caused by mild and moderate chilling were systematically identified and analyzed in China's most important banana cultivar with an annual yield of several million tons.…”

“…Low temperature (LT) is one of the major environmental factors which not only limit the productivity and the geographical distribution of crops but also cause significant losses [1,2]. In recent years, modern high-throughput expression profiling techniques, such as genomics, transcriptomics, and proteomics, have provided useful tools for better understanding the roles of genes when responding to LT stresses [3][4][5][6][7]. However, most of these studies reported about the effects of severe LT (≤10 • C) on temperate [5,[7][8][9], tropical, and subtropical [3,4,10] plants.…”

Characterization and analysis of some chilling-response WRKY transcription factors in tomato

“…CBF, also known as dehydration responsive element (DRE) binding factor (DREB) proteins, are key factors in plant cold response (Liu et al, 1998;Shi et al, 2018). In rice, WRKY genes expressed highly under cold stress and may be involved in ICE-CBF-COR pathway (Guo et al, 2019). In this study, we mainly identi ed 27 chilling response SlWRKY genes based on RNA-seq and qRT-PCR analysis (Fig.…”