# Antioxidant Defense and Transcriptional Reprogramming Account for the Differential Cold Tolerance of Two Japonica Rice Cultivars During Germination Under Low-Temperature Stress

## TL;DR

This study compares two rice varieties to understand how they respond to cold stress during germination, focusing on antioxidant defenses and gene expression changes.

## Contribution

The study reveals how antioxidant defense and transcriptional reprogramming contribute to cold tolerance differences in rice cultivars during germination.

## Key findings

- JND815 showed lower MDA accumulation than Jiyu Japonica, indicating better membrane stability and oxidative stress tolerance.
- Transcriptomic analysis identified thousands of differentially expressed genes linked to phenylpropanoid biosynthesis and carbon metabolism.
- qRT-PCR confirmed the expression trends of six cold-responsive genes, aligning with transcriptomic data.

## Abstract

Background: Low-temperature stress represents a significant constraint on rice production, especially during the germination stage. Consequently, comprehending the mechanisms underlying cold tolerance is of utmost importance for the breeding of resilient rice varieties. This research systematically examined the phenotypic and physiological responses of a cold-tolerant cultivar (JND815) and a cold-sensitive cultivar (Jiyu Japonica) to low-temperature stress (15 °C) during the germination process. Methods: Following a 17-day incubation period, physiological analyses were conducted. Transcriptomic analysis was performed to identify differentially expressed genes (DEGs), which were further subjected to KEGG enrichment analysis and Gene Ontology (GO) annotation. Additionally, the expression trends of selected cold-responsive DEGs were verified via qRT-PCR. Results: Following a 17-day incubation period, physiological analyses indicated that, in comparison to the control group (28 °C), the stress treatment notably reduced the activities of superoxide dismutase (SOD) and catalase (CAT), while increasing the activity of peroxidase (POD) and the content of malondialdehyde (MDA). Significantly, JND815 accumulated a substantially lower amount of MDA than Jiyu Japonica, suggesting superior membrane stability and oxidative stress tolerance. Transcriptomic analysis identified 11,234 and 14,164 differentially expressed genes (DEGs) in JND815 and Jiyu Japonica, respectively. KEGG enrichment analysis demonstrated that these DEGs were significantly associated with phenylpropanoid biosynthesis and carbon metabolism, and Gene Ontology (GO) annotation classified them into biological processes, cellular components, and molecular functions. The expression trends of six cold-responsive DEGs were verified by qRT-PCR to be consistent with the transcriptomic data. Conclusions: These findings offer insights into the molecular mechanisms of the low-temperature response during rice germination and lay a foundation for the genetic improvement of cold-tolerant rice varieties.