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Published on: January 3, 2025

Machine Learning and CRISPR-Based Validation Elucidate OsWOX13 Involvement in Rice Heat Stress Tolerance and

Muhammad Ikram^1,2, Muhammad Farhan³, Behnam Derakhshani⁴

¹School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya, China.

Physiologia Plantarum

|December 22, 2025

Summary

This summary is machine-generated.

Researchers identified OsWOX13 as a key gene for heat stress tolerance in rice using machine learning and functional validation. This discovery aids in developing climate-resilient rice varieties to combat global food security challenges.

Keywords:

OsWOX13 SHAP antioxidant defense differential expression machine learning proteomics rice

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Area of Science:

Plant Biology
Genetics
Biotechnology

Background:

Rice yield is significantly impacted by heat stress, a critical threat to global food security.
Understanding the genetic basis of heat stress tolerance in rice is crucial for developing resilient crop varieties.
Existing research on rice heat stress responses is limited compared to other stress factors.

Purpose of the Study:

To identify key genes conferring heat stress tolerance in rice using an integrated approach.
To validate the role of identified candidate genes in enhancing rice heat tolerance.
To explore the potential of machine learning in discovering stress-responsive genes in plants.

Main Methods:

Combined meta-transcriptomics, machine learning (Random Forest, XGBoost), and proteomic analysis.
Functional validation of candidate genes using CRISPR/Cas9-mediated knockout (KO).
Physiological and biochemical assays to assess heat stress response and antioxidant activities.

Main Results:

Identified 409 meta-differentially expressed genes (meta-DEGs) associated with various stress response pathways.
OsWOX13 was identified as a top candidate gene for heat stress tolerance by machine learning models.
OsWOX13 knockout lines showed reduced survival and altered physiological responses under heat stress, confirming its positive role.

Conclusions:

OsWOX13 acts as a positive regulator of heat stress tolerance in rice, potentially by modulating ABA signaling and antioxidant defense.
Machine learning models are effective tools for identifying crucial stress-responsive genes in plants.
OsWOX13 is a promising candidate gene for breeding climate-resilient rice varieties.