# Integrated Transcriptomics and Metabolomics with Machine Learning Identify Flavonoids as Key Effectors in Wheat Root Thermotolerance

## TL;DR

This study identifies flavonoids as key players in helping wheat roots withstand heat stress, using a combination of transcriptomics, metabolomics, and machine learning.

## Contribution

The study reveals flavonoid biosynthesis as a central pathway in wheat root thermotolerance and identifies a regulatory hub involving FERONIA and heat shock factors.

## Key findings

- Wheat cultivar YM158 maintains root growth and redox balance under heat stress, unlike YM15.
- Flavonoid biosynthesis is central to thermotolerance, supported by WGCNA and random forest analysis.
- FERONIA and heat shock factors form a regulatory hub linking hormonal signaling and secondary metabolism.

## Abstract

Root plasticity is vital for crop survival amid global warming. Yet, the molecular mechanisms governing wheat root thermotolerance remain largely unknown. In this study, we combined phenomics, transcriptomics, and metabolomics with machine learning to analyze the performance of heat-tolerant cultivar YM158 and heat-sensitive cultivar YM15 under varying heat stress. While high temperatures (35 °C) severely inhibited root growth and caused oxidative damage in YM15, YM158 maintained robust root architecture and redox balance. Using weighted gene co-expression network analysis (WGCNA) alongside the random forest feature selection algorithm, we identified the flavonoid biosynthesis pathway as central to thermotolerance. Protein–protein interaction network analysis revealed that wheat root adaptability to high temperatures involves maintaining protein homeostasis via the endoplasmic reticulum protein processing system, specifically activating the flavonoid biosynthesis pathway and enhancing the antioxidant enzyme system. Furthermore, we identified a potential regulatory hub involving the cell wall sensor FERONIA (FER) and heat shock factors (HSFs), highlighting a complex interaction between hormonal signaling and secondary metabolism. Our study offers a detailed map of root heat adaptation and positions the flavonoid-mediated antioxidant system as a promising target for breeding climate-resilient crops.