# Chromatin Topology Reconfiguration Orchestrates Thermotolerant Male Fertility via GhAL5 in Cotton

## TL;DR

The study reveals how chromatin structure changes help cotton plants maintain male fertility under heat stress, with a key gene, GhAL5, playing a central role in this adaptation.

## Contribution

The study identifies GhAL5 as a chromatin-regulated transcription factor that enhances thermotolerance in cotton and other crops through 3D genome reorganization.

## Key findings

- Heat-tolerant cotton lines exhibit controlled chromatin dynamics, while heat-sensitive lines show structural hyperactivation.
- GhAL5 overexpression improves thermotolerance in cotton and rice, indicating cross-species functionality.
- Dynamic chromatin topology reorganization is central to male fertility under heat stress.

## Abstract

Cotton, a globally vital crop, faces severe yield losses due to heat‐induced male sterility. To decipher the thermotolerance mechanisms, we conducted multi‐omics analyses (3D chromatin architecture, transcriptome, and epigenome profiling) on heat‐tolerant (84021) and heat‐sensitive (H05) lines across critical anther developmental stages. We identified subgenome homoeologous gene expression bias linked to thermotolerance, driven by high temperature (HT)‐induced dynamic chromatin topology reorganization. The sensitive line exhibited aberrant 3D structural hyperactivation during anther dehiscence, causing deleterious gene overexpression. Central to this regulation is GhAL5, an Alfin‐like transcription factor modulated through chromatin loop dynamics and TAD‐like boundary reorganization under heat stress. Functional studies confirmed the pivotal role of GhAL5: overexpression enhanced thermotolerance, while RNAi/CRISPR lines showed compromised heat resilience. Remarkably, GhAL5 conferred cross‐species heat protection when expressed in rice. Mechanistically, GhAL5 potentially orchestrates male thermotolerance through bidirectional chromatin structure modulation. This study establishes 3D genome plasticity and chromatin remodeling as key drivers of plant thermal adaptation, proposing chromatin‐aware breeding strategies for climate‐resilient crops.

This study investigates cotton’s high‐temperature (HT) response using multi‑omics. Dynamic 3D genome changes drive expression bias affecting male fertility. The tolerant line shows controlled chromatin dynamics, while the sensitive line exhibits overactivation. A key chromatin‑regulated gene, GhAL5, enhances thermotolerance when overexpressed in different crops, revealing genomic HT‑adaptation mechanisms and cross‑species potential for breeding heat‑resilient crops.