# Mining Key Drought-Resistant Genes of Upland Cotton Based on RNA-Seq and WGCNA Analysis

## TL;DR

This study identifies WRKY22 as a key gene in cotton's drought resistance, offering insights for breeding more resilient cotton varieties.

## Contribution

The study reveals WRKY22's dual regulatory role in drought resistance through osmotic regulation and membrane protection.

## Key findings

- Jin variety showed higher proline accumulation and delayed chlorophyll degradation under drought stress.
- WRKY22 was identified as a key hub gene with 3.2 times higher expression in Jin compared to TM-1 under drought.
- WRKY22 activates genes involved in proline synthesis and jasmonic acid signaling pathways.

## Abstract

Cotton, as a globally important fiber crop, is significantly affected by drought stress during production. This study uses the drought-resistant variety Jin and the drought-sensitive variety TM-1 as test materials. Through multi-period drought stress treatments at 0 d, 7 d, 10 d, 15 d, and 25 d, combined with dynamic monitoring of physiological indicators, RNA sequencing, and weighted gene co-expression network analysis, the molecular mechanism of cotton drought resistance is systematically analyzed. Dynamic monitoring of physiological indicators showed that Jin significantly accumulated proline, maintained superoxide dismutase activity, reduced malondialdehyde accumulation, and delayed chlorophyll degradation. Transcriptome analysis revealed that Jin specifically activated 8544 differentially expressed genes after stress, which were significantly enriched in lipid metabolism (α-linolenic acid, ether lipids) and secondary metabolic pathways. Weighted gene co-expression network analysis identified co-expression modules significantly correlated with proline (r = 0.81) and malondialdehyde (r = 0.86) and selected the key hub gene Gh_A08G154500 (WRKY22), which was expressed 3.2 times higher in Jin than in TM-1 at 15 days of drought stress. Functional validation suggested that WRKY22 may form a “osmotic regulation–membrane protection” co-regulatory network by activating Pro synthesis genes (P5CS) and genes involved in the jasmonic acid signaling pathway. This study reveals, for the first time, the possible dual regulatory mechanism of WRKY22 in cotton’s drought resistance, providing a theoretical basis for cotton drought-resistant breeding.