# Transcriptional Regulation and WGCNA Studies of Leaf Abscission in Cotton Cultivars FU75 and 518-48 Under Chemical Defoliant Treatment

## TL;DR

This study explores how chemical defoliants cause leaf shedding in cotton by analyzing gene expression differences between two cotton varieties.

## Contribution

The study identifies SnRK2 as a key gene in the ABA pathway involved in TDZ-induced leaf abscission in cotton.

## Key findings

- Phytohormone signal transduction and MAPK pathways are important in TDZ-induced leaf abscission.
- SnRK2 is a potential key regulatory gene in the ABA signaling pathway for leaf abscission.
- 35,739 differentially expressed genes were identified, mainly enriched in hormone and metabolic pathways.

## Abstract

In cotton production, defoliation treatment using chemicals before picking is a conventional cultivation measurement for mechanical harvesting. However, the mechanism by which defoliants induce cotton leaf shedding still remains not fully understood. After treating the defoliant thidiazuron (TDZ) on its sensitive variety FU75 and insensitive variety 518-48, this study found that phytohormone signal transduction and MAPK signaling pathway might play important roles in TDZ-induced leaf abscission. Further analysis of the DEGs using Short Time-series Expression Miner (STEM) and Weighted Gene Co-expression Network Analysis (WGCNA) revealed that sucrose non-fermenting 1 (SNF1)-related protein kinase 2 (SnRK2) is a key candidate gene in the abscisic acid (ABA) pathway. These findings provide new insights into the molecular mechanism of chemical defoliant-induced cotton leaf abscission and lay a foundation for subsequent research and potential applications in cotton production.

Leaf abscission is a cell separation process that occurs throughout the entire plant life cycle, leading to the detachment of tissues or organs. The application of chemical defoliants to induce cotton leaf abscission not only saves the energy required for maintaining life processes but also facilitates mechanical harvesting. However, the molecular mechanisms underlying cotton leaf abscission remain poorly understood. In this study, multiple comparative analyses of gene expression differences were conducted between two cotton cultivars with different sensitivities to chemical defoliant Thidiazuron (TDZ) after TDZ application, resulting in 1,505,720,260 clean reads together with the average 92.77% of Q30 base percentage and 43.13% of GC content. A total of 35,739 differentially expressed genes (DEGs) were identified and these DEGs were mainly enriched in pathways of zeatin biosynthesis, secondary metabolite biosynthesis, and hormone metabolic processes. Integration of temporal expression pattern analysis and weighted gene co-expression network analysis (WGCNA) revealed that plant hormone signal transduction and MAPK signaling pathways might play important roles in TDZ-induced leaf abscission. Among them, a sucrose non-fermenting 1 (SNF1)-related protein kinase 2 gene (SnRK2, GH_A11G1981 and GH_D11G2017) in the abscisic acid (ABA) signaling pathway might be a potential key regulatory factor in defoliant induced leaf abscission. These findings provide novel insights into understanding the molecular mechanisms of chemical defoliant-induced leaf abscission in cotton and lay a foundation for future breeding programs and practical applications in cotton production.