Abstract
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.