ATAC-Seq and Transcriptomics Reveal Mechanisms of Waterlogging Tolerance and Identify CaMYB96 as a Key Positive Regulator in Chili Pepper ( <i>Capsicum annuum</i> Var. <i>conoides</i> )

It is vital to investigate waterlogging-tolerant regulatory mechanisms in chili pepper. Waterlogging stress in pepper "ZHC2" resulted in numerous adventitious roots appearing and an increase in stem diameter and average root diameter. Under waterlogging stress, the contents of amino acids, soluble proteins, and reduced glutathione, as well as the activities of cellulase, phenylalanine ammonia lyase, and peroxidase, increased significantly compared with the control. Under waterlogging stress, 80296 peaks and 8900 differentially expressed genes (DEGs) were identified by for transposase-accessible chromatin with sequencing (ATAC-seq) coupled with transcriptomics analysis. The associated upregulated DEGs were mainly enriched in the "plant hormone signal transduction", "biosynthesis of amino acids", and "phenylalanine metabolism" pathways. Compared with the control, waterlogging tolerance of <i>CaMYB96-</i>silenced plants decreased, while that of overexpression lines increased significantly. CaMYB96 increased the levels of cellulase, soluble proteins, and antioxidants to enhance pepper waterlogging tolerance by regulating <i>CaTIFY5A</i> expression.