ATAC-sequence and transcriptomics jointly reveal the mechanisms underlying waterlogging tolerance and CaMYB96 as a key positive regulator in chili pepper (Capsicum annuum var. Conoides)
It is of great significance to investigate the mechanisms of waterlogging responses in pepper. In this study, numerous adventitious roots appeared, and stem diameter and average root diameter showed an upward trend under waterlogging stress in chili pepper 'ZHC2'. Meanwhile, the contents of cellulase, amino acids, soluble proteins, and reduced glutathione, as well as phenylalanine ammonia lyase and peroxidase activities increased significantly than those of the control under waterlogging stress. Under waterlogging stress, a total of 80296 peaks and 3671 up-regulated DEGs, 5229 down-regulated DEGs were identified by transposase-accessible chromatin with sequencing (ATAC-seq) coupled with transcriptomics (RNA-seq) analysis. The associated up-regulated DEGs were mainly enriched in the "plant hormone signal transduction", "amino acid biosynthesis", "peroxisome", and "glutathione metabolism" pathways. Addtionally, 17 differentially expressed transcription factors with binding motifs were identified under waterlogging stress. According to both transcriptional regulatory networks and gene expression levels, key gene CaMYB96 was screened. Compared with the control, waterlogging tolerance of CaMYB96-silenced pepper plants decreased, while that of OE tobacco lines increased. DNA affinity purification sequencing (DAP-seq) analysis indicated that distal intergenic regions were main binding sites for CaMYB96. The target genes selected by DAP-seq combined with RNA-seq analysis were mainly enriched in the terms like "regulation of root development", "cellulose decomposition metabolism", and "hormone-mediated signaling pathways". Among them, hormone-related target genes including CaPIN5L (auxin efflux carrier), CaTify, and CaGRP (GA-regulated protein) were explored. These results provided new insights for understanding waterlogging regulation mechanisms and breeding waterlogging-tolerant pepper varieties.