Integrated genome-wide chromatin accessibility and expression profile identify key transcription factors involved in bud endodormancy break in tea plants

Abstract

It is essential for tea plants (Camellia sinensis) to undergo bud endodormancy in order to survive winter and grow again the following spring. Molecular pathways underlying the release and break of endodormancy, however, remain unclear. Accessible chromatin regions play a crucial role in precise gene expression regulation. Here, we profiled the chromatin accessibility and transcriptional features of transcription factors (TFs) using ATAC- and RNA-seq technologies. We revealed dynamic changes during bud dormancy break in tea plants and detected open chromatin regions and TF binding sites. Numerous transcripts associated with open chromatin regions were found to exhibit dormant-preferential expression among TF-target genes. We focused on several crucial TF motifs, including MADS-box, AP2EREBP, bZIP, MYB, bHLH, E2FDP, REMB3, TCP, and G2-like factors, that were enriched in open chromatin regions at different budbreak stages, and predicted networks of TF-target genes. Then, we used qRT-PCR to investigate the expression patterns of budbreak-related genes.We found a set of differentially regulated peaks of MADS-box TFs and related genes enriched in plant hormone signal transduction pathway, photosynthesis, secondary metabolism, plant-pathogen interaction functions. Correlation analysis with the phytohormones abscisic acid and indole-3-acetic acid also provided details of the regulation network. Moreover, we identified the core TFs (SVP, CO, AP1, SOC, ABI, CBF, FRUITFULL, and ULTRAPETALA) of several pathways related to budbreak, providing the guideposts for future study.