Integration of chromatin accessibility and gene expression reveals new regulators of cold hardening to enhance freezing tolerance in Prunus mume.

Low temperature is one of the most important abiotic factors limiting the growth, development and geographical distribution of plants. Prunus mume is a special woody ornamental plant that blooms in early spring in Beijing. However, the molecular mechanism underlying cold hardening to enhance freezing tolerance in Prunus genus remains elusive. This study examined the dynamic physiological responses induced by cold hardening, and identified freezing-tolerance genes by RNA-seq and ATAC-seq analyses. Cold hardening elevated the content of soluble substances and enhanced the freezing-resistance in P. mume. Transcriptome analysis that the important differentially expressed genes (DEGs) enriched in Ca2+ signaling, MAPK cascade, ABA signaling, and ICE-CBF signaling pathways. The openness of gene chromatin was positively correlated with the expression level of these genes. Thirteen motifs were identified in the open chromatin regions in the freezing after cold hardening treatment group. The chromatin opening of transcription start site (TSS) at proximal -177 region of PmCSL was markedly increased, meanwhile the expression level of PmCSL was significantly upregulated. Overexpression of PmCSL in Arabidopsis significantly improved the freezing tolerance of transgenic plants. These findings provide new insights into the regulatory mechanism of freezing tolerance for improving the freezing tolerance breeding in P. mume.