Fig. 3

Transcriptional landscape differences between the two ecotypes under cold stress. a Phenotypic changes of JJ31 and Alamo on days 0, 28, and 56 under cold stress at 4 °C and recover at room temperature for 28 days. Scale bar indicates 7 cm. b Changes in physiological indicators of JJ31 under control (room temperature) and cold stress (4 °C). From left to right: RWC, REC, and MDA. ** indicates P < 0.005. c Changes in physiological indicators of Alamo under control (room temperature) and cold stress (4 °C). From left to right: RWC, REC, and MDA. ** indicates P < 0.005. d KEGG enrichment of all compared DEGs identified in leaves and roots of JJ31 and Alamo under cold stress. e Expression changes of cold-tolerance-related genes in the circadian rhythm, MAPK signaling pathway, and plant hormone signaling transduction pathways in two ecotypes. f Expression changes of key genes in the CBF-dependent cold response pathway in the two ecotypes