PHD17 acts as a target of miR1320 to negatively control cold tolerance via JA-activated signaling in rice

Plant Homeo Domain (PHD) proteins are involved in diverse biological processes during plant growth. However, the regulation of PHD genes on rice cold stress response remains largely unknown. Here, we reported that PHD17 negatively regulated cold tolerance in rice seedlings as a cleavage target of miR1320 . PHD17 expression was greatly induced by cold stress, and was down-regulated by miR1320 overexpression and up-regulated by miR1320 knockdown. Through 5′RACE and dual luciferase assays, we found that miR1320 targeted and cleaved the 3′UTR region of PHD17 . PHD17 was a nuclear-localized protein and acted as a transcriptional activator in yeast. PHD17 overexpression reduced cold tolerance of rice seedlings, while knockout of PHD17 increased cold tolerance, partially via the CBF cold signaling. By combining transcriptomic and physiological analyses, we demonstrated that PHD17 modulated ROS homeostasis and flavonoid accumulation under cold stress. K-means clustering analysis revealed that differentially expressed genes in PHD17 transgenic lines were significantly enriched in the jasmonic acid (JA) biosynthesis pathway, and expression of JA biosynthesis and signaling genes was verified to be affected by PHD17 . Cold stress tests applied with MeJA or IBU (JA synthesis inhibitor) further suggested the involvement of PHD17 in JA-mediated cold signaling. Taken together, our results suggest that PHD17 acts downstream of miR1320 and negatively regulates cold tolerance of rice seedlings through JA-mediated signaling pathway.