Multi-omics approach reveals the contribution of to rice cold tolerance.

As low environmental temperature adversely affects the growth, development and geographical distribution, plants have evolved multiple mechanisms involving changing physiological and metabolic processes to adapt to cold stress. In this study, we revealed that nucleoporin-coding gene was a positive regulator of cold stress in rice. Physiological assays showed that the activity of antioxidant enzymes showed a significant difference between knock-out lines and wild type under cold stress. Metabolome analysis revealed that the contents of large-scale flavonoids serving as ROS scavengers were lower in mutants compared with wild type under cold stress. Transcriptome analysis indicated that the DEGs between knock-out lines and wild type plants were enriched in defense response, regulation of hormone levels and oxidation-reduction process. Integration of transcriptomic and metabolic profiling revealed that plays a role in the oxidation-reduction process by coordinately regulating genes expression and metabolite accumulation involved in phenylpropanoid and flavonoid biosynthetic pathway. In addition, Exogenous ABA application assays indicated that lines had hypersensitive phenotypes compared with wild type plants, suggesting that may mediate cold tolerance by regulating ABA levels.