Integrated transcriptome, small RNA and degradome analysis provide insights into the transcriptional regulatory networks underlying cold acclimation in jojoba

Abstract

Jojoba (Simmondsia chinensis) is an emerging industrial oil crop cultivated in desert dry land. Jojoba is sensitive to cold stress, which hinders its domestication in the arid areas of temperate climate regions. Here, the effects of cold acclimation on physiological parameters and gene expression in jojoba leaves were analyzed. The tolerance to cold stress in cold-acclimated jojoba seedlings was enhanced as revealed by delayed fluorescence and photosynthetic parameter measurement. The expression levels of 7520 genes were changed significantly after cold acclimation, and these genes were related to multiple biological processes including the stability of photosynthetic machinery, the enhancement of ROS scavenging ability, and protein folding and RNA processing. A total of 144 miRNAs were identified in jojoba, including 133 conserved miRNAs and 11 species-specific miRNAs, and 106 targets with high confidence of miRNA were identified by degradome sequencing, including 18 novel targets of the conserved miRNAs. Forty-two miRNAs were differentially expressed in jojoba under cold acclimation, and these miRNAs were involved in cold acclimation by negatively regulating their targets. Integrated analysis revealed that multiple gene modules might play central roles in the transcriptional regulatory networks underlying cold acclimation in jojoba, in which the ICE1-CBF-SFR6 pathway activated stress response and plant defense, miR398-CSD1/2 and miR396-glutaredoxin regulated ROS homeostasis, and miR167-GDC1 modulated the protection of photosynthetic machinery. Our study will promote understanding of the molecular mechanism of cold acclimation and provide gene markers for the genetic breeding of jojoba for improving cold stress tolerance.