Transcriptomic profiling and identification of candidate genes in two Phoebe bournei ecotypes with contrasting cold stress responses

Abstract

We identified a set of ecotype-specific cold-responsive genes, providing candidate genes for enhancing cold resistance in Phoebe bournei (Hemsl.) Yang and other woody plants. Phoebe bournei (Hemsl.) Yang is an indigenous, endangered, precious timber and ornamental tree in China. Cold stress greatly affects the survival of Phoebe species. To elucidate the molecular mechanisms of cold response and identify candidate genes for improving cold resistance, we used RNA-Seq and qRT-PCR to compare the transcriptomic profiles of two ecotypes of P. bournei, cold-resistant Wuyuan (WY) and cold-sensitive Wuping (WP), under cold stress. A total of 3970 and 4433 genes were differentially expressed in WY and WP, respectively, with 2030 differentially expressed genes (DEGs) were specific to WY. Specifically, the categories “defense response”, “secondary metabolites”, and “ABC transporters” were enriched among WY-specific DEGs. Several transcription factor genes might involve in cold stress response, including RAP2-3, NAC2, NAC43, WRKY47, and WRKY51, were induced only in WY, and CBF3, ZAT10, MYB308, and WER exhibited greater cold stress-induced expression changes in WY compared with WP, which may partially explain the distinct transcriptomic changes induced by cold stress between the two ecotypes. Greater fold changes in the expression of starch metabolism-related genes such as BAM1/3 and lower fold changes in the expression of DPE2 were detected in WY, which was consistent with its greater abundance of total soluble sugars. The stronger transcriptional differentiation of related genes under cold stress in WY may explain its greater cold resistance compared with the WP ecotype, providing important genetic resources for improving cold-resistant characteristics in P. bournei. In addition, two interaction networks were constructed, resulting in identification of a series of hub genes, which facilitates functional dissection of the molecular mechanisms involved in the response to cold stress of P. bournei and extends our ability to improve cold resistance in this valued species.