Time-course RNA-seq analysis provides an improved understanding of genetic regulation in response to cold stress from white clover (Trifolium repens L.)

Abstract

AbstractWhite clover (Trifolium repens L.) is an important legume forage, which is widely distributed in cool-season regions. Therefore, cold stress is a major environmental factor limiting its growth and production, while little is known about the its cold tolerance at molecular level. In the present study, we performed time-course RNA-seq analysis under cold stress. RNA-seq results suggested that genes associated with “oxidoreductase activity” and “transcription regulator activity” are more likely related to the response of white clover to cold stress. To identify the specific gene modules and the hub genes of white clover in response to cold stress, we applied weighted gene co-expression network analyses (WGCNA) to transcriptome data. We also found that gene modules that focus on protein kinase activity, DNA-binding transcription factor activity and oxidoreductase activity, are more likely to be involved in the response of white clover to cold stress. Especially, we identified several AP2/ERF TF genes and CDPK genes as pivotal genes in white clover in response to cold stress, which would provide helpful insights into the molecular mechanisms underlying the response of white clover to cold stress.

Keywords

• Trifolium repens
• oxidoreductase
• WGCNA
• AP2/ERF
• CDPK