Comparative Transcriptome and Weighted Gene Co-expression Network Analysis Identify Key Transcription Factors of Rosa chinensis 'Old Blush' After Exposure to a Gradual Drought Stress Followed by Recovery.

Xin Jia,Shiwei Zhao,Hui Feng,Yanhua Bu,Naizhe Ji,Yingmin Lyu

doi:10.3389/fgene.2021.690264

Abstract

Rose is one of the most fundamental ornamental crops, but its yield and quality are highly limited by drought. The key transcription factors (TFs) and co-expression networks during rose’s response to drought stress and recovery after drought stress are still limited. In this study, the transcriptomes of leaves of 2-year-old cutting seedlings of Rosa chinensis ‘Old Blush’ from three continuous droughted stages (30, 60, 90 days after full watering) and rewatering were analyzed using RNA sequencing. Weighted gene co-expression network analysis (WGCNA) was used to construct a co-expression network, which was associated with the physiological traits of drought response to discovering the hub TFs involved in drought response. More than 45 million high-quality clean reads were generated from the sample and used for comparison with the rose reference genome. A total of 46433 differentially expressed genes (DEGs) were identified. Gene Ontology (GO) term enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis indicated that drought stress caused significant changes in signal transduction, plant hormones including ABA, auxin, brassinosteroid (BR), cytokinin, ethylene (ET), jasmonic acid (JA) and salicylic acid (SA), primary and secondary metabolism, and a certain degree of recovery after rewatering. Gene co-expression analysis identified 18 modules, in which four modules showed a high degree of correlation with physiological traits. In addition, 42 TFs including members of NACs, WRKYs, MYBs, AP2/ERFs, ARFs, and bHLHs with high connectivity in navajowhite1 and blue modules were screened. This study provides the transcriptome sequencing report of R. chinensis ‘Old Blush’ during drought stress and rewatering process. The study also identifies the response of candidate TFs to drought stress, providing guidelines for improving the drought tolerance of the rose through molecular breeding in the future.

Highlights

Rose is one of the most fundamental ornamental crops
At 60 days, the relative water content of the leaves decreased significantly compared with the control, which was consistent with the phenotype (Figure 2B)
With the deepening degree of drought stress, the content of MDA rises in fluctuation and reached the highest point after 90 days of the drought treatment (Figure 2D)

Summary

Introduction

Rose is one of the most fundamental ornamental crops. Cultural, and symbolic value, the rose has a significant market share in the floriculture industry. The rose occupies nearly a quarter of the Netherlands floriculture market (Mordor Intelligence, 2020). Their growth conditions are closely related to changes in the external environment. Most roses suffer from various degrees of drought, which result in a sizable loss of productivity and quality around the world. Changes in the earth’s climate have an adverse impact on plant growth, crop production, and distribution (Zhu, 2002). It is pressing to identify the response mechanism in rose under the drought stress

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