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

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.

Drought-Responsive NAC Transcription Factor RcNAC72 Is Recognized by RcABF4, Interacts with RcDREB2A to Enhance Drought Tolerance in Arabidopsis

“…Rosa chinensis 'Old Blush' is an ancient Chinese species involved in modern rose breeding, and can be used as a model plant for studying the response of roses to drought stress. In our previous study, RcNAC72 was found to be a key transcription factor gene in response to drought stress in roses [36]. We conducted further studies on RcNAC72 in this report.…”

“…The preparation method of R. chinenesis 'Old Blush' materials used in this study was described in our previous study [36]. Normally growing rose leaves, petals, roots and stems were removed and quickly putted into liquid nitrogen and stored at −80 • C for tissue specific analysis of RcNAC72.…”

“…The MDA content was measured following the method described previously [36]. The soluble sugar content was evaluated with related detection kits.…”

Gene Co-Expression Network Tools and Databases for Crop Improvement

“…A previous study has found that WGCNA is more sensitive to noise in datasets and outperforms other clustering methods in detecting non-overlapping clusters or modules [39]. The WGCNA has been reported in several publications related to crop improvement [40][41][42][43][44].…”

Comparative analysis of drought stress-induced physiological and transcriptional changes of two black sesame cultivars during anthesis

“…Among diverse abiotic stresses, numerous studies have shown that drought is the most adverse one, and it causes significant decreases in crop yields and quality traits ( Wang et al., 2011 ; Wang et al., 2019 ). To mitigate the harmful effects of drought, plants have evolved various physiological and molecular mechanisms, such as induction of diverse family genes and antioxidant defense systems, reinforcement or maintenance of biological membranes’ structure and properties, and accumulation of osmoprotectants (sugar, proteins, proline, and glutathione, GSH) in cells ( Chaves et al., 2003 ; El-Sharkawy, 2004 ; Najla et al., 2016 ; Sharma et al., 2017 ; Mahmood et al., 2020 ; Jia et al., 2021 ). Under drought stress conditions, the expression patterns of numerous genes are altered or induced to activate physiological and defense systems ( Savoi et al., 2016 ).…”