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

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.

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Comparative Transcriptome Analysis Reveals Molecular Mechanism and Regulatory Network of Rosa Chinensis ‘Old Blush’ Leaves in Response to Drought Stress

10.21203/rs.3.rs-112819/v1 ◽

2020 ◽

Author(s):

Xin Jia ◽

Hui Feng ◽

Yanhua Bu ◽

Yingmin Lu ◽

Naizhe Ji ◽

...

Keyword(s):

Transcription Factors ◽

Drought Stress ◽

Molecular Mechanism ◽

Physiological Traits ◽

Drought Response ◽

Rosa Chinensis ◽

Primary And Secondary Metabolism ◽

Term Enrichment ◽

Stress Related Genes ◽

The Rose

Abstract Background: Rose is one of the most important ornamental crops, but drought limits its yield and quality seriously. Although serval abiotic stress related genes have been identified, the molecular mechanism during rose’s responding to drought stress is still limited. In this study, the transcriptomes of leaves of two-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. Meanwhile, weighted gene co-expression network analysis (WGCNA) was used to construct a co-expression network associated with the physiological traits of drought response to discover the hub transcription factors involved in drought response.Results: More than 45 million high-quality clean reads were generated from samples and used for comparison with the rose reference genome. A total of 46433 differentially expressed genes 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, primary and secondary metabolism, and a certain degree of recovery after rewatering. Gene co-expression analysis identified 18 modules, in which four modules have highly degree of correlation with physiological traits. In addition, twenty-two transcription factors including members of NACs, WRKYs, MYBs, ERFs, ARFs and bHLHs with high connectivity in these four modules were screened. Conclusions: The results of this study provided the first transcriptome sequencing report of the drought stress in R.chinensis, and also provided candidate transcription factors in response to drought stress, providing clues for improving the drought tolerance of the rose through molecular breeding in the future.

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Whole-genome characterization of Rosa chinensis AP2/ERF transcription factors and analysis of negative regulator RcDREB2B in Arabidopsis

BMC Genomics ◽

10.1186/s12864-021-07396-6 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Wei Li ◽

Ziwen Geng ◽

Cuiping Zhang ◽

Kuiling Wang ◽

Xinqiang Jiang

Keyword(s):

Drought Stress ◽

Gene Structure ◽

Growth And Development ◽

Negative Regulator ◽

Yeast Cells ◽

Severe Drought ◽

Rosa Chinensis ◽

Number Pattern ◽

Erf Family ◽

The Rose

Abstract Background Rose (Rosa chinensis) is a traditional famous flower with valuable ornamental characteristics. However, drought stress restricts its growth and development, leading to an abnormal phenotype. One of the main transcription factor (TF) protein groups in the plant kingdom are the APETALA2/ethylene-responsive factor (AP2/ERF) proteins and are potentially involved in the growth and stress responses of various plants. Results Our investigation mainly focused on exploring the genome of rose and thereby we discovered 135 apparent AP2/ERF TFs. Phylogenic analyses revealed that RcAP2/ERF genes are categorized into DREB, Soloist, AP2, and ERF subfamilies, and are further classified these into 17 groups, with the same as Malus domestica and Arabidopsis thaliana. The analysis of the gene structure revealed that the introns ranged from 0 to 9 in number. Pattern examination demonstrated that the RcAP2/ERF predominantly consists of typical AP2 domains, of which the 2nd motif is the most ubiquitous. Distributions of cis-acting elements indicated that members of the AP2/ERF family are frequently involved in growth and development, phytohormone and stress response in rose species. Also, the distribution mapping of the rose chromosomes indicated that AP2/ERF class genes are dispersed among all seven chromosomes. Additionally, we isolated a novel DREB A2 subgroup gene and named it RcDREB2B. Subsequently, the RcDREB2B transcript accumulation was repressed under the mild and severe drought stress in the root samples of rose. RcDREB2B was targeted to the nucleus and exhibited transactivation in yeast cells. The overexpression of RcDREB2B was found to promote sensitivity to a higher salt concentration, ABA, and PEG at the germination and post-germination stages. Twelve putative osmotic and ABA-related genes were impaired in RcDREB2B-overexpressing plants. Conclusions The results provide comprehensive information regarding the gene structure, phylogenic, and distribution of the rose AP2/ERF family and bring insight into the complex transcriptional gene regulation of RcAP2/ERF. Findings in this study would also contribute to further understanding of the RcDREB2B gene in rose.

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Whole-genome characterization of Rosa chinensis AP2/ERF transcription factors and analysis of negative regulator RcDREB2B in Arabidopsis

10.21203/rs.3.rs-74171/v3 ◽

2021 ◽

Author(s):

Wei Li ◽

Ziwen Geng ◽

Cuiping Zhang ◽

Kuiling Wang ◽

Xinqiang Jiang

Keyword(s):

Drought Stress ◽

Gene Structure ◽

Growth And Development ◽

Negative Regulator ◽

Yeast Cells ◽

Severe Drought ◽

Rosa Chinensis ◽

Number Pattern ◽

Erf Family ◽

The Rose

Abstract Background: Rose (Rosa chinensis) is a traditional famous flower with valuable ornamental characteristics. However, drought stress restricts its growth and development, leading to an abnormal phenotype. One of the main transcription factor (TF) protein groups in the plant kingdom are the APETALA2/ethylene-responsive factor (AP2/ERF) proteins and are potentially involved in the growth and stress responses of various plants. Results: Our investigation mainly focused on exploring the genome of rose and thereby we discovered 135 apparent AP2/ERF TFs. Phylogenic analyses revealed that RcAP2/ERF genes are categorized into DREB, Soloist, AP2, and ERF subfamilies, and are further classified these into 17 groups, with the same as Malus domestica and Arabidopsis thaliana. The analysis of the gene structure revealed that the introns ranged from 0 to 9 in number. Pattern examination demonstrated that the RcAP2/ERF predominantly consists of typical AP2 domains, of which the 2nd motif is the most ubiquitous. Distributions of cis-acting elements indicated that members of the AP2/ERF family are frequently involved in growth and development, phytohormone and stress response in rose species. Also, the distribution mapping of the rose chromosomes indicated that AP2/ERF class genes are dispersed among all seven chromosomes. Additionally, we isolated a novel DREB A2 subgroup gene and named it RcDREB2B. Subsequently, the RcDREB2B transcript accumulation was repressed under the mild and severe drought stress in the root samples of rose. RcDREB2B was targeted to the nucleus and exhibited transactivation in yeast cells. The overexpression of RcDREB2B was found to promote sensitivity to a higher salt concentration, ABA, and PEG at the germination and post-germination stages. Twelve putative osmotic and ABA-related genes were impaired in RcDREB2B-overexpressing plants. Conclusions: The results provide comprehensive information regarding the gene structure, phylogenic, and distribution of the rose AP2/ERF family and bring insight into the complex transcriptional gene regulation of RcAP2/ERF. Findings in this study would also contribute to further understanding of the RcDREB2B gene in rose.

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Whole-genome characterization of Rosa chinensis AP2/ERF transcription factors and analysis of negative regulator RcDREB2B in Arabidopsis

10.21203/rs.3.rs-74171/v2 ◽

2020 ◽

Author(s):

Li Wei ◽

Ziwen Geng ◽

Zhang Cuiping ◽

Wang Kuiling ◽

Jiang Xinqiang

Keyword(s):

Drought Stress ◽

Gene Structure ◽

Growth And Development ◽

Negative Regulator ◽

Yeast Cells ◽

Severe Drought ◽

Rosa Chinensis ◽

Number Pattern ◽

Erf Family ◽

The Rose

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Discovery of Drought-Responsive Transposable Element-Related Peach miRNAs

10.1101/143115 ◽

2017 ◽

Author(s):

Asli Kurden Pekmezci ◽

Gökhan Karakülah ◽

Turgay Unver

Keyword(s):

Transcription Factors ◽

Drought Stress ◽

Stress Response ◽

Transposable Element ◽

Small Rna ◽

Computational Analysis ◽

Drought Response ◽

Specific Target ◽

Specific Manner ◽

Regulatory Rnas

AbstractMicroRNAs (miRNA) are small non-coding regulatory RNAs that suppress their specific target transcripts either by cleavage or inhibition of translation. Transposable element related miRNAs (TE-miRNA) have been subjected to various studies so far, and some of them were found to be involved in stress response in plants. Here, small RNA (sRNA) sequencing libraries generated from drought stress treated peach tissues were utilized to identify TE-miRNAs. Our computational analysis led to the identification of 63 TE-miRNAs, which were either locating nearby of any TE (TE-related), or overlapping with a TE (TE-derived). Furthermore, 13 out of 63 TE-miRNAs were designated as drought-responsive. Expression pattern of the identified drought-responsive TE-miRNAs are observed as tissue-specific manner, and their specific target transcripts are mostly related to transcription factors and growth-associated genes. Our findings suggest that miRNAs in relation with transposable elements might be key molecular players in the regulation of drought response.

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The Impact of Drought Stress on some Morpho-Physiological Traits and RAPD Markers in Wheat Genotypes

Journal of Plant Production Sciences ◽

10.21608/jpps.2015.7396 ◽

2015 ◽

Vol 4 (1) ◽

pp. 27-37 ◽

Cited By ~ 1

Author(s):

Bayoumi Y. ◽

Amal Abd EL-Mageed ◽

Enas Ibrahim ◽

Soad Mahmoud ◽

I. El-Demardash ◽

...

Keyword(s):

Drought Stress ◽

Rapd Markers ◽

Physiological Traits ◽

Wheat Genotypes ◽

The Impact

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Ectopic Overexpression of Histone H3K4 Methyltransferase CsSDG36 from Tea Plant Decreases Hyperosmotic Stress Tolerance in Arabidopsis thaliana

International Journal of Molecular Sciences ◽

10.3390/ijms22105064 ◽

2021 ◽

Vol 22 (10) ◽

pp. 5064

Author(s):

Qinghua Chen ◽

Linghui Guo ◽

Yanwen Yuan ◽

Shuangling Hu ◽

Fei Guo ◽

...

Keyword(s):

Drought Stress ◽

Transmembrane Domain ◽

Tea Plant ◽

Microtubule Assembly ◽

Pcr Analysis ◽

Drought Response ◽

Stomatal Development ◽

Wild Type ◽

Over Expression ◽

Histone H3k4

Histone methylation plays an important regulatory role in the drought response of many plants, but its regulatory mechanism in the drought response of the tea plant remains poorly understood. Here, drought stress was shown to induce lower relative water content and significantly downregulate the methylations of histone H3K4 in the tea plant. Based on our previous analysis of the SET Domain Group (SDG) gene family, the full-length coding sequence (CDS) of CsSDG36 was cloned from the tea cultivar ‘Fuding Dabaicha’. Bioinformatics analysis showed that the open reading frame (ORF) of the CsSDG36 gene was 3138 bp, encoding 1045 amino acids and containing the conserved structural domains of PWWP, PHD, SET and PostSET. The CsSDG36 protein showed a close relationship to AtATX4 of the TRX subfamily, with a molecular weight of 118,249.89 Da, and a theoretical isoelectric point of 8.87, belonging to a hydrophilic protein without a transmembrane domain, probably located on the nucleus. The expression of CsSDG36 was not detected in the wild type, while it was clearly detected in the over-expression lines of Arabidopsis. Compared with the wild type, the over-expression lines exhibited lower hyperosmotic resistance by accelerating plant water loss, increasing reactive oxygen species (ROS) pressure, and increasing leaf stomatal density. RNA-seq analysis suggested that the CsSDG36 overexpression caused the differential expression of genes related to chromatin assembly, microtubule assembly, and leaf stomatal development pathways. qRT-PCR analysis revealed the significant down-regulation of stomatal development-related genes (BASL, SBT1.2(SDD1), EPF2, TCX3, CHAL, TMM, SPCH, ERL1, and EPFL9) in the overexpression lines. This study provides a novel sight on the function of histone methyltransferase CsSDG36 under drought stress.

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Water uptake dynamics under progressive drought stress in diverse accessions of the OryzaSNP panel of rice (Oryza sativa)

Functional Plant Biology ◽

10.1071/fp12015 ◽

2012 ◽

Vol 39 (5) ◽

pp. 402 ◽

Cited By ~ 28

Author(s):

Veeresh R. P. Gowda ◽

Amelia Henry ◽

Vincent Vadez ◽

H. E. Shashidhar ◽

Rachid Serraj

Keyword(s):

Oryza Sativa ◽

Drought Stress ◽

Root Growth ◽

Water Uptake ◽

Root Length Density ◽

Oryza Sativa L ◽

Root Water Uptake ◽

Snp Markers ◽

Drought Response ◽

Genotypic Differences

In addition to characterising root architecture, evaluating root water uptake ability is important for understanding drought response. A series of three lysimeter studies were conducted using the OryzaSNP panel, which consists of 20 diverse rice (Oryza sativa L.) genotypes. Large genotypic differences in drought response were observed in this genotype panel in terms of plant growth and water uptake. Total water uptake and daily water uptake rates in the drought-stress treatment were correlated with root length density, especially at depths below 30 cm. Patterns of water uptake among genotypes remained consistent throughout the stress treatments: genotypes that initially extracted more water were the same genotypes that extracted more water at the end of the study. These results suggest that response to drought by deep root growth, rather than a conservative soil water pattern, seems to be important for lowland rice. Genotypes in the O. sativa type aus group showed some of the greatest water uptake and root growth values. Since the OryzaSNP panel has been genotyped in detail with SNP markers, we expect that these results will be useful for understanding the genetics of rice root growth and function for water uptake in response to drought.

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