Integrated transcriptomics and metabolomics analysis to characterize alkali stress responses in canola (Brassica napus L.)

DNA methylation is a process through which methyl groups are added to the DNA molecule, thereby modifying the activity of a DNA segment without changing the sequence. Increasing evidence has shown that DNA methylation is involved in various aspects of plant growth and development via a number of key processes including genomic imprinting and repression of transposable elements. DNA methylase and demethylase are two crucial enzymes that play significant roles in dynamically maintaining genome DNA methylation status in plants. In this work, 22 DNA methylase genes and six DNA demethylase genes were identified in rapeseed (Brassica napus L.) genome. These DNA methylase and DNA demethylase genes can be classified into four (BnaCMTs, BnaMET1s, BnaDRMs and BnaDNMT2s) and three (BnaDMEs, BnaDML3s and BnaROS1s) subfamilies, respectively. Further analysis of gene structure and conserved domains showed that each sub-class is highly conserved between rapeseed and Arabidopsis. Expression analysis conducted by RNA-seq as well as qRT-PCR suggested that these DNA methylation/demethylation-related genes may be involved in the heat/salt stress responses in rapeseed. Taken together, our findings may provide valuable information for future functional characterization of these two types of epigenetic regulatory enzymes in polyploid species such as rapeseed, as well as for analyzing their evolutionary relationships within the plant kingdom.

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Identification and Expression Analysis of SLAC/SLAH Gene Family in Brassica napus L.

International Journal of Molecular Sciences ◽

10.3390/ijms22094671 ◽

2021 ◽

Vol 22 (9) ◽

pp. 4671

Author(s):

Yunyou Nan ◽

Yuyu Xie ◽

Ayub Atif ◽

Xiaojun Wang ◽

Yanfeng Zhang ◽

...

Keyword(s):

Brassica Napus ◽

Gene Family ◽

Expression Analysis ◽

Stress Responses ◽

Structural Characteristics ◽

Brassica Napus L ◽

Nitrate Treatment ◽

Genome Wide ◽

Slow Type ◽

Hormone Responses

Slow type anion channels (SLAC/SLAHs) play important roles during anion transport, growth and development, abiotic stress responses and hormone responses in plants. However, there is few report on SLAC/SLAHs in rapeseed (Brassica napus). Genome-wide identification and expression analysis of SLAC/SLAH gene family members were performed in B. napus. A total of 23 SLAC/SLAH genes were identified in B. napus. Based on the structural characteristics and phylogenetic analysis of these members, the SLAC/SLAHs could be classified into three main groups. Transcriptome data demonstrated that BnSLAH3 genes were detected in various tissues of the rapeseed and could be up-regulated by low nitrate treatment in roots. BnSLAC/SLAHs were exclusively localized on the plasma membrane in transient expression of tobacco leaves. These results will increase our understanding of the evolution and expression of the SLAC/SLAHs and provide evidence for further research of biological functions of candidates in B. napus.

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Gradual Exposure to Salinity Improves Tolerance to Salt Stress in Rapeseed (Brassica napus L.)

Water ◽

10.3390/w11081667 ◽

2019 ◽

Vol 11 (8) ◽

pp. 1667 ◽

Cited By ~ 4

Author(s):

Michael Santangeli ◽

Concetta Capo ◽

Simone Beninati ◽

Fabrizio Pietrini ◽

Cinzia Forni

Keyword(s):

Salt Stress ◽

Brassica Napus ◽

Salt Tolerance ◽

Soil Salinity ◽

Stress Responses ◽

Prolonged Exposure ◽

Relative Reduction ◽

Brassica Napus L ◽

Salt Stress Response ◽

Psii Photochemistry

Soil salinity is considered one of the most severe abiotic stresses in plants; plant acclimation to salinity could be a tool to improve salt tolerance even in a sensitive genotype. In this work we investigated the physiological mechanisms underneath the response to gradual and prolonged exposure to sodium chloride in cultivars of Brassica napus L. Fifteen days old seedlings of the cultivars Dynastie (salt tolerant) and SY Saveo (salt sensitive) were progressively exposed to increasing soil salinity conditions for 60 days. Salt exposed plants of both cultivars showed reductions of biomass, size and number of leaves. However, after 60 days the relative reduction in biomass was lower in sensitive cultivar as compared to tolerant ones. An increase of chlorophylls content was detected in both cultivars; the values of the quantum efficiency of PSII photochemistry (ΦPSII) and those of the electron transport rate (ETR) indicated that the photochemical activity was only partially reduced by NaCl treatments in both cultivars. Ascorbate peroxidase (APX) activity was higher in treated samples with respect to the controls, indicating its activation following salt exposure, and confirming its involvement in salt stress response. A gradual exposure to salt could elicit different salt stress responses, thus preserving plant vitality and conferring a certain degree of tolerance, even though the genotype was salt sensitive at the seed germination stage. An improvement of salt tolerance in B. napus could be obtained by acclimation to saline conditions.

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In Silico Identification of the Complex Interplay between Regulatory SNPs, Transcription Factors, and Their Related Genes in Brassica napus L. Using Multi-Omics Data

International Journal of Molecular Sciences ◽

10.3390/ijms22020789 ◽

2021 ◽

Vol 22 (2) ◽

pp. 789

Author(s):

Selina Klees ◽

Thomas Martin Lange ◽

Hendrik Bertram ◽

Abirami Rajavel ◽

Johanna-Sophie Schlüter ◽

...

Keyword(s):

Transcription Factors ◽

Brassica Napus ◽

Stress Responses ◽

Oil Content ◽

Regulation Of Gene Expression ◽

Proteomics Data ◽

Brassica Napus L ◽

Essential Information ◽

Expression Of Genes ◽

Regulatory Snps

Regulatory SNPs (rSNPs) are a special class of SNPs which have a high potential to affect the phenotype due to their impact on DNA-binding of transcription factors (TFs). Thus, the knowledge about such rSNPs and TFs could provide essential information regarding different genetic programs, such as tissue development or environmental stress responses. In this study, we use a multi-omics approach by combining genomics, transcriptomics, and proteomics data of two different Brassica napus L. cultivars, namely Zhongshuang11 (ZS11) and Zhongyou821 (ZY821), with high and low oil content, respectively, to monitor the regulatory interplay between rSNPs, TFs and their corresponding genes in the tissues flower, leaf, stem, and root. By predicting the effect of rSNPs on TF-binding and by measuring their association with the cultivars, we identified a total of 41,117 rSNPs, of which 1141 are significantly associated with oil content. We revealed several enriched members of the TF families DOF, MYB, NAC, or TCP, which are important for directing transcriptional programs regulating differential expression of genes within the tissues. In this work, we provide the first genome-wide collection of rSNPs for B. napus and their impact on the regulation of gene expression in vegetative and floral tissues, which will be highly valuable for future studies on rSNPs and gene regulation.

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Genome-Wide Identification and Expression Profiling of Cytokinin Oxidase/Dehydrogenase (CKX) Genes Reveal Likely Roles in Pod Development and Stress Responses in Oilseed Rape (Brassica napus L.)

Genes ◽

10.3390/genes9030168 ◽

2018 ◽

Vol 9 (3) ◽

pp. 168 ◽

Cited By ~ 15

Author(s):

Pu Liu ◽

Chao Zhang ◽

Jin-Qi Ma ◽

Li-Yuan Zhang ◽

Bo Yang ◽

...

Keyword(s):

Brassica Napus ◽

Oilseed Rape ◽

Stress Responses ◽

Expression Profiling ◽

Cytokinin Oxidase ◽

Brassica Napus L ◽

Genome Wide ◽

Pod Development

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The impact of cerium oxide nanoparticles on the salt stress responses of Brassica napus L.

Environmental Pollution ◽

10.1016/j.envpol.2016.09.060 ◽

2016 ◽

Vol 219 ◽

pp. 28-36 ◽

Cited By ~ 54

Author(s):

Lorenzo Rossi ◽

Weilan Zhang ◽

Leonardo Lombardini ◽

Xingmao Ma

Keyword(s):

Salt Stress ◽

Brassica Napus ◽

Cerium Oxide ◽

Stress Responses ◽

Cerium Oxide Nanoparticles ◽

Oxide Nanoparticles ◽

Brassica Napus L ◽

The Impact

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Genome-wide identification and functional analysis of the TIFY gene family in the response to multiple stresses in Brassica napus L.

BMC Genomics ◽

10.1186/s12864-020-07128-2 ◽

2020 ◽

Vol 21 (1) ◽

Author(s):

Xin He ◽

Yu Kang ◽

Wenqian Li ◽

Wei Liu ◽

Pan Xie ◽

...

Keyword(s):

Brassica Napus ◽

Stress Responses ◽

Expression Patterns ◽

Specific Protein ◽

Vital Role ◽

Evolutionary Analysis ◽

Brassica Napus L ◽

Multiple Stress ◽

Biotic Stresses ◽

Genome Wide

Abstract Background TIFY is a plant-specific protein family with a diversity of functions in plant development and responses to stress and hormones, which contains JASMONATE ZIM-domain (JAZ), TIFY, PPD and ZML subfamilies. Despite extensive studies of TIFY family in many other species, TIFY has not yet been characterized in Brassica napus. Results In this study, we identified 77, 36 and 39 TIFY family genes in the genome of B. napus, B. rapa and B. oleracea, respectively. Results of the phylogenetic analysis indicated the 170 TIFY proteins from Arabidopsis, B. napus, B. rapa and B. oleracea could be divided into 11 groups: seven JAZ groups, one PPD group, one TIFY group, and two ZIM/ZML groups. The molecular evolutionary analysis showed that TIFY genes were conserved in Brassicaceae species. Gene expression profiling and qRT-PCR revealed that different groups of BnaTIFY members have distinct spatiotemporal expression patterns in normal conditions or following treatment with different abiotic/biotic stresses and hormones. The BnaJAZ subfamily genes were predominantly expressed in roots and up-regulated by NaCl, PEG, freezing, methyl jasmonate (MeJA), salicylic acid (SA) and Sclerotinia sclerotiorum in leaves, suggesting that they have a vital role in hormone signaling to regulate multiple stress tolerance in B. napus. Conclusions The extensive annotation and expression analysis of the BnaTIFY genes contributes to our understanding of the functions of these genes in multiple stress responses and phytohormone crosstalk in B. napus.

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Transcriptome Profile Analysis of Winter Rapeseed (Brassica napus L.) in Response to Freezing Stress, Reveal Potentially Connected Events to Freezing Stress

International Journal of Molecular Sciences ◽

10.3390/ijms20112771 ◽

2019 ◽

Vol 20 (11) ◽

pp. 2771 ◽

Cited By ~ 8

Author(s):

Yuanyuan Pu ◽

Lijun Liu ◽

Junyan Wu ◽

Yuhong Zhao ◽

Jing Bai ◽

...

Keyword(s):

Signal Transduction ◽

Brassica Napus ◽

Molecular Mechanism ◽

Stress Responses ◽

Soluble Sugars ◽

Enrichment Analysis ◽

Freezing Stress ◽

Oilseed Crop ◽

Brassica Napus L ◽

Winter Rapeseed

Winter rapeseed is not only an important oilseed crop, but also a winter cover crop in Northern China, where its production was severely limited by freezing stress. As an overwinter crop, the production is severely limited by freezing stress. Therefore, understanding the physiological and molecular mechanism of winter rapeseed (Brassica napus L.) in freezing stress responses becomes essential for the improvement and development of freezing-tolerant varieties of Brassica napus. In this study, morphological, physiological, ultrastructure and transcriptome changes in the Brassica napus line “2016TS(G)10” (freezing-tolerance line) that was exposed to –2 °C for 0 h, 1 h, 3 h and 24 h were characterized. The results showed that freezing stress caused seedling dehydration, and chloroplast dilation and degradation. The content of malondialdehyde (MDA), proline, soluble protein and soluble sugars were increased, as well as the relative electrolyte leakage (REL) which was significantly increased at frozen 24 h. Subsequently, RNA-seq analysis revealed a total of 98,672 UniGenes that were annotated in Brassica napus and 3905 UniGenes were identified as differentially expressed genes after being exposed to freezing stress. Among these genes, 2312 (59.21%) were up-regulated and 1593 (40.79%) were down-regulated. Most of these DEGs were significantly annotated in the carbohydrates and energy metabolism, signal transduction, amino acid metabolism and translation. Most of the up-regulated DEGs were especially enriched in plant hormone signal transduction, starch and sucrose metabolism pathways. Transcription factor enrichment analysis showed that the AP2/ERF, WRKY and MYB families were also significantly changed. Furthermore, 20 DEGs were selected to validate the transcriptome profiles via quantitative real-time PCR (qRT-PCR). In conclusion, the results provide an overall view of the dynamic changes in physiology and insights into the molecular regulation mechanisms of winter Brassica napus in response to freezing treatment, expanding our understanding on the complex molecular mechanism in plant response to freezing stress.

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Characterization of Glutamate-Mediated Hormonal Regulatory Pathway of the Drought Responses in Relation to Proline Metabolism in Brassica napus L.

Plants ◽

10.3390/plants9040512 ◽

2020 ◽

Vol 9 (4) ◽

pp. 512 ◽

Cited By ~ 2

Author(s):

Van Hien La ◽

Bok-Rye Lee ◽

Md. Tabibul Islam ◽

Md. Al Mamun ◽

Sang-Hyun Park ◽

...

Keyword(s):

Salicylic Acid ◽

Drought Stress ◽

Brassica Napus ◽

Stress Responses ◽

Plant Stress ◽

Dependent Manner ◽

Proline Metabolism ◽

Regulatory Pathway ◽

Brassica Napus L ◽

Reducing Potential

Proline metabolism influences the metabolic and/or signaling pathway in regulating plant stress responses. This study aimed to characterize the physiological significance of glutamate (Glu)-mediated proline metabolism in the drought stress responses, focusing on the hormonal regulatory pathway. The responses of cytosolic Ca2+ signaling, proline metabolism, and redox components to the exogenous application of Glu in well-watered or drought-stressed plants were interpreted in relation to endogenous hormone status and their signaling genes. Drought-enhanced level of abscisic acid (ABA) was concomitant with the accumulation of ROS and proline, as well as loss of reducing potential, which was assessed by measuring NAD(P)H/NAD(P)+ and GSH/GSSG ratios. Glu application to drought-stressed plants increased both salicylic acid (SA) and cytosolic Ca2+ levels, with the highest expression of calcium-dependent protein kinase (CPK5) and salicylic acid synthesis-related ICS1. The SA-enhanced CPK5 expression was closely associated with further enhancement of proline synthesis-related genes (P5CS1, P5CS2, and P5CR) expression and a reset of reducing potential with enhanced expression of redox regulating genes (TRXh5 and GRXC9) in a SA-mediated NPR1- and/or PR1-dependent manner. These results clearly indicate that Glu-activated interplay between SA- and CPK5-signaling as well as Glu-enhanced proline synthesis are crucial in the amelioration of drought stress in Brassica napus.

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