scholarly journals Characterization of transcription factor genes related to cold tolerance in Brassica napus

2021 ◽  
Vol 19 (4) ◽  
pp. e45
Author(s):  
Mayur Mukut Murlidhar Sharma ◽  
Rahul Vasudeo Ramekar ◽  
Nam-Il Park ◽  
Ik-Young Choi ◽  
Seon-Kang Choi ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Cold Stress ◽  
Cold Tolerance ◽  
Stress Responses ◽  
In Silico Analysis ◽  
Oilseed Crop ◽  
Large Numbers ◽  
Transcription Factor Genes ◽  
Post Transcriptional Regulation

Brassica napus is the third most important oilseed crop in the world; however, in Korea, it is greatly affected by cold stress, limiting seed growth and production. Plants have developed specific stress responses that are generally divided into three categories: cold-stress signaling, transcriptional/post-transcriptional regulation, and stress-response mechanisms. Large numbers of functional and regulatory proteins are involved in these processes when triggered by cold stress. Here, our objective was to investigate the different genetic factors involved in the cold-stress responses of B. napus. Consequently, we treated the Korean B. napus cultivar Naehan at the 4-week stage in cold chambers under different conditions, and RNA and cDNA were obtained. An in silico analysis included 80 cold-responsive genes downloaded from the National Center for Biotechnology Information (NCBI) database. Expression levels were assessed by reverse transcription polymerase chain reaction, and 14 cold-triggered genes were identified under cold-stress conditions. The most significant genes encoded zinc-finger proteins (33.7%), followed by MYB transcription factors (7.5%). In the future, we will select genes appropriate for improving the cold tolerance of B. napus.

scholarly journals Systematic analysis of JmjC gene family of Brassica napus and KDM5 subfamily involved in abiotic stress response

2019 ◽  
Author(s):  
Xinghui He ◽  
Jiao Pan ◽  
Boyu Liu ◽  
Chengfang Tan ◽  
Ying Ruan ◽  
...  
Keyword(s):  
Stress Response ◽  
Brassica Napus ◽  
Stress Responses ◽  
Retention Rate ◽  
Sequence Similarity ◽  
Expression Profiles ◽  
Functional Characterization ◽  
Homologous Gene ◽  
Oilseed Crop

Abstract Background: Jumonji C (JmjC) proteins play an important role in plant development and stress response through the removal of lysine methylation from histones. Brassica napus, which originated from spontaneous hybridization between Brassica rapa and Brassica oleracea, is the most important oilseed crop after soybean, but evolutionary relationships and functions of JmjC proteins remain unclear. Results: 65 JmjC genes were identified from B. napus genome, 29 from B. rapa, and 23 from B. oleracea. These genes were grouped into seven clades according to conserved sequences, and their catalytic activities of demethylation were predicted. Group-KDM4/JHDM3 for H3K4/9/27/36, Group-KDM5A/B for H3K4, Group-JmjC domain-only A/B for H3K27/36, Group-KDM3/JHDM2 for H3K9, and Group-JMJD6 may be for arginine demethylases. B. napus inherited most of its JmjC genes from its parents. The average retention rate of B. napus JmjC gene from B. rapa (93.1%) and B. oleracea (82.6%) exceeded that of all homologous gene pairs (83.7%) across the whole B. napus genome. Thirteen new or duplicated JmjC genes have emerged in B. napus. Sequence similarity and domain organization analyses suggest that the functions of these genes might be diversified. Furthermore, KDM5 genes were examined under stress conditions due to H3K4 demethylation. Expression profiles indicated that the genes from B. napus are possibly involved in various stress responses. Conclusion: This study provides the first genome-wide characterization of JmjC genes in Brassica species. Its JmjC genes potentially have diverse functions, and its KDM5 genes might be involved in stress response. The results of this study facilitate the future functional characterization of the demethylation of JmjC family in Brassica crops.

scholarly journals Genome-Wide Analysis of the NAC Transcription Factor Gene Family Reveals Differential Expression Patterns and Cold-Stress Responses in the Woody Plant Prunus mume

Genes ◽  
2018 ◽  
Vol 9 (10) ◽  
pp. 494 ◽  
Author(s):  
Xiaokang Zhuo ◽  
Tangchun Zheng ◽  
Zhiyong Zhang ◽  
Yichi Zhang ◽  
Liangbao Jiang ◽  
...  
Keyword(s):  
Cold Stress ◽  
Gene Family ◽  
Cold Tolerance ◽  
Stress Responses ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Freezing Stress ◽  
Prunus Mume ◽  
Flower Bud ◽  
Freezing Resistance

NAC transcription factors (TFs) participate in multiple biological processes, including biotic and abiotic stress responses, signal transduction and development. Cold stress can adversely impact plant growth and development, thereby limiting agricultural productivity. Prunus mume, an excellent horticultural crop, is widely cultivated in Asian countries. Its flower can tolerate freezing-stress in the early spring. To investigate the putative NAC genes responsible for cold-stress, we identified and analyzed 113 high-confidence PmNAC genes and characterized them by bioinformatics tools and expression profiles. These PmNACs were clustered into 14 sub-families and distributed on eight chromosomes and scaffolds, with the highest number located on chromosome 3. Duplicated events resulted in a large gene family; 15 and 8 pairs of PmNACs were the result of tandem and segmental duplicates, respectively. Moreover, three membrane-bound proteins (PmNAC59/66/73) and three miRNA-targeted genes (PmNAC40/41/83) were identified. Most PmNAC genes presented tissue-specific and time-specific expression patterns. Sixteen PmNACs (PmNAC11/19/20/23/41/48/58/74/75/76/78/79/85/86/103/111) exhibited down-regulation during flower bud opening and are, therefore, putative candidates for dormancy and cold-tolerance. Seventeen genes (PmNAC11/12/17/21/29/42/30/48/59/66/73/75/85/86/93/99/111) were highly expressed in stem during winter and are putative candidates for freezing resistance. The cold-stress response pattern of 15 putative PmNACs was observed under 4 °C at different treatment times. The expression of 10 genes (PmNAC11/20/23/40/42/48/57/60/66/86) was upregulated, while 5 genes (PmNAC59/61/82/85/107) were significantly inhibited. The putative candidates, thus identified, have the potential for breeding the cold-tolerant horticultural plants. This study increases our understanding of functions of the NAC gene family in cold tolerance, thereby potentially intensifying the molecular breeding programs of woody plants.

scholarly journals Identification of cold stress responsive microRNAs in cold tolerant and susceptible Hemerocallis fulva by high throughput sequencing

2020 ◽  
Author(s):  
Changbing Huang ◽  
Chun Jiang ◽  
limin Jin ◽  
Huanchao Zhang
Keyword(s):  
Low Temperature ◽  
Cold Stress ◽  
Cold Tolerance ◽  
Temperature Stress ◽  
Stress Responses ◽  
Target Genes ◽  
Low Temperature Stress ◽  
Differentially Expressed ◽  
Differentially Expressed Mirnas ◽  
Cold Tolerant

Abstract Background:Hemerocallis fulva is a perennial herb belonging to Hemerocallis of Hemerocallis. Because of the large and bright colors, it is often used as a garden ornamental plant. But most varieties of H. fulva on the market will wither in winter, which will affect their beauty. It is very important to study the effect of low temperature stress on the physiological indexes of H. fulva and understand the cold tolerance of different H. fulva. MiRNA is a kind of endogenous non coding small molecular RNA with length of 21-24nt. It mainly inhibits protein translation by cutting target genes, and plays an important role in the development of organisms, gene expression and biological stress. Low temperature is the main abiotic stress affecting the production of H. fulva in China, which hinders the growth and development of plants. A comprehensive understanding of the expression pattern of microRNA in H. fulva under low temperature stress can improve our understanding of microRNA mediated stress response. Although there are many studies on miRNAs of various plants under cold stress at home and abroad, there are few studies on miRNAs related to cold stress of H. fulva. It is of great significance to explore the cold stress resistant gene resources of H. fulva, especially the identification and functional research of miRNA closely related to cold stress, for the breeding of excellent H. fulva.Results A total of 5619 cold-responsive miRNAs, 315 putative novel and 5 304 conserved miRNAs, were identified from the leaves and roots of two different varieties ‘Jinyan’ (cold-tolerant) and ‘Lucretius ’ (cold-sensitive), which were stressed under -4 oC for 24 h. Twelve conserved and three novel miRNAs (novel-miR10, novel-miR19 and novel-miR48) were differentially expressed in leaves of ‘Jinyan’ under cold stress. Novel-miR19, novel-miR29 and novel-miR30 were up-regulated in roots of ‘Jinyan’ under cold stress. Thirteen and two conserved miRNAs were deferentially expressed in leaves and roots of ‘Lucretius’ after cold stress. The deferentially expressed miRNAs between two cultivars under cold stress include novel miRNAs and the members of the miR156, miR166 and miR319 families. A total of 6 598 target genes for 6 516 known miRNAs and 82 novel miRNAs were predicted by bioinformatic analysis, mainly involved in metabolic processes and stress responses. Ten differentially expressed miRNAs and predicted target genes were confirmed by quantitative reverse transcription PCR(q-PCR), and the expressional changes of target genes were negatively correlated to differentially expressed miRNAs. Our data indicated that some candidate miRNAs (e.g., miR156a-3-p, miR319a, and novel-miR19) may play important roles in plant response to cold stress.Conclusions Our study indicates that some putative target genes and miRNA mediated metabolic processes and stress responses are significant to cold tolerance in H. fulva.

scholarly journals Genome-Wide Identification and Characterization of the RCI2 Gene Family in Allotetraploid Brassica napus Compared with Its Diploid Progenitors

2022 ◽  
Vol 23 (2) ◽  
pp. 614
Author(s):  
Weiqi Sun ◽  
Mengdi Li ◽  
Jianbo Wang
Keyword(s):  
Brassica Napus ◽  
Gene Family ◽  
Gene Structure ◽  
Stress Responses ◽  
Stress Protein ◽  
Purifying Selection ◽  
Cis Acting ◽  
Genome Wide ◽  
Duplication Events

Brassica napus and its diploid progenitors (B. rapa and B. oleracea) are suitable for studying the problems associated with polyploidization. As an important anti-stress protein, RCI2 proteins widely exist in various tissues of plants, and are crucial to plant growth, development, and stress response. In this study, the RCI2 gene family was comprehensively identified and analyzed, and 9, 9, and 24 RCI2 genes were identified in B. rapa, B. oleracea, and B. napus, respectively. Phylogenetic analysis showed that all of the identified RCI2 genes were divided into two groups, and further divided into three subgroups. Ka/Ks analysis showed that most of the identified RCI2 genes underwent a purifying selection after the duplication events. Moreover, gene structure analysis showed that the structure of RCI2 genes is largely conserved during polyploidization. The promoters of the RCI2 genes in B. napus contained more cis-acting elements, which were mainly involved in plant development and growth, plant hormone response, and stress responses. Thus, B. napus might have potential advantages in some biological aspects. In addition, the changes of RCI2 genes during polyploidization were also discussed from the aspects of gene number, gene structure, gene relative location, and gene expression, which can provide reference for future polyploidization analysis.

scholarly journals Characterization of cold stress responses in different rapeseed ecotypes based on metabolomics and transcriptomics analyses

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8704 ◽  
Author(s):  
Hongju Jian ◽  
Ling Xie ◽  
Yanhua Wang ◽  
Yanru Cao ◽  
Mengyuan Wan ◽  
...  
Keyword(s):  
Gene Expression ◽  
Amino Acids ◽  
Cold Stress ◽  
Stress Responses ◽  
Differentially Expressed ◽  
Regulatory Mechanisms ◽  
Primary Metabolites ◽  
Stress Treatment ◽  
Organic Acids And Sugars

The winter oilseed ecotype is more tolerant to low temperature than the spring ecotype. Transcriptome and metabolome analyses of leaf samples of five spring Brassica napus L. (B. napus) ecotype lines and five winter B. napus ecotype lines treated at 4 °C and 28 °C were performed. A total of 25,460 differentially expressed genes (DEGs) of the spring oilseed ecotype and 28,512 DEGs of the winter oilseed ecotype were identified after cold stress; there were 41 differentially expressed metabolites (DEMs) in the spring and 47 in the winter oilseed ecotypes. Moreover, more than 46.2% DEGs were commonly detected in both ecotypes, and the extent of the changes were much more pronounced in the winter than spring ecotype. By contrast, only six DEMs were detected in both the spring and winter oilseed ecotypes. Eighty-one DEMs mainly belonged to primary metabolites, including amino acids, organic acids and sugars. The large number of specific genes and metabolites emphasizes the complex regulatory mechanisms involved in the cold stress response in oilseed rape. Furthermore, these data suggest that lipid, ABA, secondary metabolism, signal transduction and transcription factors may play distinct roles in the spring and winter ecotypes in response to cold stress. Differences in gene expression and metabolite levels after cold stress treatment may have contributed to the cold tolerance of the different oilseed ecotypes.

scholarly journals Genome-wide identification and comparative analysis of Dof gene family in Brassica napus

2020 ◽  
Author(s):  
Neeta Lohani ◽  
Saeid Babaei ◽  
Mohan B. Singh ◽  
Prem L. Bhalla
Keyword(s):  
Abiotic Stress ◽  
Brassica Napus ◽  
Gene Family ◽  
Stress Responses ◽  
Structure Evolution ◽  
Oilseed Crop ◽  
Evolutionary Analysis ◽  
Abiotic Stress Response ◽  
Protein Motifs ◽  
Genome Wide

AbstractDOF, DNA binding with one finger proteins are plant-specific transcription factors shown to play roles in diverse plant functions. However, a—little is known about DOF protein repertoire of the allopolyploid crop, Brassica napus. Here, we report genome-wide identification and systematic analysis of the Dof transcription factor family in this important oilseed crop. We identified 117 Brassica napus Dof genes (BnaDofs). So far, this is the largest number of Dof genes reported in a single eudicot species. Based on phylogenetic analysis, BnaDofs were classified into nine groups (A, B1, B2. C1, C2.1, C2.2, C3, D1, D2). Most members belonging to a particular group displayed conserved gene structural organisation and similar protein motifs distribution. Chromosomal localisation analysis highlighted the uneven distribution of BnaDofs across all chromosomes. Evolutionary analysis exemplified that the divergence of Brassica genus from Arabidopsis, the whole genome triplication event, and the hybridisation of B. oleracea and B. rapa to form B. napus, followed by gene loss and rearrangements, led to the expansion and divergence of Dof TF gene family in B. napus. Functional annotation of BnaDof proteins, cis-element analysis of their promoters suggested potential roles in organ development, the transition from vegetative to the reproductive stage, light responsiveness, phytohormone responsiveness as well as abiotic stress responses. Furthermore, the transcriptomic analysis highlighted the preferential tissue-specific expression patters of BnaDofs and their role in response to various abiotic stress. Overall, this study provides a comprehensive understanding of the molecular structure, evolution, and potential functional roles of Dof genes in plant development and abiotic stress response.

scholarly journals SiFBA5, a cold-responsive factor from Saussurea involucrate promotes cold resilience and biomass increase in transgenic tomato plants under cold stress

2020 ◽  
Author(s):  
Jianqiang Mu ◽  
Yajuan Fu ◽  
Bucang Liu ◽  
Yao Zhang ◽  
Aiying Wang ◽  
...  
Keyword(s):  
Low Temperature ◽  
Cold Stress ◽  
Cold Tolerance ◽  
Stress Responses ◽  
Transgenic Tomato ◽  
Dihydroxyacetone Phosphate ◽  
Tomato Plants ◽  
Transgenic Tomato Plants ◽  
Photosynthesis Efficiency ◽  
Fructose 1,6 Bisphosphate

Abstract Background Saussurea involucrate survives in extreme arctic conditions with strong cold resistant ability. The species occurs in rocky, mountainous habitats at elevations of approximately 2400-4100m with year-round snowfall and freezing temperatures providing a magnificent model and abundant gene pool for dissecting plant stress responses. Fructose-1,6-Bisphosphate Aldolase (FBA) mediates the reverse conversion of fructose 1,6-bisphosphate (FBP) into dihydroxyacetone phosphate (DHAP) and glycerol triphosphate (GAP) during glycolysis or gluconeogenesis, which is the key enzyme in this reaction. Saussurea involucrate can survive in extremely low temperature environment, which shows that it has extremely high photosynthesis efficiency. Significantly, the underlying mechanism of its cold tolerance is yet to be unveiled. Therefore, our work aims to explore potential molecular mechanisms. Results In this study, we identified a cold-responsive gene SiFBA5 that based on a preliminary low-temperature genome-wide transcriptional profiling in S. involucrata. Expression analysis showed that cold temperature rapidly induced transcriptional expression of SiFBA5, suggesting that SiFBA5 participates in initial stress responses. Subcellular localization showed that SiFBA5 is localized to the chloroplast. We then generated transgenic tomato plants overexpressing SiFBA5 derived by a CaMV 35S promoter. Phenotypic observation suggested that the transgenic overexpress plants displayed increased cold tolerance, photosynthesis efficiency, and carbohydrate accumulation in comparison with wild-type plants. Conclusion Collectively, our results demonstrated that SiFBA5 positively regulates plant response to cold stress, making it a promising candidate for improving cold tolerance in crops.

scholarly journals CmRCC1 Gene From Pumpkin Confers Cold Tolerance in Tobacco by Modulating Root Architecture and Photosynthetic Activity

2021 ◽  
Vol 12 ◽  
Author(s):  
Mengmeng Wang ◽  
Shu Zhou ◽  
Junyang Lu ◽  
Anqi Xu ◽  
Yuan Huang ◽  
...  
Keyword(s):  
Quantum Yield ◽  
Cold Stress ◽  
Cold Tolerance ◽  
Stress Responses ◽  
Root Architecture ◽  
Lateral Roots ◽  
Root Diameter ◽  
Limiting Factor ◽  
Effective Quantum Yield ◽  
Ps Ii

Low-temperature stress is the main limiting factor of cucurbit crop cultivation as it affects crop yield and quality. The identification of genes involved in cold tolerance is a crucial aspect of pumpkin rootstock breeding. Here, we examined the function of a pumpkin Regulator of Chromosome Condensation 1 (CmRCC1) gene in the root development and cold stress responses of tobacco (Nicotiana benthamiana). CmRCC1 expression was differentially induced in pumpkin root, stem, and leaf under cold stress. Transient transformation showed that CmRCC1 is located in the nucleus. CmRCC1 overexpression in tobacco increased the gravitropic set-point angle in lateral roots, as well as root diameter and volume. The expression of auxin polar transport factors, PIN1 and PIN3, decreased and increased in CmRCC1-overexpressed plants, respectively. Yeast two-hybrid verification and luciferase complementation imaging assay showed that CmRCC1 interacts with CmLAZY1. Furthermore, the decreases in maximum quantum yield of PS II, the effective quantum yield of PS II, and electron transfer rate and the increases in quantum yield of nonregulated energy dissipation and malondialdehyde content were compromised in transgenic plants compared with wild-type plants under cold stress. The results suggest that CmRCC1 plays an important role in the regulation of root architecture and positively modulates cold tolerance.

scholarly journals Quantitative Proteomic Analysis of Castor (Ricinus communis L.) Seeds During Early Imbibition Provided Novel Insights into Cold Stress Response

2019 ◽  
Vol 20 (2) ◽  
pp. 355 ◽  
Author(s):  
Xiaoyu Wang ◽  
Min Li ◽  
Xuming Liu ◽  
Lixue Zhang ◽  
Qiong Duan ◽  
...  
Keyword(s):  
Fatty Acid ◽  
Stress Response ◽  
Cold Stress ◽  
Cold Tolerance ◽  
Stress Responses ◽  
Fatty Acid Biosynthesis ◽  
Ricinus Communis ◽  
Seedling Emergence ◽  
Proteomics Data ◽  
Castor Seeds

Early planting is one of the strategies used to increase grain yield in temperate regions. However, poor cold tolerance in castor inhibits seed germination, resulting in lower seedling emergence and biomass. Here, the elite castor variety Tongbi 5 was used to identify the differential abundance protein species (DAPS) between cold stress (4 °C) and control conditions (30 °C) imbibed seeds. As a result, 127 DAPS were identified according to isobaric tag for relative and absolute quantification (iTRAQ) strategy. These DAPS were mainly involved in carbohydrate and energy metabolism, translation and posttranslational modification, stress response, lipid transport and metabolism, and signal transduction. Enzyme-linked immunosorbent assays (ELISA) demonstrated that the quantitative proteomics data collected here were reliable. This study provided some invaluable insights into the cold stress responses of early imbibed castor seeds: (1) up-accumulation of all DAPS involved in translation might confer cold tolerance by promoting protein synthesis; (2) stress-related proteins probably protect the cell against damage caused by cold stress; (3) up-accumulation of key DAPS associated with fatty acid biosynthesis might facilitate resistance or adaptation of imbibed castor seeds to cold stress by the increased content of unsaturated fatty acid (UFA). The data has been deposited to the ProteomeXchange with identifier PXD010043.

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