scholarly journals RNA N6-Methyladenosine Responds to Low-Temperature Stress in Tomato Anthers

2021 ◽  
Vol 12 ◽  
Author(s):  
Dandan Yang ◽  
Huachao Xu ◽  
Yue Liu ◽  
Mengzhuo Li ◽  
Muhammad Ali ◽  
...  
Keyword(s):  
Low Temperature ◽  
Cold Stress ◽  
Temperature Stress ◽  
Pollen Development ◽  
Adenosine Triphosphatase ◽  
Gene Expression Regulation ◽  
Anther Development ◽  
Low Temperature Stress ◽  
Atp Binding ◽  
Pollen Abortion

Cold stress is a serious threat to subtropical crop pollen development and induces yield decline. N6-methyladenosine (m6A) is the most frequent mRNA modification and plays multiple physiological functions in plant development. However, whether m6A regulates pollen development is unclear, and its putative role in cold stress response remains unknown. Here, we observed that moderate low-temperature (MLT) stress induced pollen abortion in tomato. This phenotype was caused by disruption of tapetum development and pollen exine formation, accompanied by reduced m6A levels in tomato anther. Analysis of m6A-seq data revealed 1,805 transcripts displayed reduced m6A levels and 978 transcripts showed elevated m6A levels in MLT-stressed anthers compared with those in anthers under normal temperature. These differentially m6A enriched transcripts under MLT stress were mainly related to lipid metabolism, adenosine triphosphatase (ATPase) activity, and ATP-binding pathways. An ATP-binding transcript, SlABCG31, had significantly upregulated m6A modification levels, which was inversely correlated to the dramatically downregulated expression level. These changes correlated with higher abscisic acid (ABA) levels in anthers and disrupted pollen wall formation under low-temperature stress. Our findings characterized m6A as a novel layer of complexity in gene expression regulation and established a molecular link between m6A methylation and tomato anther development under low-temperature conditions.

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 Membrane Lipids’ Metabolism and Transcriptional Regulation in Maize Roots Under Cold Stress

2021 ◽  
Vol 12 ◽  
Author(s):  
Xunchao Zhao ◽  
Yulei Wei ◽  
Jinjie Zhang ◽  
Li Yang ◽  
Xinyu Liu ◽  
...  
Keyword(s):  
Lipid Metabolism ◽  
Low Temperature ◽  
Cold Stress ◽  
Temperature Stress ◽  
Membrane Lipids ◽  
Membrane Lipid ◽  
Metabolic Changes ◽  
Low Temperature Stress ◽  
Maize Seedlings ◽  
Maize Roots

Low temperature is one of the major abiotic stresses that restrict the growth and development of maize seedlings. Membrane lipid metabolism and remodeling are key strategies for plants to cope with temperature stresses. In this study, an integrated lipidomic and transcriptomic analysis was performed to explore the metabolic changes of membrane lipids in the roots of maize seedlings under cold stress (5°C). The results revealed that major extraplastidic phospholipids [phosphatidylcholine (PC), phosphatidylethanolamine (PE), phosphatidic acid (PA), and phosphatidylinositol (PI)] were dominant membrane lipids in maize root tissues, accounting for more than 70% of the total lipids. In the transcriptome data of maize roots under cold stress, a total of 189 lipid-related differentially expressed genes (DEGs) were annotated and classified into various lipid metabolism pathways, and most of the DEGs were enriched in the “Eukaryotic phospholipid synthesis” (12%), “Fatty acid elongation” (12%), and “Phospholipid signaling” (13%) pathways. Under low temperature stress, the molar percentage of the most abundant phospholipid PC decreased around 10%. The significantly up-regulated expression of genes encoding phospholipase [phospholipase D (PLD)] and phosphatase PAP/LPP genes implied that PC turnover was triggered by cold stress mainly via the PLD pathway. Consequently, as the central product of PC turnover, the level of PA increased drastically (63.2%) compared with the control. The gene-metabolite network and co-expression network were constructed with the prominent lipid-related DEGs to illustrate the modular regulation of metabolic changes of membrane lipids. This study will help to explicate membrane lipid remodeling and the molecular regulation mechanism in field crops encountering low temperature stress.

scholarly journals Antioxidant Defense, Chlorophyll Fluorescence and VvCBF4-VvNAC1 Genes Expression in Grapevine Cultivars (Vitis Vinifera L.) in Response to Cold Stress

2021 ◽  
Author(s):  
M. A. Aazami ◽  
M. Asghari Aruq ◽  
M. B. Hassanpouraghdam
Keyword(s):  
Chlorophyll Fluorescence ◽  
Low Temperature ◽  
Cold Stress ◽  
Temperature Stress ◽  
Low Temperature Stress ◽  
Vitis Vinifera L ◽  
Agricultural Industry ◽  
Genes Expression ◽  
Significant Damage ◽  
Photochemical Quantum Yield

Abstract Background: Cold stress is one of the limitative factors of different species of crops on the planet, causing significant damage to the Iranian agricultural industry every year. Grapes are the product of temperate warm zones and sensitive to early autumn cold and spring cold. The current study the effects of cold stress (+1 °C for 4, 8, and 16 hours) on three grapevine cultivars (Ghiziluzum, Khalili, and Perllete) were investigated. Results: The results showed that cold stress caused significant changes in the antioxidant and biochemicals content in the studied cultivars. Furthermore, examining the chlorophyll fluorescence indices, cold stress caused a significant increase in minimal fluorescence (F0), a decrease in maximal fluorescence (Fm), and the maximum photochemical quantum yield of photosystem II (Fv/Fm) in all cultivars. According to the obtained results, among the three studied cultivars, ‘Perllete’ with the highest increase in proline content and the activity of antioxidant enzymes and also, having the lowest accumulation of malondialdehyde, hydrogen peroxide, electrolyte leakage, and F0 as well as less decrease in Fm and Fv/Fm had the higher tolerance to the cold stress than ‘Ghiziluzum’ and ‘Khalili’ cultivars. VvCBF4 and VvNAC1 genes expression was increased in all three cultivars at +1 °C at 8 hours and then decreased. The increase in VvCBF4 and VvNAC1 genes expression in ‘Perllete’ cultivar was higher than the other two cultivars. Conclusion: ‘Perllete’ and ‘Ghiziluzum’ showed the highest tolerance to low temperature stress, respectively. ‘Khalili’ was sensitive to low temperature stress.

scholarly journals The Methylation Patterns and Transcriptional Responses to Chilling Stress at the Seedling Stage in Rice

2019 ◽  
Vol 20 (20) ◽  
pp. 5089 ◽  
Author(s):  
Hui Guo ◽  
Tingkai Wu ◽  
Shuxing Li ◽  
Qiang He ◽  
Zhanlie Yang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Low Temperature ◽  
Cold Stress ◽  
Cold Tolerance ◽  
Temperature Stress ◽  
Chilling Stress ◽  
Low Temperature Stress ◽  
Expression Level ◽  
Altered Expression ◽  
Cold Tolerant

Chilling stress is considered the major abiotic stress affecting the growth, development, and yield of rice. To understand the transcriptomic responses and methylation regulation of rice in response to chilling stress, we analyzed a cold-tolerant variety of rice (Oryza sativa L. cv. P427). The physiological properties, transcriptome, and methylation of cold-tolerant P427 seedlings under low-temperature stress (2–3 °C) were investigated. We found that P427 exhibited enhanced tolerance to low temperature, likely via increasing antioxidant enzyme activity and promoting the accumulation of abscisic acid (ABA). The Methylated DNA Immunoprecipitation Sequencing (MeDIP-seq) data showed that the number of methylation-altered genes was highest in P427 (5496) and slightly lower in Nipponbare (Nip) and 9311 (4528 and 3341, respectively), and only 2.7% (292) of methylation genes were detected as common differentially methylated genes (DMGs) related to cold tolerance in the three varieties. Transcriptome analyses revealed that 1654 genes had specifically altered expression in P427 under cold stress. These genes mainly belonged to transcription factor families, such as Myeloblastosis (MYB), APETALA2/ethylene-responsive element binding proteins (AP2-EREBP), NAM-ATAF-CUC (NAC) and WRKY. Fifty-one genes showed simultaneous methylation and expression level changes. Quantitative RT-PCR (qRT-PCR) results showed that genes involved in the ICE (inducer of CBF expression)-CBF (C-repeat binding factor)—COR (cold-regulated) pathway were highly expressed under cold stress, including the WRKY genes. The homologous gene Os03g0610900 of the open stomatal 1 (OST1) in rice was obtained by evolutionary tree analysis. Methylation in Os03g0610900 gene promoter region decreased, and the expression level of Os03g0610900 increased, suggesting that cold stress may lead to demethylation and increased gene expression of Os03g0610900. The ICE-CBF-COR pathway plays a vital role in the cold tolerance of the rice cultivar P427. Overall, this study demonstrates the differences in methylation and gene expression levels of P427 in response to low-temperature stress, providing a foundation for further investigations of the relationship between environmental stress, DNA methylation, and gene expression in rice.

Gene-Coexpression Network Analysis Identifies Specific Modules and Hub Genes Related to Cold Stress in Rice

2021 ◽  
Author(s):  
Zhichi Zeng ◽  
Sichen Zhang ◽  
Wenyan Li ◽  
Baoshan Chen ◽  
Wenlan Li
Keyword(s):  
Network Analysis ◽  
Low Temperature ◽  
Cold Stress ◽  
Cold Tolerance ◽  
Temperature Stress ◽  
Low Temperature Stress ◽  
Rice Cultivars ◽  
Hub Genes ◽  
New Genes ◽  
Short Period

Abstract Background: When plants are subjected to cold stress, they undergo a series of molecular and physiological changes to protect themselves from injury. Indica cultivars can usually withstand only mild cold stress in a relatively short period. Hormone-mediated defence response plays an important role in cold stress. Weighted gene co-expression network analysis (WGCNA) is a very useful tool for studying the correlation between genes, identifying modules with high phenotype correlation, and identifying Hub genes in different modules. Many studies have elucidated the molecular mechanisms of cold tolerance in different plants, but little information about the recovery process after cold stress is available.Results: To understand the molecular mechanism of cold tolerance in rice, we performed comprehensive transcriptome analyses during cold treatment and recovery stage in two cultivars of near-isogenic lines (9311 and DC907). Twelve transcriptomes in two rice cultivars were determined. A total of 2509 new genes were predicted by fragment splicing and assembly, and 7506 differentially expressed genes were identified by pairwise comparison. A total of 26 modules were obtained by expression-network analysis, 12 of which were highly correlated with cold stress or recovery treatment. We further identified candidate Hub genes associated with specific modules and analysed their regulatory relationships based on coexpression data. Results showed that various plant-hormone regulatory genes acted together to protect plants from physiological damage under short-term low-temperature stress. We speculated that this may be common in rice. Under long-term cold stress, rice improved the tolerance to low-temperature stress by promoting autophagy, sugar synthesis, and metabolism.Conclusion: Through WGCNA analysis at the transcriptome level, we provided a potential regulatory mechanism for the cold stress and recovery of rice cultivars and identified candidate central genes. Our findings provided an important reference for the future cultivation of rice strains with good tolerance.

scholarly journals Low Temperature Stress Mediates the Antioxidants Pool and Chlorophyll Fluorescence in Vitis vinifera L. Cultivars

Plants ◽  
2021 ◽  
Vol 10 (9) ◽  
pp. 1877
Author(s):  
Mohammad A. Aazami ◽  
Majid Asghari-Aruq ◽  
Mohammad B. Hassanpouraghdam ◽  
Sezai Ercisli ◽  
Mojmir Baron ◽  
...  
Keyword(s):  
Chlorophyll Fluorescence ◽  
Low Temperature ◽  
Cold Stress ◽  
Temperature Stress ◽  
Early Spring ◽  
Low Temperature Stress ◽  
Rapid Screening ◽  
Vitis Vinifera L ◽  
Temperature Damage ◽  
Photochemical Quantum Yield

Grapes are sensitive to early autumn and spring low temperature damage. The current study aimed to assay the effects of cold stress (+1 °C for 4, 8, and 16 h) on three grapevine cultivars (Ghiziluzum, Khalili, and Perllete). The results showed that cold stress caused significant changes in the antioxidant and biochemicals content in the studied cultivars. Furthermore, examining the chlorophyll fluorescence indices, cold stress caused a significant increase in minimal fluorescence (F0), a decrease in maximal fluorescence (Fm), and the maximum photochemical quantum yield of photosystem II (Fv/Fm) in all cultivars. Among the studied cultivars, ‘Perllete’ had the highest increase in proline content and activity of antioxidant enzymes and also had the lowest accumulation of malondialdehyde, hydrogen peroxide, electrolyte leakage, and F0, as well as less of a decrease in Fm and Fv/Fm, and had a higher tolerance to cold stress than ‘Ghiziluzum’ and ‘Khalili’. ‘Perllete’ and ‘Ghiziluzum’ showed reasonable tolerance to the low temperature stress. ‘Khalili’ was sensitive to the stress. The rapid screening of grapevine cultivars in early spring low temperatures is applicable with the assaying of some biomolecules and chlorophyll fluorescence.

scholarly journals The Low Temperature Induced Physiological Responses ofAvena nudaL., a Cold-Tolerant Plant Species

2013 ◽  
Vol 2013 ◽  
pp. 1-7 ◽  
Author(s):  
Wenying Liu ◽  
Kenming Yu ◽  
Tengfei He ◽  
Feifei Li ◽  
Dongxu Zhang ◽  
...  
Keyword(s):  
Low Temperature ◽  
Cold Stress ◽  
Chlorophyll Content ◽  
Temperature Stress ◽  
Physiological Mechanism ◽  
Low Temperature Stress ◽  
Cold Tolerant ◽  
Avena Nuda ◽  
Mda Content ◽  
Naked Oats

The paperaim of the was to study the effect of low temperature stress onAvena nudaL. seedlings. Cold stress leads to many changes of physiological indices, such as membrane permeability, free proline content, malondialdehyde (MDA) content, and chlorophyll content. Cold stress also leads to changes of some protected enzymes such as peroxidase (POD), superoxide dismutase (SOD), and catalase (CAT). We have measured and compared these indices of seedling leaves under low temperature and normal temperature. The proline and MDA contents were increased compared with control; the chlorophyll content gradually decreased with the prolongation of low temperature stress. The activities of SOD, POD, and CAT were increased under low temperature. The study was designated to explore the physiological mechanism of cold tolerance in naked oats for the first time and also provided theoretical basis for cultivation and antibiotic breeding inAvena nudaL.

scholarly journals Integrated Isoform Sequencing and Dynamic Transcriptome Analysis Reveals Diverse Transcripts Responsible for Low Temperature Stress at Anther Meiosis Stage in Rice

2021 ◽  
Vol 12 ◽  
Author(s):  
Zhaojun Qu ◽  
Yan Jia ◽  
Yuyang Duan ◽  
Hongyang Chen ◽  
Xinpeng Wang ◽  
...  
Keyword(s):  
Low Temperature ◽  
Cold Stress ◽  
Cold Tolerance ◽  
Temperature Stress ◽  
Expression Profiles ◽  
Pollen Viability ◽  
Enrichment Analysis ◽  
Pollen Sterility ◽  
Low Temperature Stress ◽  
Amino Acid Contents

Low temperatures stress is one of the important factors limiting rice yield, especially during rice anther development, and can cause pollen sterility and decrease grain yield. In our study, low-temperature stress decreased pollen viability and spikelet fertility by affecting the sugar, nitrogen and amino acid contents of anthers. We performed RNA-seq and ISO-seq experiments to study the genome-wide transcript expression profiles in low-temperature anthers. A total of 4,859 differentially expressed transcripts were detected between the low-temperature and control groups. Gene ontology enrichment analysis revealed significant terms related to cold tolerance. Hexokinase and glutamate decarboxylase participating in starch and sucrose metabolism may play important roles in the response to cold stress. Using weighted gene co-expression network analysis, nine hub transcripts were found that could improve cold tolerance throughout the meiosis period of rice: Os02t0219000-01 (interferon-related developmental regulator protein), Os01t0218350-00 (tetratricopeptide repeat-containing thioredoxin), Os08t0197700-00 (luminal-binding protein 5), Os11t0200000-01 (histone deacetylase 19), Os03t0758700-01 (WD40 repeat domain-containing protein), Os06t0220500-01 (7-deoxyloganetin glucosyltransferase), Pacbio.T01382 (sucrose synthase 1), Os01t0172400-01 (phospholipase D alpha 1), and Os01t0261200-01 (NAC domain-containing protein 74). In the PPI network, the protein minichromosome maintenance 4 (MCM4) may play an important role in DNA replication induced by cold stress.

scholarly journals Physiological Attributes and Transcriptomics Analysis Reveal the Response Mechanism of Helictotrichon Virescens to Low-Temperature Stress

2021 ◽  
Author(s):  
Mingjun Cheng ◽  
Mingmin Zheng ◽  
Kuoshu Cui ◽  
Ruizhen Zhang ◽  
Tao Yang ◽  
...  
Keyword(s):  
Low Temperature ◽  
Cold Stress ◽  
Temperature Stress ◽  
Leaf Tissue ◽  
Low Temperature Stress ◽  
Tibet Plateau ◽  
Perennial Herb ◽  
Optical Antenna ◽  
Response Mechanism ◽  
Antenna Complex

Abstract Background: Helictotrichon Virescens is a perennial herb mainly distributed in high altitude areas of 2000 ~ 4500 m. It is widely cultivated in the Qinghai-Tibet Plateau of China, strongly resistant to cold, and an essential part of wild herbage in this region. However, the molecular mechanism of Helictotrichon virescens response to low-temperature stress is unclear, and the key regulating genes to specific biological processes are poorly known. Results: It was used physiological and transcriptome analysis to study the cold stress response mechanism in Helictotrichon Virescens. Under low-temperature treatment at 0℃, the leaves reduced chlorophyll content and light energy absorption through light antenna complex (LHCs). As the content of chlorophyll, a and b decreased, as evident were the photoprotection effects. Besides, circadian pathway-plant is crucial for the response to cold stress in Helictotrichon Virescens. Among them, DEG encoding LHY and HY5 showed strongly up-regulated expression during cold stress in Helictotrichon Virescens. Conclusions: This study provides an opportunity to fully understand the response process of Helictotrichon Virescens to low-temperature stress. It answers the pertinent questions in perennial herbaceous cold stress research, how leaves integrate light and low-temperature signals to regulate circadian rhythms in crops, and how leaf tissue reduces light absorption and enhances light protection through optical antenna complex (LHCs).

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