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

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.

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

10.21203/rs.3.rs-41470/v1 ◽

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.

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An R2R3-MYB Transcription Factor RmMYB108 Responds to Chilling Stress of Rosa multiflora and Conferred Cold Tolerance of Arabidopsis

Frontiers in Plant Science ◽

10.3389/fpls.2021.696919 ◽

2021 ◽

Vol 12 ◽

Author(s):

Jie Dong ◽

Lei Cao ◽

Xiaoying Zhang ◽

Wuhua Zhang ◽

Tao Yang ◽

...

Keyword(s):

Low Temperature ◽

Transgenic Plants ◽

Plant Growth ◽

Cold Tolerance ◽

Temperature Stress ◽

Chilling Stress ◽

Low Temperature Stress ◽

Myb Transcription Factor ◽

Rosa Multiflora ◽

R2r3 Myb

A sudden cooling in the early spring or late autumn negatively impacts the plant growth and development. Although a number of studies have characterized the role of the transcription factors (TFs) of plant R2R3-myeloblastosis (R2R3-MYB) in response to biotic and abiotic stress, plant growth, and primary and specific metabolisms, much less is known about their role in Rosa multiflora under chilling stress. In the present study, RmMYB108, which encodes a nuclear-localized R2R3-MYB TF with a self-activation activity, was identified based on the earlier published RNA-seq data of R. multiflora plants exposed to short-term low-temperature stress and also on the results of prediction of the gene function referring Arabidopsis. The RmMYB108 gene was induced by stress due to chilling, salt, and drought and was expressed in higher levels in the roots than in the leaves. The heterologous expression of RmMYB108 in Arabidopsis thaliana significantly enhanced the tolerance of transgenic plants to freezing, water deficit, and high salinity, enabling higher survival and growth rates, earlier flowering and silique formation, and better seed quantity and quality compared with the wild-type (WT) plants. When exposed to a continuous low-temperature stress at 4°C, transgenic Arabidopsis lines–overexpressing RmMYB108 showed higher activities of superoxide dismutase and peroxidase, lower relative conductivity, and lower malondialdehyde content than the WT. Moreover, the initial fluorescence (Fo) and maximum photosynthetic efficiency of photosystem II (Fv/Fm) changed more dramatically in the WT than in transgenic plants. Furthermore, the expression levels of cold-related genes involved in the ICE1 (Inducer of CBF expression 1)-CBFs (C-repeat binding factors)-CORs (Cold regulated genes) cascade were higher in the overexpression lines than in the WT. These results suggest that RmMYB108 was positively involved in the tolerance responses when R. multiflora was exposed to challenges against cold, freeze, salt, or drought and improved the cold tolerance of transgenic Arabidopsis by reducing plant damage and promoting plant growth.

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

10.21203/rs.3.rs-737261/v1 ◽

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.

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Cold tolerance in rice plants is partially controlled by root responses

10.1101/2020.01.25.919464 ◽

2020 ◽

Author(s):

Angie Geraldine Sierra Rativa ◽

Artur Teixeira de Araújo Junior ◽

Daniele da Silva Friedrich ◽

Rodrigo Gastmann ◽

Thainá Inês Lamb ◽

...

Keyword(s):

Low Temperature ◽

Cold Tolerance ◽

Temperature Stress ◽

Cold Treatment ◽

Membrane Integrity ◽

Root Hairs ◽

Acc Oxidase ◽

Dry Weight ◽

Low Temperature Stress ◽

Cold Tolerant

AbstractRice (Oryza sativa L.) ssp. indica is the most cultivated species in the South of Brazil. However, these plants face low temperature stress from September to November, which is the period of early sowing, affecting plant development during the initial stages of growth, and reducing rice productivity. This study aimed to characterize the root response to low temperature stress during the early vegetative stage of two rice genotypes contrasting in their cold tolerance (CT, cold-tolerant; and CS, cold-sensitive). Root dry weight and length, as well as number of root hairs, were higher in CT than CS when exposed to cold treatment. Histochemical analyses indicated that roots of CS genotype present higher levels of lipid peroxidation and H2O2 accumulation, along with lower levels of plasma membrane integrity than CT under low temperature stress. RNAseq analyses revealed that the contrasting genotypes present completely different molecular responses to cold stress. The number of over-represented functional categories was lower in CT than CS under cold condition, suggesting that CS genotype is more impacted by low temperature stress than CT. Several genes might contribute to rice cold tolerance, including the ones related with cell wall remodeling, cytoskeleton and growth, signaling, antioxidant system, lipid metabolism, and stress response. On the other hand, high expression of the genes SRC2 (defense), root architecture associated 1 (growth), ACC oxidase, ethylene-responsive transcription factor, and cytokinin-O-glucosyltransferase 2 (hormone-related) seems to be related with cold sensibility. Since these two genotypes have a similar genetic background (sister lines), the differentially expressed genes found here can be considered candidate genes for cold tolerance and could be used in future biotechnological approaches aiming to increase rice tolerance to low temperature.

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Near-Isogenic Lines of Japonica Rice Revealed New QTLs for Cold Tolerance at Booting Stage

Agronomy ◽

10.3390/agronomy9010040 ◽

2019 ◽

Vol 9 (1) ◽

pp. 40 ◽

Cited By ~ 1

Author(s):

Zhenghai Sun ◽

Juan Du ◽

Xiaoying Pu ◽

Muhammad Kazim Ali ◽

Xiaomeng Yang ◽

...

Keyword(s):

Low Temperature ◽

Cold Tolerance ◽

Temperature Stress ◽

Mixed Linear Model ◽

Low Temperature Stress ◽

Japonica Rice ◽

Near Isogenic Lines ◽

Booting Stage ◽

Isogenic Lines ◽

Cold Tolerant

Low temperature stress severely hampers rice productivity, and hence elaborating chilling-mediated physiochemical alterations and unravelling cold tolerance pathways will facilitate cold resilient rice breeding. Various cold tolerant Near-isogenic lines (NILs) selected at the booting stage through backcrossing of a japonica landrace Lijing2 (cold tolerant) with cold sensitive Towada (a japonica cultivar). The cold tolerance attributes of NILs was validated over two years by evaluating the spikelet fertility followed by correlation of nineteen morphological traits with the rate of seed setting (RSS). Results revealed BG, FG, 1-2IL, RSLL, and UIL were significantly correlated with RSS and had nearer marker interval distance with cold tolerance in QTL analysis. Two QTLs, qCTB-7-a and qCTB-7-b, were found for RSS based on a mixed linear model. Alleles of two QTLs were contributed by Lijing2 and genetic distances between the peaks were 0.00 and 0.06cM, which explained 5.70% and 8.36% variation, respectively, One QTL for 1-2IL, RSLL, and ILBS, while two QTLs for FG, BG, and UIL were also identified. These findings can be exploited to engineer low temperature stress tolerant rice in times of climate change.

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

The Scientific World JOURNAL ◽

10.1155/2013/658793 ◽

2013 ◽

Vol 2013 ◽

pp. 1-7 ◽

Cited By ~ 18

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.

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

Frontiers in Plant Science ◽

10.3389/fpls.2021.795834 ◽

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.

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