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

Agronomy ◽  
2019 ◽  
Vol 9 (1) ◽  
pp. 40 ◽  
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.

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 Detection of QTLs for cold tolerance at the booting stage in near-isogenic lines derived from rice landrace Lijiangxintuanheigu

2018 ◽  
Vol 54 (No. 3) ◽  
pp. 93-100
Author(s):  
Yang Shu Ming ◽  
Zhang Su Hua ◽  
Yang Tao ◽  
Wang Li
Keyword(s):  
Cold Tolerance ◽  
Interval Mapping ◽  
Near Isogenic Lines ◽  
Booting Stage ◽  
Isogenic Lines ◽  
Cold Tolerant ◽  
Cold Sensitive ◽  
Inclusive Composite Interval Mapping ◽  
Rice Landrace ◽  
Best Linear Unbiased

Chilling damage significantly reduces grain yield in rice, while exploring major quantitative trait loci (QTLs) has the potential to improve rice production. Mapping of QTLs for 5 cold tolerance-related traits at the booting stage was conducted with SSR markers and inclusive composite interval mapping (ICIM) approach, based on 105 near-isogenic lines derived from a backcross between Lijiangxintuanheigu (LTH, cold-tolerant landrace) and Towada (cold-sensitive cultivar). Phenotype values were investigated under five cold-stress environments and analysed by the best linear unbiased prediction (BLUP). Twenty-one QTLs were identified on chromosomes 1, 2, 3, 4, 6, 7, 10 and 11, and the amount of variation (R<sup>2</sup>) explained by each QTL ranged from 7.71 to 29.66%, with five co-located QTL regions. Eight novel major loci (qSF-2, qSF-6a, qSF-7, qGW-6, qDGWP-4, qDSWPP-4, qDWPP-1 and qDWPP-4b) were detected in several environments and BLUP, and their alleles were contributed by LTH with R<sup>2 </sup>variance from 12.24 to 29.66%. These favourable QTLs would facilitate elucidation of the genetic mechanism of cold tolerance and provide strategies for breeding high-productive rice.    

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.

scholarly journals Cold tolerance in rice plants is partially controlled by root responses

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.

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

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.

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 Hormone Profiles and Antioxidant Activity of Cultivated and Wild Tomato Seedlings under Low-Temperature Stress

Agronomy ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 1146
Author(s):  
Parviz Heidari ◽  
Mohammad Reza Amerian ◽  
Gianni Barcaccia
Keyword(s):  
Oxidative Stress ◽  
Antioxidant Activity ◽  
Low Temperature ◽  
Temperature Stress ◽  
Expression Patterns ◽  
Low Temperature Stress ◽  
Ros Scavenging ◽  
Tomato Species ◽  
Tolerant Species ◽  
Cold Tolerant

Low temperature is a major limiting factor for the growth and reproduction of some plant species, such as tomato. So far, few studies have been conducted on the effects of low temperature, and the mechanisms of plants’ response to this type of stress is not fully clear. In the current study, the effects of low, nonfreezing temperature (10 °C for three days) on the hormone content, antioxidant activity, and expression patterns of cold-related genes in the leaves of cold-tolerant species (Solanum habrochaites Accession ‘LA1777′) and cold-susceptible species (Solanum lycopersicum cultivar ‘Moneymaker’) were investigated. Low temperature increased the abscisic acid (ABA) content in both tomato species, while the content of zeatin-type cytokinins (ZT) increased in the cold-tolerant species. However, the content of indole-3-acetic acid (IAA) and gibberellic acid (GA) reduced in response to low temperature in susceptible species. Accordingly, cytokinin (CK) is identified as an important hormone associated with low-temperature stress in tomato. In addition, our results indicate that the C-repeat/DRE binding factor 1 (CBF1) gene is less induced in response to low temperature in tomato, although transcription of the inducer of CBF expression 1 (ICE1) gene was upregulated under low temperature in both tomato species. It seems that ICE1 may modulate cold-regulated (COR) genes in a CBF-independent way. In addition, in response to low temperature, the malondialdehyde (MDA) level and membrane stability index (MSI) increased in the susceptible species, indicating that low temperature induces oxidative stress. Additionally, we found that glutathione peroxidase is highly involved in reactive oxygen species (ROS) scavenging induced by low temperature, and antioxidants are more induced in tolerant species. Overall, our results suggest that sub-optimal temperatures promote oxidative stress in tomato and CK is introduced as a factor related to the response to low temperature that requires deeper attention in future breeding programs of tomato.

scholarly journals Exogenous EBR Ameliorates Endogenous Hormone Contents in Tomato Species under Low-Temperature Stress

Horticulturae ◽  
2021 ◽  
Vol 7 (4) ◽  
pp. 84
Author(s):  
Parviz Heidari ◽  
Mahdi Entazari ◽  
Amin Ebrahimi ◽  
Mostafa Ahmadizadeh ◽  
Alessandro Vannozzi ◽  
...  
Keyword(s):  
Low Temperature ◽  
Temperature Stress ◽  
Low Temperatures ◽  
Low Temperature Stress ◽  
Sensitive Species ◽  
Tomato Species ◽  
Tolerant Species ◽  
Cold Tolerant ◽  
Cold Sensitive ◽  
Stress Dependent

Low-temperature stress is a type of abiotic stress that limits plant growth and production in both subtropical and tropical climate conditions. In the current study, the effects of 24-epi-brassinolide (EBR) as analogs of brassinosteroids (BRs) were investigated, in terms of hormone content, antioxidant enzyme activity, and transcription of several cold-responsive genes, under low-temperature stress (9 °C) in two different tomato species (cold-sensitive and cold-tolerant species). Results indicated that the treatment with exogenous EBR increases the content of gibberellic acid (GA3) and indole-3-acetic acid (IAA), whose accumulation is reduced by low temperatures in cold-sensitive species. Furthermore, the combination or contribution of BR and abscisic acid (ABA) as a synergetic interaction was recognized between BR and ABA in response to low temperatures. The content of malondialdehyde (MDA) and proline was significantly increased in both species, in response to low-temperature stress; however, EBR treatment did not affect the MDA and proline content. Moreover, in the present study, the effect of EBR application was different in the tomato species under low-temperature stress, which increased the catalase (CAT) activity in the cold-tolerant species and increased the glutathione peroxidase (GPX) activity in the cold-sensitive species. Furthermore, expression levels of cold-responsive genes were influenced by low-temperature stress and EBR treatment. Overall, our findings revealed that a low temperature causes oxidative stress while EBR treatment may decrease the reactive oxygen species (ROS) damage into increasing antioxidant enzymes, and improve the growth rate of the tomato by affecting auxin and gibberellin content. This study provides insight into the mechanism by which BRs regulate stress-dependent processes in tomatoes, and provides a theoretical basis for promoting cold resistance of the tomato.

scholarly journals Responses of Grain Yield and Yield Related Parameters to Post-Heading Low-Temperature Stress in Japonica Rice

Plants ◽  
2021 ◽  
Vol 10 (7) ◽  
pp. 1425
Author(s):  
Iftikhar Ali ◽  
Liang Tang ◽  
Junjie Dai ◽  
Min Kang ◽  
Aqib Mahmood ◽  
...  
Keyword(s):  
Low Temperature ◽  
Grain Yield ◽  
Temperature Stress ◽  
Grain Filling ◽  
Low Temperature Stress ◽  
Maximum Temperature ◽  
Surface Model ◽  
Japonica Rice ◽  
Rice Productivity ◽  
Grain Filling Duration

There is unprecedented increase in low-temperature stress (LTS) during post-heading stages in rice as a consequence of the recent climate changes. Quantifying the effect of LTS on yields is key to unraveling the impact of climatic changes on crop production, and therefore developing corresponding mitigation strategies. The present research was conducted to analyze and quantify the effect of post-heading LTS on rice yields as well as yield and grain filling related parameters. A two-year experiment was conducted during rice growing season of 2018 and 2019 using two Japonica cultivars (Huaidao 5 and Nanjing 46) with different low-temperature sensitivities, at four daily minimum/maximum temperature regimes of 21/27 °C (T1), 17/23 °C (T2), 13/19 °C (T3) and 9/15 °C (T4). These temperature treatments were performed for 3 (D1), 6 (D2) or 9 days (D3), at both flowering and grain filling stages. We found LTS for 3 days had no significant effect on grain yield, even when the daily mean temperature was as low as 12 °C. However, LTS of between 6 and 9 days at flowering but not at filling stage significantly reduced grain yield of both cultivars. Comparatively, Huaidao 5 was more cold tolerant than Nanjing 46. LTS at flowering and grain filling stages significantly reduced both maximum and mean grain filling rates. Moreover, LTS prolonged the grain filling duration of both cultivars. Additionally, there was a strong correlation between yield loss and spikelet fertility, spikelet weight at maturity, grain filling duration as well as mean and maximum grain filling rates under post-heading LTS (p < 0.001). Moreover, the effect of post-heading LTS on rice yield can be well quantified by integrating the canopy temperature (CT) based accumulated cold degree days (ACDDCT) with the response surface model. The findings of this research are useful in modeling rice productivity under LTS and for predicting rice productivity under future climates.

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