scholarly journals Comparative Transcriptome-Based Mining and Expression Profiling of Transcription Factors Related to Cold Tolerance in Peanut

2020 ◽  
Vol 21 (6) ◽  
pp. 1921 ◽  
Author(s):  
Chunji Jiang ◽  
He Zhang ◽  
Jingyao Ren ◽  
Jiale Dong ◽  
Xinhua Zhao ◽  
...  
Keyword(s):  
Cold Stress ◽  
Cold Tolerance ◽  
Expression Profiling ◽  
Gene Networks ◽  
Functional Enrichment ◽  
Differentially Expressed ◽  
Regulation Of Transcription ◽  
Evolutionary Analysis ◽  
Comparative Transcriptome ◽  
Cold Tolerant

Plants tolerate cold stress by regulating gene networks controlling cellular and physiological traits to modify growth and development. Transcription factor (TF)-directed regulation of transcription within these gene networks is key to eliciting appropriate responses. Identifying TFs related to cold tolerance contributes to cold-tolerant crop breeding. In this study, a comparative transcriptome analysis was carried out to investigate global gene expression of entire TFs in two peanut varieties with different cold-tolerant abilities. A total of 87 TF families including 2328 TF genes were identified. Among them, 445 TF genes were significantly differentially expressed in two peanut varieties under cold stress. The TF families represented by the largest numbers of differentially expressed members were bHLH (basic helix—loop—helix protein), C2H2 (Cys2/His2 zinc finger protein), ERF (ethylene-responsive factor), MYB (v-myb avian myeloblastosis viral oncogene homolog), NAC (NAM, ATAF1/2, CUC2) and WRKY TFs. Phylogenetic evolutionary analysis, temporal expression profiling, protein–protein interaction (PPI) network, and functional enrichment of differentially expressed TFs revealed the importance of plant hormone signal transduction and plant-pathogen interaction pathways and their possible mechanism in peanut cold tolerance. This study contributes to a better understanding of the complex mechanism of TFs in response to cold stress in peanut and provides valuable resources for the investigation of evolutionary history and biological functions of peanut TFs genes involved in cold tolerance.

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 Transcriptome sequencing and iTRAQ of different rice cultivars provide insight into molecular mechanisms of cold-tolerance response in japonica rice

2020 ◽  
Author(s):  
Yan Jia ◽  
Hualong Liu ◽  
Zhaojun Qu ◽  
Jin Wang ◽  
Xinpeng Wang ◽  
...  
Keyword(s):  
Cold Stress ◽  
Cold Tolerance ◽  
Nitrogen Metabolism ◽  
N Uptake ◽  
Differentially Expressed ◽  
Japonica Rice ◽  
Rice Cultivars ◽  
Gene And Protein Expression ◽  
Cold Tolerant ◽  
Cold Sensitive

Abstract Background: Rice ( Oryza sativa L.), one of the most important crops cultivated in both tropical and temperate regions, has a high sensitivity to cold stress. Chilling stress limits N uptake and nitrogen metabolism in rice. To identify the genes and pathways involved in cold tolerance, specifically within the nitrogen metabolism pathway, we compared gene and protein expression differences between a cold-tolerant cultivar, Dongnong428 (DN), and a cold-sensitive cultivar, Songjing10 (SJ). Results: Using isobaric tags for relative or absolute quantification (iTRAQ) with high-throughput mRNA sequencing (RNA-seq) techniques, we identified 5,549 genes and 450 proteins in DN and 6,145 genes and 790 proteins in SJ, that were differentially expressed during low water temperature (T w ) treatment. There were 354 transcription factor (TF) genes (212 down, 142 up), and 366 TF genes (220 down, 146 up), including 47 gene families, differentially expressed in the DN under control (CKDN) vs. DN under low-T w (D15DN) and CKSJ vs. D15SJ, respectively. Genes related to rice cold-related biosynthesis pathways, particularly the mitogen-activated protein kinase (MAPK) signaling pathway, zeatin biosynthesis, and plant hormone signal transduction pathways, were significantly differentially expressed in both rice cultivars. Differentially expressed proteins (DEPs) related to rice cold-related biosynthesis pathways and particularly glutathione metabolism were significantly differentially expressed in both rice cultivars. Transcriptome and proteome analysis of the nitrogen metabolism pathways showed that major genes and proteins that participated in γ-aminobutyric acid (GABA) and glutamine synthesis were downregulated. Conclusion: Under cold stress conditions during reproductive growth, genes and proteins related to the biosynthesis pathways of cold stress were significantly differentially expressed in DN and SJ. The present study confirmed the known cold stress-associated genes and identified a number of putative new cold-responsive genes. We also found that translational regulation under cold stress plays an important role in cold-tolerant DN. Low-T w treatments affected N uptake and N metabolism in rice, and promoted Glu metabolism, and the synthesis of ornithine and proline in cold-sensitive SJ.

scholarly journals Rootstock-Mediated Transcriptional Changes Associated with Cold Tolerance in Prunus mume Leaves

Horticulturae ◽  
2021 ◽  
Vol 7 (12) ◽  
pp. 572
Author(s):  
Faisal Hayat ◽  
Chengdong Ma ◽  
Shahid Iqbal ◽  
Xiao Huang ◽  
Ouma Kenneth Omondi ◽  
...  
Keyword(s):  
Oxidative Damage ◽  
Cold Stress ◽  
Cold Tolerance ◽  
Molecular Mechanisms ◽  
Mapk Signaling ◽  
Differentially Expressed ◽  
Prunus Mume ◽  
Japanese Apricot ◽  
Cold Tolerant ◽  
Cold Sensitive

Japanese apricot (Prunus mume) is remarkably valuable for its high ornamental and economic importance due to its distinctive features. Low temperature is a serious environmental constraint for this species, restricting its cultivation and dispersal in the north of China. To address this issue, breeding requires an understanding of the molecular mechanisms underlying responses to cold stress. We examined the leaf physiological and transcriptome profile by RNA sequencing in ‘Bungo’ scion cultivar grafted onto Prunus mume (cold-sensitive) and Prunus armeniaca (cold-tolerant) rootstocks at 4 °C for 0, 6, and 24 h. Our results revealed that the increased MDA concentration in the leaves of P. mume cultivar (cold-sensitive) suggests that cold stress might cause oxidative damage and increased sensitivity. Moreover, the cold-tolerant cultivar (P. armeniaca) considerably enhances the enzyme activities (i.e., SOD, POD, and CAT), as well as osmo-protectants (soluble sugars and proline) compared with sensitive cultivar, which helps plants to withstand oxidative damage caused by cold stress. Additionally, differentially expressed genes were shown to be enriched in plant hormone signal transduction, ribosome, MAPK signaling, and circadian rhythm pathway. After 24 h of cold stress, genes related to PYL4, histidine kinase 1, SAUR36, bHLH130, bHLH123, TIFY 6B-like, WRKY 40, WRKY 57, and 60S acidic ribosomal protein P1 were differentially expressed, implying that these DEGs involved in multiple pathways are involved in cold tolerance in Japanese apricot. This study improved our current understanding of the mechanism of cold tolerance in Japanese apricot, and the findings could be utilized for other related fruit species.

scholarly journals An association between the nitrogen metabolism pathway and cold tolerance in rice was identified using comparative transcriptome and proteome profiling

2020 ◽  
Author(s):  
Jia Yan ◽  
Liu Hualong ◽  
Qu Zhaojun ◽  
Wang Jin ◽  
Wang Xinpeng ◽  
...  
Keyword(s):  
Cold Stress ◽  
Cold Tolerance ◽  
Nitrogen Metabolism ◽  
N Uptake ◽  
Differentially Expressed ◽  
Rice Cultivars ◽  
Metabolism Pathway ◽  
Gene And Protein Expression ◽  
Cold Tolerant ◽  
Cold Sensitive

Abstract BackgroundRice (Oryza sativa L.), one of the most important crops cultivated in both tropical and temperate regions, has a high sensitivity to cold stress. Chilling stress limits the N uptake and nitrogen metabolism in rice. To identify the genes and pathways involved in cold tolerance, and specifically associations with the nitrogen metabolism pathway, we have compared the gene and protein expression changes between a cold-tolerant cultivar, Dongnong428 (DN), and a cold-sensitive cultivar, Songjing10(SJ).ResultsUsing absolute quantification (iTRAQ) with high-throughput mRNA sequencing (RNA-seq) techniques, we identified 5,549 genes and 450 proteins in DN and 6,145 genes and 790 proteins in SJ, that were differentially expressed during low- water temperature (Tw) treatment. There were 354 transcription factor (TF) genes (212down, 142 up), 366 TF genes (220 down, 146 up), including 47 gene families, differentially expressed in the DN under control (CKDN) vs. DN under low-Tw (D15DN) and CKSJ vs. D15SJ, respectively. These results indicated that TF genes play a major role in post-translational regulations. Genes related to rice cold-related biosynthesis pathways, particularly the MAPK signaling pathway, zeatin biosynthesis, and plant hormone signal transduction pathways, were significantly differentially expressed in both rice cultivars. Differentially expressed proteins (DEPs) related to rice cold-related biosynthesis pathways and particularly glutathione metabolism were significantly differentially expressed in both rice cultivars. Transcriptome and proteome analysis of the nitrogen metabolism pathways showed that major genes and proteins were down-regulated that participated in γ-aminobutyric acid (GABA) and glutamine synthesis. ConclusionUnder cold stress conditions during reproductive growth, genes and proteins related to the biosynthesis pathways of cold stress, were significantly differentially expressed in the DN and SJ. The present study confirmed the known cold stress-associated genes and identified a number of putative new cold-responsive genes. It has also revealed that translational regulation under cold stress plays an important role in cold-tolerant DN. Low-Tw treatments affect the N uptake and N metabolism in rice, and promote Glu metabolism, and the synthesis of ornithine and proline in cold-sensitive SJ.

Systems Biology Approaches Reveal a Multi-stress Responsive WRKY Transcription Factor and Stress Associated Gene Co-expression Networks in Chickpea

2019 ◽  
Vol 14 (7) ◽  
pp. 591-601 ◽  
Author(s):  
Aravind K. Konda ◽  
Parasappa R. Sabale ◽  
Khela R. Soren ◽  
Shanmugavadivel P. Subramaniam ◽  
Pallavi Singh ◽  
...  
Keyword(s):  
Expression Pattern ◽  
Gene Networks ◽  
Molecular Mechanisms ◽  
Enrichment Analysis ◽  
Functional Enrichment Analysis ◽  
Wrky Transcription Factor ◽  
Functional Enrichment ◽  
Differentially Expressed ◽  
Callose Deposition ◽  
Significant Probability

Background: Chickpea is a nutritional rich premier pulse crop but its production encounters setbacks due to various stresses and understanding of molecular mechanisms can be ascribed foremost importance. Objective: The investigation was carried out to identify the differentially expressed WRKY TFs in chickpea in response to herbicide stress and decipher their interacting partners. Methods: For this purpose, transcriptome wide identification of WRKY TFs in chickpea was done. Behavior of the differentially expressed TFs was compared between other stress conditions. Orthology based cofunctional gene networks were derived from Arabidopsis. Gene ontology and functional enrichment analysis was performed using Blast2GO and STRING software. Gene Coexpression Network (GCN) was constructed in chickpea using publicly available transcriptome data. Expression pattern of the identified gene network was studied in chickpea-Fusarium interactions. Results: A unique WRKY TF (Ca_08086) was found to be significantly (q value = 0.02) upregulated not only under herbicide stress but also in other stresses. Co-functional network of 14 genes, namely Ca_08086, Ca_19657, Ca_01317, Ca_20172, Ca_12226, Ca_15326, Ca_04218, Ca_07256, Ca_14620, Ca_12474, Ca_11595, Ca_15291, Ca_11762 and Ca_03543 were identified. GCN revealed 95 hub genes based on the significant probability scores. Functional annotation indicated role in callose deposition and response to chitin. Interestingly, contrasting expression pattern of the 14 network genes was observed in wilt resistant and susceptible chickpea genotypes, infected with Fusarium. Conclusion: This is the first report of identification of a multi-stress responsive WRKY TF and its associated GCN in chickpea.

scholarly journals Comparative Transcriptome Analysis Reveals Potential Gene Modules Associated with Cold Tolerance in Sugarcane (Saccharum officinarum L.)

2021 ◽  
Author(s):  
Xing Huang ◽  
Yongsheng Liang ◽  
Baoqing Zhang ◽  
Xiupeng Song ◽  
Yangrui Li ◽  
...  
Keyword(s):  
Cold Stress ◽  
Cold Tolerance ◽  
Cold Resistance ◽  
Soluble Sugar ◽  
Resistance Mechanism ◽  
Saccharum Officinarum ◽  
Calcium Signal ◽  
Protein Kinase Activity ◽  
Comparative Transcriptome ◽  
Climate Conditions

AbstractSugarcane is an important crop worldwide, and most sugar is derived directly from sugarcane. Due to its thermophilic nature, the yield of sugarcane is largely influenced by extreme climate conditions, especially cold stress. Therefore, the development of sugarcane with improved cold tolerance is an important goal. However, little is known about the multiple mechanisms underlying cold acclimation at the bud stage in sugarcane. In this study, we emphasized that sensitivity to cold stress was higher for the sugarcane variety ROC22 than for GT42, as determined by physical signs, including bud growth capacity, relative conductivity, malonaldehyde contents, and soluble sugar contents. To understand the factors contributing to the difference in cold tolerance between ROC22 and GT42, comparative transcriptome analyses were performed. We found that genes involved in the regulation of the stability of the membrane system were the relative determinants of difference in cold tolerance. Additionally, genes related to protein kinase activity, starch metabolism, and calcium signal transduction were associated with cold tolerance. Finally, 25 candidate genes, including 23 variety-specific and 2 common genes, and 7 transcription factors were screened out for understanding the possible cold resistance mechanism. The findings of this study provide candidate gene resources for cold resistance and will improve our understanding of the regulation of cold tolerance at the bud stage in sugarcane.

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.

THE BEHAVIOR OF THREE COLD-TOLERANT AND A STANDARD SOYBEAN VARIETY IN RELATION TO THE LEVEL AND THE DURATION OF A COLD STRESS

1980 ◽  
Vol 60 (3) ◽  
pp. 821-829 ◽  
Author(s):  
J. SCHMID ◽  
E. R. KELLER
Keyword(s):  
Cold Stress ◽  
Cold Tolerance ◽  
Growth Chamber ◽  
Cool Temperature ◽  
Federal Republic Of Germany ◽  
Average Growth ◽  
Cold Temperatures ◽  
Temperature Regimes ◽  
Cold Tolerant ◽  
The Stability

The cold tolerance of the varieties Gieso (Federal Republic of Germany), Amurskaja 41 (Russia), ISZ-7 and I-1 (Hungary) was investigated in growth chamber and greenhouse experiments. In the growth chamber trial, cool and cold temperatures reduced the grain yield of Gieso whereas ISZ-7 and I-1 increased their yields from the high temperature level to the coldest one. Amurskaja 41 had about the same yield in the warm and cool temperature regimes but in the coldest treatment, yields decreased compared with those of Gieso. The high quality of ISZ-7 and I-1 to compensate for stress periods as compared with Gieso and also with Amurskaja 41 is reflected in the average growth rate, the flower and pod formation and the dry matter production per plant. In the greenhouse experiment, duration of a cold stress at vegetative stages V1 and V3 and at the beginning of flowering was investigated. All tested varieties were able to compensate for cold stress of 10 days whereas only ISZ-7 and I-1 showed good yields under a long period of stress. These more cold tolerant varieties were particularly able to make good use of subsequent higher temperatures as expressed by the grain weight per degree Celsius. The stability of harvest index is also an important factor in cold tolerance investigations.

scholarly journals Comparative transcriptome profiling reveals the cold stress responsiveness in two contrasting Chinese jujube cultivars

2020 ◽  
Author(s):  
Heying Zhou(Former Corresponding Author) ◽  
Xiaoming Pang(New Corresponding Author) ◽  
Ying He ◽  
Yongsheng Zhu ◽  
Meiyu Li ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Enrichment Analysis ◽  
Transcriptome Profiling ◽  
Functional Enrichment Analysis ◽  
Functional Enrichment ◽  
Freezing Stress ◽  
Comparative Transcriptome ◽  
Chinese Jujube ◽  
Cold Tolerant ◽  
C 30

Abstract Background Low temperature is a major factor influences the growth and development of Chinese jujube ( Ziziphus jujuba Mill.) in cold winter and spring. Little is known about the molecular mechanisms for coping with different freezing stress conditions in jujube. To gain insight into the freezing-related molecular changes, we conducted comparative transcriptome analyses from the cold-sensitive cultivar ‘Dongzao’ and cold-tolerant cultivar ‘Jinsixiaozao’ using RNA-Seq. Results In our study, more than 20,000 genes were detected at chilling (4°C) and freezing (-10°C, -20°C, -30°C and -40°C) stress between two cultivars. The numbers of differentially expressed genes (DEGs) between the two cultivars was 1831, 2030, 1993, 1845 and 2137 under the five treatments, respectively. Functional enrichment analysis suggested that metabolic pathway, response to stimulus and catalytic activity were significantly enriched at stronger freezing stress. Among them, nine DEGs participated in the pathway of Ca 2+ signal, thirty-two DEGs were identified to take part in sucrose metabolism, and other DEGs were identified to participate in the regulation of ROS, plant hormones and antifreeze protein. In addition, important transcription factors ( WRKY , AP2 / ERF , NAC and bZIP ) participating in the freezing stress were activated under different degrees of freezing stress. Conclusions Our research provides a more comprehensive understanding of DEGs involved in freezing stress at the transcriptome levels in Z. jujuba , especially two cultivars with different cold tolerance. These results expanding our understanding on the complex molecular mechanism of jujube, which also provide new insights and candidate genes for genetic improvement of jujube tolerance to freezing stress.

The genetic architecture and breeding towards cold tolerance in maize: review.

2021 ◽  
pp. 282-294
Author(s):  
Hai-xiao Dong ◽  
Zhao Li ◽  
Guang-hui Hu ◽  
Ya-ping Yuan ◽  
Zhi-wu Zhang
Keyword(s):  
Cold Tolerance ◽  
Expression Profiling ◽  
Genetic Architecture ◽  
Association Studies ◽  
Genome Wide Association Studies ◽  
Cold Response ◽  
Genome Wide ◽  
Maize Varieties ◽  
Cold Tolerant ◽  
Cold Sensitive

Abstract This chapter reviews the global adaptation of maize, the effect of cold stress, existing cold-tolerant or cold-sensitive maize varieties or mutants, research on linkage analysis, and genome-wide association studies and gene expression profiling in maize cold response. In addition, the potential usage of genomic selection to accelerate the breeding process is explored. The objectives are to integrate knowledge for the benefit of geneticists to understand the genetic architecture of cold tolerance and for breeders to select 'hyper-tolerant' maize varieties adapted to broader and changeable environments.

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