scholarly journals Cold tolerance of ScCBL6 is associated with photosynthesis and tonoplast transporters in Arabidopsis

2019 ◽  
Author(s):  
Yanli Zhou ◽  
Changhong Zhao ◽  
Guangqiang Long ◽  
Chengli Zhou ◽  
Xudong Sun ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Cold Stress ◽  
Cold Tolerance ◽  
Ectopic Expression ◽  
Tibet Plateau ◽  
Integrated Analysis ◽  
Rna Seq ◽  
Stipa Purpurea ◽  
Multiple Processes ◽  
Differential Expressed Genes

Abstract Plant adapted in the fragile zone offer enormous opportunity to understand the stress biology under ecological scenario . Stipa capillacea is widely distributed in the frigid and arid region of Tibet Plateau, but its signal system has never been investigated yet. In this study, we isolated a signal transduction gene, ScCBL6 , in Stipa capillacea , to characterize its cold tolerance capacity by ectopic expression in Arabidopsis . The results suggested that full length ScCBL6 encodes 227 amino acids, and phylogenetically clustered with CBL6 protein in Stipa purpurea and Oryza sativa . In comparison with wild type (WT) plants, ScCBL6 overexpressing plants ( ScCBL6- OXP) are tolerant to cold stress but not drought stress, which attested by the higher photosynthetic capacity (Fv/Fm) and survival rate of ScCBL6- OXP under cold stress. We further compared their cold-responsive transcriptome profiles through RNA-Seq. Totally, 3931 genes were differentially expressed by introduction of ScCBL6. They are participated in multiple processes like immune system, lipid catabolic, secondary metabolic and mainly enriched in plant hormone signal transduction and biomacro-molecule metabolism as regard to KEGG pathway. Differential expressed genes (DEGs) were predicted to locate in chloroplast, mitochondrion, vacuole, and so on, suggesting multitudinous function of ScCBL6. Based on the integrated analysis of ScCBL6-OXP, we inferred that ScCBL6 improve plant cold stress tolerance via regulate photosynthesis redox and vacuole metabolites transport in Arabidopsis .

GRAS-domain transcription factor PAT1 regulates jasmonic acid biosynthesis in grape cold stress response

2021 ◽  
Author(s):  
Zemin Wang ◽  
Darren Chern Jan Wong ◽  
Yi Wang ◽  
Guangzhao Xu ◽  
Chong Ren ◽  
...  
Keyword(s):  
Stress Response ◽  
Cold Stress ◽  
Cold Tolerance ◽  
Cold Treatment ◽  
Ectopic Expression ◽  
Bimolecular Fluorescence Complementation ◽  
Luciferase Reporter ◽  
Vitis Amurensis ◽  
Mobility Shift

Abstract Cultivated grapevine (Vitis) is a highly valued horticultural crop, and cold stress affects its growth and productivity. Wild Amur grape (Vitis amurensis) PAT1 (Phytochrome A signal transduction 1, VaPAT1) is induced by low temperature, and ectopic expression of VaPAT1 enhances cold tolerance in Arabidopsis (Arabidopsis thaliana). However, little is known about the molecular mechanism of VaPAT1 during the cold stress response in grapevine. Here, we confirmed the overexpression of VaPAT1 in transformed grape calli enhanced cold tolerance. Yeast two-hybrid and bimolecular fluorescence complementation assays highlighted an interaction between VaPAT1 with INDETERMINATE-DOMAIN 3 (VaIDD3). A role of VaIDD3 in cold tolerance was also indicated. Transcriptome analysis revealed VaPAT1 and VaIDD3 overexpression and cold treatment coordinately modulate the expression of stress-related genes including lipoxygenase 3 (LOX3), a gene encoding a key jasmonate biosynthesis enzyme. Co-expression network analysis indicated LOX3 might be a downstream target of VaPAT1. Both electrophoretic mobility shift and dual luciferase reporter assays showed the VaPAT1-IDD3 complex binds to the IDD-box (AGACAAA) in the VaLOX3 promoter to activate its expression. Overexpression of both VaPAT1 and VaIDD3 increased the transcription of VaLOX3 and JA levels in transgenic grape calli. Conversely, VaPAT1-SRDX (dominant repression) and CRISPR/Cas9-mediated mutagenesis of PAT1-ED causing the loss of the C-terminus in grape calli dramatically prohibited the accumulation of VaLOX3 and JA levels during cold treatment. Together, these findings point to a pivotal role of VaPAT1 in the cold stress response in grape by regulating JA biosynthesis.

Transcriptome profiling of rice seedlings under cold stress

2017 ◽  
Vol 44 (4) ◽  
pp. 419 ◽  
Author(s):  
Luciano C. da Maia ◽  
Pablo R. B. Cadore ◽  
Leticia C. Benitez ◽  
Rodrigo Danielowski ◽  
Eugenia J. B. Braga ◽  
...  
Keyword(s):  
Cold Stress ◽  
Cold Tolerance ◽  
Food Production ◽  
Genetic Model ◽  
Rice Yield ◽  
Oryza Sativa L ◽  
Abiotic Factors ◽  
Transcriptome Profiling ◽  
Important Species ◽  
Differential Expressed Genes

Rice (Oryza sativa L.) is one of the most important species for food production worldwide, besides being an excellent genetic model among the grasses. Cold is one of the major abiotic factors reducing rice yield, primarily affecting germination and reproduction phases. Currently, the RNAseq technique allows the identification of differential expressed genes in response to a given treatment, such as cold stress. In the present work, a transcriptome (RNAseq) analysis was performed in the V3 phase for contrasting genotypes Oro (tolerant) and Tio Taka (sensitive), in response to cold (13°C). A total of 241 and 244 M readings were obtained, resulting in the alignment of 25.703 and 26.963 genes in genotypes Oro and Tio Taka respectively. The analyses revealed 259 and 5579 differential expressed genes in response to cold in the genotypes Oro and Tio Taka respectively. Ontology classes with larger changes were metabolic process ~27%, cellular process ~21%, binding ~30% and catalytic activity ~22%. In the genotype Oro, 141 unique genes were identified, 118 were common between Oro and Tio Taka and 5461 were unique to Tio Taka. Genes involved in metabolic routes of signal transduction, phytohormones, antioxidant system and biotic stress were identified. These results provide an understanding that breeding for a quantitative trait, such as cold tolerance at germination, several gene loci must be simultaneously selected. In general, few genes were identified, but it was not possible to associate only one gene function as responsible for the cultivar tolerance; since different genes from different metabolic routes were identified. The genes described in the present work will be useful for future investigations and for the detailed validation in marker assisted selection projects for cold tolerance in the germination of rice.

scholarly journals Integrated RNA-seq Analysis and Meta-QTLs Mapping Provide Insights into Cold Stress Response in Rice Seedling Roots

2020 ◽  
Vol 21 (13) ◽  
pp. 4615 ◽  
Author(s):  
Weilong Kong ◽  
Chenhao Zhang ◽  
Yalin Qiang ◽  
Hua Zhong ◽  
Gangqing Zhao ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Stress Response ◽  
Cold Stress ◽  
Molecular Mechanisms ◽  
Oryza Sativa L ◽  
Growth And Yield ◽  
Rna Seq ◽  
Cold Tolerant ◽  
Stress Related Genes ◽  
Qtls Mapping

Rice (Oryza sativa L.) is a widely cultivated food crop around the world, especially in Asia. However, rice seedlings often suffer from cold stress, which affects their growth and yield. Here, RNA-seq analysis and Meta-QTLs mapping were performed to understand the molecular mechanisms underlying cold tolerance in the roots of 14-day-old seedlings of rice (RPY geng, cold-tolerant genotype). A total of 4779 of the differentially expressed genes (DEGs) were identified, including 2457 up-regulated and 2322 down-regulated DEGs. The GO, COG, KEEG, and Mapman enrichment results of DEGs revealed that DEGs are mainly involved in carbohydrate transport and metabolism, signal transduction mechanisms (plant hormone signal transduction), biosynthesis, transport and catabolism of secondary metabolites (phenylpropanoid biosynthesis), defense mechanisms, and large enzyme families mechanisms. Notably, the AP2/ERF-ERF, NAC, WRKY, MYB, C2H2, and bHLH transcription factors participated in rice’s cold–stress response and tolerance. On the other hand, we mapped the identified DEGs to 44 published cold–stress-related genes and 41 cold-tolerant Meta-QTLs regions. Of them, 12 DEGs were the published cold–stress-related genes and 418 DEGs fell into the cold-tolerant Meta-QTLs regions. In this study, the identified DEGs and the putative molecular regulatory network can provide insights for understanding the mechanism of cold stress tolerance in rice. In addition, DEGs in KEGG term-enriched terms or cold-tolerant Meta-QTLs will help to secure key candidate genes for further functional studies on the molecular mechanism of cold stress response in rice.

scholarly journals Enhancement of plant cold tolerance by soybean RCC1 family gene GmTCF1a

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Zhanghui Dong ◽  
Hui Wang ◽  
Xia Li ◽  
Hongtao Ji
Keyword(s):  
Low Temperature ◽  
Cold Stress ◽  
Cold Tolerance ◽  
Ectopic Expression ◽  
Growth Yield ◽  
Freezing Stress ◽  
Homologous Gene ◽  
Plant Tolerance ◽  
Transgenic Lines ◽  
Soybean Plants

Abstract Background Low temperature severely limits the growth, yield, and geographic distributions of soybean. Soybean plants respond to cold stress by reprogramming the expression of a series of cold-responsive genes. However, the intrinsic mechanism underlying cold-stress tolerance in soybean remains unclear. A. thaliana tolerant to chilling and freezing 1 (AtTCF1) is a regulator of chromosome condensation 1 (RCC1) family protein and regulates freezing tolerance through an independent C-repeat binding transcription factor (CBF) signaling pathway. Results In this study, we identified a homologous gene of AtTCF1 in soybean (named GmTCF1a), which mediates plant tolerance to low temperature. Like AtTCF1, GmTCF1a contains five RCC1 domains and is located in the nucleus. GmTCF1a is strongly and specifically induced by cold stress. Interestingly, ectopic overexpression of GmTCF1a in Arabidopsis greatly increased plant survival rate and decreased electrolyte leakage under freezing stress. A cold-responsive gene, COR15a, was highly induced in the GmTCF1a-overexpressing transgenic lines. Conclusions GmTCF1a responded specifically to cold stress, and ectopic expression of GmTCF1a enhanced cold tolerance and upregulated COR15a levels. These results indicate that GmTCF1a positively regulates cold tolerance in soybean and may provide novel insights into genetic improvement of cold tolerance in crops.

scholarly journals Transcriptomic profiling of germinating seeds under cold stress and characterization of the cold-tolerant gene LTG5 in rice

2020 ◽  
Author(s):  
yinghua Pan ◽  
Haifu Liang ◽  
Lijun Gao ◽  
Gaoxing Dai ◽  
Weiwei Chen ◽  
...  
Keyword(s):  
Low Temperature ◽  
Cold Stress ◽  
Cold Tolerance ◽  
Wild Rice ◽  
Expression Patterns ◽  
Molecular Genetic ◽  
Oryza Rufipogon ◽  
Rna Seq ◽  
Cold Tolerant ◽  
Cold Sensitive

Abstract Background: Wild rice ( Oryza rufipogon Griff.) is an important germplasm resource for rice improvement. It has superior tolerance for many abiotic stresses including cold stress, but little is known about the mechanism underlying its resistance to cold. Low temperature is one of the most prevalent factors that limit rice productivity and geographical distribution.Results: This study aimed to elucidate the molecular genetic mechanisms of wild rice in tolerating low temperature. Comprehensive transcriptome profiles of two rice genotypes (cold-sensitive ce 253 and cold-tolerant Y12-4) at the germinating stage under cold stress were comparatively analyzed. A total of 42.44–68.71 million readings were obtained, resulting in the alignment of 29128 and 30131 genes in genotypes 253 and Y12-4, respectively. Many common and differentially expressed genes (DEGs) were analyzed in cold-sensitive and cold-tolerant genotypes. Results showed more upregulated DEGs in cold-tolerant genotypes than in cold-sensitive genotypes at four stages under cold stress. Gene ontology enrichment analyses indicated more upregulated genes than downregulated ones in cold-tolerant genotypes based on cellular process, metabolic process, response stimulus, membrane part, and catalytic activity. To confirm the RNA Sequencing (RNA-seq) data, Quantitative real time polymerase chain reaction (qRT-PCR) was performed on seven randomly selected DEGs. These genes showed similar expression patterns corresponding with the RNA-Seq method. We also explored a gene for cold tolerance LTG5 , encoding a UDP-glucosyltransferase. The overexpression of LTG5 gene conferred cold tolerance to indica rice.Conclusion: Overall, our results suggested that gene resources related to cold stress from wild rice can be valuable for improving the cold tolerance of crop plants.

scholarly journals Characterization of Chromatin Accessibility and Gene Expression Upon Cold Stress Reveals the Transcription Factor RAV1 Functions in Cold Response in Vitis amurensis

2021 ◽  
Author(s):  
Chong Ren ◽  
Li Huayang ◽  
Zemin Wang ◽  
Zhanwu Dai ◽  
Fatma Lecourieux ◽  
...  
Keyword(s):  
Cold Stress ◽  
Cold Tolerance ◽  
Regulatory Networks ◽  
Cold Hardiness ◽  
Target Genes ◽  
Plant Cell Wall ◽  
Cold Treatment ◽  
Vitis Amurensis ◽  
Rna Seq ◽  
Cold Response

Abstract Cold tolerance is regulated by a variety of transcription factors (TFs) and their target genes. Except for the well-characterized C-repeat binding factors (CBFs)-dependent transcriptional cascade, the mechanisms of cold tolerance mediated by other transcriptional regulatory networks are still largely unknown. Here we used the assay for transposase-accessible chromatin with sequencing (ATAC-seq) and RNA-seq to identify cold responsive TFs in Vitis amurensis, a grape species with high cold hardiness. A number of 9 TFs, including CBF4, RAV1 and ERF104, were identified after cold treatment. Weighted gene co-expression network analysis (WGCNA) and gene ontology (GO) analysis revealed that these TFs may regulate cold response through different pathways. As a prime candidate TF, overexpression of VaRAV1 in grape cells improved its cold tolerance. The transgenic cells exhibited low electrolyte leakage and malondialdehyde (MDA) content and high peroxidase (POD) activity. Moreover, the TF gene TCP8 and a gene involving in homogalacturonan biosynthesis were found to be regulated by VaRAV1, suggesting that the contribution of VaRAV1 to cold tolerance may be achieved by enhancing stability of cell membrane and regulating the expression of target genes involved in plant cell wall composition. Our work provides novel insights into plant response to cold stress and demonstrates the utility of ATAC-seq and RNA-seq for rapid identification of TFs in response to cold stress in grapevine. The VaRAV1 may play an important role in adaption to cold stress.

scholarly journals Transcriptomic profiling of germinating seeds under cold stress and characterization of the cold-tolerant gene LTG5 in rice

2020 ◽  
Author(s):  
Yinghua Pan ◽  
Haifu Liang ◽  
Lijun Gao ◽  
Gaoxing Dai ◽  
Weiwei Chen ◽  
...  
Keyword(s):  
Low Temperature ◽  
Cold Stress ◽  
Cold Tolerance ◽  
Wild Rice ◽  
Expression Patterns ◽  
Rna Seq ◽  
Cold Tolerant ◽  
Cold Sensitive ◽  
Sensitive Genotype ◽  
Tolerant Genotype

Abstract Background: Low temperature is a limiting factor of rice productivity and geographical distribution. Wild rice (Oryza rufipogon Griff.) is an important germplasm resource for rice improvement. It has superior tolerance to many abiotic stresses, including cold stress, but little is known about the mechanism underlying its resistance to cold. Results: This study elucidated the molecular genetic mechanisms of wild rice in tolerating low temperature. Comprehensive transcriptome profiles of two rice genotypes (cold-sensitive ce 253 and cold-tolerant Y12-4) at the germinating stage under cold stress were comparatively analyzed. A total of 42.44–68.71 million readings were obtained, resulting in the alignment of 29 128 and 30 131 genes in genotypes 253 and Y12-4, respectively. Many common and differentially expressed genes (DEGs) were analyzed in the cold-sensitive and cold-tolerant genotypes. Results showed more upregulated DEGs in the cold-tolerant genotype than in the cold-sensitive genotype at four stages under cold stress. Gene ontology enrichment analyses based on cellular process, metabolic process, response stimulus, membrane part, and catalytic activity indicated more upregulated genes than downregulated ones in the cold-tolerant genotype than in the cold-sensitive genotype. Quantitative real-time polymerase chain reaction was performed on seven randomly selected DEGs to confirm the RNA Sequencing (RNA-seq) data. These genes showed similar expression patterns corresponding with the RNA-Seq method. Weighted gene co-expression network analysis（WGCNA）revealed Y12-4 showed more positive genes than 253 under cold stress. We also explored the cold tolerance gene LTG5 (Low Temperature Growth 5) encoding a UDP-glucosyltransferase. The overexpression of the LTG5 gene conferred cold tolerance to indica rice. Conclusion: Gene resources related to cold stress from wild rice can be valuable for improving the cold tolerance of crops.

scholarly journals Combining QTL-seq and linkage mapping to fine map a candidate gene in qCTS6 for cold tolerance at the seedling stage in rice

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Luomiao Yang ◽  
Jingguo Wang ◽  
Zhenghong Han ◽  
Lei Lei ◽  
Hua Long Liu ◽  
...  
Keyword(s):  
Cold Stress ◽  
Cold Tolerance ◽  
Regulatory Gene ◽  
Snp Markers ◽  
Seedling Stage ◽  
Pcr Analysis ◽  
Sequencing Data ◽  
Coding Region ◽  
Rice Varieties ◽  
Major Qtl

Abstract Background Cold stress caused by low temperatures is an important factor restricting rice production. Identification of cold-tolerance genes that can stably express in cold environments is crucial for molecular rice breeding. Results In this study, we employed high-throughput quantitative trait locus sequencing (QTL-seq) analyses in a 460-individual F2:3 mapping population to identify major QTL genomic regions governing cold tolerance at the seedling stage in rice. A novel major QTL (qCTS6) controlling the survival rate (SR) under low-temperature conditions of 9°C/10 days was mapped on the 2.60-Mb interval on chromosome 6. Twenty-seven single-nucleotide polymorphism (SNP) markers were designed for the qCST6 region based on re-sequencing data, and local QTL mapping was conducted using traditional linkage analysis. Eventually, we mapped qCTS6 to a 96.6-kb region containing 13 annotated genes, of which seven predicted genes contained 13 non-synonymous SNP loci. Quantitative reverse transcription PCR analysis revealed that only Os06g0719500, an OsbZIP54 transcription factor, was strongly induced by cold stress. Haplotype analysis confirmed that +376 bp (T>A) in the OsbZIP54 coding region played a key role in regulating cold tolerance in rice. Conclusion We identified OsbZIP54 as a novel regulatory gene associated with rice cold-responsive traits, with its Dongfu-104 allele showing specific cold-induction expression serving as an important molecular variation for rice improvement. This result is expected to further exploration of the genetic mechanism of rice cold tolerance at the seedling stage and improve cold tolerance in rice varieties by marker-assisted selection.

scholarly journals Gene Expression Profile and Co-Expression Network of Pearl Gentian Grouper under Cold Stress by Integrating Illumina and PacBio Sequences

Animals ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 1745
Author(s):  
Ben-Ben Miao ◽  
Su-Fang Niu ◽  
Ren-Xie Wu ◽  
Zhen-Bang Liang ◽  
Bao-Gui Tang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cold Stress ◽  
Differential Expression Analysis ◽  
Endocrine System ◽  
Control Group ◽  
Regulation Mechanism ◽  
Rna Seq ◽  
Cold Tolerant ◽  
Stress Signals ◽  
Membrane Changes

Pearl gentian grouper (Epinephelus fuscoguttatus ♀ × Epinephelus lanceolatus ♂) is a fish of high commercial value in the aquaculture industry in Asia. However, this hybrid fish is not cold-tolerant, and its molecular regulation mechanism underlying cold stress remains largely elusive. This study thus investigated the liver transcriptomic responses of pearl gentian grouper by comparing the gene expression of cold stress groups (20, 15, 12, and 12 °C for 6 h) with that of control group (25 °C) using PacBio SMRT-Seq and Illumina RNA-Seq technologies. In SMRT-Seq analysis, a total of 11,033 full-length transcripts were generated and used as reference sequences for further RNA-Seq analysis. In RNA-Seq analysis, 3271 differentially expressed genes (DEGs), two low-temperature specific modules (tan and blue modules), and two significantly expressed gene sets (profiles 0 and 19) were screened by differential expression analysis, weighted gene co-expression networks analysis (WGCNA), and short time-series expression miner (STEM), respectively. The intersection of the above analyses further revealed some key genes, such as PCK, ALDOB, FBP, G6pC, CPT1A, PPARα, SOCS3, PPP1CC, CYP2J, HMGCR, CDKN1B, and GADD45Bc. These genes were significantly enriched in carbohydrate metabolism, lipid metabolism, signal transduction, and endocrine system pathways. All these pathways were linked to biological functions relevant to cold adaptation, such as energy metabolism, stress-induced cell membrane changes, and transduction of stress signals. Taken together, our study explores an overall and complex regulation network of the functional genes in the liver of pearl gentian grouper, which could benefit the species in preventing damage caused by cold stress.

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.

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