scholarly journals Full-length transcriptome profiling reveals insight into the cold response of two kiwifruit genotypes (A. arguta) with contrasting freezing tolerances

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Shihang Sun ◽  
Miaomiao Lin ◽  
Xiujuan Qi ◽  
Jinyong Chen ◽  
Hong Gu ◽  
...  
Keyword(s):  
Low Temperature ◽  
Cold Stress ◽  
Freezing Tolerance ◽  
Plant Hormone ◽  
Inositol Phosphate ◽  
Mapk Signaling ◽  
Sucrose Metabolism ◽  
Cold Response ◽  
Inositol Phosphate Metabolism ◽  
Key Genes

Abstract Background Kiwifruit (Actinidia Lindl.) is considered an important fruit species worldwide. Due to its temperate origin, this species is highly vulnerable to freezing injury while under low-temperature stress. To obtain further knowledge of the mechanism underlying freezing tolerance, we carried out a hybrid transcriptome analysis of two A. arguta (Actinidi arguta) genotypes, KL and RB, whose freezing tolerance is high and low, respectively. Both genotypes were subjected to − 25 °C for 0 h, 1 h, and 4 h. Results SMRT (single-molecule real-time) RNA-seq data were assembled using the de novo method, producing 24,306 unigenes with an N50 value of 1834 bp. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of DEGs showed that they were involved in the ‘starch and sucrose metabolism’, the ‘mitogen-activated protein kinase (MAPK) signaling pathway’, the ‘phosphatidylinositol signaling system’, the ‘inositol phosphate metabolism’, and the ‘plant hormone signal transduction’. In particular, for ‘starch and sucrose metabolism’, we identified 3 key genes involved in cellulose degradation, trehalose synthesis, and starch degradation processes. Moreover, the activities of beta-GC (beta-glucosidase), TPS (trehalose-6-phosphate synthase), and BAM (beta-amylase), encoded by the abovementioned 3 key genes, were enhanced by cold stress. Three transcription factors (TFs) belonging to the AP2/ERF, bHLH (basic helix-loop-helix), and MYB families were involved in the low-temperature response. Furthermore, weighted gene coexpression network analysis (WGCNA) indicated that beta-GC, TPS5, and BAM3.1 were the key genes involved in the cold response and were highly coexpressed together with the CBF3, MYC2, and MYB44 genes. Conclusions Cold stress led various changes in kiwifruit, the ‘phosphatidylinositol signaling system’, ‘inositol phosphate metabolism’, ‘MAPK signaling pathway’, ‘plant hormone signal transduction’, and ‘starch and sucrose metabolism’ processes were significantly affected by low temperature. Moreover, starch and sucrose metabolism may be the key pathway for tolerant kiwifruit to resist low temperature damages. These results increase our understanding of the complex mechanisms involved in the freezing tolerance of kiwifruit under cold stress and reveal a series of candidate genes for use in breeding new cultivars with enhanced freezing tolerance.

scholarly journals Physiological and transcriptome analysis of Poa pratensis var. anceps cv. Qinghai in response to cold stress

2020 ◽  
Author(s):  
Wenke Dong ◽  
Xiang Ma ◽  
Hanyu Jiang ◽  
Chunxu Zhao ◽  
Huiling Ma
Keyword(s):  
Low Temperature ◽  
Cold Stress ◽  
Molecular Mechanisms ◽  
Cold Resistance ◽  
Poa Pratensis ◽  
Tca Cycle ◽  
Sucrose Metabolism ◽  
Tibet Plateau ◽  
Glutathione Metabolism ◽  
Cold Response

Abstract Background Low temperature limits the growth and geographical distribution of plants. Poa pratensis is a cool-season turfgrass mainly grown in urban areas. However, low winter temperature or cold events in spring and autumn may cause P.pratensis mortality, affecting the appearance of lawns. P.pratensis var. anceps cv. Qinghai (PQ) is widely distributed in the Qinghai-Tibet Plateau above 3000 m. PQ has greater cold resistance than the commercially cultivated P.pratensis varieties. However, existing studies on the response mechanism of PQ to low temperatures have mainly focused on physiological and biochemical perspectives, while changes in the PQ transcriptome during the response to cold stress have not been reported. Results To investigate the molecular mechanism of the PQ cold response and identify genes to improve the low-temperature resistance of P.pratensis, we analyzed and compared the transcriptomes of PQ and the cold-sensitive P.pratensis cv. ‘Baron’ (PB) under cold stress using RNA sequencing. We identified 4878 and 1871 differentially expressed genes (DEGs) between the treatment vs control comparison of PQ and PB, respectively, with 4494 DEGs specific to PQ. Based on the DEGs, important Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, such as “starch and sucrose metabolism”, “protein processing in endoplasmic reticulum”, “phenylalanine metabolism” and “glycolysis/gluconeogenesis” were significantly enriched in PQ, and “starch and sucrose metabolism”, “phenylpropanoid biosynthesis”, “galactose metabolism” and “glutathione metabolism” were significantly enriched in PB. In addition, the “glycolysis” and “citrate cycle (TCA cycle)” pathways were identified as involved in cold resistance of P.pratensis. Conclusions As we know, this is the first study to explore the transcriptome of P.pratensis var. anceps cv. Qinghai. Our study not noly provides important insights into the molecular mechanisms of P.pratensis var. anceps cv. Qinghai responds to cold stress, but also systematically reveals the changes of key genes and products of glycolysis and TCA cycle in response to cold stress, which is conductive to the breeding of cold-resistant P.pratensis genotype.

scholarly journals Identification of Genes Differentially Expressed in Response to Cold in Pisum sativum Using RNA Sequencing Analyses

Plants ◽  
2019 ◽  
Vol 8 (8) ◽  
pp. 288 ◽  
Author(s):  
Nasser Bahrman ◽  
Emilie Hascoët ◽  
Odile Jaminon ◽  
Frédéric Dépta ◽  
Jean-François Hû ◽  
...  
Keyword(s):  
Low Temperature ◽  
Pisum Sativum ◽  
Rna Sequencing ◽  
Differentially Expressed Genes ◽  
Freezing Tolerance ◽  
Cold Treatment ◽  
Temperature Treatment ◽  
Differentially Expressed ◽  
Cold Response ◽  
Chilling Response

Low temperature stress affects growth and development in pea (Pisum sativum L.) and decreases yield. In this study, RNA sequencing time series analyses performed on lines, Champagne frost-tolerant and Térèse frost-sensitive, during a low temperature treatment versus a control condition, led us to identify 4981 differentially expressed genes. Thanks to our experimental design and statistical analyses, we were able to classify these genes into three sets. The first one was composed of 2487 genes that could be related to the constitutive differences between the two lines and were not regulated during cold treatment. The second gathered 1403 genes that could be related to the chilling response. The third set contained 1091 genes, including genes that could be related to freezing tolerance. The identification of differentially expressed genes related to cold, oxidative stress, and dehydration responses, including some transcription factors and kinases, confirmed the soundness of our analyses. In addition, we identified about one hundred genes, whose expression has not yet been linked to cold stress. Overall, our findings showed that both lines have different characteristics for their cold response (chilling response and/or freezing tolerance), as more than 90% of differentially expressed genes were specific to each of them.

scholarly journals Understanding the early cold response mechanism in IR64 indica rice variety through comparative transcriptome analysis

2020 ◽  
Author(s):  
Pratiti Dasgupta ◽  
Abhishek Das ◽  
Sambit Datta New ◽  
Ishani Banerjee New ◽  
Sucheta Tripathy ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Low Temperature ◽  
Cold Stress ◽  
Cold Shock ◽  
Indica Rice ◽  
Cellular Reprogramming ◽  
Early Gene ◽  
Signaling Proteins ◽  
Cold Response

Abstract Background Cellular reprogramming in response to environmental stress involves alteration of gene expression, changes in the protein and metabolite profile for ensuring better stress management in plants. Similar to other plant species originating in tropical and sub-tropical areas, indica rice is highly sensitive to low temperature that adversely affects its growth and grain productivity. Substantial work has been done to understand cold induced changes in gene expression in rice plants. However, adequate information is not available for early gene expression, especially in indica variety. Therefore, a transcriptome profile was generated for cold shock treated seedlings of IR64 variety to identify early responsive genes. Results The functional annotation of early DEGs shows enrichment of genes involved in altered membrane rigidity and electrolytic leakage, the onset of calcium signaling, ROS generation and activation of stress responsive transcription factors in IR64. Gene regulatory network suggests that cold shock induces Ca 2+ signaling to activate DREB/CBF pathway and other groups of transcription factors such as MYB, NAC and ZFP; for activating various cold-responsive genes. The analysis also indicates that cold induced signaling proteins like RLKs, RLCKs, CDPKs and MAPKK and ROS signaling proteins. Further, several LEA, dehydrins and Low temperature-induced-genes were upregulated under early cold shock condition, indicating the onset of water-deficit conditions. Expression profiling in different high yielding cultivars shows high expression of cold-responsive genes in Heera and CB1 indica varieties, These varieties show low levels of cold induced ROS production, electrolytic leakage and high germination rate post-cold stress, compared to IR36 and IR64. Collectively, these results suggest that these varieties may have improved adaptability to cold stress. Conclusions The results of this study provide insights about early responsive events in Oryza sativa L.ssp. indica cv IR64 in response to cold stress. Our data shows the onset of cold response is associated with upregulation of stress responsive TFs, hydrophilic proteins and signaling molecules, whereas, the genes coding for cellular biosynthetic enzymes, cell cycle control and growth-related TFs are downregulated. This study reports that the generation of ROS is integral to the early response to trigger the ROS mediated signaling events during later stages.

Synthesis of inositol phosphate ligands of plant hormone–receptor complexes: pathways of inositol hexakisphosphate turnover

2012 ◽  
Vol 444 (3) ◽  
pp. 601-609 ◽  
Author(s):  
David E. Hanke ◽  
Paroo N. Parmar ◽  
Samuel E. K. Caddick ◽  
Porntip Green ◽  
Charles A. Brearley
Keyword(s):  
Hormone Receptor ◽  
Plant Hormone ◽  
Inositol Phosphates ◽  
Inositol Phosphate ◽  
Leaf Tissue ◽  
Phosphate Metabolism ◽  
Inositol Hexakisphosphate ◽  
Receptor Complexes ◽  
Inositol Phosphate Metabolism ◽  
Phosphate Ligands

Reduction of phytate is a major goal of plant breeding programs to improve the nutritional quality of crops. Remarkably, except for the storage organs of crops such as barley, maize and soybean, we know little of the stereoisomeric composition of inositol phosphates in plant tissues. To investigate the metabolic origins of higher inositol phosphates in photosynthetic tissues, we have radiolabelled leaf tissue of Solanum tuberosum with myo-[2-3H]inositol, undertaken a detailed analysis of inositol phosphate stereoisomerism and permeabilized mesophyll protoplasts in media containing inositol phosphates. We describe the inositol phosphate composition of leaf tissue and identify pathways of inositol phosphate metabolism that we reveal to be common to other kingdoms. Our results identify the metabolic origins of a number of higher inositol phosphates including ones that are precursors of cofactors, or cofactors of plant hormone–receptor complexes. The present study affords alternative explanations of the effects of disruption of inositol phosphate metabolism reported in other species, and identifies different inositol phosphates from that described in photosynthetic tissue of the monocot Spirodela polyrhiza. We define the pathways of inositol hexakisphosphate turnover and shed light on the occurrence of a number of inositol phosphates identified in animals, for which metabolic origins have not been defined.

scholarly journals Identification of key Genes and Pathways Associated With Thermal Stress in Peripheral Blood Mononuclear Cells of Holstein Dairy Cattle

2021 ◽  
Vol 12 ◽  
Author(s):  
Hao Fang ◽  
Ling Kang ◽  
Zaheer Abbas ◽  
Lirong Hu ◽  
Yumei Chen ◽  
...  
Keyword(s):  
Heat Stress ◽  
Thermal Stress ◽  
Dairy Cattle ◽  
Cold Stress ◽  
Signaling Pathway ◽  
Mononuclear Cells ◽  
Mapk Signaling ◽  
Chinese Holstein ◽  
Apoptosis Protein ◽  
Key Genes

The objectives of the present study were to identify key genes and biological pathways associated with thermal stress in Chinese Holstein dairy cattle. Hence, we constructed a cell-model, applied various molecular biology experimental techniques and bioinformatics analysis. A total of 55 candidate genes were screened from published literature and the IPA database to examine its regulation under cold (25°C) or heat (42°C) stress in PBMCs. We identified 29 (3 up-regulated and 26 down-regulated) and 41 (15 up-regulated and 26 down-regulated) significantly differentially expressed genes (DEGs) (fold change ≥ 1.2-fold and P < 0.05) after cold and heat stress treatments, respectively. Furthermore, bioinformatics analyses confirmed that major biological processes and pathways associated with thermal stress include protein folding and refolding, protein phosphorylation, transcription factor binding, immune effector process, negative regulation of cell proliferation, autophagy, apoptosis, protein processing in endoplasmic reticulum, estrogen signaling pathway, pathways related to cancer, PI3K- Akt signaling pathway, and MAPK signaling pathway. Based on validation at the cellular and individual levels, the mRNA expression of the HIF1A gene showed upregulation during cold stress and the EIF2A, HSPA1A, HSP90AA1, and HSF1 genes showed downregulation after heat exposure. The RT-qPCR and western blot results revealed that the HIF1A after cold stress and the EIF2A, HSPA1A, HSP90AA1, and HSF1 after heat stress had consistent trend changes at the cellular transcription and translation levels, suggesting as key genes associated with thermal stress response in Holstein dairy cattle. The cellular model established in this study with PBMCs provides a suitable platform to improve our understanding of thermal stress in dairy cattle. Moreover, this study provides an opportunity to develop simultaneously both high-yielding and thermotolerant Chinese Holstein cattle through marker-assisted selection.

scholarly journals Acclimation, priming and memory in the response of Arabidopsis thaliana seedlings to cold stress

2019 ◽  
Author(s):  
Jan Erik Leuendorf ◽  
Manuel Frank ◽  
Thomas Schmülling
Keyword(s):  
Arabidopsis Thaliana ◽  
Cold Stress ◽  
Freezing Tolerance ◽  
Physiological State ◽  
Cold Treatment ◽  
Freezing Resistance ◽  
Cold Response ◽  
Stress Memory ◽  
The Impact

Because stress experiences are often recurrent plants have developed strategies to remember a first so-called priming stress to eventually respond more effectively to a second triggering stress. Here, we have studied the impact of discontinuous or sustained cold stress (4 °C) on in vitro grown Arabidopsis thaliana seedlings of different age and their ability to get primed and respond differently to a later triggering stress. Cold treatment of 7-d-old seedlings induced the expression of cold response genes but did not cause a significantly enhanced freezing resistance. The competence to increase the freezing resistance in response to cold was associated with the formation of true leaves. Discontinuous exposure to cold only during the night led to a stepwise modest increase in freezing tolerance provided that the intermittent phase at ambient temperature was less than 32 h. Seedlings exposed to sustained cold treatment developed a higher freezing tolerance which was further increased in response to a triggering stress during three days after the priming treatment had ended indicating cold memory. Interestingly, in all scenarios the primed state was lost as soon as the freezing tolerance had reached the level of naïve plants indicating that an effective memory was associated with an altered physiological state. Known mutants of the cold stress response (cbfs, erf105) and heat stress memory (fgt1) did not show an altered behaviour indicating that their roles do not extend to memory of cold stress.

scholarly journals Genome-Wide Identification and Low Temperature Responsive Pattern of Actin Depolymerizing Factor (ADF) Gene Family in Wheat (Triticum aestivum L.)

2021 ◽  
Vol 12 ◽  
Author(s):  
Ke Xu ◽  
Yong Zhao ◽  
Sihang Zhao ◽  
Haodong Liu ◽  
Weiwei Wang ◽  
...  
Keyword(s):  
Low Temperature ◽  
Cold Stress ◽  
Gene Family ◽  
Plant Development ◽  
Expression Profiles ◽  
Actin Depolymerizing Factor ◽  
Ros Scavenging ◽  
Cold Response ◽  
Expression Levels ◽  
Genome Wide

The actin depolymerizing factor (ADF) gene family, which is conserved in eukaryotes, is important for plant development, growth, and stress responses. Cold stress restricts wheat growth, development, and distribution. However, genome-wide identification and functional analysis of the ADF family in wheat is limited. Further, because of the promising role of ADF genes in cold response, there is need for an understanding of the function of this family on wheat under cold stress. In this study, 25 ADF genes (TaADFs) were identified in the wheat genome and they are distributed on 15 chromosomes. The TaADF gene structures, duplication events, encoded conversed motifs, and cis-acting elements were investigated. Expression profiles derived from RNA-seq data and real-time quantitative PCR analysis revealed the tissue- and temporal-specific TaADF expression patterns. In addition, the expression levels of TaADF13/16/17/18/20/21/22 were significantly affected by cold acclimation or freezing conditions. Overexpression of TaADF16 increased the freezing tolerance of transgenic Arabidopsis, possibly because of enhanced ROS scavenging and changes to the osmotic regulation in cells. The expression levels of seven cold-responsive genes were up-regulated in the transgenic Arabidopsis plants, regardless of whether the plants were exposed to low temperature. These findings provide fundamental information about the wheat ADF genes and may help to elucidate the regulatory effects of the encoded proteins on plant development and responses to low-temperature stress.

scholarly journals Understanding the early cold response mechanism in IR64 indica rice variety through comparative transcriptome analysis

2020 ◽  
Author(s):  
Pratiti Dasgupta ◽  
Abhishek Das ◽  
Sambit Datta ◽  
Ishani Banerjee ◽  
Sucheta Tripathy ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Low Temperature ◽  
Cold Stress ◽  
Cold Shock ◽  
Rice Variety ◽  
Cellular Reprogramming ◽  
Early Gene ◽  
Signaling Proteins ◽  
Cold Response

Abstract Background: Cellular reprogramming in response to environmental stress involves alteration of gene expression, changes in the protein and metabolite profile for ensuring better stress management in plants. Similar to other plant species originating in tropical and sub-tropical areas, indica rice is highly sensitive to low temperature that adversely affects its growth and grain productivity. Substantial work has been done to understand cold induced changes in gene expression in rice plants. However, adequate information is not available for early gene expression, especially in indica variety. Therefore, a transcriptome profile was generated for cold shock treated seedlings of IR64 variety to identify early responsive genes. Results: The functional annotation of early DEGs shows enrichment of genes involved in altered membrane rigidity and electrolytic leakage, the onset of calcium signaling, ROS generation and activation of stress responsive transcription factors in IR64. Gene regulatory network suggests that cold shock induced Ca2+ signaling activates DREB/CBF pathway and other groups of transcription factors such as MYB, NAC and ZFP; for activating various cold-responsive genes. The analysis also indicates that cold induced signaling proteins like RLKs, RLCKs, CDPKs and MAPKK and ROS signaling proteins. Further, several late-embryogenesis-abundant (LEA), dehydrins and low temperature-induced-genes were upregulated under early cold shock condition, indicating the onset of water-deficit conditions. Expression profiling in different high yielding cultivars shows high expression of cold-responsive genes in Heera and CB1 indica varieties. These varieties show low levels of cold induced ROS production, electrolytic leakage and high germination rate post-cold stress, compared to IR36 and IR64. Collectively, these results suggest that these varieties may have improved adaptability to cold stress.Conclusions: The results of this study provide insights about early responsive events in Oryza sativa L.ssp. indica cv IR64 in response to cold stress. Our data shows the onset of cold response is associated with upregulation of stress responsive TFs, hydrophilic proteins and signaling molecules, whereas, the genes coding for cellular biosynthetic enzymes, cell cycle control and growth-related TFs are downregulated. This study reports that the generation of ROS is integral to the early response to trigger the ROS mediated signaling events during later stages.

scholarly journals Transcriptome profiling reveals the crucial biological pathways involved in cold response in Moso bamboo (Phyllostachys edulis)

2019 ◽  
Vol 40 (4) ◽  
pp. 538-556
Author(s):  
Yuanyuan Liu ◽  
Chu Wu ◽  
Xin Hu ◽  
Hongye Gao ◽  
Yue Wang ◽  
...  
Keyword(s):  
Low Temperature ◽  
Cold Stress ◽  
Early Stage ◽  
Cold Treatment ◽  
Well Being ◽  
Moso Bamboo ◽  
Differentially Expressed ◽  
Phyllostachys Edulis ◽  
Transcriptomic Response ◽  
Cold Response

Abstract Most bamboo species including Moso bamboo (Phyllostachys edulis) are tropical or subtropical plants that greatly contribute to human well-being. Low temperature is one of the main environmental factors restricting bamboo growth and geographic distribution. Our knowledge of the molecular changes during bamboo adaption to cold stress remains limited. Here, we provided a general overview of the cold-responsive transcriptional profiles in Moso bamboo by systematically analyzing its transcriptomic response under cold stress. Our results showed that low temperature induced strong morphological and biochemical alternations in Moso bamboo. To examine the global gene expression changes in response to cold, 12 libraries (non-treated, cold-treated 0.5, 1 and 24 h at −2 °C) were sequenced using an Illumina sequencing platform. Only a few differentially expressed genes (DEGs) were identified at early stage, while a large number of DEGs were identified at late stage in this study, suggesting that the majority of cold response genes in bamboo are late-responsive genes. A total of 222 transcription factors from 24 different families were differentially expressed during 24-h cold treatment, and the expressions of several well-known C-repeat/dehydration responsive element-binding factor negative regulators were significantly upregulated in response to cold, indicating the existence of special cold response networks. Our data also revealed that the expression of genes related to cell wall and the biosynthesis of fatty acids were altered in response to cold stress, indicating their potential roles in the acquisition of bamboo cold tolerance. In summary, our studies showed that both plant kingdom-conserved and species-specific cold response pathways exist in Moso bamboo, which lays the foundation for studying the regulatory mechanisms underlying bamboo cold stress response and provides useful gene resources for the construction of cold-tolerant bamboo through genetic engineering in the future.

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