scholarly journals Transcriptome analysis of harvest blueberries (Vaccinium corymbosum ‘Duke’) in response to cold stress

2019 ◽  
Author(s):  
Fan Zhang ◽  
ShuJuan Ji ◽  
BaoDong Wei ◽  
Shunchang Cheng ◽  
Jia Hao ◽  
...  
Keyword(s):  
Cold Stress ◽  
High Throughput ◽  
Cold Storage ◽  
Stress Responses ◽  
Chilling Injury ◽  
Vaccinium Corymbosum ◽  
Membrane Lipid ◽  
Transcriptional Level ◽  
Biological Processes ◽  
As Stress

Abstract Background Blueberry ( Vaccinium spp. ) is a small berry with high economic value. Although cold storage can extend the storage time of blueberry to more than 60 days, it leads to chilling injury (CI) displayed as pedicle pits; and the samples of 0°C-30 days was the critical point of chilling injury (CI). However, little is known about the mechanism and the molecular basis response to cold stress in blueberry have not been explained definitely.Methods To comprehensively reveal the CI mechanisms in response to cold stress, we performed high-throughput RNA Seq analysis to investigate the gene regulation network in blueberries at different storage temperatures (20°C and 0°C) in this study. At the same time, the pitting and decay rate, electrolyte leakage, malondialdehyde (MDA) and proline content were also measured.Results High-throughput transcriptome sequences were assembled into 35,060 unique transcripts with an N50 length of 1,348bp. A total of 1,167 up-regulated and 685 down-regulated differentially expressed genes (DEGs) were annotated and classified between the CI group and control. Forty-five cold-induced transcription factor (TF) families containing 1,023 TFs were identified. The DEGs indicated in biological processes such as stress responses; cell wall metabolism; abscisic acid, gibberellin, membrane lipid, energy metabolism, cellular components, and molecular functions were significantly responsed to low temperature storage. The transcriptional level of 40 DEGs were verified by qRT-PCR.Conclusions The harvest cold storage leads serious CI in blueberries, which substantially decreases the quality, storability and consumer acceptance. In our research, the physiological changes during the cold storage were determined; the biological processes such as stress responses, hormone metabolic processes were significantly affected by CI. Overall, the results obtained here are valuable for preventing pitting under cold storage and could serve as new targets for enhancing blueberry fruit post harvest storage.

scholarly journals Transcriptome analysis of postharvest blueberries (Vaccinium corymbosum‘Duke’) in response to cold stress

2020 ◽  
Author(s):  
Fan Zhang ◽  
ShuJuan Ji ◽  
BaoDong Wei ◽  
Shunchang Cheng ◽  
Jia Hao ◽  
...  
Keyword(s):  
Cold Stress ◽  
Cold Storage ◽  
Stress Responses ◽  
Chilling Injury ◽  
Membrane Lipid ◽  
Proline Content ◽  
Cdna Libraries ◽  
Transcriptional Level ◽  
Biological Processes ◽  
As Stress

Abstract Background: Blueberry ( Vaccinium spp. ) is a small berry with high economic value. Although cold storage can extend the storage time of blueberry to more than 60 days, it leads to chilling injury (CI) displayed as pedicle pits; and the samples of 0°C-30 days was the critical point of CI. However, little is known about the mechanism and the molecular basis response to cold stress in blueberry have not been explained definitely. Methods: To comprehensively reveal the CI mechanisms in response to cold stress, we performed high-throughput RNA Seq analysis to investigate the gene regulation network in 0d (control) and 30d chilled blueberry. At the same time, the pitting and decay rate, electrolyte leakage (EL), malondialdehyde (MDA) proline content and GSH content were also measured. Results: Two cDNA libraries from 0d (control) and 30d chilled samples were constructed and sequenced, generating a total of 35,060 unigenes with an N50 length of 1,348bp. Of these, 1852 were differentially expressed, with 1,167 upregulated and 685 downregulated. Forty-five cold-induced transcription factor (TF) families containing 1,023 TFs were identified. The DEGs indicated in biological processes such as stress responses; cell wall metabolism; abscisic acid, gibberellin, membrane lipid, energy metabolism, cellular components, and molecular functions were significantly responsed to cold storage. The transcriptional level of 40 DEGs were verified by qRT-PCR. Conclusions: The postharvest cold storage leads serious CI in blueberry, which substantially decreases the quality, storability and consumer acceptance. The MDA content, proline content, EL increased and the GSH content decreased in this chilled process. The biological processes such as stress responses, hormone metabolic processes were significantly affected by CI. Overall, the results obtained here are valuable for preventing CI under cold storage and could help to perfect the lack of the genetic information of non-model plant species.

scholarly journals Transcriptome analysis of postharvest blueberries (Vaccinium corymbosum ‘Duke’) in response to cold stress

2019 ◽  
Author(s):  
Fan Zhang ◽  
ShuJuan Ji ◽  
BaoDong Wei ◽  
Shunchang Cheng ◽  
Jia Hao ◽  
...  
Keyword(s):  
Cold Stress ◽  
Cold Storage ◽  
Stress Responses ◽  
Chilling Injury ◽  
Vaccinium Corymbosum ◽  
Proline Content ◽  
Cdna Libraries ◽  
Transcriptional Level ◽  
Biological Processes ◽  
As Stress

Abstract Background: Blueberry (Vaccinium spp.) is a small berry with high economic value. Although cold storage can extend the storage time of blueberry to more than 60 days, it leads to chilling injury (CI) displayed as pedicle pits; and the samples of 0°C-30 days was the critical point of CI. However, little is known about the mechanism and the molecular basis response to cold stress in blueberry have not been explained definitely. Methods: To comprehensively reveal the CI mechanisms in response to cold stress, we performed high-throughput RNA Seq analysis to investigate the gene regulation network in 0d (control) and 30d chilled blueberry. At the same time, the pitting and decay rate, electrolyte leakage (EL), malondialdehyde (MDA) proline content and GSH content were also measured.Results: Two cDNA libraries from 0d (control) and 30d chilled samples were constructed and sequenced, generating a total of 35,060 unigenes with an N50 length of 1,348bp. Of these, 1852 were differentially expressed, with 1,167 upregulated and 685 downregulated. Forty-five cold-induced transcription factor (TF) families containing 1,023 TFs were identified. The DEGs indicated in biological processes such as stress responses; cell wall metabolism; abscisic acid, gibberellin, membrane lipid, energy metabolism, cellular components, and molecular functions were significantly responsed to cold storage. The transcriptional level of 40 DEGs were verified by qRT-PCR. Conclusions: The postharvest cold storage leads serious CI in blueberry, which substantially decreases the quality, storability and consumer acceptance. The MDA content, proline content, EL increased and the GSH content decreased in this chilled process. The biological processes such as stress responses, hormone metabolic processes were significantly affected by CI. Overall, the results obtained here are valuable for preventing CI under cold storage and could help to perfect the lack of the genetic information of non-model plant species.

scholarly journals Transcriptome analysis of postharvest blueberries (Vaccinium corymbosum‘Duke’) in response to cold stress

2020 ◽  
Author(s):  
Fan Zhang ◽  
ShuJuan Ji ◽  
BaoDong Wei ◽  
Shunchang Cheng ◽  
YaJuan Wang ◽  
...  
Keyword(s):  
Cold Stress ◽  
Cold Storage ◽  
Transcriptome Analysis ◽  
Stress Responses ◽  
Chilling Injury ◽  
Proline Content ◽  
Differentially Expressed ◽  
Transcriptional Level ◽  
Biological Processes ◽  
As Stress

Abstract Background: Blueberry (Vaccinium spp.) is a small berry with high economic value. Although cold storage can extend the storage time of blueberry to more than 60 days, it leads to chilling injury (CI) displaying as pedicle pits; and the samples of 0°C-30 days was the critical point of CI. However, little is known about the mechanism and the molecular basis response to cold stress in blueberry have not been explained definitely. To comprehensively reveal the CI mechanisms in response to cold stress, we performed high-throughput RNA Seq analysis to investigate the gene regulation network in 0d (control) and 30d chilled blueberry. At the same time, the pitting and decay rate, electrolyte leakage (EL), malondialdehyde (MDA) proline content and GSH content were measured. Results: Two cDNA libraries from 0d (control) and 30d chilled samples were constructed and sequenced, generating a total of 35,060 unigenes with an N50 length of 1,348bp. Of these, 1852 were differentially expressed, with 1,167 upregulated and 685 downregulated. Forty-five cold-induced transcription factor (TF) families containing 1,023 TFs were identified. The DEGs indicated biological processes such as stress responses; cell wall metabolism; abscisic acid, gibberellin, membrane lipid, energy metabolism, cellular components, and molecular functions were significantly responsed to cold storage. The transcriptional level of 40 DEGs were verified by qRT-PCR. Conclusions: The postharvest cold storage leads serious CI in blueberry, which substantially decreases the quality, storability and consumer acceptance. The MDA content, proline content, EL increased and the GSH content decreased in this chilled process. The biological processes such as stress responses, hormone metabolic processes were significantly affected by CI. Overall, the results obtained here are valuable for preventing CI under cold storage and could help to perfect the lack of the genetic information of non-model plant species. Keywords: Blueberry; Differentially expressed genes; Low temperature storage; Pathways; Pitting; Transcriptome analysis

scholarly journals De novo sequencing and analysis of the transcriptome of two highbush blueberry (Vaccinium corymbosum L.) cultivars ‘Bluecrop’ and ‘Legacy’ at harvest and following post-harvest storage

PLoS ONE ◽  
2021 ◽  
Vol 16 (8) ◽  
pp. e0255139
Author(s):  
María Cárcamo de la Concepción ◽  
Daniel James Sargent ◽  
Nada Šurbanovski ◽  
Richard John Colgan ◽  
Marco Moretto
Keyword(s):  
Fruit Quality ◽  
Cold Storage ◽  
Stress Responses ◽  
De Novo ◽  
Transcript Abundance ◽  
Vaccinium Corymbosum ◽  
Moisture Loss ◽  
Biological Processes ◽  
Significant Differential Expression ◽  
Post Harvest

Fruit firmness and in particular the individual components of texture and moisture loss, are considered the key quality traits when describing blueberry fruit quality, and whilst these traits are genetically regulated, the mechanisms governing their control are not clearly understood. In this investigation, RNAseq was performed on fruits of two blueberry cultivars with very different storage properties, ‘Bluecrop’ and ‘Legacy’, at harvest, three weeks storage in a non-modified environment at 4 °C and after three weeks storage at 4 °C followed by three days at 21 °C, with the aim of understanding the transcriptional changes that occur during storage in cultivars with very different post-harvest fruit quality. De novo assemblies of the transcriptomes of the two cultivars were performed separately and a total of 39,335 and 41,896 unigenes for ‘Bluecrop’ and ‘Legacy’ respectively were resolved. Differential gene expression analyses were grouped into four cluster profiles based on changes in transcript abundance between harvest and 24 days post-harvest. A total of 290 unigenes were up-regulated in ‘Legacy’ only, 685 were up-regulated in ‘Bluecrop’, 252 were up-regulated in both cultivars and 948 were down-regulated in both cultivars between harvest and 24 days post-harvest. Unigenes showing significant differential expression between harvest and following post-harvest cold-storage were grouped into classes of biological processes including stress responses, cell wall metabolism, wax metabolism, calcium metabolism, cellular components, and biological processes. In total 21 differentially expressed unigenes with a putative role in regulating the response to post-harvest cold-storage in the two cultivars were identified from the de novo transcriptome assemblies performed. The results presented provide a stable foundation from which to perform further analyses with which to functionally validate the candidate genes identified, and to begin to understand the genetic mechanisms controlling changes in firmness in blueberry fruits post-harvest.

EARLY RESPONSE TO DEHYDRATION 7 Remodels Cell Membrane Lipid Composition during Cold Stress in Arabidopsis

2020 ◽  
Author(s):  
Juan de Dios Barajas-Lopez ◽  
Arjun Tiwari ◽  
Xavier Zarza ◽  
Molly W Shaw ◽  
Jesús Pascual ◽  
...  
Keyword(s):  
Cold Stress ◽  
Stress Responses ◽  
Lipid Composition ◽  
Plant Stress ◽  
Early Response ◽  
Membrane Lipid ◽  
Mutant Line ◽  
Triple Mutant ◽  
Membrane Lipid Composition ◽  
Plant Stress Responses

  Plants adjust to unfavorable conditions by altering physiological activities, such as gene expression. Although previous studies have identified multiple stress-induced genes, the function of many genes during the stress responses remains unclear. Expression of ERD7 (EARLY RESPONSE TO DEHYDRATION 7) is induced in response to dehydration. Here, we show that ERD7 plays essential roles in both plant stress responses and development. In Arabidopsis, ERD7 protein accumulated under various stress conditions, including exposure to low temperature. A triple mutant of Arabidopsis lacking ERD7 and two closely related homologs had an embryonic lethal phenotype, whereas a mutant lacking the two homologs and one ERD7 allele had relatively round leaves, indicating that the ERD7 gene family has essential roles in development. Moreover, the importance of the ERD7 family in stress responses was evidenced by the susceptibility of the mutant lines to cold stress. ERD7 protein was found to bind to several, but not all, negatively charged phospholipids and was associated with membranes. Lipid components and cold-induced reduction in PIP2 in the mutant line were altered relative to wild type. Furthermore, membranes from the mutant line had reduced fluidity. Taken together, ERD7 and its homologs are important for plant stress responses and development and associated with the modification in membrane lipid composition.

scholarly journals De novo sequencing and analysis of the transcriptome of two highbush blueberry (V. corymbosum L.) cultivars ‘Bluecrop’ and ‘Legacy’ at harvest and following post-harvest storage

2020 ◽  
Author(s):  
Maria Carcamo de la Concepcion ◽  
Daniel James Sargent ◽  
Nada Surbanovski ◽  
Richard Colgan ◽  
Marco Moretto
Keyword(s):  
Fruit Quality ◽  
Cold Storage ◽  
Stress Responses ◽  
De Novo ◽  
Transcript Abundance ◽  
Moisture Loss ◽  
Biological Processes ◽  
Significant Differential Expression ◽  
Post Harvest ◽  
The Individual

Abstract Background: Fruit firmness and in particular the individual components of texture and moisture loss, are considered the key quality traits when describing blueberry fruit quality, and whilst these traits are genetically regulated, the mechanisms governing their control are not clearly understood. In this investigation, RNAseq was performed on fruits of two blueberry cultivars with very different storage properties, ‘Bluecrop’ and ‘Legacy’, at harvest, three weeks storage in a non-modified environment at 4 oC and after three weeks storage at 4 oC followed by three days at 21 oC, with the aim of understanding the transcriptional changes that occur during storage in cultivars with very different post-harvest fruit quality.Results: De novo assemblies of the transcriptomes of the two cultivars were performed separately and a total of 39,335 and 41,896 unigenes for ‘Bluecrop’ and ‘Legacy’ respectively were resolved. Differential gene expression analyses were grouped into four cluster profiles based on changes in transcript abundance between harvest and 24 days post-harvest. A total of 264 unigenes were up-regulated in ‘Legacy’ and down-regulated in ‘Bluecrop’, 103 were down-regulated in ‘Legacy’ and up-regulated in ‘Bluecrop’, 43 were up-regulated in both cultivars and 355 were down-regulated in both cultivars between harvest and 24 days post-harvest. Unigenes showing significant differential expression between harvest and following post-harvest cold-storage were grouped into classes of biological processes including stress responses, cell wall metabolism, wax metabolism, calcium metabolism, cellular components, and biological processes.Conclusions: In total 21 differentially expressed unigenes with a putative role in regulating the response to post-harvest cold-storage in the two cultivars were identified from the de novo transcriptome assemblies performed. The results presented provide a stable foundation from which to perform further analyses with which to functionally validate the candidate genes identified, and to begin to understand the genetic mechanisms controlling changes in firmness in blueberry fruits post-harvest.

scholarly journals Role of Membrane Lipid Peroxidation, Enzymatic and Non-enzymatic Antioxidative Systems in the Development of Chilling Injury in Japanese Plums

2012 ◽  
Vol 137 (6) ◽  
pp. 473-481 ◽  
Author(s):  
Sukhvinder Pal Singh ◽  
Zora Singh
Keyword(s):  
Oxidative Stress ◽  
Lipid Peroxidation ◽  
Cold Storage ◽  
Chilling Injury ◽  
Membrane Lipid ◽  
Enzymatic Antioxidants ◽  
Membrane Lipid Peroxidation ◽  
Stress Theory ◽  
Antioxidative Systems ◽  
Duration Of Storage

Chilling injury (CI) is a major postharvest constraint in the long-term cold storage, transportation, and distribution of japanese plums (Prunus salicina). The aim of the work was to explain the development and severity of CI in japanese plums based on the oxidative stress theory following time course analysis of enzymatic and non-enzymatic antioxidants. Changes in membrane lipid peroxidation and enzymatic and non-enzymatic antioxidative systems in japanese plum cultivar Blackamber were determined at weekly intervals during 5 weeks of cold storage at 0 °C and at 2-day intervals during poststorage simulated shelf conditions (21 ± 1 °C) for 8 days after each week of cold storage. Fruit respiration and ethylene production rates showed typical climacteric patterns after removal from cold storage and these rates were relatively high after 4 and 5 weeks compared with 0 to 3 weeks of storage. The CI symptoms first appeared after 3 weeks of cold storage after fruit had been transferred to simulated shelf conditions. The incidence and severity of CI intensified with increasing storage duration. The extent of lipid peroxidation indicated by concentration of thiobarbituric acid-reactive substances and membrane damage manifested as electrolyte leakage increased with increasing duration of storage and subsequent simulated shelf conditions. Membrane lipid peroxidation exhibited positive correlation with the severity of CI. Activities of primary antioxidant enzymes and the enzymes involved in the ascorbate–glutathione cycle were determined to explain the levels of reduced and oxidized forms of cellular redox buffers, ascorbate and glutathione. In response to chilling stress, antioxidative protection systems operated efficiently during the first 3 weeks of cold storage, but extended storage resulted in loss of ability to ameliorate increasing levels of oxidative stress. In this study, the comprehensive analyses of various metabolites and antioxidative systems explain the series of events involved in development of CI in japanese plums in support of the oxidative stress theory.

scholarly journals Genome-Wide Identification of WRKY Genes and Their Response to Cold Stress in Coffea canephora

Forests ◽  
2019 ◽  
Vol 10 (4) ◽  
pp. 335 ◽  
Author(s):  
Xiangshu Dong ◽  
Yanan Yang ◽  
Ziying Zhang ◽  
Ziwei Xiao ◽  
Xuehui Bai ◽  
...  
Keyword(s):  
Cold Stress ◽  
Stress Responses ◽  
Gene Expression Analysis ◽  
Target Genes ◽  
Coffea Canephora ◽  
Biological Processes ◽  
Genome Wide ◽  
A Genome ◽  
Cold Responses ◽  
Insight Into

WRKY transcription factors are known to play roles in diverse stress responses in plants. Low temperatures limit the geographic distribution of Coffea canephora Pierre ex A.Froehner. The WRKYs of C. canephora are still not well characterized, and the response of C. canephora WRKYs (CcWRKYs) under cold stress is still largely unknown. We identified 49 CcWRKYs from the C. canephora genome to gain insight into these mechanisms. These CcWRKYs were divided into three groups that were based on the conserved WRKY domains and zinc-finger structure. Gene expression analysis demonstrated that 14 CcWRKYs were induced during the cold acclimation stage, 17 CcWRKYs were preferentially upregulated by 4 °C treatment, and 12 CcWRKYs were downregulated by cold stress. Subsequently, we carried out a genome-wide analysis to predict 14,513 potential CcWRKY target genes in C. canephora. These isolated genes were involved in multiple biological processes, and most of them could be grouped by the response to stimulus. Among the putative CcWRKY target genes, 235 genes were categorized into response to the cold process, including carbohydrate metabolic, lipid metabolic, and photosynthesis process-related genes. Furthermore, the qRT-PCR and correlation analysis indicated that CcWRKY might control their putative targets that respond to cold stress. These results provide a basis for understanding the molecular mechanism for CcWRKY-mediated cold responses.

scholarly journals De novo sequencing and analysis of the transcriptome of two highbush blueberry (V. corymbosum L.) cultivars ‘Bluecrop’ and ‘Legacy’ at harvest and following post-harvest storage

2021 ◽  
Author(s):  
Maria Carcamo de la Concepcion ◽  
Daniel James Sargent ◽  
Nada Surbanovski ◽  
Richard Colgan ◽  
Marco Moretto
Keyword(s):  
Fruit Quality ◽  
Cold Storage ◽  
Stress Responses ◽  
De Novo ◽  
Transcript Abundance ◽  
Moisture Loss ◽  
Biological Processes ◽  
Significant Differential Expression ◽  
Post Harvest ◽  
The Individual

Abstract Background: Fruit firmness and in particular the individual components of texture and moisture loss, are considered the key quality traits when describing blueberry fruit quality, and whilst these traits are genetically regulated, the mechanisms governing their control are not clearly understood. In this investigation, RNAseq was performed on fruits of two blueberry cultivars with very different storage properties, ‘Bluecrop’ and ‘Legacy’, at harvest, three weeks storage in a non-modified environment at 4 oC and after three weeks storage at 4 oC followed by three days at 21 oC, with the aim of understanding the transcriptional changes that occur during storage in cultivars with very different post-harvest fruit quality.Results: De novo assemblies of the transcriptomes of the two cultivars were performed separately and a total of 39,335 and 41,896 unigenes for ‘Bluecrop’ and ‘Legacy’ respectively were resolved. Differential gene expression analyses were grouped into four cluster profiles based on changes in transcript abundance between harvest and 24 days post-harvest. A total of 264 unigenes were up-regulated in ‘Legacy’ and down-regulated in ‘Bluecrop’, 103 were down-regulated in ‘Legacy’ and up-regulated in ‘Bluecrop’, 43 were up-regulated in both cultivars and 355 were down-regulated in both cultivars between harvest and 24 days post-harvest. Unigenes showing significant differential expression between harvest and following post-harvest cold-storage were grouped into classes of biological processes including stress responses, cell wall metabolism, wax metabolism, calcium metabolism, cellular components, and biological processes.Conclusions: In total 21 differentially expressed unigenes with a putative role in regulating the response to post-harvest cold-storage in the two cultivars were identified from the de novo transcriptome assemblies performed. The results presented provide a stable foundation from which to perform further analyses with which to functionally validate the candidate genes identified, and to begin to understand the genetic mechanisms controlling changes in firmness in blueberry fruits post-harvest.

An Insight into Oligopeptide Transporter 3 (OPT3) family proteins

2020 ◽  
Vol 27 ◽  
Author(s):  
Fırat Kurt
Keyword(s):  
Stress Responses ◽  
Chelating Agent ◽  
Biological Processes ◽  
Biotic And Abiotic Stress ◽  
Oligopeptide Transporter ◽  
Binding Residues ◽  
Fe Homeostasis ◽  
Proteins Interactions ◽  
Insight Into ◽  
Selection Of

: Oligopeptide transporter 3 (OPT3) proteins are one of the subsets of OPT clade, yet little is known about these transporters. Therefore, homolog OPT3 proteins in several plant species were investigated and characterized using bioinformatical tools. Motif and co-expression analyses showed that OPT3 proteins may be involved in both biotic and abiotic stress responses as well as growth and developmental processes. AtOPT3 usually seemed to take part in Fe homeostasis whereas ZmOPT3 putatively interacted with proteins involved in various biological processes from plant defense system to stress responses. Glutathione (GSH), as a putative alternative chelating agent, was used in the AtOPT3 and ZmOPT3 docking analyses to identify their putative binding residues. The information given in this study will contribute to the understanding of OPT3 proteins’ interactions in various pathways and to the selection of potential ligands for OPT3s.

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