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

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

10.21203/rs.2.16686/v3 ◽

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.

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

10.21203/rs.2.16686/v2 ◽

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.

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

10.21203/rs.2.16686/v1 ◽

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.

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Transcriptome Analysis of Pre-Storage 1-MCP and High CO2-Treated ‘Madoka’ Peach Fruit Explains the Reduction in Chilling Injury and Improvement of Storage Period by Delaying Ripening

International Journal of Molecular Sciences ◽

10.3390/ijms22094437 ◽

2021 ◽

Vol 22 (9) ◽

pp. 4437

Author(s):

Han Ryul Choi ◽

Min Jae Jeong ◽

Min Woo Baek ◽

Jong Hang Choi ◽

Hee Cheol Lee ◽

...

Keyword(s):

Cold Storage ◽

Transcriptome Analysis ◽

Molecular Mechanisms ◽

Chilling Injury ◽

Chemical Properties ◽

Storage Period ◽

Differentially Expressed ◽

Peach Fruit ◽

High Co2 ◽

Physico Chemical

Cold storage of peach fruit at low temperatures may induce chilling injury (CI). Pre-storage 1-MCP and high CO2 treatments were reported among the methods to ameliorate CI and reduce softening of peach fruit. However, molecular data indicating the changes associated with pre-storage 1-MCP and high CO2 treatments during cold storage of peach fruit are insufficient. In this study, a comparative analysis of the difference in gene expression and physico-chemical properties of fruit at commercial harvest vs. stored fruit for 12 days at 0 °C (cold-stored (CS), pre-storage 1-MCP+CS, and pre-storage high CO2+CS) were used to evaluate the variation among treatments. Several genes were differentially expressed in 1-MCP+CS- and CO2+CS-treated fruits as compared to CS. Moreover, the physico-chemical and sensory data indicated that 1-MCP+CS and CO2+CS suppressed CI and delayed ripening than the CS, which could lead to a longer storage period. We also identified the list of genes that were expressed commonly and exclusively in the fruit treated by 1-MCP+CS and CO2+CS and compared them to the fruit quality parameters. An attempt was also made to identify and categorize genes related to softening, physiological changes, and other ripening-related changes. Furthermore, the transcript levels of 12 selected representative genes from the differentially expressed genes (DEGs) in the transcriptome analysis were confirmed via quantitative real-time PCR (qRT-PCR). These results add information on the molecular mechanisms of the pre-storage treatments during cold storage of peach fruit. Understanding the genetic response of susceptible cultivars such as ‘Madoka’ to CI-reducing pre-storage treatments would help breeders release CI-resistant cultivars and could help postharvest technologists to develop more CI-reducing technologies.

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Identification of cold stress responsive microRNAs in cold tolerant and susceptible Hemerocallis fulva by high throughput sequencing

10.21203/rs.3.rs-41470/v1 ◽

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.

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IDENTIFICATION AND QUANTIFICATION OF DIFFERENTIALLY EXPRESSED GENES ASSOCIATED WITH CITRUS BLIGHT (Citrus spp.)

Ciência e Agrotecnologia ◽

10.1590/s1413-70542015000100004 ◽

2015 ◽

Vol 39 (1) ◽

pp. 32-38

Author(s):

José Renato de Abreu ◽

Luciano Vilela Paiva ◽

Miguel Angel Dita Rodríguez ◽

Anderson Tadeu Silva ◽

Ariadne Ribeiro Henriques ◽

...

Keyword(s):

Stress Responses ◽

Plant Stress ◽

Control Measures ◽

Differentially Expressed ◽

Cdna Libraries ◽

Suppressive Subtractive Hybridization ◽

Transcriptional Level ◽

Hybridization Technique ◽

Tree Roots ◽

Citrus Blight

Brazil is the largest citrus producer in the world, being responsible for more than 20% of its production, which is, however still low due to phytosanitary issues such as citrus blight. Citrus blight is an anomaly whose causes still have not yet been determined, therefore there are no efficient control measures to minimize the production losses with the use of resistant varieties being considered the most appropriate method. However, little is known about the genes involved in the defense response of the plants to this anomaly. Considering that many physiological alterations associated with plant stress responses are controlled at a transcriptional level, in this study we sought the identification and characterization of the gene expression products differentially expressed in the response to the citrus blight. Through the suppressive subtractive hybridization technique, expressed cDNA libraries were built using mRNAs isolated from "Cravo" lemon tree roots (Citrus limonia L. Osbeck) under "Pera" orange (Citrus sinensis L. Osbeck) of healthy and sick plants. 129 clones were obtained by subtraction and their sequences were compared in databases. 34 of them linked to proteins associated to stress processes, while the others were similar to sequences of unknown functions or did not present similarity with sequences deposited in the databases. 3 genes were selected and their expressions were studied by RT - qPCR in real-time. Plants with citrus blight presented an increase of the expression level in two of those genes, suggesting that these can be directly involved with this anomaly.

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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

10.21203/rs.3.rs-42248/v1 ◽

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.

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Characterization of cold stress responses in different rapeseed ecotypes based on metabolomics and transcriptomics analyses

PeerJ ◽

10.7717/peerj.8704 ◽

2020 ◽

Vol 8 ◽

pp. e8704 ◽

Cited By ~ 2

Author(s):

Hongju Jian ◽

Ling Xie ◽

Yanhua Wang ◽

Yanru Cao ◽

Mengyuan Wan ◽

...

Keyword(s):

Gene Expression ◽

Amino Acids ◽

Cold Stress ◽

Stress Responses ◽

Differentially Expressed ◽

Regulatory Mechanisms ◽

Primary Metabolites ◽

Stress Treatment ◽

Organic Acids And Sugars

The winter oilseed ecotype is more tolerant to low temperature than the spring ecotype. Transcriptome and metabolome analyses of leaf samples of five spring Brassica napus L. (B. napus) ecotype lines and five winter B. napus ecotype lines treated at 4 °C and 28 °C were performed. A total of 25,460 differentially expressed genes (DEGs) of the spring oilseed ecotype and 28,512 DEGs of the winter oilseed ecotype were identified after cold stress; there were 41 differentially expressed metabolites (DEMs) in the spring and 47 in the winter oilseed ecotypes. Moreover, more than 46.2% DEGs were commonly detected in both ecotypes, and the extent of the changes were much more pronounced in the winter than spring ecotype. By contrast, only six DEMs were detected in both the spring and winter oilseed ecotypes. Eighty-one DEMs mainly belonged to primary metabolites, including amino acids, organic acids and sugars. The large number of specific genes and metabolites emphasizes the complex regulatory mechanisms involved in the cold stress response in oilseed rape. Furthermore, these data suggest that lipid, ABA, secondary metabolism, signal transduction and transcription factors may play distinct roles in the spring and winter ecotypes in response to cold stress. Differences in gene expression and metabolite levels after cold stress treatment may have contributed to the cold tolerance of the different oilseed ecotypes.

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Transcriptome Analysis of Resistance to Fusarium Wilt in Mung Bean (Vigna radiata L.)

Frontiers in Plant Science ◽

10.3389/fpls.2021.679629 ◽

2021 ◽

Vol 12 ◽

Author(s):

Yujie Chang ◽

Feifei Sun ◽

Suli Sun ◽

Lanfen Wang ◽

Jing Wu ◽

...

Keyword(s):

Candidate Genes ◽

Fusarium Wilt ◽

Transcriptome Analysis ◽

Stress Responses ◽

Mung Bean ◽

Differential Expression Analysis ◽

Differentially Expressed ◽

Post Inoculation ◽

Wilt Resistance ◽

Fusarium Wilt Resistance

Fusarium wilt is a destructive soil-borne disease that threatens the production of mung bean. Mung bean lines Zheng8-4 and Zheng8-20 show high resistance and high susceptibility to Fusarium wilt, respectively. Transcriptome analysis was carried out to identify candidate genes involved in Fusarium wilt resistance using Zheng8-4 and Zheng8-20 at 0, 0.5, 1, 2, and 4 days post inoculation (dpi). Differential expression analysis showed that 3,254 genes responded to pathogen infection and were differentially expressed in the resistant and susceptible lines. Weighted gene co-expression network analysis (WGCNA) was also performed to identify five modules highly correlated with Fusarium wilt resistance, in which 453 differentially expressed genes (DEGs) were considered likely to be involved in Fusarium wilt resistance. Among these DEGs, we found 24 genes encoding resistance (R) proteins, 22 encoding protein kinases, 20 belonging to transcription factor families, 34 encoding proteins with oxidoreductase activity, 17 involved in stimulation/stress responses, and 54 annotated to pathogen resistance-related pathways. Finally, 27 annotated genes were further selected as candidate genes of Fusarium wilt resistance in mung bean. This study identifies novel potential resistance-related genes against Fusarium wilt and provides a theoretical basis for further investigation of Fusarium wilt resistance in mung bean breeding.

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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 ◽

10.1371/journal.pone.0255139 ◽

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.

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