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.

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

2020 ◽  
Author(s):  
Changbing Huang ◽  
Chun Jiang ◽  
limin Jin ◽  
Huanchao Zhang
Keyword(s):  
Low Temperature ◽  
Cold Stress ◽  
Cold Tolerance ◽  
Temperature Stress ◽  
Stress Responses ◽  
Target Genes ◽  
Low Temperature Stress ◽  
Differentially Expressed ◽  
Differentially Expressed Mirnas ◽  
Cold Tolerant

Abstract Background:Hemerocallis fulva is a perennial herb belonging to Hemerocallis of Hemerocallis. Because of the large and bright colors, it is often used as a garden ornamental plant. But most varieties of H. fulva on the market will wither in winter, which will affect their beauty. It is very important to study the effect of low temperature stress on the physiological indexes of H. fulva and understand the cold tolerance of different H. fulva. MiRNA is a kind of endogenous non coding small molecular RNA with length of 21-24nt. It mainly inhibits protein translation by cutting target genes, and plays an important role in the development of organisms, gene expression and biological stress. Low temperature is the main abiotic stress affecting the production of H. fulva in China, which hinders the growth and development of plants. A comprehensive understanding of the expression pattern of microRNA in H. fulva under low temperature stress can improve our understanding of microRNA mediated stress response. Although there are many studies on miRNAs of various plants under cold stress at home and abroad, there are few studies on miRNAs related to cold stress of H. fulva. It is of great significance to explore the cold stress resistant gene resources of H. fulva, especially the identification and functional research of miRNA closely related to cold stress, for the breeding of excellent H. fulva.Results A total of 5619 cold-responsive miRNAs, 315 putative novel and 5 304 conserved miRNAs, were identified from the leaves and roots of two different varieties ‘Jinyan’ (cold-tolerant) and ‘Lucretius ’ (cold-sensitive), which were stressed under -4 oC for 24 h. Twelve conserved and three novel miRNAs (novel-miR10, novel-miR19 and novel-miR48) were differentially expressed in leaves of ‘Jinyan’ under cold stress. Novel-miR19, novel-miR29 and novel-miR30 were up-regulated in roots of ‘Jinyan’ under cold stress. Thirteen and two conserved miRNAs were deferentially expressed in leaves and roots of ‘Lucretius’ after cold stress. The deferentially expressed miRNAs between two cultivars under cold stress include novel miRNAs and the members of the miR156, miR166 and miR319 families. A total of 6 598 target genes for 6 516 known miRNAs and 82 novel miRNAs were predicted by bioinformatic analysis, mainly involved in metabolic processes and stress responses. Ten differentially expressed miRNAs and predicted target genes were confirmed by quantitative reverse transcription PCR(q-PCR), and the expressional changes of target genes were negatively correlated to differentially expressed miRNAs. Our data indicated that some candidate miRNAs (e.g., miR156a-3-p, miR319a, and novel-miR19) may play important roles in plant response to cold stress.Conclusions Our study indicates that some putative target genes and miRNA mediated metabolic processes and stress responses are significant to cold tolerance in H. fulva.

scholarly journals Light Regulates the Cytokinin-Dependent Cold Stress Responses in Arabidopsis

2021 ◽  
Vol 11 ◽  
Author(s):  
Sylva Prerostova ◽  
Martin Černý ◽  
Petre I. Dobrev ◽  
Vaclav Motyka ◽  
Lucia Hluskova ◽  
...  
Keyword(s):  
Light Intensity ◽  
Cold Stress ◽  
Stress Tolerance ◽  
Stress Responses ◽  
Cold Treatment ◽  
Cytokinin Oxidase ◽  
Low Light ◽  
Cold Response ◽  
The Impact ◽  
Effect Of Light

To elucidate the effect of light intensity on the cold response (5°C; 7 days) in Arabidopsis thaliana, we compared the following parameters under standard light (150 μmol m–2 s–1), low light (20 μmol m–2 s–1), and dark conditions: membrane damage, photosynthetic parameters, cytokinin oxidase/dehydrogenase (CKX) activity, phytohormone levels, and transcription of selected stress- and hormone-related genes and proteome. The impact of cytokinins (CKs), hormones directly interacting with the light signaling pathway, on cold responses was evaluated using transformants overexpressing CK biosynthetic gene isopentenyl transferase (DEX:IPT) or CK degradation gene HvCKX2 (DEX:CKX) under a dexamethasone-inducible promoter. In wild-type plants, cold treatment under light conditions caused down-regulation of CKs (in shoots) and auxin, while abscisic acid (ABA), jasmonates, and salicylic acid (SA) were up-regulated, especially under low light. Cold treatment in the dark strongly suppressed all phytohormones, except ABA. DEX:IPT plants showed enhanced stress tolerance associated with elevated CK and SA levels in shoots and auxin in apices. Contrarily, DEX:CKX plants had weaker stress tolerance accompanied by lowered levels of CKs and auxins. Nevertheless, cold substantially diminished the impact from the inserted genes. Cold stress in dark minimized differences among the genotypes. Cold treatments in light strongly up-regulated stress marker genes RD29A, especially in roots, and CBF1-3 in shoots. Under control conditions, their levels were higher in DEX:CKX plants, but after 7-day stress, DEX:IPT plants exhibited the highest transcription. Transcription of genes related to CK metabolism and signaling showed a tendency to re-establish, at least partially, CK homeostasis in both transformants. Up-regulation of strigolactone-related genes in apices and leaves indicated their role in suppressing shoot growth. The analysis of leaf proteome revealed over 20,000 peptides, representing 3,800 proteins and 2,212 protein families (data available via ProteomeXchange, identifier PXD020480). Cold stress induced proteins involved in ABA and jasmonate metabolism, antioxidant enzymes, and enzymes of flavonoid and glucosinolate biosynthesis. DEX:IPT plants up-regulated phospholipase D and MAP-kinase 4. Cold stress response at the proteome level was similar in all genotypes under optimal light intensity, differing significantly under low light. The data characterized the decisive effect of light–CK cross-talk in the regulation of cold stress responses.

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 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.

scholarly journals iTRAQ-based quantitative proteomics analysis of cantaloupe (Cucumis melo var. saccharinus) after cold storage

2020 ◽  
Author(s):  
Wen Song ◽  
Fengxian Tang ◽  
Wenchao Cai ◽  
Qin Zhang ◽  
Fake Zhou ◽  
...  
Keyword(s):  
Cold Stress ◽  
Cold Tolerance ◽  
Proteomic Analysis ◽  
Molecular Mechanisms ◽  
Treatment Time ◽  
Chilling Injury ◽  
Cold Treatment ◽  
Cold Response ◽  
Low Temperature Storage ◽  
Metabolic Analysis

Abstract Background: During the low temperature storage, cantaloupe is susceptible to the cold stress, resulting in the loss of edible and commercial quality. To ascertain the molecular mechanisms of cold tolerance in cantaloupe, cold-sensitive cultivar Goldqueen-308 (GE) and cold-tolerant cultivar Jiashi-310 (JS) were used for quantitative proteomic analysis with iTRAQ in parallel. Results: In this work, two commercial cultivars were treated at 0.5℃ for 0, 12 and 24 days. Phenotypes assays showed that GE suffered a more severe damage as the cold treatment time extended. Proteomic analysis revealed that the number of differentially expressed proteins (DEPs) changed significantly over time in cold-exposed cantaloupe. Comparing with GE, JS responded in a prompter manner in terms of expressing cold-responding proteins during the similarly cold treatment. Furthermore, much more different groups of proteins were mobilized in response to the cold treatment in JS comparing with GE. Metabolic analysis indicated that more amino acids were up-regulated in JS during the early phases of cold stress. This study also identified some DEPs since they were up-regulated in JS or down-regulated in GE in terms of molecular mechanisms, which were mainly related to carbohydrate and energy metabolism, structure proteins, ROS scavening, amino acid metabolic and signaling transduction. Moreover, iTRAQ analysis was confirmed to be reliable via the results of phenotypes assays, metabolic analysis and q-PCR validation. Conclusion: By proteomics information,we found that the prompt response and the significant mobilization of proteins in JS maintained a higher level of cold tolerance, and the delay of cold response in GE could be a critical reason for the severe chilling injury. The candidate proteins we found will be the basis of future studies for further investigations and our findings may help to better understand the novel mechanisms of cold tolerance in cantaloupe.

scholarly journals Cold Response of the Mediterranean Fruit Fly (Ceratitis capitata) on a Lab Diet

Insects ◽  
2019 ◽  
Vol 10 (2) ◽  
pp. 48 ◽  
Author(s):  
Farhan Al-Behadili ◽  
Vineeta Bilgi ◽  
Junxi Li ◽  
Penghao Wang ◽  
Miyuki Taniguchi ◽  
...  
Keyword(s):  
Low Temperature ◽  
Ceratitis Capitata ◽  
Sex Ratios ◽  
Cold Treatment ◽  
Adult Emergence ◽  
Fruit Fly ◽  
Mediterranean Fruit Fly ◽  
Pest Species ◽  
Cold Response ◽  
The Mediterranean

Cold treatment at 0.0 °C with different exposure durations (0–12 days) was applied to the Mediterranean fruit fly Ceratitis capitata (Wiedemann) fed on a lab diet. The examined developmental stages were early eggs (<6 h), late eggs (>42 h), first instar, second instar and third instar larvae. Pupation, adult emergence and sex ratios of survived flies were investigated to study the C. capitata responses to this low temperature treatment. Our results showed that exposure time at low temperature has a clear effect on pupation and adult emergence. Based on pupation ratios, the first and third instar are the most cold tolerant stages, with LT99 = 7.3 for both of them. Cold tolerance at both stages are very close and no significant differences were detected. There were no significant differences on C. capitata sex ratios among different stages after treatment. This study improves our understanding of C. capitata responses to cold treatment, which may assist in the improvement of the current treatment strategies to control this destructive horticulture pest species.

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 Genome-Wide Analysis and Expression Profiling of the Heat Shock Factor Gene Family in Phyllostachys edulis during Development and in Response to Abiotic Stresses

Forests ◽  
2019 ◽  
Vol 10 (2) ◽  
pp. 100 ◽  
Author(s):  
Lihua Xie ◽  
Xiangyu Li ◽  
Dan Hou ◽  
Zhanchao Cheng ◽  
Jun Liu ◽  
...  
Keyword(s):  
Heat Shock ◽  
Gene Family ◽  
Protein Interaction ◽  
Structural Characteristics ◽  
Quantitative Polymerase Chain Reaction ◽  
Expression Patterns ◽  
Cold Treatment ◽  
Moso Bamboo ◽  
Phyllostachys Edulis ◽  
Class A

Heat shock transcription factors (Hsfs) play crucial roles in regulating plant responses to heat and other stresses, as well as in plant development. As the largest monopodial bamboo species in the world, how to adapt to various stresses under the background of global climate change is very important for the sustainable development of bamboo forest. However, our understanding of the function of Hsfs in moso bamboo (Phyllostachys edulis) is limited. In this study, a total of 22 non-redundant Hsf genes were identified in the moso bamboo genome. Structural characteristics and phylogenetic analysis revealed that members of the PheHsf family can be clustered into three classes (A, B and C). Furthermore, PheHsfs promoters contained a number of stress-, hormone- and development-related cis-acting elements. Transcriptome analysis indicated that most PheHsfs participate in rapid shoot growth and flower development in moso bamboo. Moreover, the expression patterns of all 12 members of class A were analyzed under various stresses (heat, drought, salt and cold treatment) through Figurereal-time quantitative polymerase chain reaction (qRT-PCR). Within the class A PheHsf members, PheHsfA1a was expressed mainly during moso bamboo development. Expression of four PheHsfA4s and one PheHsfA2 (PheHsfA4a-1, PheHsfA4a-2, PheHsfA4d-1, PheHsfA4d-2, and PheHsfA2a-2) was up-regulated in response to various stresses. PheHsfA2a-2, PheHsfA4d-1 and PheHsfA4d-2 were strongly induced respectively by heat, drought and NaCl stress. Through co-expression analysis we found that two hub genes PheHsfA4a-2 and PheHsfA4a-1 were involved in a complex protein interaction network. Based on the prediction of protein interaction networks, five PheHsfAs (PheHsfA4a-1, PheHsfA4a-2, PheHsfA4d-1, PheHsfA4d-2, and PheHsfA2a-2) were predicted to play an important role in flower and shoot development and abiotic stress response of moso bamboo. This study provides an overview of the complexity of the PheHsf gene family and a basis for analyzing the functions of PheHsf genes of interest.

scholarly journals Global analysis of differentially expressed genes between two Japonica rice varieties induced by low temperature during the booting stage by RNA-Seq

2020 ◽  
Vol 7 (6) ◽  
pp. 192243
Author(s):  
Zhenhua Guo ◽  
Lijun Cai ◽  
Chuanxue Liu ◽  
Cuihong Huang ◽  
Zhiqiang Chen ◽  
...  
Keyword(s):  
Low Temperature ◽  
Differentially Expressed Genes ◽  
Chilling Stress ◽  
Cold Treatment ◽  
Chilling Tolerance ◽  
Differentially Expressed ◽  
Antioxidant Enzyme Activities ◽  
Japonica Rice ◽  
Rice Varieties ◽  
Booting Stage

As one of the abiotic stresses, low temperature severely threatens rice production during its entire growth period, especially during the booting stage. In the present study, transcriptome analysis was performed comparing Longjing (LJ) 25 (chilling-tolerant) and LJ 11 (chilling-sensitive) rice varieties to identify genes associated with chilling tolerance in rice spikelets. A total of 23 845 expressed genes and 13 205 differentially expressed genes (DEGs) were identified, respectively. Gene ontology (GO) enrichment analyses revealed ‘response to cold’ (containing 180 DEGs) as the only category enriched in both varieties during the entire cold treatment period. Through M ap M an analysis, we identified nine and six DEGs related to the Calvin cycle and antioxidant enzymes, respectively, including OsRBCS3 , OsRBCS2 , OsRBCS4 , OsAPX2 and OsCATC , that under chilling stress were markedly downregulated in LJ11 compared with LJ25. Furthermore, we predicted their protein–protein interaction (PPI) network and identified nine hub genes (the threshold of co-expressed gene number ≥ 11) in Cytoscape, including three RuBisCO-related genes with 14 co-expressed genes. Under chilling stress, antioxidant enzyme activities (peroxidase (POD) and catalase (CAT)) were downregulated in LJ11 compared with LJ25. However, the content of malondialdehyde (MDA) was higher in LJ11 compared with LJ25. Collectively, our findings identify low temperature responsive genes that can be effectively used as candidate genes for molecular breeding programmes to increase the chilling tolerance of rice.

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