scholarly journals Use of Comparative Transcriptomic Analysis of Different Potato Varieties to Elucidate the Molecular Mechanism Underlying Differences in Cold Resistance

2021 ◽  
Author(s):  
Huiju Yang ◽  
Mingwei Chen ◽  
Can Kou ◽  
Huachun Guo
Keyword(s):  
Signal Transduction ◽  
Low Temperature ◽  
Plant Hormone ◽  
Cold Resistance ◽  
Expression Patterns ◽  
Temperature Response ◽  
Crop Productivity ◽  
Transcriptomic Analysis ◽  
Tolerant Variety ◽  
Cold Tolerant

Abstract Background Among the various abiotic stresses, cold is an essential factor that limits crop productivity worldwide. Low temperature affects the growth, development and distribution of agronomic species around the world. To improve the understanding of the physiological and genetic properties and functions affecting potato cold tolerance, in this study, transcriptomic analysis was performed on two potato strains (HZ88 and LS6) with different cold tolerances that were treated at low temperature for 0, 1, 3, and 6 hours. Results Transcriptomic analysis showed that there were large differences between HZ88 and LS6 regarding the expression levels of low-temperature response genes. Notably, HZ88 responds to low-temperature stress, its low-temperature response genes are primarily enriched in plant hormone signal transduction; cutin, suberine and wax biosynthesis; and photosynthesis-antenna proteins. Conversely, the most significant low-temperature response genes of the LS6 strain were determined to be enriched in plant-pathogen interactions, zeatin biosynthesis, and plant hormone signal transduction. The cuticle, composed of a horny waxy layer, is an important protective barrier formed by plants to resist biotic/abiotic stress during the long-term ecological adaptation process, and the HZ88 strain may strengthen its cold resistance by enhancing this physical defence measure. In the LS6 strain, potatoes tend to cope with cold stress by strengthening their immune system and regulating hormone signal transduction. In addition, hormone pathway-related genes (such as ABA), ICE-CBF signalling pathway-related genes, and genes encoding TFs all exhibited different expression patterns between HZ88 and LS6. Conclusions To the best of our knowledge, this study is the first to elucidate the genetic mechanisms underlying the difference in cold resistance between the strongly cold-tolerant variety LS6 and the weakly cold-tolerant variety HZ88, thereby establishing a foundation for further analysis and genetic breeding.

scholarly journals Comparative transcriptome analysis of the cold resistance of the sterile rice line 33S

PLoS ONE ◽  
2022 ◽  
Vol 17 (1) ◽  
pp. e0261822
Author(s):  
Hongjun Xie ◽  
Mingdong Zhu ◽  
Yaying Yu ◽  
Xiaoshan Zeng ◽  
Guohua Tang ◽  
...  
Keyword(s):  
Low Temperature ◽  
Cold Resistance ◽  
Temperature Response ◽  
Enrichment Analysis ◽  
Abiotic Factor ◽  
Comparative Transcriptome ◽  
Important Species ◽  
Expression Of Genes ◽  
Nutrient Reserve ◽  
Cold Tolerant

Rice (Oryza sativa L.) is one of the most important species for food production worldwide. Low temperature is a major abiotic factor that affects rice germination and reproduction. Here, the underlying regulatory mechanism in seedlings of a TGMS variety (33S) and a cold-sensitive variety (Nipponbare) was investigated by comparative transcriptome. There were 795 differentially expressed genes (DEGs) identified only in cold-treated 33S, suggesting that 33S had a unique cold-resistance system. Functional and enrichment analysis of these DEGs revealed that, in 33S, several metabolic pathways, such as photosynthesis, amino acid metabolism, secondary metabolite biosynthesis, were significantly repressed. Moreover, pathways related to growth and development, including starch and sucrose metabolism, and DNA biosynthesis and damage response/repair, were significantly enhanced. The expression of genes related to nutrient reserve activity were significantly up-regulated in 33S. Finally, three NAC and several ERF transcription factors were predicted to be important in this transcriptional reprogramming. This present work provides valuable information for future investigations of low-temperature response mechanisms and genetic improvement of cold-tolerant rice seedlings.

scholarly journals Hormone Profiles and Antioxidant Activity of Cultivated and Wild Tomato Seedlings under Low-Temperature Stress

Agronomy ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 1146
Author(s):  
Parviz Heidari ◽  
Mohammad Reza Amerian ◽  
Gianni Barcaccia
Keyword(s):  
Oxidative Stress ◽  
Antioxidant Activity ◽  
Low Temperature ◽  
Temperature Stress ◽  
Expression Patterns ◽  
Low Temperature Stress ◽  
Ros Scavenging ◽  
Tomato Species ◽  
Tolerant Species ◽  
Cold Tolerant

Low temperature is a major limiting factor for the growth and reproduction of some plant species, such as tomato. So far, few studies have been conducted on the effects of low temperature, and the mechanisms of plants’ response to this type of stress is not fully clear. In the current study, the effects of low, nonfreezing temperature (10 °C for three days) on the hormone content, antioxidant activity, and expression patterns of cold-related genes in the leaves of cold-tolerant species (Solanum habrochaites Accession ‘LA1777′) and cold-susceptible species (Solanum lycopersicum cultivar ‘Moneymaker’) were investigated. Low temperature increased the abscisic acid (ABA) content in both tomato species, while the content of zeatin-type cytokinins (ZT) increased in the cold-tolerant species. However, the content of indole-3-acetic acid (IAA) and gibberellic acid (GA) reduced in response to low temperature in susceptible species. Accordingly, cytokinin (CK) is identified as an important hormone associated with low-temperature stress in tomato. In addition, our results indicate that the C-repeat/DRE binding factor 1 (CBF1) gene is less induced in response to low temperature in tomato, although transcription of the inducer of CBF expression 1 (ICE1) gene was upregulated under low temperature in both tomato species. It seems that ICE1 may modulate cold-regulated (COR) genes in a CBF-independent way. In addition, in response to low temperature, the malondialdehyde (MDA) level and membrane stability index (MSI) increased in the susceptible species, indicating that low temperature induces oxidative stress. Additionally, we found that glutathione peroxidase is highly involved in reactive oxygen species (ROS) scavenging induced by low temperature, and antioxidants are more induced in tolerant species. Overall, our results suggest that sub-optimal temperatures promote oxidative stress in tomato and CK is introduced as a factor related to the response to low temperature that requires deeper attention in future breeding programs of tomato.

scholarly journals Transcriptome Analysis of Photosynthetic Characteristics was Induced by Low Temperature Stress in Brassica napus L.

2019 ◽  
Author(s):  
Jin Jiaojiao ◽  
Liu Zigang ◽  
Mi Wenbo ◽  
Sun Wancang ◽  
Wu Junyan ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Low Temperature ◽  
Temperature Stress ◽  
Photosynthetic Characteristics ◽  
Low Temperature Stress ◽  
Rna Seq ◽  
Brassica Napus L ◽  
Regulated Expression ◽  
Tolerant Variety ◽  
Cold Tolerant

Abstract Background RNA Sequencing (RNA-Seq) technique could be utilized to compare the transcription groups of two different cold-resistant rapeseed leaves responding to low temperature at the seedling stage, analyze the photosynthetic characteristics of rapeseed subjected to low temperature stress, and identify the related genes for low temperature induction in rapeseed leaves. Results Using cold-tolerant variety 17NS and sensitive variety NF24 as experimental materials, carrying out RNA-Seq analysis by photosynthetic parameter determination and Illumina HiSeqTM platform. and screen out the KEGG significant enrichment pathway related to photosynthetic characteristics under low temperature stress. Differential Expressed Genes (DEGs) were used for real-time PCR to verify the reliability of RNA-Seq results. The results showed that the response of Brassica napus L. to low temperature stress mainly was achieved by inhibiting photosynthesis, the cold-tolerant variety 17NS had a strong ability to maintain membrane system stability and structural integrity after 24 h of low temperature stress, while the sensitive variety NF24 photosynthesis was significantly inhibited. Two pathways of Photosynthesis and Photosynthesis-antennas, which were significantly correlated with photosynthetic characteristics and low temperature stress were screened by KEGG enrichment. The results of DEGs indicated that 64 differentially expressed genes in these two pathways were induced by low temperature stress, and 8 of them were up-regulated expression and 56 of them were down-regulated expression. The expression pattern of DEGs was consistent with the results of RNA-Seq analysis by qRT-PCR detection and confirmed the reliability of RNA-Seq results. Conclusion Our study analysis and identified 17 low-temperature-induced photosynthetic-related candidate genes in Brassica napus L., and the GO and KEGG metabolic pathways clarified the molecular function of differentially expressed genes.

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

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

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

scholarly journals Transcriptome Analysis of Gene Expression Patterns Potentially Associated with Premature Senescence in Nicotiana tabacum L.

Molecules ◽  
2018 ◽  
Vol 23 (11) ◽  
pp. 2856 ◽  
Author(s):  
Zhe Zhao ◽  
Yifan Li ◽  
Songchao Zhao ◽  
Jiawen Zhang ◽  
Hong Zhang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Signal Transduction ◽  
Plant Hormone ◽  
Expression Patterns ◽  
Signal Transduction Pathway ◽  
Dynamic Network ◽  
Gene Expression Patterns ◽  
Premature Senescence ◽  
Chlorophyll Metabolism ◽  
Three Stages

Senescence affects the remobilization of nutrients and adaption of the plant to the environment. Combined stresses can result in premature senescence in plants which exist in the field. In this study, transcriptomic analysis was performed on mature leaves and leaves in three stages of premature senescence to understand the molecular mechanism. With progressive premature senescence, a declining chlorophyll (chl) content and an increasing malonaldehyde (MDA) content were observed, while plasmolysis and cell nucleus pyknosis occurred, mitochondria melted, thylakoid lamellae were dilated, starch grains in chloroplast decreased, and osmiophilic granules increased gradually. Moreover, in total 69 common differentially expressed genes (DEGs) in three stages of premature senescing leaves were found, which were significantly enriched in summarized Gene Ontology (GO) terms of membrane-bounded organelle, regulation of cellular component synthesis and metabolic and biosynthetic processes. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis suggested that the plant hormone signal transduction pathway was significantly enriched. The common DEGs and four senescence-related pathways, including plant hormone signal transduction, porphyrin and chlorophyll metabolism, carotenoid biosynthesis, and regulation of autophagy were selected to be discussed further. This work aimed to provide potential genes signaling and modulating premature senescence as well as the possible dynamic network of gene expression patterns for further study.

scholarly journals Integrated Transcriptomics and Metabolomics Analysis Reveal Key Metabolism Pathways Contributing to Cold Tolerance in Peanut

2021 ◽  
Vol 12 ◽  
Author(s):  
Xin Wang ◽  
Yue Liu ◽  
Zhongkui Han ◽  
Yuning Chen ◽  
Dongxin Huai ◽  
...  
Keyword(s):  
Low Temperature ◽  
Cold Tolerance ◽  
Gene Networks ◽  
Cold Resistance ◽  
Chilling Stress ◽  
Soluble Sugar ◽  
Growth Yield ◽  
Limiting Factors ◽  
Accumulation Pattern ◽  
Cold Tolerant

Low temperature (non-freezing) is one of the major limiting factors in peanut (Arachis hypogaea L.) growth, yield, and geographic distribution. Due to the complexity of cold-resistance trait in peanut, the molecular mechanism of cold tolerance and related gene networks were largely unknown. In this study, metabolomic analysis of two peanut cultivars subjected to chilling stress obtained a set of cold-responsive metabolites, including several carbohydrates and polyamines. These substances showed a higher accumulation pattern in cold-tolerant variety SLH than cold-susceptible variety ZH12 under cold stress, indicating their importance in protecting peanut from chilling injuries. In addition, 3,620 cold tolerance genes (CTGs) were identified by transcriptome sequencing, and the CTGs were most significantly enriched in the “phenylpropanoid biosynthesis” pathway. Two vital modules and several novel hub genes were obtained by weighted gene co-expression network analysis (WGCNA). Several key genes involved in soluble sugar, polyamine, and G-lignin biosynthetic pathways were substantially higher and/or responded more quickly in SLH (cold tolerant) than ZH12 (cold susceptible) under low temperature, suggesting they might be crucial contributors during the adaptation of peanut to low temperature. These findings will not only provide valuable resources for study of cold resistance in peanut but also lay a foundation for genetic modification of cold regulators to enhance stress tolerance in crops.

scholarly journals De novo transcriptome assembly and comparative transcriptomic analysis provide molecular insights into low temperature stress response of Canarium album

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Ruilian Lai ◽  
Xin Feng ◽  
Jin Chen ◽  
Yongyan Zhang ◽  
Xiaoxia Wei ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Plant Hormone ◽  
Acid Metabolism ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Chilling Stress ◽  
Transcriptomic Analysis ◽  
Glutathione Metabolism ◽  
Pathway Enrichment Analysis ◽  
De Novo Transcriptome

AbstractA de novo transcriptome analysis was performed in C. album, a temperature sensitive fruit tree in China, after treatment with varied temperatures. A total number of 168,385 transcripts were assembled, comprising of 109,439 unigenes, of which 70,530 were successfully annotated. Compared with control check group (CK), which was treated under 25 °C, the chilling stress (4 °C) treated group (CT), showed about 2810 up-regulated and 2567 down-regulated genes. Whereas, group treated under freezing (− 3 °C) stress (FT) showed an up-regulation and a down-regulation of 1748 and 1459 genes, respectively. GO classification analysis revealed that DEGs related to metabolic processes, single-organism metabolic process, and catalytic activity are significantly enriched in both CT and FT conditions. KEGG pathway enrichment analysis for both CT and FT treatments showed an enrichment of genes encoding or related to glycine/serine and threonine metabolism, alpha-linolenic acid metabolism, carotenoid biosynthesis, photosynthesis-antenna proteins, and circadian rhythm. However, genes related to photosynthesis, carbon fixation in photosynthetic organisms, glutathione metabolism, pyruvate metabolism, nicotinate and nicotinamide metabolism were specifically enriched in CT condition. Nevertheless, FT treatment induced genes related to plant-pathogen interaction, linoleic acid metabolism, plant hormone signal transduction and pentose phosphate pathway. Many of the genes involved in plant hormone signal transduction showed significantly different expression in both FT and CT conditions. However, the change was more evident in FT. Here we present the first of the reports for a de novo transcriptomic analysis in C. album, suggesting that the plant shows differential responses in chilling and freezing temperatures, where the hormone signaling and transduction contribute greatly to FT responses. Our study thus paves way for future research regarding functions of these potentially identified genes.

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

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

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

scholarly journals MaMAPK3-MaICE1-MaPOD P7 pathway, a positive regulator of cold tolerance in banana

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Jie Gao ◽  
Tongxin Dou ◽  
Weidi He ◽  
Ou Sheng ◽  
Fangcheng Bi ◽  
...  
Keyword(s):  
Transgenic Plants ◽  
Cold Tolerance ◽  
Molecular Breeding ◽  
Cold Resistance ◽  
Oxidoreductase Activity ◽  
Tropical Fruit ◽  
Over Expression ◽  
Cavendish Banana ◽  
Cold Tolerant ◽  
Necrotic Symptoms

Abstract Background Banana is a tropical fruit with a high economic impact worldwide. Cold stress greatly affects the development and production of banana. Results In the present study, we investigated the functions of MaMAPK3 and MaICE1 involved in cold tolerance of banana. The effect of RNAi of MaMAPK3 on Dajiao (Musa spp. ‘Dajiao’; ABB Group) cold tolerance was evaluated. The leaves of the MaMAPK3 RNAi transgenic plants showed wilting and severe necrotic symptoms, while the wide-type (WT) plants remained normal after cold exposure. RNAi of MaMAPK3 significantly changed the expressions of the cold-responsive genes, and the oxidoreductase activity was significantly changed in WT plants, while no changes in transgenic plants were observed. MaICE1 interacted with MaMAPK3, and the expression level of MaICE1 was significantly decreased in MaMAPK3 RNAi transgenic plants. Over-expression of MaICE1 in Cavendish banana (Musa spp. AAA group) indicated that the cold resistance of transgenic plants was superior to that of the WT plants. The POD P7 gene was significantly up-regulated in MaICE1-overexpressing transgenic plants compared with WT plants, and the POD P7 was proved to interact with MaICE1. Conclusions Taken together, our work provided new and solid evidence that MaMAPK3-MaICE1-MaPOD P7 pathway positively improved the cold tolerance in monocotyledon banana, shedding light on molecular breeding for the cold-tolerant banana or other agricultural species.

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