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 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 profiling reveals the cold stress responsiveness in two contrasting Chinese jujube cultivars

2020 ◽  
Author(s):  
Heying Zhou(Former Corresponding Author) ◽  
Xiaoming Pang(New Corresponding Author) ◽  
Ying He ◽  
Yongsheng Zhu ◽  
Meiyu Li ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Enrichment Analysis ◽  
Transcriptome Profiling ◽  
Functional Enrichment Analysis ◽  
Functional Enrichment ◽  
Freezing Stress ◽  
Comparative Transcriptome ◽  
Chinese Jujube ◽  
Cold Tolerant ◽  
C 30

Abstract Background Low temperature is a major factor influences the growth and development of Chinese jujube ( Ziziphus jujuba Mill.) in cold winter and spring. Little is known about the molecular mechanisms for coping with different freezing stress conditions in jujube. To gain insight into the freezing-related molecular changes, we conducted comparative transcriptome analyses from the cold-sensitive cultivar ‘Dongzao’ and cold-tolerant cultivar ‘Jinsixiaozao’ using RNA-Seq. Results In our study, more than 20,000 genes were detected at chilling (4°C) and freezing (-10°C, -20°C, -30°C and -40°C) stress between two cultivars. The numbers of differentially expressed genes (DEGs) between the two cultivars was 1831, 2030, 1993, 1845 and 2137 under the five treatments, respectively. Functional enrichment analysis suggested that metabolic pathway, response to stimulus and catalytic activity were significantly enriched at stronger freezing stress. Among them, nine DEGs participated in the pathway of Ca 2+ signal, thirty-two DEGs were identified to take part in sucrose metabolism, and other DEGs were identified to participate in the regulation of ROS, plant hormones and antifreeze protein. In addition, important transcription factors ( WRKY , AP2 / ERF , NAC and bZIP ) participating in the freezing stress were activated under different degrees of freezing stress. Conclusions Our research provides a more comprehensive understanding of DEGs involved in freezing stress at the transcriptome levels in Z. jujuba , especially two cultivars with different cold tolerance. These results expanding our understanding on the complex molecular mechanism of jujube, which also provide new insights and candidate genes for genetic improvement of jujube tolerance to freezing stress.

Comparative transcriptome analysis of two different genotypes of wheat (Triticum aestivum L.) in response to spring freeze-stress

2019 ◽  
Author(s):  
Ziyang Zhang ◽  
Zhiwei Wang ◽  
Zhiyu Wang ◽  
Qidi Zhu
Keyword(s):  
Low Temperature ◽  
Cold Resistance ◽  
Signal Transduction Pathway ◽  
Temperature Treatment ◽  
Transduction Pathway ◽  
Comparative Transcriptome ◽  
Seed Setting ◽  
Low Temperature Treatment ◽  
Freeze Stress ◽  
Seed Setting Rate

Abstract Frequent cold spells in spring can lead to significant yield loss in wheat, which seriously affects the spike differentiation and formation. Aikang58 (AK58) and Zhengmai366 (ZM366) are two important wheat cultivars in China, especially in the main wheat-producing areas of the Yellow River and the Huaihe River. This study investigated the response of AK58 and ZM366 to spring-freeze stress using comparative transcriptome analysis. The yield per plant decreased by 12% (AK58) and 89% (ZM366) after three days of low-temperature treatment during the differentiation of pistil and stamen primordia. Low-temperature treatment had a greater effect on the seed-setting rate of ZM366 than of AK58. RNA-seq analysis of AK58 and ZM366 treated at low temperature found 5835 and 8413 differentially expressed genes (DEGs), respectively, of which 3434 genes were common to both varieties. Further analysis of the higher cold resistance in spring of AK58 compared to ZM366 found: a) In response to low-temperature stress, the expression of gene encoding of antioxidant enzymes in AK58 were much higher than that in ZM366; b) The DEGs expression in the hormone signal transduction pathway under low temperature conditions found that AK58 activated abscisic acid and jasmonic acid signal transduction pathway more effectively; c) Under low-temperature conditions, the metabolic pathway for selenium compounds in AK58 was inhibited; d) Low-temperature stress caused abnormal expression of flowering genes in ZM366, resulting in the final seed setting rate of ZM366 being far lower than AK58. These results provide a sound basis for further screening of genes that may improve the cold resistance of wheat in spring.

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 Genome-Wide Transcriptional Changes of Rhodosporidium kratochvilovae at Low Temperature

2021 ◽  
Vol 12 ◽  
Author(s):  
Rui Guo ◽  
Meixia He ◽  
Xiaoqing Zhang ◽  
Xiuling Ji ◽  
Yunlin Wei ◽  
...  
Keyword(s):  
Low Temperature ◽  
Temperature Response ◽  
Sugar Metabolism ◽  
Enrichment Analysis ◽  
Amino Sugar ◽  
Mapk Signaling ◽  
Pathway Enrichment Analysis ◽  
Rna Seq ◽  
Deep Sequencing Technology ◽  
Rhodosporidium Kratochvilovae

Rhodosporidium kratochvilovae strain YM25235 is a cold-adapted oleaginous yeast strain that can grow at 15°C. It is capable of producing polyunsaturated fatty acids. Here, we used the Nanopore Platform to first assemble the R. kratochvilovae strain YM25235 genome into a 23.71 Mb size containing 46 scaffolds and 8,472 predicted genes. To explore the molecular mechanism behind the low temperature response of R. kratochvilovae strain YM25235, we analyzed the RNA transcriptomic data from low temperature (15°C) and normal temperature (30°C) groups using the next-generation deep sequencing technology (RNA-seq). We identified 1,300 differentially expressed genes (DEGs) by comparing the cultures grown at low temperature (15°C) and normal temperature (30°C) transcriptome libraries, including 553 significantly upregulated and 747 significantly downregulated DEGs. Gene ontology and pathway enrichment analysis revealed that DEGs were primarily related to metabolic processes, cellular processes, cellular organelles, and catalytic activity, whereas the overrepresented pathways included the MAPK signaling pathway, metabolic pathways, and amino sugar and nucleotide sugar metabolism. We validated the RNA-seq results by detecting the expression of 15 DEGs using qPCR. This study provides valuable information on the low temperature response of R. kratochvilovae strain YM25235 for further research and broadens our understanding for the response of R. kratochvilovae strain YM25235 to low temperature.

scholarly journals Comparative transcriptome profiling reveals cold stress responsiveness in two contrasting Chinese jujube cultivars

2020 ◽  
Author(s):  
Heying Zhou ◽  
Ying He ◽  
Yongsheng Zhu ◽  
Meiyu Li ◽  
Shuang Song ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Enrichment Analysis ◽  
Transcriptome Profiling ◽  
Functional Enrichment Analysis ◽  
Functional Enrichment ◽  
Freezing Stress ◽  
Comparative Transcriptome ◽  
Chinese Jujube ◽  
Cold Tolerant ◽  
C 30

Abstract Background: Low temperature is a major factor influencing the growth and development of Chinese jujube (Ziziphus jujuba Mill.) in cold winter and spring. Little is known about the molecular mechanisms enabling jujube to cope with different freezing stress conditions. To elucidate the freezing-related molecular changes, we conducted comparative transcriptome analyses from the cold-sensitive cultivar ‘Dongzao’ and cold-tolerant cultivar ‘Jinsixiaozao’ using RNA-Seq. Results: In our study, more than 20,000 genes were detected at chilling (4°C) and freezing (-10°C, -20°C, -30°C and -40°C) stress between the two cultivars. The numbers of differentially expressed genes (DEGs) between the two cultivars were 1831, 2030, 1993, 1845 and 2137 under the five treatments. Functional enrichment analysis suggested that the metabolic pathway, response to stimulus and catalytic activity were significantly enriched under stronger freezing stress. Among the DEGs, nine participated in the Ca2+ signal pathway, thirty-two were identified to participate in sucrose metabolism, and others were identified to participate in the regulation of ROS, plant hormones and antifreeze proteins. In addition, important transcription factors (WRKY, AP2/ERF, NAC and bZIP) participating in freezing stress were activated under different degrees of freezing stress. Conclusions: Our research first provides a more comprehensive understanding of DEGs involved in freezing stress at the transcriptome level in two Z. jujuba cultivars with different freezing tolerances. These results may help to elucidate the molecular mechanism of freezing tolerance in jujube and also provides new insights and candidate genes for genetically enhancing freezing stress tolerance.

scholarly journals Exosome-Mediated Activation of Neuronal Cells Triggered by γ-Aminobutyric Acid (GABA)

Nutrients ◽  
2021 ◽  
Vol 13 (8) ◽  
pp. 2544
Author(s):  
Ryo Inotsuka ◽  
Miyako Udono ◽  
Atsushi Yamatsu ◽  
Mujo Kim ◽  
Yoshinori Katakura
Keyword(s):  
Oral Administration ◽  
Memory Function ◽  
Neuronal Cells ◽  
Neuronal Cell ◽  
Enrichment Analysis ◽  
Gene Set Enrichment Analysis ◽  
Aminobutyric Acid ◽  
Intestinal Cells ◽  
Cell Functions ◽  
Expression Of Genes

γ-Aminobutyric acid (GABA) is a potent bioactive amino acid, and several studies have shown that oral administration of GABA induces relaxation, improves sleep, and reduces psychological stress and fatigue. In a recent study, we reported that exosomes derived from GABA-treated intestinal cells serve as signal transducers that mediate brain–gut interactions. Therefore, the purpose of this study was to verify the functionality of GABA-derived exosomes and to examine the possibility of improving memory function following GABA administration. The results showed that exosomes derived from GABA-treated intestinal cells (Caco-2) activated neuronal cells (SH-SY5Y) by regulating genes related to neuronal cell functions. Furthermore, we found that exosomes derived from the serum of GABA-treated mice also activated SH-SY5Y cells, indicating that exosomes, which are capable of activating neuronal cells, circulate in the blood of mice orally administered GABA. Finally, we performed a microarray analysis of mRNA isolated from the hippocampus of mice that were orally administered GABA. The results revealed changes in the expression of genes related to brain function. Gene Set Enrichment Analysis (GSEA) showed that oral administration of GABA affected the expression of genes related to memory function in the hippocampus.

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.

scholarly journals Comparative Transcriptome Analysis Reveals Potential Gene Modules Associated with Cold Tolerance in Sugarcane (Saccharum officinarum L.)

2021 ◽  
Author(s):  
Xing Huang ◽  
Yongsheng Liang ◽  
Baoqing Zhang ◽  
Xiupeng Song ◽  
Yangrui Li ◽  
...  
Keyword(s):  
Cold Stress ◽  
Cold Tolerance ◽  
Cold Resistance ◽  
Soluble Sugar ◽  
Resistance Mechanism ◽  
Saccharum Officinarum ◽  
Calcium Signal ◽  
Protein Kinase Activity ◽  
Comparative Transcriptome ◽  
Climate Conditions

AbstractSugarcane is an important crop worldwide, and most sugar is derived directly from sugarcane. Due to its thermophilic nature, the yield of sugarcane is largely influenced by extreme climate conditions, especially cold stress. Therefore, the development of sugarcane with improved cold tolerance is an important goal. However, little is known about the multiple mechanisms underlying cold acclimation at the bud stage in sugarcane. In this study, we emphasized that sensitivity to cold stress was higher for the sugarcane variety ROC22 than for GT42, as determined by physical signs, including bud growth capacity, relative conductivity, malonaldehyde contents, and soluble sugar contents. To understand the factors contributing to the difference in cold tolerance between ROC22 and GT42, comparative transcriptome analyses were performed. We found that genes involved in the regulation of the stability of the membrane system were the relative determinants of difference in cold tolerance. Additionally, genes related to protein kinase activity, starch metabolism, and calcium signal transduction were associated with cold tolerance. Finally, 25 candidate genes, including 23 variety-specific and 2 common genes, and 7 transcription factors were screened out for understanding the possible cold resistance mechanism. The findings of this study provide candidate gene resources for cold resistance and will improve our understanding of the regulation of cold tolerance at the bud stage in sugarcane.

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