scholarly journals Differential expression analysis of genes in the root crown of alfalfa under low-temperature stress

2019 ◽  
Author(s):  
Xiaolong Wang ◽  
Huiqing Jin ◽  
Kai Meng ◽  
Zhenyu Jia ◽  
Shiyuan Yan ◽  
...  
Keyword(s):  
Low Temperature ◽  
Temperature Stress ◽  
Expression Patterns ◽  
Differential Expression Analysis ◽  
Northern China ◽  
Winter Hardiness ◽  
Low Temperature Stress ◽  
Rna Seq ◽  
Real Time Quantitative Pcr ◽  
Alfalfa Varieties

Abstract Background: Alfalfa ( Medicago sativa ) is a perennial forage crop widely cultivated in northern China. The root crown is an important storage organ of alfalfa, especially in the wintering process, as it is closely related to winter hardiness. However, the molecular mechanism underlying the winter hardiness of the alfalfa root crown remains unclear. To investigate these gaps in knowledge, the RNA sequencing (RNA-Seq) technology was used to identify critical genes related to winter hardiness. Results: In this study, the winter survival rate of the Lomgmu 806 variety was approximately 3.68-fold higher than that of the Sardi variety. We sequenced the transcriptomes of the root crown of the two alfalfa varieties. Among the 57,712 unigenes identified, 2,299 differentially expressed genes (DEGs) were upregulated, and 2,143 DEGs were downregulated. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway annotations showed that 1,159 unigenes were mainly annotated in 116 pathways. Seven DEGs belonging to the “plant hormone signalling transduction” pathway, the “peroxisome” pathway and transcription factor family (MYB, B3, AP2/ERF, and WRKY) and involved in alfalfa winter hardiness were identified. As a result, the expression patterns of seven DEGs were verified by real-time quantitative PCR (RT-qPCR) analyses, which verified the reliability of the RNA-Seq analyses. Conclusions: The RNA-Seq data revealed the gene regulation response of alfalfa to low-temperature stress, which provides a valuable resource for the further identification and functional analysis of candidate genes related to winter hardiness in alfalfa. Furthermore, these data provide references for future in-depth studies of winter hardiness mechanisms in alfalfa.

scholarly journals Different Genes Express Analysis of root crown of alfalfa under low temperature stress

2019 ◽  
Author(s):  
Xiaolong Wang ◽  
Huiqing Jin ◽  
Kai Meng ◽  
Zhenyu Jia ◽  
Shiyuan Yan ◽  
...  
Keyword(s):  
Survival Rate ◽  
Low Temperature ◽  
Temperature Stress ◽  
Expression Patterns ◽  
Northern China ◽  
Winter Hardiness ◽  
Low Temperature Stress ◽  
Winter Survival ◽  
Rna Seq ◽  
Alfalfa Varieties

Abstract Abstract Background: Alfalfa ( Medicago sativa ) is a perennial forage crop widely cultivated in northern China. The root crown of alfalfa is an important storage organ in the process of wintering, and it is closely related to the winter hardiness of alfalfa. At present, the specific molecular mechanism of response to winter hardiness in alfalfa root crown is unclear. The transcriptome database created by RNA sequencing (RNA-seq) is widely used to identify the critical genes related to winter hardiness. Results: The transcriptomes of alfalfa varieties, such as “Lomgmu 806” (with high winter survival rate) and “Sardi” (with low winter survival rate) have been sequenced in the study. Among the identified 57,712 unigenes, 2,299 differentially expressed genes (DEGs) were up-regulated, and 2,143 unigenes were down-regulated in the Lomgmu 806 vs Sardi root crown. The KEGG pathway annotations showed that 1,159 unigenes were mainly annotated to 116 pathways. Seven DEGs belonging to “plant hormone signaling transduction”, “peroxidase” pathway and transcription factors family (MYB, B3, AP2/ERF, WRKY) genes involved in alfalfa winter hardiness. Among them, the expression patterns of seven DEGs were verified by real-time quantitative PCR (RT-qPCR) analyses, which verified the reliable results of transcriptome sequencing analyses. Conclusions: RNA-Seq was used to discover genes associated with the wintering differences between alfalfa varieties. The transcriptome data showed that the gene regulation response of alfalfa to low temperature stress, which provides a valuable resource for further identification and functional analysis of candidate genes for winter hardiness of alfalfa. In addition, these data provide references for future study of genetic breeding and winter hardiness in alfalfa.

scholarly journals Identification of proteins involved in response to cold stress and genome-wide identification and analysis of the APX gene family in winter rapeseed (Brassica rapa L.)

2021 ◽  
Author(s):  
Li Ma ◽  
Jing Bai ◽  
Jia Xu ◽  
Weiliang Qi ◽  
Haiyun Li ◽  
...  
Keyword(s):  
Low Temperature ◽  
Gene Family ◽  
Temperature Stress ◽  
Brassica Rapa ◽  
Cold Resistance ◽  
Resistance Mechanism ◽  
Northern China ◽  
Low Temperature Stress ◽  
Oilseed Crop ◽  
Cold Response

Abstract Winter Brassica rapa is an important oilseed crop in northern China, but the mechanism of its cold resistance remains unclear. APX plays important roles in response of this plant to abiotic stress and in scavenging free radicals. In this study, 59 DEPs were isolated and identified from winter B. rapa and B. napus using bidirectional electrophoresis, and APX was found to be differentially expressed in these two species. Therefore, the roles of APX proteins in the cold response and superoxide metabolism pathways in both rapeseed species were further investigated. And comprehensive analysis of phylogeny, chromosome distribution, motif identification, sequence structure, gene duplication, and RNA-seq expression profile in APX gene family. Most of the BrAPX genes were specifically expressed under low temperature stress and behaved significantly differently in cold-tolerant and cold-sensitive varieties. qPCR was also used to verify the differences in expression between these two varieties under cold, freezing, drought and heat stress, and these candidate genes and proteins may play important roles in the response of B. rapa to low temperature stress and provide new information for the elucidation of the cold resistance mechanism in B. rapa.

scholarly journals Full-length transcriptome sequencing reveals the low-temperature-tolerance mechanism of Medicago falcata roots

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Guowen Cui ◽  
Hua Chai ◽  
Hang Yin ◽  
Mei Yang ◽  
Guofu Hu ◽  
...  
Keyword(s):  
Low Temperature ◽  
Temperature Stress ◽  
Electrolyte Leakage ◽  
Temperature Tolerance ◽  
Low Temperature Stress ◽  
Full Length ◽  
Rna Seq ◽  
Smrt Sequencing ◽  
Tolerance Mechanism ◽  
Low Temperature Tolerance

Abstract Background Low temperature is one of the main environmental factors that limits crop growth, development, and production. Medicago falcata is an important leguminous herb that is widely distributed worldwide. M. falcata is related to alfalfa but is more tolerant to low temperature than alfalfa. Understanding the low temperature tolerance mechanism of M. falcata is important for the genetic improvement of alfalfa. Results In this study, we explored the transcriptomic changes in the roots of low-temperature-treated M. falcata plants by combining SMRT sequencing and NGS technologies. A total of 115,153 nonredundant sequences were obtained, and 8849 AS events, 73,149 SSRs, and 4189 lncRNAs were predicted. A total of 111,587 genes from SMRT sequencing were annotated, and 11,369 DEGs involved in plant hormone signal transduction, protein processing in endoplasmic reticulum, carbon metabolism, glycolysis/gluconeogenesis, starch and sucrose metabolism, and endocytosis pathways were identified. We characterized 1538 TF genes into 45 TF gene families, and the most abundant TF family was the WRKY family, followed by the ERF, MYB, bHLH and NAC families. A total of 134 genes, including 101 whose expression was upregulated and 33 whose expression was downregulated, were differentially coexpressed at all five temperature points. PB40804, PB75011, PB110405 and PB108808 were found to play crucial roles in the tolerance of M. falcata to low temperature. WGCNA revealed that the MEbrown module was significantly correlated with low-temperature stress in M. falcata. Electrolyte leakage was correlated with most genetic modules and verified that electrolyte leakage can be used as a direct stress marker in physiological assays to indicate cell membrane damage from low-temperature stress. The consistency between the qRT-PCR results and RNA-seq analyses confirmed the validity of the RNA-seq data and the analysis of the regulatory mechanism of low-temperature stress on the basis of the transcriptome. Conclusions The full-length transcripts generated in this study provide a full characterization of the transcriptome of M. falcata and may be useful for mining new low-temperature stress-related genes specific to M. falcata. These new findings could facilitate the understanding of the low-temperature-tolerance mechanism of M. falcata.

scholarly journals Cloning and Functional Analysis of Expansin TaEXPA9 Homologs in Winter Wheat in Frigid Regions

2021 ◽  
Author(s):  
Ziyi Zhao ◽  
Baozhong Hu ◽  
Xu Feng ◽  
Fenglan li ◽  
Fumeng He ◽  
...  
Keyword(s):  
Low Temperature ◽  
Plant Growth ◽  
Winter Wheat ◽  
Temperature Stress ◽  
Cold Hardiness ◽  
Expression Patterns ◽  
Fluorescent Labeling ◽  
Low Temperature Stress ◽  
Wild Type ◽  
In The Wild

Abstract BackgroundLow temperature is an important factor that influences the ability of winter wheat to safely overwinter. Excessive low temperatures restrict the regrowth of winter wheat, thus decreasing agricultural output. Non-enzymatic expansins, which are related to plant growth, have been reported to respond to drought, salinity, and low temperature stress. We obtained an expansin gene, TaEXPA9, that is induced by low temperature from a transcriptome analysis of ‘Dongnong winter wheat no. 2’—a winter wheat with high cold hardiness—but the expression pattern and function of this gene were unknown. We therefore analyzed the expression patterns of TaEXPA9-A/B/D in D2 in response to different abiotic stresses and exogenous phytohormone treatments in different organs. The entire length of TaEXPA9-A/B/D was obtained, and green fluorescent labeling was used for subcellular localization analysis of TaEXPA9-A/B/D on onion epidermis. The 35S::TaEXPA9-A/B/D expression vector was constructed, and an overexpression transgenic Arabidopsis thaliana line was obtained to examine the effects of the homologs of this expansin on plant growth and low temperature stress resistance. ResultsThe results showed that TaEXPA9-A/B/D transcription significantly increased at 4°C low temperature stress, its expression level was higher in the roots, and TaEXPA9-A/B/D was localized to the cell wall. The roots were well-developed in the overexpression A. thaliana, and the growth-related markers and setting rate were better than in the wild-type. Recovery was stronger in the overexpression plants after frost stress. At 4°C low temperature stress, the antioxidant enzyme activity and osmoregulatory substance content in the TaEXPA9-A/B/D-overexpressing A. thaliana plants were significantly higher than in the wild-type plants, and the degree of membrane lipid peroxidation was lower. ConclusionsIn summary, TaEXPA9-A/B/D participates in the low-temperature stress response and may increase the scavenging of reactive oxygen species caused by low temperature stress through the protective enzyme system. Additionally, TaEXPA9-A/B/D can increase the levels of small molecular organic substances to resist osmotic stress caused by low temperature.

Transcriptomic Analysis of Stropharia Rugosoannulata Reveals Potential Carbohydrate Metabolism and Cold Resistance Mechanisms Under Low-Temperature Stress

2021 ◽  
Author(s):  
Haibo Hao ◽  
Jinjing Zhang ◽  
Shengdong Wu ◽  
Jing Bai ◽  
Xinyi Zhuo ◽  
...  
Keyword(s):  
Heat Shock ◽  
Low Temperature ◽  
Heat Shock Protein ◽  
Carbohydrate Metabolism ◽  
Temperature Stress ◽  
Molecular Mechanisms ◽  
Low Temperature Stress ◽  
Rna Seq ◽  
Oxidoreductase Activity ◽  
Heat Shock Protein Genes

Abstract Low temperature is an important environmental factor that restricts the growth of Stropharia rugosoannulata; however, the molecular mechanisms underlying S. rugosoannulata responses to low-temperature stress are largely unknown. In this study, we performed a transcriptome analysis of a high-sensitivity strain (DQ-1) and low-sensitivity strain (DQ-3) under low-temperature stress. The liquid hyphae of S. rugosoannulata treated at 25°C and 10°C were analyzed by RNA-Seq, and a total of 9499 differentially expressed genes (DEGs) were identified. GO and KEGG enrichment analyses showed that these genes were enriched in “xenobiotic biodegradation and metabolism”, “carbohydrate metabolism”, “lipid metabolism” and “oxidoreductase activity”. Further research found that carbohydrate enzyme (AA, GH, CE, and GT) genes were downregulated more significantly in DQ-1 than DQ-3 and several cellulase activities were also reduced to a greater extent. Moreover, the CAT1, CAT2, GR, and POD genes and more heat shock protein genes (HSP20, HSP78 and sHSP) were upregulated in the two strains after low-temperature stress, and the GPX gene and more heat shock protein genes were upregulated in DQ-3. In addition, the enzyme activity and qRT–PCR results showed trends similar to those of the RNA-Seq results. This result indicates that low-temperature stress reduces the expression of different AA, GH, CE, and GT enzyme genes and reduces the secretion of cellulase, thereby reducing the carbohydrate metabolism process and mycelial growth of S. rugosoannulata. Moreover, the expression levels of different types of antioxidant enzymes and heat shock proteins are also crucial for S. rugosoannulata to resist low-temperature stress. In short, this study will provide a basis for further research on important signaling pathways, gene functions and variety breeding of S. rugosoannulata related to low-temperature stress.

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 miR-151 Affects Low-Temperature Tolerance of Penaeus vannamei by Modulating Autophagy Under Low-Temperature Stress

2021 ◽  
Vol 9 ◽  
Author(s):  
QingJian Liang ◽  
WenNa Dong ◽  
MuFei Ou ◽  
ZhongHua Li ◽  
Can Liu ◽  
...  
Keyword(s):  
Low Temperature ◽  
Temperature Stress ◽  
Expression Patterns ◽  
Temperature Tolerance ◽  
Low Temperature Stress ◽  
Low Temperature Tolerance ◽  
Total Hemocyte Count ◽  
Increased Sensitivity ◽  
Novel Strategy ◽  
Environment Stress

MicroRNAs (miRNAs) play key roles in many physiologic and pathologic processes, including autophagy. Autophagy is cellular in an emergency response mechanism of environment stress, but their complex molecular regulatory mechanism under low-temperature stress is largely unknown in shrimp, especially miRNA-mediated regulation of autophagy in low-temperature tolerance. In this article, a shrimp PvTOR and miRNA pva-miR-151 cooperation in response to low-temperature stress has been reported. Pva-miR-151 showed expression patterns opposite to target PvTOR under low-temperature stress. The pva-miR-151 targets the 3′-UTR region of PvTOR, regulate the formation of autophagosome, which contribute to the degradation and recycling of damaged organelles. In addition, the low-temperature tolerance was correlated positively with autophagy in shrimp. Silenced pva-miR-151 increased sensitivity to low-temperature stress, whereas overexpression pva-miR-151 decreased the expression of PvTOR and p-TOR and increased tolerance to low-temperature stress by improving the formation of autophagosome and total hemocyte count. In addition, the TOR activator 3BDO can partially rescue autophagy induced by overexpression of pva-miR-151; these results indicate that miR-151 was necessary for the low-temperature tolerance in shrimp. Taken together, we provide a novel strategy and mechanism for shrimp breeding to improve shrimp low-temperature tolerance.

scholarly journals Full-length transcriptome sequencing reveals a low-temperature-tolerance mechanism in Medicago falcata roots

2019 ◽  
Author(s):  
Guowen Cui ◽  
Hua Chai ◽  
Hang Yin ◽  
Mei Yang ◽  
Guofu Hu ◽  
...  
Keyword(s):  
Low Temperature ◽  
Temperature Stress ◽  
Electrolyte Leakage ◽  
Temperature Tolerance ◽  
Low Temperature Stress ◽  
Full Length ◽  
Rna Seq ◽  
Tolerance Mechanism ◽  
Medicago Falcata ◽  
Low Temperature Tolerance

Abstract Background Low temperature is one of the main environmental factors that limits crop growth, development and production. Medicago falcata is an economically and ecologically important legume that is closely related to alfalfa and exhibits better tolerance to low temperature than alfalfa. Understanding the low-temperature-tolerance mechanism of M. falcata is important for the genetic improvement of alfalfa. Results In this study, we explored the transcriptomic changes in low-temperature-treated M. falcata roots by combining SMRT and NGS technologies. A total of 115,153 nonredundant sequences were obtained, and 8,849 AS events, 73,149 SSRs and 4,189 LncRNAs were predicted. A total of 111,587 genes from SMRT were annotated, and 11,369 DEGs were identified in this paper that are involved in plant hormone signal transduction, protein processing in endoplasmic reticulum, carbon metabolism, glycolysis/gluconeogenesis, starch and sucrose metabolism, and endocytosis pathways. We characterized 1,538 TF genes into 45 TF gene families, and the most abundant TF family was WRKY, followed by ERF, MYB, bHLH and NAC. A total of 134 genes were differentially coexpressed at all five temperature points, including 101 upregulated genes and 33 downregulated genes. PB40804, PB75011, PB110405 and PB108808 were found to play crucial roles in the tolerance of M. falcata to low temperature. The WGCNA results showed that the MEbrown module was significantly correlated with low-temperature stress in M. falcata. Electrolyte leakage was correlated with most genetic modules and corroborated that electrolyte leakage can be used as direct stress markers to reflect cell membrane damage from low-temperature stress in physiological assays. The consistency between the qRT-PCR results and RNA-Seq analyses confirm the validity of the RNA-Seq data and the analysis of the regulation of low-temperature stress in the transcriptome. Conclusions The full-length transcripts generated in this study provided a full characterization of the gene transcription of M. falcata and are useful for mining new low-temperature stress-related genes specific to M. falcata. These new findings facilitate the understanding of low-temperature-tolerance mechanisms in M. falcata.

scholarly journals Characterization of PcLEA14, a Group 5 Late Embryogenesis Abundant Protein Gene from Pear (Pyrus communis)

Plants ◽  
2020 ◽  
Vol 9 (9) ◽  
pp. 1138
Author(s):  
Tomoki Shibuya ◽  
Ryota Itai ◽  
Minori Maeda ◽  
Hiroyasu Kitashiba ◽  
Kanji Isuzugawa ◽  
...  
Keyword(s):  
Low Temperature ◽  
Stress Tolerance ◽  
Temperature Stress ◽  
Expression Patterns ◽  
Fruit Trees ◽  
Regulatory Elements ◽  
Late Embryogenesis Abundant ◽  
Low Temperature Stress ◽  
Late Embryogenesis ◽  
Protein Group

Fruit trees need to overcome harsh winter climates to ensure perennially; therefore, they are strongly influenced by environmental stress. In the present study, we focused on the pear homolog PcLEA14 belonging to the unique 5C late embryogenesis abundant (LEA) protein group for which information is limited on fruit trees. PcLEA14 was confirmed to belong to this protein group using phylogenetic tree analysis, and its expression was induced by low-temperature stress. The seasonal fluctuation in its expression was considered to be related to its role in enduring overwinter temperatures, which is particularly important in perennially. Moreover, the function of PcLEA14 in low-temperature stress tolerance was revealed in transgenic Arabidopsis. Subsequently, the pear homolog of dehydration-responsive element-binding protein/C-repeat binding factor1 (DREB1), which is an important transcription factor in low-temperature stress tolerance and is uncharacterized in pear, was analyzed after bioinformatics analysis revealed the presence of DREB cis-regulatory elements in PcLEA14 and the dormancy-related gene, both of which are also expressed during low temperatures. Among the five PcDREBs, PcDREB1A and PcDREB1C exhibited similar expression patterns to PcLEA14 whereas the other PcDREBs were not expressed in winter, suggesting their different physiological roles. Our findings suggest that the low-temperature tolerance mechanism in overwintering trees is associated with group 5C LEA proteins and DREB1.

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