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 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 The Methylation Patterns and Transcriptional Responses to Chilling Stress at the Seedling Stage in Rice

2019 ◽  
Vol 20 (20) ◽  
pp. 5089 ◽  
Author(s):  
Hui Guo ◽  
Tingkai Wu ◽  
Shuxing Li ◽  
Qiang He ◽  
Zhanlie Yang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Low Temperature ◽  
Cold Stress ◽  
Cold Tolerance ◽  
Temperature Stress ◽  
Chilling Stress ◽  
Low Temperature Stress ◽  
Expression Level ◽  
Altered Expression ◽  
Cold Tolerant

Chilling stress is considered the major abiotic stress affecting the growth, development, and yield of rice. To understand the transcriptomic responses and methylation regulation of rice in response to chilling stress, we analyzed a cold-tolerant variety of rice (Oryza sativa L. cv. P427). The physiological properties, transcriptome, and methylation of cold-tolerant P427 seedlings under low-temperature stress (2–3 °C) were investigated. We found that P427 exhibited enhanced tolerance to low temperature, likely via increasing antioxidant enzyme activity and promoting the accumulation of abscisic acid (ABA). The Methylated DNA Immunoprecipitation Sequencing (MeDIP-seq) data showed that the number of methylation-altered genes was highest in P427 (5496) and slightly lower in Nipponbare (Nip) and 9311 (4528 and 3341, respectively), and only 2.7% (292) of methylation genes were detected as common differentially methylated genes (DMGs) related to cold tolerance in the three varieties. Transcriptome analyses revealed that 1654 genes had specifically altered expression in P427 under cold stress. These genes mainly belonged to transcription factor families, such as Myeloblastosis (MYB), APETALA2/ethylene-responsive element binding proteins (AP2-EREBP), NAM-ATAF-CUC (NAC) and WRKY. Fifty-one genes showed simultaneous methylation and expression level changes. Quantitative RT-PCR (qRT-PCR) results showed that genes involved in the ICE (inducer of CBF expression)-CBF (C-repeat binding factor)—COR (cold-regulated) pathway were highly expressed under cold stress, including the WRKY genes. The homologous gene Os03g0610900 of the open stomatal 1 (OST1) in rice was obtained by evolutionary tree analysis. Methylation in Os03g0610900 gene promoter region decreased, and the expression level of Os03g0610900 increased, suggesting that cold stress may lead to demethylation and increased gene expression of Os03g0610900. The ICE-CBF-COR pathway plays a vital role in the cold tolerance of the rice cultivar P427. Overall, this study demonstrates the differences in methylation and gene expression levels of P427 in response to low-temperature stress, providing a foundation for further investigations of the relationship between environmental stress, DNA methylation, and gene expression in rice.

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 Genome-Wide Association Mapping Unravels the Genetic Control of Seed Vigor under Low-Temperature Conditions in Rapeseed (Brassica napus L.)

Plants ◽  
2021 ◽  
Vol 10 (3) ◽  
pp. 426
Author(s):  
Tao Luo ◽  
Yuting Zhang ◽  
Chunni Zhang ◽  
Matthew N. Nelson ◽  
Jinzhan Yuan ◽  
...  
Keyword(s):  
Low Temperature ◽  
Stress Tolerance ◽  
Candidate Genes ◽  
Temperature Stress ◽  
Seed Vigor ◽  
Low Temperature Stress ◽  
Brassica Napus L ◽  
Temperature Conditions ◽  
Genome Wide ◽  
Tolerance Indices

Low temperature inhibits rapid germination and successful seedling establishment of rapeseed (Brassica napus L.), leading to significant productivity losses. Little is known about the genetic diversity for seed vigor under low-temperature conditions in rapeseed, which motivated our investigation of 13 seed germination- and emergence-related traits under normal and low-temperature conditions for 442 diverse rapeseed accessions. The stress tolerance index was calculated for each trait based on performance under non-stress and low-temperature stress conditions. Principal component analysis of the low-temperature stress tolerance indices identified five principal components that captured 100% of the seedling response to low temperature. A genome-wide association study using ~8 million SNP (single-nucleotide polymorphism) markers identified from genome resequencing was undertaken to uncover the genetic basis of seed vigor related traits in rapeseed. We detected 22 quantitative trait loci (QTLs) significantly associated with stress tolerance indices regarding seed vigor under low-temperature stress. Scrutiny of the genes in these QTL regions identified 62 candidate genes related to specific stress tolerance indices of seed vigor, and the majority were involved in DNA repair, RNA translation, mitochondrial activation and energy generation, ubiquitination and degradation of protein reserve, antioxidant system, and plant hormone and signal transduction. The high effect variation and haplotype-based effect of these candidate genes were evaluated, and high priority could be given to the candidate genes BnaA03g40290D, BnaA06g07530D, BnaA09g06240D, BnaA09g06250D, and BnaC02g10720D in further study. These findings should be useful for marker-assisted breeding and genomic selection of rapeseed to increase seed vigor under low-temperature stress.

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 Cold tolerance in rice plants is partially controlled by root responses

2020 ◽  
Author(s):  
Angie Geraldine Sierra Rativa ◽  
Artur Teixeira de Araújo Junior ◽  
Daniele da Silva Friedrich ◽  
Rodrigo Gastmann ◽  
Thainá Inês Lamb ◽  
...  
Keyword(s):  
Low Temperature ◽  
Cold Tolerance ◽  
Temperature Stress ◽  
Cold Treatment ◽  
Membrane Integrity ◽  
Root Hairs ◽  
Acc Oxidase ◽  
Dry Weight ◽  
Low Temperature Stress ◽  
Cold Tolerant

AbstractRice (Oryza sativa L.) ssp. indica is the most cultivated species in the South of Brazil. However, these plants face low temperature stress from September to November, which is the period of early sowing, affecting plant development during the initial stages of growth, and reducing rice productivity. This study aimed to characterize the root response to low temperature stress during the early vegetative stage of two rice genotypes contrasting in their cold tolerance (CT, cold-tolerant; and CS, cold-sensitive). Root dry weight and length, as well as number of root hairs, were higher in CT than CS when exposed to cold treatment. Histochemical analyses indicated that roots of CS genotype present higher levels of lipid peroxidation and H2O2 accumulation, along with lower levels of plasma membrane integrity than CT under low temperature stress. RNAseq analyses revealed that the contrasting genotypes present completely different molecular responses to cold stress. The number of over-represented functional categories was lower in CT than CS under cold condition, suggesting that CS genotype is more impacted by low temperature stress than CT. Several genes might contribute to rice cold tolerance, including the ones related with cell wall remodeling, cytoskeleton and growth, signaling, antioxidant system, lipid metabolism, and stress response. On the other hand, high expression of the genes SRC2 (defense), root architecture associated 1 (growth), ACC oxidase, ethylene-responsive transcription factor, and cytokinin-O-glucosyltransferase 2 (hormone-related) seems to be related with cold sensibility. Since these two genotypes have a similar genetic background (sister lines), the differentially expressed genes found here can be considered candidate genes for cold tolerance and could be used in future biotechnological approaches aiming to increase rice tolerance to 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.

Differential Proteomic Analysis and Photosynthetic Characteristics of Winter Rapeseed under Low Temperature Stress

2016 ◽  
Vol 42 (10) ◽  
pp. 1541
Author(s):  
Zi-Gang LIU ◽  
Jin-Hai YUAN ◽  
Wan-Cang SUN ◽  
Xiu-Cun ZENG ◽  
Yan FANG ◽  
...  
Keyword(s):  
Low Temperature ◽  
Temperature Stress ◽  
Proteomic Analysis ◽  
Photosynthetic Characteristics ◽  
Low Temperature Stress ◽  
Winter Rapeseed
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