scholarly journals Transcriptomic, proteomic, and physiological comparative analyses of flooding mitigation of the damage induced by low-temperature stress in direct seeded early indica rice at the seedling stage

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Wenxia Wang ◽  
Jie Du ◽  
Liming Chen ◽  
Yongjun Zeng ◽  
Xueming Tan ◽  
...  
Keyword(s):  
Low Temperature ◽  
Temperature Stress ◽  
Molecular Mechanisms ◽  
Tricarboxylic Acid Cycle ◽  
Indica Rice ◽  
Low Temperature Stress ◽  
Seedling Stage ◽  
Differentially Expressed ◽  
Rice Seedlings ◽  
Direct Seeded

Abstract Background Low temperature (LT) often occurs at the seedling stage in the early rice-growing season, especially for direct seeded early-season indica rice, and using flooding irrigation can mitigate LT damage in rice seedlings. The molecular mechanism by which flooding mitigates the damage induced by LT stress has not been fully elucidated. Thus, LT stress at 8 °C, LT accompanied by flooding (LTF) and CK (control) treatments were established for 3 days to determine the transcriptomic, proteomic and physiological response in direct seeded rice seedlings at the seedling stage. Results LT damaged chloroplasts, and thylakoid lamellae, and increased osmiophilic bodies and starch grains compared to CK, but LTF alleviated the damage to chloroplast structure caused by LT. The physiological characteristics of treated plants showed that compared with LT, LTF significantly increased the contents of rubisco, chlorophyll, PEPCK, ATP and GA3 but significantly decreased soluble protein, MDA and ABA contents. 4D-label-free quantitative proteomic profiling showed that photosynthesis-responsive proteins, such as phytochrome, as well as chlorophyll and the tricarboxylic acid cycle were significantly downregulated in LT/CK and LTF/CK comparison groups. However, compared with LT, phytochrome, chlorophyllide oxygenase activity and the glucan branching enzyme in LTF were significantly upregulated in rice leaves. Transcriptomic and proteomic studies identified 72,818 transcripts and 5639 proteins, and 4983 genes that were identified at both the transcriptome and proteome levels. Differentially expressed genes (DEGs) and differentially expressed proteins (DEPs) were significantly enriched in glycine, serine and threonine metabolism, biosynthesis of secondary metabolites, glycolysis/gluconeogenesis and metabolic pathways. Conclusion Through transcriptomic, proteomic and physiological analyses, we determined that a variety of metabolic pathway changes were induced by LT and LTF. GO and KEGG enrichment analyses demonstrated that DEGs and DEPs were associated with photosynthesis pathways, antioxidant enzymes and energy metabolism pathway-related proteins. Our study provided new insights for efforts to reduce the damage to direct seeded rice caused by low-temperature stress and provided a breeding target for low temperature flooding-resistant cultivars. Further analysis of translational regulation and metabolites may help to elucidate the molecular mechanisms by which flooding mitigates low-temperature stress in direct seeded early indica rice at the seedling stage.

scholarly journals Transcriptomic, proteomic, and physiological comparative analyses of flooding mitigating low temperature stress on direct-seeded early indica rice at seedling stage

2020 ◽  
Author(s):  
WENXIA WANG ◽  
Jie Du ◽  
Liming Chen ◽  
Yongjun Zeng ◽  
Xueming Tan ◽  
...  
Keyword(s):  
Low Temperature ◽  
Metabolic Regulation ◽  
Indica Rice ◽  
Physiological Activity ◽  
Growth Characteristic ◽  
Seedling Stage ◽  
Differentially Expressed ◽  
Rice Seedlings ◽  
Direct Seeded ◽  
Early Rice

Abstract Background Low temperature (LT) often occurs at seedling stage in early rice-growing season, especially for direct-seeded early-season indica rice seedlings, and adopting flooding irrigation could mitigate LT damage. However, it is not clear on the response mechanisms of a mitigating effect on LT stress at early rice seedling stage. Results In this study, LT stress with 10/6°C (day/night), LT accompanied by flooding (LTF) and CK (control) treatments were established for 3d to aim to determine the response mechanisms on physiological, transcriptomic, and proteomic of direct-seeded rice seedlings at seedling stage. The results showed that the chloroplasts was severely degraded, thylakoid lamellae were seriously damaged and osmiophilic body increased gradually in LT contrast to CK, but LTF could alleviate the damage of low temperature on chloroplast structure. Compared with LT, LTF significantly increased the contents of Rubisco, chlorophyll, PEPCK, ATP and GA3 of rice seedlings whereas significantly decreased soluble protein, MDA and ABA content, suggesting the higher photosynthetic traits, antioxidant ability and better growth characteristic, although it could also affect the physiological activity contrast to CK. The identified differentially expressed genes and differentially expressed proteins indicated that photosynthesis metabolism pathway, reactive oxygen species and metabolic regulation had significant differences between LT and LTF stress, which were the main reasons that reduced the LT damage of rice seedlings for LTF. Conclusions Our results could provide comprehensive interpretation of physiological characteristics, genes and proteins expression changes in low temperature and low temperature flooding.

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.

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.

A snapshot of the low temperature stress transcriptome of developing rice seedlings (Oryza sativa L.) via ESTs from subtracted cDNA library

2003 ◽  
Vol 107 (6) ◽  
pp. 1071-1082 ◽  
Author(s):  
B. G. de los Reyes ◽  
M. Morsy ◽  
J. Gibbons ◽  
T. S. N. Varma ◽  
W. Antoine ◽  
...  
Keyword(s):  
Oryza Sativa ◽  
Low Temperature ◽  
Cdna Library ◽  
Temperature Stress ◽  
Oryza Sativa L ◽  
Low Temperature Stress ◽  
Rice Seedlings

scholarly journals Transcriptome Sequencing Analysis of Birch (Betula platyphylla Sukaczev) under Low-Temperature Stress

Forests ◽  
2020 ◽  
Vol 11 (9) ◽  
pp. 970
Author(s):  
Siyu Yan ◽  
Dawei Zhang ◽  
Song Chen ◽  
Su Chen
Keyword(s):  
Low Temperature ◽  
Temperature Stress ◽  
Calcium Binding ◽  
Enrichment Analysis ◽  
Glutamate Synthase ◽  
Functional Enrichment Analysis ◽  
Low Temperature Stress ◽  
Functional Enrichment ◽  
Differentially Expressed ◽  
Sequencing Analysis

Low temperature is one of the common abiotic stresses that adversely affect the growth and development of plants. In this study, we used RNA-Seq to identify low-temperature-responsive genes in birch and further analyzed the underlying molecular mechanism. Birch seedlings were treated by the low temperature (6 °C) for 0, 1, 1.5, 2, 2.5, and 3 h, respectively. A total of 3491 genes were differentially expressed after low-temperature stress. Gene Ontology (GO) and Kyoto Encyclopedia of Gene and Genomes (KEGG) functional enrichment analysis were performed for the differentially expressed genes (DEGs). GO analysis indicated that 3491 DEGs were distributed into 1002 categories, and these DEGs were enriched in “cell process”, “metabolic process”, and “stimulus response”, under the “biological process” category; in “organelles” and “cell components”, under the “cell component” category; and in “catalytic activity” and “adhesion”, under the “molecular function” category. The KEGG enrichment indicated that 119 DEGs were involved in Ca2+ and plant hormone signal transduction; 205 DEGs were involved in secondary metabolic processes, such as lipid metabolism and phenylpropanoid biosynthesis pathway; and 20 DEGs were involved in photosynthesis. In addition, a total of 362 transcription factors (TFs) were differentially expressed under low-temperature stress, including AP2/ERF, C2H2, MYB-HB-like, WRKY, bHLH, WD40-like, and GRAS families. Gene Bpev01.c0480.g0081 (calmodulin-like CML38), Bpev01.c1074.g0005 (calmodulin-like CML25), Bpev01.c1074.g0001 (Calcium-binding EF-hand family protein), Bpev01.c2029.g0005 (calmodulin-like protein), Bpev01.c0154.g0008 (POD), Bpev01.c0015.g0143 (N-acetyl-1-glutamate synthase), and Bpev01.c0148.g0010 (branched chain amino acid transferase) were up-regulated at a high level, under low-temperature stress.

Sign in / Sign up

Export Citation Format

Share Document