Global analysis of differentially expressed genes between two Japonica rice varieties induced by low temperature during the booting stage by RNA-Seq

As one of the abiotic stresses, low temperature severely threatens rice production during its entire growth period, especially during the booting stage. In the present study, transcriptome analysis was performed comparing Longjing (LJ) 25 (chilling-tolerant) and LJ 11 (chilling-sensitive) rice varieties to identify genes associated with chilling tolerance in rice spikelets. A total of 23 845 expressed genes and 13 205 differentially expressed genes (DEGs) were identified, respectively. Gene ontology (GO) enrichment analyses revealed ‘response to cold’ (containing 180 DEGs) as the only category enriched in both varieties during the entire cold treatment period. Through M ap M an analysis, we identified nine and six DEGs related to the Calvin cycle and antioxidant enzymes, respectively, including OsRBCS3 , OsRBCS2 , OsRBCS4 , OsAPX2 and OsCATC , that under chilling stress were markedly downregulated in LJ11 compared with LJ25. Furthermore, we predicted their protein–protein interaction (PPI) network and identified nine hub genes (the threshold of co-expressed gene number ≥ 11) in Cytoscape, including three RuBisCO-related genes with 14 co-expressed genes. Under chilling stress, antioxidant enzyme activities (peroxidase (POD) and catalase (CAT)) were downregulated in LJ11 compared with LJ25. However, the content of malondialdehyde (MDA) was higher in LJ11 compared with LJ25. Collectively, our findings identify low temperature responsive genes that can be effectively used as candidate genes for molecular breeding programmes to increase the chilling tolerance of rice.

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Identification of Genes Differentially Expressed in Response to Cold in Pisum sativum Using RNA Sequencing Analyses

Plants ◽

10.3390/plants8080288 ◽

2019 ◽

Vol 8 (8) ◽

pp. 288 ◽

Cited By ~ 2

Author(s):

Nasser Bahrman ◽

Emilie Hascoët ◽

Odile Jaminon ◽

Frédéric Dépta ◽

Jean-François Hû ◽

...

Keyword(s):

Low Temperature ◽

Pisum Sativum ◽

Rna Sequencing ◽

Differentially Expressed Genes ◽

Freezing Tolerance ◽

Cold Treatment ◽

Temperature Treatment ◽

Differentially Expressed ◽

Cold Response ◽

Chilling Response

Low temperature stress affects growth and development in pea (Pisum sativum L.) and decreases yield. In this study, RNA sequencing time series analyses performed on lines, Champagne frost-tolerant and Térèse frost-sensitive, during a low temperature treatment versus a control condition, led us to identify 4981 differentially expressed genes. Thanks to our experimental design and statistical analyses, we were able to classify these genes into three sets. The first one was composed of 2487 genes that could be related to the constitutive differences between the two lines and were not regulated during cold treatment. The second gathered 1403 genes that could be related to the chilling response. The third set contained 1091 genes, including genes that could be related to freezing tolerance. The identification of differentially expressed genes related to cold, oxidative stress, and dehydration responses, including some transcription factors and kinases, confirmed the soundness of our analyses. In addition, we identified about one hundred genes, whose expression has not yet been linked to cold stress. Overall, our findings showed that both lines have different characteristics for their cold response (chilling response and/or freezing tolerance), as more than 90% of differentially expressed genes were specific to each of them.

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Global Analysis of Gene Expression Profiles in Glutinous Rice 89-1 (Oryza sativa L.) Seedlings Exposed to Chilling Stress

Plant Molecular Biology Reporter ◽

10.1007/s11105-020-01278-z ◽

2021 ◽

Author(s):

Xiaoxue Pan ◽

Hong Wu ◽

Mingyu Hu ◽

Zhongwei Wang ◽

Xiaoying Jiang ◽

...

Keyword(s):

Cell Wall ◽

Oryza Sativa ◽

Differentially Expressed Genes ◽

Oryza Sativa L ◽

Expression Profiles ◽

Global Analysis ◽

Chilling Stress ◽

Cold Treatment ◽

Differentially Expressed ◽

Glutinous Rice

AbstractRice (Oryza sativa) is a tropical cereal crop that is severely affected by chilling stress at the seedling stage, although glutinous rice 89-1 (Gr89-1) in Chongqing, China, shows tolerance to low temperatures and overwintering ability. However, little research has been conducted on the mechanisms regulating chilling stress in Gr89-1. In this study, a comprehensive of transcriptional profiles of Gr89-1 seedlings at the three-leaf stage was conducted after a 4 °C treatment for 2, 6, 12, 24, or 48 h. Overall, 2993 differentially expressed genes were detected in Gr89-1 seedlings upon cold exposure. Gene Ontology testing and pathway analysis revealed differentially expressed genes involved in transcriptional regulation, carbohydrate metabolism, plant hormone signal, and cell wall composition. A total of 243 transcription factors were differentially expressed during the cold treatment; in particular, the AP2/EREBP, bHLH, NAC, WRKY, C2H2, and TIFY families were generally upregulated after cold treatment, whereas the mTERF and GNAT families were downregulated. Chilling stress changed the starch and sucrose metabolism, coupled with the accumulation of sucrose and trehalose level, and increases in jasmonic acid level in Gr89-1 seedlings. Furthermore, a number of the cell wall-related genes identified in the present study were also differentially expressed during the cold treatment. The genes and pathways identified in the current study increase our understanding of the mechanisms underlying cold resistance in rice seedlings.

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HARDENING PRETREATMENT BY DROUGHT AND LOW TEMPERATURE ENHANCED CHILLING STRESS TOLERANCE OF CUCUMBER SEEDLINGS

Acta Scientiarum Polonorum Hortorum Cultus ◽

10.24326/asphc.2019.2.4 ◽

2019 ◽

Vol 18 (2) ◽

pp. 29-37 ◽

Cited By ~ 1

Author(s):

Fardin Ghanbari ◽

Sajad Kordi

Keyword(s):

Low Temperature ◽

Chilling Stress ◽

Chilling Injury ◽

Warm Season ◽

Chilling Tolerance ◽

Limiting Factors ◽

Antioxidant Enzyme Activities ◽

Cucumber Seedlings ◽

Injury Index ◽

Randomized Design

Chilling stress is of major limiting factors influencing the growth and development of warm-season crops like cucumber. In this research, the possibility of chilling tolerance of cucumber seedlings was investigated through employing the drought and low-temperature pretreatments. The factorial experiment consisted of two factors including cucumber cultivars (i.e. ‘Super Dominos’ and ‘Super Star’) and hardening treatments (control, low temperatures at 10°C, and 15°C and drought simulated by 10% and 20% PEG) based on completely randomized design (CRD) in 3 replications. After applying treatments and providing them 48 h opportunity to be recovered, the seedlings were subjected to 3°C for a six-day period and 6 h for each day. All hardening treatments improved seedlings’ growth, chlorophyll content, total phenol (TP) and antioxidant enzyme activities, while reducing chilling injury index and malondialdehyde (MDA) content. Comparing to temperature hardening, the drought pretreatment showed to have a better effect on inducing the chilling tolerance into cultivars. Overall, the results of this experiment showed that employing drought and low-temperature pretreatments enabled cucumber seedlings to mitigate the harmful effects of chilling.

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Identification of candidate genes controlling chilling tolerance of rice in the cold region at the booting stage by BSA-Seq and RNA-Seq

Royal Society Open Science ◽

10.1098/rsos.201081 ◽

2020 ◽

Vol 7 (11) ◽

pp. 201081

Author(s):

Zhenhua Guo ◽

Lijun Cai ◽

Zhiqiang Chen ◽

Ruiying Wang ◽

Lanming Zhang ◽

...

Keyword(s):

Candidate Genes ◽

Bulked Segregant Analysis ◽

Expression Patterns ◽

Enrichment Analysis ◽

Chilling Tolerance ◽

Pathway Enrichment Analysis ◽

Potential Candidate ◽

Rice Varieties ◽

Booting Stage ◽

F2 Population

Rice is sensitive to low temperatures, specifically at the booting stage. Chilling tolerance of rice is a quantitative trait loci that is governed by multiple genes, and thus, its precise identification through the conventional methods is an arduous task. In this study, we investigated the candidate genes related to chilling tolerance at the booting stage of rice. The F2 population was derived from Longjing25 (chilling-tolerant) and Longjing11 (chilling-sensitive) cross. Two bulked segregant analysis pools were constructed. A 0.82 Mb region containing 98 annotated genes on chromosomes 6 and 9 was recognized as the candidate region associated with chilling tolerance of rice at the booting stage. Transcriptomic analysis of Longjing25 and Longjing11 revealed 50 differentially expressed genes (DEGs) on the candidate intervals. KEGG pathway enrichment analysis of DEGs was performed. Nine pathways were found to be enriched, which contained 10 DEGs. A total of four genes had different expression patterns or levels between Longjing25 and Longjing11. Four out of the 10 DEGs were considered as potential candidate genes for chilling tolerance. This study will assist in the cloning of the candidate genes responsible for chilling tolerance and molecular breeding of rice for the development of chilling-tolerant rice varieties.

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Effect of Low Temperature Pre-Treatment on Anther Culture in Selected Indica, Japonica Rice Varieties and their Inter Sub-Specific Hybrids

Ceylon Journal of Science (Biological Sciences) ◽

10.4038/cjsbs.v38i1.1322 ◽

2009 ◽

Vol 38 (1) ◽

pp. 11 ◽

Cited By ~ 5

Author(s):

HNI Herath ◽

DC Bandara ◽

PK Samarajeewa ◽

DSA Wijesundara

Keyword(s):

Low Temperature ◽

Anther Culture ◽

Japonica Rice ◽

Rice Varieties ◽

Pre Treatment

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Differentially expressed genes in sensitive and tolerant rice varieties in response to salt-stress

Journal of Plant Biochemistry and Biotechnology ◽

10.1007/s13562-010-0022-5 ◽

2011 ◽

Vol 20 (2) ◽

pp. 149-154 ◽

Cited By ~ 16

Author(s):

Awadhesh Pandit ◽

Vandna Rai ◽

Tilak R. Sharma ◽

Prakash C. Sharma ◽

Nagendra K. Singh

Keyword(s):

Salt Stress ◽

Differentially Expressed Genes ◽

Differentially Expressed ◽

Rice Varieties

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Identification and characterization of heat-responsive microRNAs at the booting stage in two rice varieties 9311 and Nagina 22

Genome ◽

10.1139/gen-2020-0175 ◽

2021 ◽

Author(s):

Ying Luo ◽

Tao Wang ◽

Dan Yang ◽

Biao Luo ◽

Weiping Wang ◽

...

Keyword(s):

Stress Responses ◽

High Throughput Sequencing ◽

Target Genes ◽

Elevated Temperatures ◽

Differentially Expressed ◽

Control Group ◽

Microrna Target ◽

Rice Varieties ◽

Booting Stage ◽

Differentially Expressed Mirnas

Abstract: MicroRNAs (miRNAs) are small, non-coding, regulatory RNAs that play important roles in abiotic stress responses in plants. but their regulatory roles in the adaptive response to heat stress at the booting stage in two rice varieties 9311 and Nagina 22, remain largely unknown. In this study, 464 known miRNAs and 123 potential novel miRNAs were identified. Of these miRNAs, a total of 90 differential expressed miRNAs were obtained with 9311 libraries as control group, of which 54 upregulated and 36 downregulated miRNAs. To gain insight into functional significance, 2773 potential target genes of these 90 differentially expressed miRNAs were predicted. GO enrichment showed that the predicted target genes of differentially expressed miRNAs including NACs, LACs, CSD, and Hsp40. KEGG pathway analysis showed that target genes of these differentially expressed miRNAs were significantly enriched in plant hormone signal transduction pathway. The expression levels of ten differentially expressed miRNAs and their target genes obtained by qRT-PCR were largely consistent with the sequencing results. This study lays a foundation for the elucidation of the miRNA-mediated regulatory mechanism in rice at elevated temperatures. Key words: rice, heat-responsive, microRNA, target gene, booting stage, high-throughput sequencing

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Cell Type-Specific Differentiation Between Indica and Japonica Rice Root Tip Responses to Different Environments Based on Single-Cell RNA Sequencing

Frontiers in Genetics ◽

10.3389/fgene.2021.659500 ◽

2021 ◽

Vol 12 ◽

Author(s):

Zhe Wang ◽

Daofu Cheng ◽

Chengang Fan ◽

Cong Zhang ◽

Chao Zhang ◽

...

Keyword(s):

Rna Sequencing ◽

Differentially Expressed Genes ◽

Rice Root ◽

Differentially Expressed ◽

Bzip Transcription Factor ◽

Quiescent Center ◽

Cell Type ◽

Rice Varieties ◽

Specific Differentiation ◽

Cell Type Specific

Background: As Oryza sativa ssp. indica and Oryza sativa ssp. japonica are the two major subspecies of Asian cultivated rice, the adaptative evolution of these varieties in divergent environments is an important topic in both theoretical and practical studies. However, the cell type-specific differentiation between indica and japonica rice varieties in response to divergent habitat environments, which facilitates an understanding of the genetic basis underlying differentiation and environmental adaptation between rice subspecies at the cellular level, is little known.Methods: We analyzed a published single-cell RNA sequencing dataset to explore the differentially expressed genes between indica and japonica rice varieties in each cell type. To estimate the relationship between cell type-specific differentiation and environmental adaptation, we focused on genes in the WRKY, NAC, and BZIP transcription factor families, which are closely related to abiotic stress responses. In addition, we integrated five bulk RNA sequencing datasets obtained under conditions of abiotic stress, including cold, drought and salinity, in this study. Furthermore, we analyzed quiescent center cells in rice root tips based on orthologous markers in Arabidopsis.Results: We found differentially expressed genes between indica and japonica rice varieties with cell type-specific patterns, which were enriched in the pathways related to root development and stress reposes. Some of these genes were members of the WRKY, NAC, and BZIP transcription factor families and were differentially expressed under cold, drought or salinity stress. In addition, LOC_Os01g16810, LOC_Os01g18670, LOC_Os04g52960, and LOC_Os08g09350 may be potential markers of quiescent center cells in rice root tips.Conclusion: These results identified cell type-specific differentially expressed genes between indica-japonica rice varieties that were related to various environmental stresses and provided putative markers of quiescent center cells. This study provides new clues for understanding the development and physiology of plants during the process of adaptative divergence, in addition to identifying potential target genes for the improvement of stress tolerance in rice breeding applications.

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Transcriptomic Analysis of Viable but Non-Culturable Escherichia coli O157:H7 Formation Induced by Low Temperature

Microorganisms ◽

10.3390/microorganisms7120634 ◽

2019 ◽

Vol 7 (12) ◽

pp. 634 ◽

Cited By ~ 1

Author(s):

Junliang Zhong ◽

Xihong Zhao

Keyword(s):

Escherichia Coli ◽

Low Temperature ◽

Differentially Expressed Genes ◽

Pathogenic Bacteria ◽

Differentially Expressed ◽

Transmembrane Transport ◽

Pathway Enrichment Analysis ◽

Escherichia Coli O157 ◽

Vbnc State ◽

E Coli

Escherichia coli O157:H7 is one of the most common pathogenic bacteria that pose a threat to food safety. The aim of this study was to investigate the mechanisms of the formation of viable but non-culturable (VBNC) E. coli O157:H7 induced by low temperature (−20 °C) using RNA sequencing (RNA-Seq) transcriptomics analysis. The results of the present investigation revealed the presence of 2298 differentially expressed genes in VBNC cells, accounting for 46.03% of the total number of genes. Additionally, GO function and KEGG pathway enrichment analysis were performed to investigate the functional and related metabolic pathways of the differentially expressed genes. We found that the ion transport, protein synthesis, and protein transmembrane transport activities were significantly improved in the VBNC cells, indicating that E. coli O157:H7 cells synthesized a considerable amount of protein to maintain the levels of their functional metabolic processes and life activities in the VBNC state. In conclusion, we suggest that the increased synthesis of proteins such as SecY, FtsY, and Ffh might indicate that they are the key proteins involved in the improvement of the transmembrane transport activities in VBNC E. coli O157:H7 cells, maintaining their functional metabolism in the VBNC state and enhancing their survival ability under low temperatures.

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