scholarly journals Comparison of Differentially Expressed Genes Involved in Drought Response between Two Elite Rice Varieties

2012 ◽  
Vol 5 (6) ◽  
pp. 1403-1405 ◽  
Author(s):  
Hai-Wen Zhang ◽  
Xiao-Wu Pan ◽  
Yong-Chao Li ◽  
Li-Yun Wan ◽  
Xiao-Xiang Li ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Differentially Expressed ◽  
Drought Response ◽  
Rice Varieties

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

2011 ◽  
Vol 20 (2) ◽  
pp. 149-154 ◽  
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

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

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.

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

2020 ◽  
Vol 7 (6) ◽  
pp. 192243
Author(s):  
Zhenhua Guo ◽  
Lijun Cai ◽  
Chuanxue Liu ◽  
Cuihong Huang ◽  
Zhiqiang Chen ◽  
...  
Keyword(s):  
Low Temperature ◽  
Differentially Expressed Genes ◽  
Chilling Stress ◽  
Cold Treatment ◽  
Chilling Tolerance ◽  
Differentially Expressed ◽  
Antioxidant Enzyme Activities ◽  
Japonica Rice ◽  
Rice Varieties ◽  
Booting Stage

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.

scholarly journals Profiling the differentially expressed genes in two rice varieties during rapid grain-filling stages

2011 ◽  
Vol 33 (6) ◽  
pp. 2259-2268 ◽  
Author(s):  
Chin-Jit Teo ◽  
Le Vinh Thuc ◽  
Keat-Ai Yeoh ◽  
Wai-Sun Chan ◽  
Sudha V. Chivukula ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Grain Filling ◽  
Differentially Expressed ◽  
Rice Varieties
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