scholarly journals Meta-Analysis of Expression of the Stress Tolerance Associated Genes and Uncover their Cis-Regulatory Elements in Rice (Oryza sativa L.)

2020 ◽  
Vol 13 (1) ◽  
pp. 39-49 ◽  
Author(s):  
Nikwan Shariatipour ◽  
Bahram Heidari
Keyword(s):  
Oryza Sativa ◽  
Stress Tolerance ◽  
Abiotic Stresses ◽  
Regulatory Networks ◽  
Oryza Sativa L ◽  
Expression Profiles ◽  
Meta Analysis ◽  
Regulatory Elements ◽  
Significant Differential Expression ◽  
Bioinformatics Tools

Background: Rice contributes to the staple food of more than half of the world’s population. However, its productivity is influenced by various biotic and abiotic stresses. Genetic engineering and plant breeding tools help to overcome the adverse effects of environmental stresses. The advanced bioinformatics tools provide information for a better understanding of the mechanisms underlying stress tolerance, gene expression profiles and functions of the important genes and cis-regulatory elements involved in better performance under abiotic stresses. Objective: To identify the key genes involved in the tolerance mechanism for abiotic stresses and their regulatory networks in rice (Oryza sativa L.). Methods: A total of 152 various microarray datasets associated with nine rice trials were retrieved for expression meta-analysis through various bioinformatics tools. Results: The results indicated that 29593, 202798, 73224 and 25241 genes represented significant differential expression under cold, drought, salinity and heat stress conditions compared with the control condition, respectively. Twenty three highly overexpressed genes were identified under the evaluated abiotic stresses. The transcription regulatory activity of differentially expressed genes was mainly due to hormone, light and stress-responsive cis-acting regulatory elements among which ABRE, ARE, CGTCA-motif, GARE-motif, TGACG-motif, G-box, G-Box, GAG-motif, GA-motif, TCT-motif, Box 4, Sp1, HSE, MBS and TC-rich repeats were the most important in the promoter sites of the identified up-regulated genes. The results of cis-acting regulatory analysis suggest that 15 cis-acting regulatory elements were contributed to the tolerance mechanisms for abiotic stresses. Conclusion: The result of expression meta-analysis in this study provides an insight for plant breeders for better understanding the function of the genes and their regulatory mechanism in plants (especially cereals) exposed to different abiotic stresses. The outcome of this study suggests practical approaches for designing unified breeding programmes to breed multi-abiotic stress-tolerant species.

Assessment of rice (Oryza sativa L.) genotypes for drought stress tolerance using morpho-physiological indices as a screening technique

2020 ◽  
Vol 53 (1) ◽  
Author(s):  
Asma Asma ◽  
Iqbal Hussain ◽  
Muhammad Yasin Ashraf ◽  
Muhammad Arslan Ashraf ◽  
Rizwan Rasheed ◽  
...  
Keyword(s):  
Oryza Sativa ◽  
Drought Stress ◽  
Stress Tolerance ◽  
Oryza Sativa L ◽  
Screening Technique ◽  
Drought Stress Tolerance ◽  
Physiological Indices

Characterization of Nucleotide Binding ­Site-Encoding Genes in Sweetpotato, Ipomoea batatas(L.) Lam., and Their Response to Biotic and Abiotic Stresses

2021 ◽  
pp. 1-15
Author(s):  
Zengzhi Si ◽  
Yake Qiao ◽  
Kai Zhang ◽  
Zhixin Ji ◽  
Jinling Han
Keyword(s):  
Binding Site ◽  
Abiotic Stresses ◽  
Ipomoea Batatas ◽  
Expression Profiles ◽  
Nucleotide Binding ◽  
Regulatory Elements ◽  
Nucleotide Binding Site ◽  
Biotic And Abiotic Stresses ◽  
Encoding Genes

Sweetpotato, <i>Ipomoea batatas</i> (L.) Lam., is an important and widely grown crop, yet its production is affected severely by biotic and abiotic stresses. The nucleotide binding site (NBS)-encoding genes have been shown to improve stress tolerance in several plant species. However, the characterization of NBS-encoding genes in sweetpotato is not well-documented to date. In this study, a comprehensive analysis of NBS-encoding genes has been conducted on this species by using bioinformatics and molecular biology methods. A total of 315 NBS-encoding genes were identified, and 260 of them contained all essential conserved domains while 55 genes were truncated. Based on domain architectures, the 260 NBS-encoding genes were grouped into 6 distinct categories. Phylogenetic analysis grouped these genes into 3 classes: TIR, CC (I), and CC (II). Chromosome location analysis revealed that the distribution of NBS-encoding genes in chromosomes was uneven, with a number ranging from 1 to 34. Multiple stress-related regulatory elements were detected in the promoters, and the NBS-encoding genes’ expression profiles under biotic and abiotic stresses were obtained. According to the bioinformatics analysis, 9 genes were selected for RT-qPCR analysis. The results revealed that <i>IbNBS75</i>, <i>IbNBS219</i>, and <i>IbNBS256</i> respond to stem nematode infection; <i>Ib­NBS240</i>, <i>IbNBS90</i>, and <i>IbNBS80</i> respond to cold stress, while <i>IbNBS208</i>, <i>IbNBS71</i>, and <i>IbNBS159</i> respond to 30% PEG treatment. We hope these results will provide new insights into the evolution of NBS-encoding genes in the sweetpotato genome and contribute to the molecular breeding of sweetpotato in the future.

scholarly journals Genome-wide characterization of MATE gene family and expression profiles in response to abiotic stresses in rice (Oryza sativa)

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Zhixuan Du ◽  
Qitao Su ◽  
Zheng Wu ◽  
Zhou Huang ◽  
Jianzhong Bao ◽  
...  
Keyword(s):  
Oryza Sativa ◽  
Gene Family ◽  
Tandem Repeats ◽  
Expression Profiles ◽  
Functional Divergence ◽  
Expression Patterns ◽  
Regulatory Elements ◽  
Genome Wide ◽  
Comprehensive Information ◽  
Family Gene

AbstractMultidrug and toxic compound extrusion (MATE) proteins are involved in many physiological functions of plant growth and development. Although an increasing number of MATE proteins have been identified, the understanding of MATE proteins is still very limited in rice. In this study, 46 MATE proteins were identified from the rice (Oryza sativa) genome by homology searches and domain prediction. The rice MATE family was divided into four subfamilies based on the phylogenetic tree. Tandem repeats and fragment replication contribute to the expansion of the rice MATE gene family. Gene structure and cis-regulatory elements reveal the potential functions of MATE genes. Analysis of gene expression showed that most of MATE genes were constitutively expressed and the expression patterns of genes in different tissues were analyzed using RNA-seq. Furthermore, qRT-PCR-based analysis showed differential expression patterns in response to salt and drought stress. The analysis results of this study provide comprehensive information on the MATE gene family in rice and will aid in understanding the functional divergence of MATE genes.

scholarly journals Regulation of ATG6/Beclin-1 homologs by abiotic stresses and hormones in rice (Oryza sativa L.)

2012 ◽  
Vol 11 (4) ◽  
pp. 3676-3687 ◽  
Author(s):  
R.M. Rana ◽  
S. Dong ◽  
Z. Ali ◽  
J. Huang ◽  
H.S. Zhang
Keyword(s):  
Oryza Sativa ◽  
Abiotic Stresses ◽  
Oryza Sativa L ◽  
Beclin 1

scholarly journals In vitro Selection of Drought Stress Tolerance in Rice (Oryza sativa L.) var. Jarava

2019 ◽  
Vol 29 (1) ◽  
pp. 127-131 ◽  
Author(s):  
Omar H Obaid ◽  
SK Reddy
Keyword(s):  
Oryza Sativa ◽  
Drought Stress ◽  
Stress Tolerance ◽  
Plant Tissue ◽  
In Vitro Selection ◽  
Oryza Sativa L ◽  
Drought Stress Tolerance ◽  
Selection Of

Abstract not available Plant Tissue Cult. & Biotech. 29(1): 127-131, 2019 (June)

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