scholarly journals Splice Variants of Superoxide Dismutases in Rice and Their Expression Profiles under Abiotic Stresses

2021 ◽  
Vol 22 (8) ◽  
pp. 3997
Author(s):  
Ajay Saini ◽  
Jai S. Rohila ◽  
Ganesan Govindan ◽  
Yong-Fang Li ◽  
Ramanjulu Sunkar
Keyword(s):  
Splice Variants ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Rice Genome ◽  
Stress Conditions ◽  
Superoxide Dismutases ◽  
Rice Seedlings ◽  
Mrna Variants ◽  
Cellular Reactive Oxygen Species ◽  
As Stress

The superoxide dismutases (SODs) play vital roles in controlling cellular reactive oxygen species (ROS) that are generated both under optimal as well as stress conditions in plants. The rice genome harbors seven SOD genes (CSD1, CSD2, CSD3, CSD4, FSD1, FSD2, and MSD) that encode seven constitutive transcripts. Of these, five (CSD2, CSD3, CSD4, FSD1, and MSD) utilizes an alternative splicing (AS) strategy and generate seven additional splice variants (SVs) or mRNA variants, i.e., three for CSD3, and one each for CSD2, CSD4, FSD1, and MSD. The exon-intron organization of these SVs revealed variations in the number and length of exons and/or untranslated regions (UTRs). We determined the expression patterns of SVs along with their constitutive forms of SODs in rice seedlings exposed to salt, osmotic, cold, heavy metal (Cu+2) stresses, as well as copper-deprivation. The results revealed that all seven SVs were transcriptionally active in both roots and shoots. When compared to their corresponding constitutive transcripts, the profiles of five SVs were almost similar, while two specific SVs (CSD3-SV4 and MSD-SV2) differed significantly, and the differences were also apparent between shoots and roots suggesting that the specific SVs are likely to play important roles in a tissue-specific and stress-specific manner. Overall, the present study has provided a comprehensive analysis of the SVs of SODs and their responses to stress conditions in shoots and roots of rice seedlings.

scholarly journals Evolutionary Understanding of Metacaspase Genes in Cultivated and Wild Oryza Species and Its Role in Disease Resistance Mechanism in Rice

Genes ◽  
2020 ◽  
Vol 11 (12) ◽  
pp. 1412
Author(s):  
Ruchi Bansal ◽  
Nitika Rana ◽  
Akshay Singh ◽  
Pallavi Dhiman ◽  
Rushil Mandlik ◽  
...  
Keyword(s):  
Disease Resistance ◽  
Wild Rice ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Resistance Mechanism ◽  
Regulatory Elements ◽  
Stress Conditions ◽  
Pcr Analysis ◽  
North East ◽  
Wild Rice Species

Metacaspases (MCs), a class of cysteine-dependent proteases found in plants, fungi, and protozoa, are predominately involved in programmed cell death processes. In this study, we identified metacaspase genes in cultivated and wild rice species. Characterization of metacaspase genes identified both in cultivated subspecies of Oryza sativa, japonica, and indica and in nine wild rice species was performed. Extensive computational analysis was conducted to understand gene structures, phylogenetic relationships, cis-regulatory elements, expression patterns, and haplotypic variations. Further, the haplotyping study of metacaspase genes was conducted using the whole-genome resequencing data publicly available for 4726 diverse genotype and in-house resequencing data generated for north-east Indian rice lines. Sequence variations observed among wild and cultivated rice species for metacaspase genes were used to understand the duplication and neofunctionalization events. The expression profiles of metacaspase genes were analyzed using RNA-seq transcriptome profiling in rice during different developmental stages and stress conditions. Real-time quantitative PCR analysis of candidate metacaspase genes in rice cultivars Pusa Basmati-1 in response to Magnaporthe oryzae infection indicated a significant role in the disease resistance mechanism. The information provided here will help to understand the evolution of metacaspases and their role under stress conditions in rice.

scholarly journals Genome-wide analysis and expression patterns of lipid phospholipid phospholipase gene family in Brassica napus L.

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Wei Su ◽  
Ali Raza ◽  
Liu Zeng ◽  
Ang Gao ◽  
Yan Lv ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Gene Family ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Stress Conditions ◽  
Motif Analysis ◽  
Genome Wide Analysis ◽  
Group I ◽  
Genome Wide ◽  
A Genome

Abstract Background Lipid phosphate phosphatases (LPP) are critical for regulating the production and degradation of phosphatidic acid (PA), an essential signaling molecule under stress conditions. Thus far, the LPP family genes have not been reported in rapeseed (Brassica napus L.). Results In this study, a genome-wide analysis was carried out to identify LPP family genes in rapeseed that respond to different stress conditions. Eleven BnLPPs genes were identified in the rapeseed genome. Based on phylogenetic and synteny analysis, BnLPPs were classified into four groups (Group I-Group IV). Gene structure and conserved motif analysis showed that similar intron/exon and motifs patterns occur in the same group. By evaluating cis-elements in the promoters, we recognized six hormone- and seven stress-responsive elements. Further, six putative miRNAs were identified targeting three BnLPP genes. Gene ontology analysis disclosed that BnLPP genes were closely associated with phosphatase/hydrolase activity, membrane parts, phosphorus metabolic process, and dephosphorylation. The qRT-PCR based expression profiles of BnLPP genes varied in different tissues/organs. Likewise, several gene expression were significantly up-regulated under NaCl, PEG, cold, ABA, GA, IAA, and KT treatments. Conclusions This is the first report to describe the comprehensive genome-wide analysis of the rapeseed LPP gene family. We identified different phytohormones and abiotic stress-associated genes that could help in enlightening the plant tolerance against phytohormones and abiotic stresses. The findings unlocked new gaps for the functional verification of the BnLPP gene family during stresses, leading to rapeseed improvement.

scholarly journals Genome-Wide Analysis of Dof Genes and Their Response to Abiotic Stress in Rose (Rosa chinensis)

2021 ◽  
Vol 12 ◽  
Author(s):  
Hong Nan ◽  
Richard A. Ludlow ◽  
Min Lu ◽  
Huaming An
Keyword(s):  
Gene Expression ◽  
Abiotic Stress ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Functional Characterization ◽  
Stress Conditions ◽  
Genome Wide Analysis ◽  
Rosa Chinensis ◽  
Genome Wide ◽  
A Genome

Dof (DNA binding with one finger) proteins play important roles in plant development and defense regulatory networks. In the present study, we report a genome-wide analysis of rose Dof genes (RchDof), including phylogenetic inferences, gene structures, chromosomal locations, gene duplications, and expression diversity. A total of 24 full-length RchDof genes were identified in Rosa chinensis, which were assigned to nine distinct subgroups. These RchDof genes were unevenly distributed on rose chromosomes. The genome-scale analysis of synteny indicated that segmental duplication events may have played a major role in the evolution of the RchDof gene family. Analysis of cis-acting elements revealed putative functions of Dofs in rose during development as well as under numerous biotic and abiotic stress conditions. Moreover, the expression profiles derived from qRT-PCR experiments demonstrated distinct expression patterns in various tissues, and gene expression divergence existed among the duplicated RchDof genes, suggesting a fundamentally functional divergence of the duplicated Dof paralogs in rose. The gene expression analysis of RchDofs under drought and salt stress conditions was also performed. The present study offered novel insights into the evolution of RchDofs and can aid in the further functional characterization of its candidate genes.

scholarly journals Comparative functional genomics analysis of cytochrome P450 gene superfamily in wheat and maize

2019 ◽  
Author(s):  
kaifa wei ◽  
YiXuan Li
Keyword(s):  
Amino Acid ◽  
Genetic Manipulation ◽  
Expression Profiles ◽  
Functional Divergence ◽  
Expression Patterns ◽  
Amino Acid Level ◽  
Rice Genome ◽  
Acid Sites ◽  
Drought Treatment ◽  
Specific Expression

Abstract The cytochrome P450s (CYP450s) as the largest enzyme family of plant metabolism participate in various physiological processes, whereas no study has demonstrated interest in comprehensive comparison of the genes in wheat and maize. Genome-wide survey, characterization and comparison of wheat and maize CYP450 gene superfamily are useful for genetic manipulation of the Gramineae crops. Results In total, 1285 and 263 full-length CYP450s were identified in wheat and maize, respectively. According to standard nomenclature, wheat CYP450s (TaCYP450s) were categorized into 45 families, while maize CYP450s (ZmCYP450s) into 43 families. Of maize CYP450s, there are 108 duplicated gene pairs and 134 genes had their syntenic counterparts in rice genome, and a total of 140 duplication events were predicted in wheat CYP450s. Functional divergence analysis at the amino acid level of representative clans CYP51, CYP74 and CYP97 in wheat, maize and rice identified some critical amino acid sites that are responsible for functional divergence of a gene family. Expression profiles of Ta-, ZmCYP450s were investigated using RNA-seq data, and we found the majority of them showed tissue-specific expression patterns such as TaCYP51H39_5B in root; TaCYP74A98_4A in leaf at cotyledon emergence stage (LCE); TaCYP71C162_5A in fruit at whole plant fruit ripening stage (FR); ZmCYP707A5 in root; ZmCYP76B18 in tassel; ZmCYP78A130 in embryo. Under water-deficit condition, 82 and 39 significantly differentially expressed CYP450s were respectively detected in wheat and maize like TaCYP71Y18_1D, TaCYP707A5_6A, TaCYP71R11_1A, TaCYP97B4_6D, ZmCYP81N4, ZmCYP81A1 and ZmCYP71C62, of which TaCYP71Y18_1D and ZmCYP81N4 were the genes most highly induced by drought treatment. Fourteen CYP450s were selected to validate their expression level through qRT-PCR. In total, 477 TaCYP450s were distributed in 22 co-expression modules, and some co-expressed genes that likely take part in the same biochemical pathway were identified. For instance, the expression of TaCYP74A98_4D was highly correlated with TaLOX9, TaLOX36, TaLOX39, TaLOX44 and TaOPR8, and all of them may be involved in jasmonate (JA) biosynthesis. TaCYP73A201_3A showed coexpression with TaPAL1.25, TaCCoAOMT1.2, TaCOMT.1, TaCCR1.6 and TaLAC5, which probably act in the wheat stem and/or root lignin synthesis pathway.

The Predominant microRNAs in β-cell Clusters for Insulin Regulation and Diabetic Control

2020 ◽  
Vol 21 (7) ◽  
pp. 722-734
Author(s):  
Adele Soltani ◽  
Arefeh Jafarian ◽  
Abdolamir Allameh
Keyword(s):  
Mirna Expression ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Diabetic Control ◽  
In Vitro Proliferation ◽  
Cell Functions ◽  
Mirna Expression Profiles ◽  
Multiple Processes ◽  
The Impact

micro (mi)-RNAs are vital regulators of multiple processes including insulin signaling pathways and glucose metabolism. Pancreatic β-cells function is dependent on some miRNAs and their target mRNA, which together form a complex regulative network. Several miRNAs are known to be directly involved in β-cells functions such as insulin expression and secretion. These small RNAs may also play significant roles in the fate of β-cells such as proliferation, differentiation, survival and apoptosis. Among the miRNAs, miR-7, miR-9, miR-375, miR-130 and miR-124 are of particular interest due to being highly expressed in these cells. Under diabetic conditions, although no specific miRNA profile has been noticed, the expression of some miRNAs and their target mRNAs are altered by posttranscriptional mechanisms, exerting diverse signs in the pathobiology of various diabetic complications. The aim of this review article is to discuss miRNAs involved in the process of stem cells differentiation into β-cells, resulting in enhanced β-cell functions with respect to diabetic disorders. This paper will also look into the impact of miRNA expression patterns on in vitro proliferation and differentiation of β-cells. The efficacy of the computational genomics and biochemical analysis to link the changes in miRNA expression profiles of stem cell-derived β-cells to therapeutically relevant outputs will be discussed as well.

scholarly journals Silicon Stimulates Plant Growth and Metabolism in Rice Plants under Conventional and Osmotic Stress Conditions

Plants ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 777
Author(s):  
Sara Monzerrat Ramírez-Olvera ◽  
Libia Iris Trejo-Téllez ◽  
Fernando Carlos Gómez-Merino ◽  
Lucero del Mar Ruíz-Posadas ◽  
Ernesto Gabriel Alcántar-González ◽  
...  
Keyword(s):  
Plant Growth ◽  
Osmotic Stress ◽  
Abiotic Factors ◽  
Stress Conditions ◽  
Chlorophyll B ◽  
Rice Seedlings ◽  
Root Volume ◽  
Total Sugars ◽  
Dry Biomass ◽  
Peg 8000

Exogenous silicon (Si) can enhance plant resistance to various abiotic factors causing osmotic stress. The objective of this research was to evaluate the application of 1 and 2 mM Si to plants under normal conditions and under osmotic stress. Morelos A-98 rice seedlings, were treated with 1 and 2 mM SiO2 for 28 d. Subsequently, half of the plants were subjected to osmotic stress with the addition of 10% polyethylene glycol (PEG) 8000; and continued with the addition of Si (0, 1 and 2 mM SiO2) for both conditions. The application of Si under both conditions increased chlorophyll b in leaves, root volume, as well as fresh and dry biomass of roots. Interestingly, the number of tillers, shoot fresh and dry biomass, shoot water content, concentration of total chlorophyll, chlorophyll a/b ratio, and the concentration of total sugars and proline in shoot increased with the addition of Si under osmotic stress conditions. The addition of Si under normal conditions decreased the concentration of sugars in the roots, K and Mn in roots, and increased the concentration of Fe and Zn in shoots. Therefore, Si can be used as a potent inorganic biostimulant in rice Morelos A-98 since it stimulates plant growth and modulates the concentration of vital biomolecules and essential nutrients.

scholarly journals Characterization of Interactions between the Soybean Salt-Stress Responsive Membrane-Intrinsic Proteins GmPIP1 and GmPIP2

Agronomy ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 1312
Author(s):  
Jia Liu ◽  
Weicong Qi ◽  
Haiying Lu ◽  
Hongbo Shao ◽  
Dayong Zhang
Keyword(s):  
Plasma Membrane ◽  
Salt Stress ◽  
Salt Tolerance ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Gene Expression Profiles ◽  
Early Gene ◽  
Plant Responses ◽  
Constitutive Overexpression ◽  
Important Trait

Salt tolerance is an important trait in soybean cultivation and breeding. Plant responses to salt stress include physiological and biochemical changes that affect the movement of water across the plasma membrane. Plasma membrane intrinsic proteins (PIPs) localize to the plasma membrane and regulate the water and solutes flow. In this study, quantitative real-time PCR and yeast two-hybridization were engaged to analyze the early gene expression profiles and interactions of a set of soybean PIPs (GmPIPs) in response to salt stress. A total of 20 GmPIPs-encoding genes had varied expression profiles after salt stress. Among them, 13 genes exhibited a downregulated expression pattern, including GmPIP1;6, the constitutive overexpression of which could improve soybean salt tolerance, and its close homologs GmPIP1;7 and 1;5. Three genes showed upregulated patterns, including the GmPIP1;6 close homolog GmPIP1;4, when four genes with earlier increased and then decreased expression patterns. GmPIP1;5 and GmPIP1;6 could both physically interact strongly with GmPIP2;2, GmPIP2;4, GmPIP2;6, GmPIP2;8, GmPIP2;9, GmPIP2;11, and GmPIP2;13. Definite interactions between GmPIP1;6 and GmPIP1;7 were detected and GmPIP2;9 performed homo-interaction. The interactions of GmPIP1;5 with GmPIP2;11 and 2;13, GmPIP1;6 with GmPIP2;9, 2;11 and GmPIP2;13, and GmPIP2;9 with itself were strengthened upon salt stress rather than osmotic stress. Taken together, we inferred that GmPIP1 type and GmPIP2 type could associate with each other to synergistically function in the plant cell; a salt-stress environment could promote part of their interactions. This result provided new clues to further understand the soybean PIP–isoform interactions, which lead to potentially functional homo- and heterotetramers for salt tolerance.

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