scholarly journals Genome Wide Characterization, Identification And Expression Analysis Of Erf Gene Family In Cotton

2020 ◽  
Author(s):  
Muhammad Mubashar Zafar ◽  
Abdul Rehman ◽  
Abdul Razzaq ◽  
Aqsa Parvaiz ◽  
Ghulam Mustafa ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Gene Family ◽  
Abiotic Stress Tolerance ◽  
Diploid Species ◽  
Pathogen Resistance ◽  
Genome Comparison ◽  
Minor Role ◽  
Genome Wide ◽  
A Genome ◽  
Ap2 Domain

AbstractERF is a subfamily of AP2/EREBP superfamily, contained single AP2 domain. The overexpression of ERF genes steered to abiotic stress tolerance and pathogen resistance in transgenic plants. Here, a genome-wide analysis of ERF gene family within two diploid species (G. arboreum & G. raimondii) and two tetraploid species (G. barbadense, G. hirsutum) was performed. A total of 118, 120, 213, 220 genes contained sequence single AP2 domain were identified in G. arboreum, G. raimondii, G. barbadense and G. hirsutum respectively. The identified genes were unevenly distributed across 13/26 chromosomes of A and D genomes of cotton. Genome comparison revealed that segmental duplication may have played crucial roles in the expansion of the cotton ERF gene family, and tandem duplication also played a minor role. Analysis of RNA-Seq data indicated that cotton ERF gene expression levels varied across different tissues and in response to different abiotic stress. Overall, our results could provide valuable information for better understanding the evolution of cotton ERF genes and lays a foundation for future investigation in cotton.

scholarly journals Genome-wide identification and expression analysis of sucrose nonfermenting-1-related protein kinase (SnRK) genes in Triticum aestivum in response to abiotic stress

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Shefali Mishra ◽  
Pradeep Sharma ◽  
Rajender Singh ◽  
Ratan Tiwari ◽  
Gyanendra Pratap Singh
Keyword(s):  
Abiotic Stress ◽  
Gene Family ◽  
Abiotic Stresses ◽  
Phylogenetic Analyses ◽  
Abiotic Stress Tolerance ◽  
Functional Characterization ◽  
Protein Motif ◽  
Element Analysis ◽  
Genome Wide ◽  
A Genome

AbstractThe SnRK gene family is a key regulator that plays an important role in plant stress response by phosphorylating the target protein to regulate subsequent signaling pathways. This study was aimed to perform a genome-wide analysis of the SnRK gene family in wheat and the expression profiling of SnRKs in response to abiotic stresses. An in silico analysis identified 174 SnRK genes, which were then categorized into three subgroups (SnRK1/2/3) on the basis of phylogenetic analyses and domain types. The gene intron–exon structure and protein-motif composition of SnRKs were similar within each subgroup but different amongst the groups. Gene duplication and synteny between the wheat and Arabidopsis genomes was also investigated in order to get insight into the evolutionary aspects of the TaSnRK family genes. The result of cis-acting element analysis showed that there were abundant stress- and hormone-related cis-elements in the promoter regions of 129 SnRK genes. Furthermore, quantitative real-time PCR data revealed that heat, salt and drought treatments enhanced TaSnRK2.11 expression, suggesting that it might be a candidate gene for abiotic stress tolerance. We also identified eight microRNAs targeting 16 TaSnRK genes which are playing important role across abiotic stresses and regulation in different pathways. These findings will aid in the functional characterization of TaSnRK genes for further research.

scholarly journals Genome-Wide Identification and Expression Profiling of the PDI Gene Family Reveals Their Probable Involvement in Abiotic Stress Tolerance in Tomato (Solanum lycopersicum L.)

Genes ◽  
2020 ◽  
Vol 12 (1) ◽  
pp. 23
Author(s):  
Antt Htet Wai ◽  
Muhammad Waseem ◽  
A B M Mahbub Morshed Khan ◽  
Ujjal Kumar Nath ◽  
Do Jin Lee ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Gene Family ◽  
Stress Tolerance ◽  
Solanum Lycopersicum ◽  
Expression Profiling ◽  
Abiotic Stress Tolerance ◽  
Dependent Manner ◽  
Solanum Lycopersicum L ◽  
Genome Wide ◽  
Protein Disulfide

Protein disulfide isomerases (PDI) and PDI-like proteins catalyze the formation and isomerization of protein disulfide bonds in the endoplasmic reticulum and prevent the buildup of misfolded proteins under abiotic stress conditions. In the present study, we conducted the first comprehensive genome-wide exploration of the PDI gene family in tomato (Solanum lycopersicum L.). We identified 19 tomato PDI genes that were unevenly distributed on 8 of the 12 tomato chromosomes, with segmental duplications detected for 3 paralogous gene pairs. Expression profiling of the PDI genes revealed that most of them were differentially expressed across different organs and developmental stages of the fruit. Furthermore, most of the PDI genes were highly induced by heat, salt, and abscisic acid (ABA) treatments, while relatively few of the genes were induced by cold and nutrient and water deficit (NWD) stresses. The predominant expression of SlPDI1-1, SlPDI1-3, SlPDI1-4, SlPDI2-1, SlPDI4-1, and SlPDI5-1 in response to abiotic stress and ABA treatment suggested they play regulatory roles in abiotic stress tolerance in tomato in an ABA-dependent manner. Our results provide new insight into the structure and function of PDI genes and will be helpful for the selection of candidate genes involved in fruit development and abiotic stress tolerance in tomato.

scholarly journals Genome-Wide Characterization of Glutathione Peroxidase (GPX) Gene Family in Rapeseed (Brassica napus L.) Revealed Their Role in Multiple Abiotic Stress Response and Hormone Signaling

Antioxidants ◽  
2021 ◽  
Vol 10 (9) ◽  
pp. 1481
Author(s):  
Wei Li ◽  
Xuemin Huai ◽  
Peitao Li ◽  
Ali Raza ◽  
Muhammad Salman Mubarik ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Brassica Napus ◽  
Gene Family ◽  
Antioxidant Defense ◽  
Main Role ◽  
Brassica Napus L ◽  
Group I ◽  
Genome Wide ◽  
A Genome ◽  
Antioxidant Defense Systems

Plant glutathione peroxidases (GPXs) are the main enzymes in the antioxidant defense system that sustain H2O2 homeostasis and normalize plant reaction to abiotic stress conditions. To understand the major roles of the GPX gene family in rapeseed (Brassica napus L.), for the first time, a genome-wide study identified 25 BnGPX genes in the rapeseed genome. The phylogenetic analysis discovered that GPX genes were grouped into four major groups (Group I–Group IV) from rapeseed and three closely interrelated plant species. The universal investigation uncovered that the BnGPXs gene experienced segmental duplications and positive selection pressure. Gene structure and motifs examination recommended that most of the BnGPX genes demonstrated a comparatively well-maintained exon-intron and motifs arrangement within the identical group. Likewise, we recognized five hormones-, four stress-, and numerous light-reactive cis-elements in the promoters of BnGPXs. Five putative bna-miRNAs from two families were also prophesied, targeting six BnGPXs genes. Gene ontology annotation results proved the main role of BnGPXs in antioxidant defense systems, ROS, and response to stress stimulus. Several BnGPXs genes revealed boosted expression profiles in many developmental tissues/organs, i.e., root, seed, leaf, stem, flower, and silique. The qRT-PCR based expression profiling exhibited that two genes (BnGPX21 and BnGPX23) were suggestively up-regulated against different hormones (ABA, IAA, and MeJA) and abiotic stress (salinity, cold, waterlogging, and drought) treatments. In short, our discoveries provide a basis for additional functional studies on the BnGPX genes in future rapeseed breeding programs.

scholarly journals Genome-wide analysis of Myo-inositol oxygenase gene family in tomato reveals their involvement in ascorbic acid accumulation

2019 ◽  
Author(s):  
Shoaib Munir ◽  
Muhammad Ali Mumtaz ◽  
John Kojo Ahiakpa ◽  
Genzhong Liu ◽  
Wei Zheng ◽  
...  
Keyword(s):  
Ascorbic Acid ◽  
Abiotic Stress ◽  
Gene Family ◽  
Stress Tolerance ◽  
Abiotic Stress Tolerance ◽  
Light Response ◽  
Genome Wide ◽  
Genes Encoding ◽  
Transgenic Lines ◽  
Distribution Mapping

Abstract Background Ascorbic acid (Vitamin C, AsA) is an antioxidant metabolite involved in plant development and environmental stimuli. AsA biosynthesis has been well studied in plants and MIOX is a critical enzyme in plants AsA biosynthesis pathway. However, myo-inositol oxygenase (MIOX) gene family members and their involvement in AsA biosynthesis and response to abiotic stress remain unclear. Results In this study, five tomato genes encoding MIOX proteins and possessing MIOX motifs were identified. Structural analysis and distribution mapping showed that 5 MIOX genes contain different intron/exon patterns and unevenly distributed among four chromosomes. In addition, expression analyses indicated the remarkable expression of SlMIOX genes in different plant tissues. Furthermore, transgenic lines were obtained by over-expression of MIOX4 gene in tomato. The overexpression lines showed a significant increase in total ascorbate in leaves and red fruits compared to control. Expression analysis revealed that increased accumulation of AsA in MIOX4 overexpression lines is possible as a consequence of the multiple genes involved in AsA biosynthesis. Myo inositol (MI) feeding in leaf and fruit implied that AsA biosynthesis was mainly improved by Myo-inositol pathway in leaves and fruits. MIOX4 overexpression lines exhibited a betterlight response, abiotic stress tolerance, and AsA biosynthesis capacity. Conclusions These results showed that MIOX4 transgenic lines contribute to AsA biosynthesis, evident as better light response and improved oxidative stress tolerance. This study provides the first comprehensive analysis of MIOX gene family and their involvement in ascorbate biosynthesis in tomato.

scholarly journals Genome-Wide Analysis and Cloning of the Apple Stress-Associated Protein Gene Family Reveals MdSAP15, Which Confers Tolerance to Drought and Osmotic Stresses in Transgenic Arabidopsis

2018 ◽  
Vol 19 (9) ◽  
pp. 2478 ◽  
Author(s):  
Qinglong Dong ◽  
Dingyue Duan ◽  
Shuang Zhao ◽  
Bingyao Xu ◽  
Jiawei Luo ◽  
...  
Keyword(s):  
Drought Tolerance ◽  
Gene Family ◽  
Transgenic Arabidopsis ◽  
Abiotic Stress Tolerance ◽  
Expression Patterns ◽  
Pcr Analysis ◽  
Sequence Alignments ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
A Genome

Stress-associated proteins (SAPs) are novel A20/AN1 zinc finger domain-containing proteins that are now favorable targets to improve abiotic stress tolerance in plants. However, the SAP gene family and their biological functions have not been identified in the important fruit crop apple (Malus × domestica Borkh.). We conducted a genome-wide analysis and cloning of this gene family in apple and determined that the overexpression of MdSAP15 enhances drought tolerance in Arabidopsis plants. We identified 30 SAP genes in the apple genome. Phylogenetic analysis revealed two major groups within that family. Results from sequence alignments and analyses of 3D structures, phylogenetics, genomics structure, and conserved domains indicated that apple SAPs are highly and structurally conserved. Comprehensive qRT-PCR analysis found various expression patterns for MdSAPs in different tissues and in response to a water deficit. A transgenic analysis showed that the overexpression of MdSAP15 in transgenic Arabidopsis plants markedly enhanced their tolerance to osmotic and drought stresses. Our results demonstrate that the SAP genes are highly conserved in plant species, and that MdSAP15 can be used as a target gene in genetic engineering approaches to improve drought tolerance.

scholarly journals Genome-Wide Identification and Characterization of Soybean GmLOR Gene Family and Expression Analysis in Response to Abiotic Stresses

2021 ◽  
Vol 22 (22) ◽  
pp. 12515
Author(s):  
Yisheng Fang ◽  
Dong Cao ◽  
Hongli Yang ◽  
Wei Guo ◽  
Wenqi Ouyang ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Gene Family ◽  
Abiotic Stresses ◽  
Expression Patterns ◽  
Plant Tolerance ◽  
Promoter Regions ◽  
Real Time Quantitative Pcr ◽  
Related Family ◽  
Genome Wide ◽  
A Genome

The LOR (LURP-one related) family genes encode proteins containing a conserved LOR domain. Several members of the LOR family genes are required for defense against Hyaloperonospora parasitica (Hpa) in Arabidopsis. However, there are few reports of LOR genes in response to abiotic stresses in plants. In this study, a genome-wide survey and expression levels in response to abiotic stresses of 36 LOR genes from Glycine max were conducted. The results indicated that the GmLOR gene family was divided into eight subgroups, distributed on 14 chromosomes. A majority of members contained three extremely conservative motifs. There were four pairs of tandem duplicated GmLORs and nineteen pairs of segmental duplicated genes identified, which led to the expansion of the number of GmLOR genes. The expansion patterns of the GmLOR family were mainly segmental duplication. A heatmap of soybean LOR family genes showed that 36 GmLOR genes exhibited various expression patterns in different tissues. The cis-acting elements in promoter regions of GmLORs include abiotic stress-responsive elements, such as dehydration-responsive elements and drought-inducible elements. Real-time quantitative PCR was used to detect the expression level of GmLOR genes, and most of them were expressed in the leaf or root except that GmLOR6 was induced by osmotic and salt stresses. Moreover, GmLOR4/10/14/19 were significantly upregulated after PEG and salt treatments, indicating important roles in the improvement of plant tolerance to abiotic stress. Overall, our study provides a foundation for future investigations of GmLOR gene functions in soybean.

Identification of stress repressive zinc finger gene family and its expression analysis in rice under abiotic constraints

2020 ◽  
Author(s):  
Chao Zhang ◽  
Yanning Tan ◽  
Jemaa Essemine ◽  
Ni Li ◽  
Zhongxiao Hu ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Gene Family ◽  
Zinc Finger ◽  
Abiotic Stresses ◽  
Expression Patterns ◽  
Rt Pcr ◽  
Conserved Domains ◽  
Genome Wide ◽  
A Genome ◽  
Genome Wide Survey

Abstract Background: Stress repressive zinc finger (SRZ) gene family in rice is one of the plant defense gene families that play a pivotal role in plant growth regulation and development, particularly under stressful conditions. However, there is no genome-wide survey regarding SRZ gene family in rice (OsSRZ) till date. Results: We studied, herein, this gene family by performing a genome-wide screening and we identified 25 OsSRZ gene members using Japonica cultivar as an investigating material. Their chromosome localizations, phylogenetic relationships, genomic structures, conserved domains and promoter cis-regulatory elements were analyzed. Besides, their spatio-temporal expression profiles and expression patterns under various hormones and stress treatments were also assessed. Based on the phylogeny and domain constitution, the OsSRZ gene family was classified into five groups (I-V). Conserved domains analysis demonstrates that OsSRZ proteins contain at least one highly conserved SRZ domain. The analysis of expression patterns of the SRZ gene family reveal that OsSRZ genes display tissue-specific expression patterns at various rice developmental stages and exhibit differential responses to both phytohormones and abiotic stresses. Furthermore, q-RT-PCR analysis reveals that Os SRZ genes exhibit different expression patterns under various abiotic stresses. We notice the presence of a single specific gene considerably or strongly up-regulated for each kind of abiotic stress. Over 12 OsSRZ genes analyzed with q-RT-PCR, solely 4 genes (OsSRZ 1, 2, 10 and 11) were found to be substantially or strongly up-regulated following abiotic stress. Notably, OsSRZ 10 and 11 were up-regulated under heat stress by 7 and 5 times, respectively. However, OsSRZ2 was up-regulated by 7 and 3.5 folds under salt and cold stresses, respectively. Interestingly, OsSRZ1 was up-regulated by about 3~11 times in 24 h following artificial oxidative stress application using 1 mM H2O2 . Conclusions: We deduce that some members of OsSRZ gene family function as abiotic stress marker in rice. At the genomic level and expression pattern, our genome-wide survey could provide promising and valuable insights to widen and strengthen further future investigation by leading a cutting edge research regarding the biological and molecular functions of this gene family.

scholarly journals Genome-wide analysis of Myo-inositol oxygenase gene family in tomato reveals their involvement in ascorbic acid accumulation

2020 ◽  
Author(s):  
Shoaib Munir ◽  
Muhammad Ali Mumtaz ◽  
John Kojo Ahiakpa ◽  
Genzhong Liu ◽  
Weifang Chen ◽  
...  
Keyword(s):  
Ascorbic Acid ◽  
Abiotic Stress ◽  
Gene Family ◽  
Stress Tolerance ◽  
Abiotic Stress Tolerance ◽  
Light Response ◽  
Genome Wide ◽  
Genes Encoding ◽  
Transgenic Lines ◽  
Distribution Mapping

Abstract Background Ascorbic acid (Vitamin C, AsA) is an antioxidant metabolite involved in plant development and environmental stimuli. AsA biosynthesis has been well studied in plants, and MIOX is a critical enzyme in plants AsA biosynthesis pathway. However, Myo-inositol oxygenase (MIOX) gene family members and their involvement in AsA biosynthesis and response to abiotic stress remain unclear. Results In this study, five tomato genes encoding MIOX proteins and possessing MIOX motifs were identified. Structural analysis and distribution mapping showed that 5 MIOX genes contain different intron/exon patterns and unevenly distributed among four chromosomes. Besides, expression analyses indicated the remarkable expression of SlMIOX genes in different plant tissues. Furthermore, transgenic lines were obtained by over-expression of the MIOX4 gene in tomato. The overexpression lines showed a significant increase in total ascorbate in leaves and red fruits compared to control. Expression analysis revealed that increased accumulation of AsA in MIOX4 overexpression lines is possible as a consequence of the multiple genes involved in AsA biosynthesis. Myo inositol (MI) feeding in leaf and fruit implied that the Myo-inositol pathway improved the AsA biosynthesis in leaves and fruits. MIOX4 overexpression lines exhibited abetter light response, abiotic stress tolerance, and AsA biosynthesis capacity. Conclusions These results showed that MIOX4 transgenic lines contribute to AsA biosynthesis, evident as better light response and improved oxidative stress tolerance. This study provides the first comprehensive analysis of the MIOX gene family and their involvement in ascorbate biosynthesis in tomato.

Genome‑wide identification and expression analysis of the ASMT gene family reveals their role in abiotic stress tolerance in apple

2022 ◽  
Vol 293 ◽  
pp. 110683
Author(s):  
Hongtao Wang ◽  
Chunhui Song ◽  
Sen Fang ◽  
Zhengyang Wang ◽  
Shangwei Song ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Gene Family ◽  
Stress Tolerance ◽  
Expression Analysis ◽  
Abiotic Stress Tolerance ◽  
Genome Wide

scholarly journals Genome-wide identification and expression analysis of the calmodulin-binding transcription activator (CAMTA) gene family in wheat (Triticum aestivum L.)

2020 ◽  
Author(s):  
Fan Yang ◽  
Fushuang Dong ◽  
Fanghui Hu ◽  
Yongwei Liu ◽  
Jianfang Chai ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Gene Family ◽  
Expression Analysis ◽  
Developmental Regulation ◽  
Expression Profiles ◽  
Transcription Activator ◽  
Tissue Specific ◽  
Calmodulin Binding ◽  
Genome Wide ◽  
A Genome

Abstract Background: Plant calmodulin-binding transcription activator (CAMTA) proteins play important roles in hormone signal transduction, developmental regulation, and environmental stress tolerance. However, in wheat, the CAMTA gene family has not been systematically characterized. Results: In this work, 15 wheat CAMTA genes were identified using a genome-wide search method. Their chromosome location, physicochemical properties, subcellular localization, gene structure, protein domain, and promoter cis-elements were systematically analyzed. Phylogenetic analysis classified the TaCAMTA genes into three groups (groups A, B, and C), numbered 7, 6, and 2, respectively. The results showed that most TaCAMTA genes contained stress-related cis-elements. Finally, to obtain tissue-specific and stress-responsive candidates, the expression profiles of the TaCAMTAs in various tissues and under biotic and abiotic stresses were investigated. Tissue-specific expression analysis showed that all of the 15 TaCAMTA genes were expressed in multiple tissues with different expression levels, as well as under abiotic stress, the expressions of each TaCAMTA gene could respond to at least one abiotic stress. It also found that 584 genes in wheat genome were predicted to be potential target genes by CAMTA, demonstrating that CAMTA can be widely involved in plant development and growth, as well as coping with stresses. Conclusions: This work systematically identified the CAMTA gene family in wheat at the whole-genome-wide level, providing important candidates for further functional analysis in developmental regulation and the stress response in wheat.

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