scholarly journals Genome-Wide Identification and Characterization of PIN-FORMED (PIN) Gene Family Reveals Role in Developmental and Various Stress Conditions in Triticum aestivum L.

2021 ◽  
Vol 22 (14) ◽  
pp. 7396
Author(s):  
Manu Kumar ◽  
Bhagwat Singh Kherawat ◽  
Prajjal Dey ◽  
Debanjana Saha ◽  
Anupama Singh ◽  
...  
Keyword(s):  
Gene Family ◽  
Auxin Transport ◽  
Expression Patterns ◽  
Triticum Aestivum L ◽  
Stress Conditions ◽  
Biotic And Abiotic Stress ◽  
Developmental Processes ◽  
Qrt Pcr ◽  
Genome Wide

PIN-FORMED (PIN) genes play a crucial role in regulating polar auxin distribution in diverse developmental processes, including tropic responses, embryogenesis, tissue differentiation, and organogenesis. However, the role of PIN-mediated auxin transport in various plant species is poorly understood. Currently, no information is available about this gene family in wheat (Triticum aestivum L.). In the present investigation, we identified the PIN gene family in wheat to understand the evolution of PIN-mediated auxin transport and its role in various developmental processes and under different biotic and abiotic stress conditions. In this study, we performed genome-wide analysis of the PIN gene family in common wheat and identified 44 TaPIN genes through a homology search, further characterizing them to understand their structure, function, and distribution across various tissues. Phylogenetic analyses led to the classification of TaPIN genes into seven different groups, providing evidence of an evolutionary relationship with Arabidopsis thaliana and Oryza sativa. A gene exon/intron structure analysis showed a distinct evolutionary path and predicted the possible gene duplication events. Further, the physical and biochemical properties, conserved motifs, chromosomal, subcellular localization, transmembrane domains, and three-dimensional (3D) structure were also examined using various computational approaches. Cis-elements analysis of TaPIN genes showed that TaPIN promoters consist of phytohormone, plant growth and development, and stress-related cis-elements. In addition, expression profile analysis also revealed that the expression patterns of the TaPIN genes were different in different tissues and developmental stages. Several members of the TaPIN family were induced during biotic and abiotic stress. Moreover, the expression patterns of TaPIN genes were verified by qRT-PCR. The qRT-PCR results also show a similar expression with slight variation. Therefore, the outcome of this study provides basic genomic information on the expression of the TaPIN gene family and will pave the way for dissecting the precise role of TaPINs in plant developmental processes and different stress conditions.

scholarly journals Genome-Wide Identification and Characterization of the Brassinazole-resistant (BZR) Gene Family and Its Expression in the Various Developmental Stage and Stress Conditions in Wheat (Triticum aestivum L.)

2021 ◽  
Vol 22 (16) ◽  
pp. 8743
Author(s):  
Mahipal Singh Kesawat ◽  
Bhagwat Singh Kherawat ◽  
Anupama Singh ◽  
Prajjal Dey ◽  
Mandakini Kabi ◽  
...  
Keyword(s):  
Triticum Aestivum ◽  
Gene Family ◽  
Evolutionary Relationship ◽  
Triticum Aestivum L ◽  
Regulatory Elements ◽  
Stress Conditions ◽  
Homology Search ◽  
Slight Variation ◽  
Developmental Processes ◽  
Genome Wide

Brassinosteroids (BRs) play crucial roles in various biological processes, including plant developmental processes and response to diverse biotic and abiotic stresses. However, no information is currently available about this gene family in wheat (Triticum aestivum L.). In the present investigation, we identified the BZR gene family in wheat to understand the evolution and their role in diverse developmental processes and under different stress conditions. In this study, we performed the genome-wide analysis of the BZR gene family in the bread wheat and identified 20 TaBZR genes through a homology search and further characterized them to understand their structure, function, and distribution across various tissues. Phylogenetic analyses lead to the classification of TaBZR genes into five different groups or subfamilies, providing evidence of evolutionary relationship with Arabidopsis thaliana, Zea mays, Glycine max, and Oryza sativa. A gene exon/intron structure analysis showed a distinct evolutionary path and predicted the possible gene duplication events. Further, the physical and biochemical properties, conserved motifs, chromosomal, subcellular localization, and cis-acting regulatory elements were also examined using various computational approaches. In addition, an analysis of public RNA-seq data also shows that TaBZR genes may be involved in diverse developmental processes and stress tolerance mechanisms. Moreover, qRT-PCR results also showed similar expression with slight variation. Collectively, these results suggest that TaBZR genes might play an important role in plant developmental processes and various stress conditions. Therefore, this work provides valuable information for further elucidate the precise role of BZR family members in wheat.

scholarly journals Characterization of MATE Gene Family And Its Role In Drought, Heat, And Salt Tolerance In Wheat (Triticum Aestivum L.)

2021 ◽  
Author(s):  
Joseph Noble Amoah ◽  
Yong Weon Seo
Keyword(s):  
Salt Stress ◽  
Expression Patterns ◽  
Triticum Aestivum L ◽  
Stress Conditions ◽  
Crop Species ◽  
Expression Levels ◽  
Cis Acting ◽  
Genome Wide ◽  
A Genome

Abstract To explore the response of multidrug and toxic compound extrusion (MATE) proteins to drought, heat, and salt stress in wheat, a genome-wide identification and expression study was performed. 20 MATE genes located on 4 of the 12 chromosomes were identified and categorized into four (I-1V) subfamilies, based on phylogenetic analysis. Wheat MATE family expansion was primarily driven by whole-genome duplication (WGD) and tandem events. In the same subfamily, gene exon-intron structures and motif composition are more similar. TaMATE genes had cis-acting elements that were implicated in stress and defense response. Tae-miR5175e was identified as the highly expressed miRNA that targets TaMATEs by miRNA prediction. When compared to controls, the relative expression patterns of seven TaMATE genes were substantially elevated during drought stress. TaMATE2, 10, 13, and 14 expression levels considerably elevated after 15 days (d) of heat stress, whereas TaMATE2, 14, 18, and 20 expression levels were highly upregulated following 15 d of salt stress treatment, indicating the crucial role of TaMATEs under these abiotic stress conditions. Furthermore, drought, heat, and salt stress decreased wheat water content, but increased malondialdehyde (MDA), electrolyte leakage (EL), and proline content, whereas the expression of the 7 putative MATE genes was correlated with physio-biochemical indicators of these stress conditions. The findings contribute to a better understanding of the complexities of MATEs and present a theoretical base for future MATE gene discovery and application in wheat and other crop species.

Genome-wide characterization and expression profiling of the MAPKKK genes in Gossypium arboreum L.

Genome ◽  
2019 ◽  
Vol 62 (9) ◽  
pp. 609-622 ◽  
Author(s):  
Weidong Zhu ◽  
Wei Tan ◽  
Qiulin Li ◽  
Xiugui Chen ◽  
Junjuan Wang ◽  
...  
Keyword(s):  
Gene Family ◽  
Stress Responses ◽  
Expression Patterns ◽  
Mitogen Activated Protein Kinase ◽  
Gossypium Arboreum ◽  
Developmental Processes ◽  
Protein Motifs ◽  
Genome Wide ◽  
A Genome ◽  
Salt And Drought Stresses

Mitogen-activated protein kinase kinase kinases (MAPKKKs) are important components of MAPK cascades, which have different functions during developmental processes and stress responses. To date, there has been no systematic investigation of this gene family in the diploid cotton Gossypium arboreum L. In this study, a genome-wide survey was performed that identified 78 MAPKKK genes in G. arboreum. Phylogenetic analysis classified these genes into three subgroups: 14 belonged to ZIK, 20 to MEKK, and 44 to Raf. Chromosome location, phylogeny, and the conserved protein motifs of the MAPKKK gene family in G. arboreum were analyzed. The MAPKKK genes had a scattered genomic distribution across 13 chromosomes. The members in the same subfamily shared similar conserved motifs. The MAPKKK expression patterns were analyzed in mature leaves, stems, roots, and at different ovule developmental stages, as well as under salt and drought stresses. Transcriptome analysis showed that 76 MAPKKK genes had different transcript accumulation patterns in the tested tissues and 38 MAPKKK genes were differentially expressed in response to salt and drought stresses. These results lay the foundation for understanding the complex mechanisms behind MAPKKK-mediated developmental processes and abiotic stress-signaling transduction pathways in cotton.

scholarly journals Genome-wide characterization and expression analysis of the Dof gene family related to abiotic stress in watermelon

2019 ◽  
Author(s):  
Yong Zhou ◽  
Yuan Cheng ◽  
Chunpeng Wan ◽  
Youxin Yang ◽  
Jinyin Chen
Keyword(s):  
Phylogenetic Analysis ◽  
Gene Family ◽  
Expression Patterns ◽  
Future Research ◽  
Biological Processes ◽  
Biological Functions ◽  
Specific Expression ◽  
Qrt Pcr ◽  
Genome Wide ◽  
Intron Structure

The plant DNA-binding with one finger (Dof) gene family is a class of plant-specific transcription factors that play vital roles in many biological processes and response to stresses. In the present study, a total of 36 ClDof genes were identified in the watermelon genome, which were unevenly distributed on 10 chromosomes. Phylogenetic analysis showed that the ClDof proteins could be divided into nine groups, and the members in a particular group had similar motif arrangement and exon-intron structure. We then analyzed the expression patterns of nine selected ClDof genes in eight specific tissues by qRT-PCR, and the results showed that they have tissue-specific expression patterns. We also evaluated the expression levels of the nine selected ClDof genes under salt stress and ABA treatments using qRT-PCR, and they showed differential expression under these treatments, suggesting their important roles in stress response. Taken together, our results provide a basis for future research on the biological functions of Dof genes in watermelon.

scholarly journals Genome-Wide Identification and Expression Profile Analysis of the Phospholipase C Gene Family in Wheat (Triticum aestivum L.)

Plants ◽  
2020 ◽  
Vol 9 (7) ◽  
pp. 885
Author(s):  
Xianguo Wang ◽  
Yang Liu ◽  
Zheng Li ◽  
Xiang Gao ◽  
Jian Dong ◽  
...  
Keyword(s):  
Gene Family ◽  
Phospholipase C ◽  
Profile Analysis ◽  
Expression Patterns ◽  
Functional Characterization ◽  
Primary Root ◽  
In Silico Analysis ◽  
Triticum Aestivum L ◽  
Stress Conditions ◽  
Phosphatase Domain

Phospholipid-hydrolyzing enzymes include members of the phospholipase C (PLC) family that play important roles in regulating plant growth and responding to stress. In the present study, a systematic in silico analysis of the wheat PLC gene family revealed a total of 26 wheat PLC genes (TaPLCs). Phylogenetic and sequence alignment analyses divided the wheat PLC genes into 2 subfamilies, TaPI-PLC (containing the typical X, Y, and C2 domains) and TaNPC (containing a phosphatase domain). TaPLC expression patterns differed among tissues, organs, and under abiotic stress conditions. The transcript levels of 8 TaPLC genes were validated through qPCR analyses. Most of the TaPLC genes were sensitive to salt stress and were up-regulated rapidly, and some were sensitive to low temperatures and drought. Overexpression of TaPI-PLC1-2B significantly improved resistance to salt and drought stress in Arabidopsis, and the primary root of P1-OE was significantly longer than that of the wild type under stress conditions. Our results not only provide comprehensive information for understanding the PLC gene family in wheat, but can also provide a solid foundation for functional characterization of the wheat PLC gene family.

scholarly journals Genome-wide characterization and expression analysis of the HD-Zip gene family in response to drought and salinity stresses in sesame

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Mengyuan Wei ◽  
Aili Liu ◽  
Yujuan Zhang ◽  
Yong Zhou ◽  
Donghua Li ◽  
...  
Keyword(s):  
Gene Family ◽  
Stress Responses ◽  
Leucine Zipper ◽  
Expression Patterns ◽  
Functional Characterization ◽  
Genome Wide ◽  
Gene Structures ◽  
Relationship Of ◽  
Zip Genes

Abstract Background The homeodomain-leucine zipper (HD-Zip) gene family is one of the plant-specific transcription factor families, involved in plant development, growth, and in the response to diverse stresses. However, comprehensive analysis of the HD-Zip genes, especially those involved in response to drought and salinity stresses is lacking in sesame (Sesamum indicum L.), an important oil crop in tropical and subtropical areas. Results In this study, 45 HD-Zip genes were identified in sesame, and denominated as SiHDZ01-SiHDZ45. Members of SiHDZ family were classified into four groups (HD-Zip I-IV) based on the phylogenetic relationship of Arabidopsis HD-Zip proteins, which was further supported by the analysis of their conserved motifs and gene structures. Expression analyses of SiHDZ genes based on transcriptome data showed that the expression patterns of these genes were varied in different tissues. Additionally, we showed that at least 75% of the SiHDZ genes were differentially expressed in responses to drought and salinity treatments, and highlighted the important role of HD-Zip I and II genes in stress responses in sesame. Conclusions This study provides important information for functional characterization of stress-responsive HD-Zip genes and may contribute to the better understanding of the molecular basis of stress tolerance in sesame.

scholarly journals Genome-wide identification, phylogeny and expression analysis of the SPL gene family in wheat

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Ting Zhu ◽  
Yue Liu ◽  
Liting Ma ◽  
Xiaoying Wang ◽  
Dazhong Zhang ◽  
...  
Keyword(s):  
Abscisic Acid ◽  
Gene Family ◽  
Gene Structure ◽  
Expression Patterns ◽  
Wheat Yield ◽  
Chromosomal Distribution ◽  
Positive Role ◽  
Qrt Pcr ◽  
Genome Wide ◽  
Duplication Events

Abstract Background Members of the plant-specific SPL gene family (squamosa promoter-binding protein -like) contain the SBP conserved domain and are involved in the regulation of plant growth and development, including the development of plant flowers and plant epidermal hair, the plant stress response, and the synthesis of secondary metabolites. This family has been identified in various plants. However, there is no systematic analysis of the SPL gene family at the genome-wide level of wheat. Results In this study, 56 putative TaSPL genes were identified using the comparative genomics method; we renamed them TaSPL001 - TaSPL056 on their chromosomal distribution. According to the un-rooted neighbor joining phylogenetic tree, gene structure and motif analyses, the 56 TaSPL genes were divided into 8 subgroups. A total of 81 TaSPL gene pairs were designated as arising from duplication events and 64 interacting protein branches were identified as involve in the protein interaction network. The expression patterns of 21 randomly selected TaSPL genes in different tissues (roots, stems, leaves and inflorescence) and under 4 treatments (abscisic acid, gibberellin, drought and salt) were detected by quantitative real-time polymerase chain reaction (qRT-PCR). Conclusions The wheat genome contains 56 TaSPL genes and those in same subfamily share similar gene structure and motifs. TaSPL gene expansion occurred through segmental duplication events. Combining the results of transcriptional and qRT-PCR analyses, most of these TaSPL genes were found to regulate inflorescence and spike development. Additionally, we found that 13 TaSPLs were upregulated by abscisic acid, indicating that TaSPL genes play a positive role in the abscisic acid-mediated pathway of the seedling stage. This study provides comprehensive information on the SPL gene family of wheat and lays a solid foundation for elucidating the biological functions of TaSPLs and improvement of wheat yield.

scholarly journals Genome-Wide Identification of the Early Flowering 4 (ELF4) Gene Family in Cotton and Silent GhELF4-1 and GhEFL3-6 Decreased Cotton Stress Resistance

2021 ◽  
Vol 12 ◽  
Author(s):  
Miaomiao Tian ◽  
Aimin Wu ◽  
Meng Zhang ◽  
Jingjing Zhang ◽  
Hengling Wei ◽  
...  
Keyword(s):  
Gene Family ◽  
Expression Patterns ◽  
Multiple Roles ◽  
Early Flowering ◽  
Qrt Pcr ◽  
Genome Wide ◽  
Gossypium Raimondii ◽  
Spatio Temporal ◽  
Gene Structures

The early flowering 4 (ELF4) family members play multiple roles in the physiological development of plants. ELF4s participated in the plant biological clock’s regulation process, photoperiod, hypocotyl elongation, and flowering time. However, the function in the ELF4s gene is barely known. In this study, 11, 12, 21, and 22 ELF4 genes were identified from the genomes of Gossypium arboreum, Gossypium raimondii, Gossypium hirsutum, and Gossypium barbadense, respectively. There ELF4s genes were classified into four subfamilies, and members from the same subfamily show relatively conservative gene structures. The results of gene chromosome location and gene duplication revealed that segmental duplication promotes gene expansion, and the Ka/Ks indicated that the ELF4 gene family has undergone purification selection during long-term evolution. Spatio-temporal expression patterns and qRT-PCR showed that GhELF4 genes were mainly related to flower, leaf, and fiber development. Cis-acting elements analysis and qRT-PCR showed that GhELF4 genes might be involved in the regulation of abscisic acid (ABA) or light pathways. Silencing of GhELF4-1 and GhEFL3-6 significantly affected the height of cotton seedlings and reduced the resistance of cotton. The identification and functional analysis of ELF4 genes in upland cotton provide more candidate genes for genetic modification.

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 identification, phylogeny and expression analysis of AP2/ERF transcription factors family in sweet potato

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Shutao He ◽  
Xiaomeng Hao ◽  
Shuli He ◽  
Xiaoge Hao ◽  
Xiaonan Chen
Keyword(s):  
Transcription Factors ◽  
Abiotic Stress ◽  
Gene Family ◽  
Sweet Potato ◽  
Stress Responses ◽  
Expression Patterns ◽  
Gene Promoters ◽  
Biotic And Abiotic Stress ◽  
Protein Motifs ◽  
Genome Wide

Abstract Background In recent years, much attention has been given to AP2/ERF transcription factors because they play indispensable roles in many biological processes, such as plant development and biotic and abiotic stress responses. Although AP2/ERFs have been thoroughly characterised in many plant species, the knowledge about this family in the sweet potato, which is a vital edible and medicinal crop, is still limited. In this study, a comprehensive genome-wide investigation was conducted to characterise the AP2/ERF gene family in the sweet potato. Results Here, 198 IbAP2/ERF transcription factors were obtained. Phylogenetic analysis classified the members of the IbAP2/ERF family into three groups, namely, ERF (172 members), AP2 (21 members) and RAV (5 members), which was consistent with the analysis of gene structure and conserved protein domains. The evolutionary characteristics of these IbAP2/ERF genes were systematically investigated by analysing chromosome location, conserved protein motifs and gene duplication events, indicating that the expansion of the IbAP2/ERF gene family may have been caused by tandem duplication. Furthermore, the analysis of cis-acting elements in IbAP2/ERF gene promoters implied that these genes may play crucial roles in plant growth, development and stress responses. Additionally, the available RNA-seq data and quantitative real-time PCR (qRT-PCR) were used to investigate the expression patterns of IbAP2/ERF genes during sweet potato root development as well as under multiple forms of abiotic stress, and we identified several developmental stage-specific and stress-responsive IbAP2/ERF genes. Furthermore, g59127 was differentially expressed under various stress conditions and was identified as a nuclear protein, which was in line with predicted subcellular localization results. Conclusions This study originally revealed the characteristics of the IbAP2/ERF superfamily and provides valuable resources for further evolutionary and functional investigations of IbAP2/ERF genes in the sweet potato.

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