scholarly journals Phenylalanine Ammonia-Lyase (PAL) Genes Family in Wheat (Triticum aestivum L.): Genome-Wide Characterization and Expression Profiling

Agronomy ◽  
2021 ◽  
Vol 11 (12) ◽  
pp. 2511
Author(s):  
Fatima Rasool ◽  
Muhammad Uzair ◽  
Muhammad Kashif Naeem ◽  
Nazia Rehman ◽  
Amber Afroz ◽  
...  
Keyword(s):  
Triticum Aestivum ◽  
Phenylalanine Ammonia Lyase ◽  
Chromosomal Rearrangements ◽  
Aegilops Tauschii ◽  
Triticum Aestivum L ◽  
Regulatory Elements ◽  
Phenylpropanoid Pathway ◽  
Evolutionary Analysis ◽  
Genome Wide ◽  
A Genome

Phenylalanine ammonia-lyase (PAL) is the first enzyme in the phenylpropanoid pathway and plays a vital role in adoption, growth, and development in plants but in wheat its characterization is still not very clear. Here, we report a genome-wide identification of TaPAL genes and analysis of their transcriptional expression, duplication, and phylogeny in wheat. A total of 37 TaPAL genes that cluster into three subfamilies have been identified based on phylogenetic analysis. These TaPAL genes are distributed on 1A, 1B, 1D, 2A, 2B, 2D, 4A, 5B, 6A, 6B, and 6D chromosomes. Gene structure, conserved domain analysis, and investigation of cis-regulatory elements were systematically carried out. Chromosomal rearrangements and gene loss were observed by evolutionary analysis of the orthologs among Triticum urartu, Aegilops tauschii, and Triticum aestivum during the origin of bread wheat. Gene ontology analysis revealed that PAL genes play a role in plant growth. We also identified 27 putative miRNAs targeting 37 TaPAL genes. The high expression level of PAL genes was detected in roots of drought-tolerant genotypes compared to drought-sensitive genotypes. However, very low expressions of TaPAL10, TaPAL30, TaPAL32, TaPAL3, and TaPAL28 were recorded in all wheat genotypes. Arogenate dehydratase interacts with TaPAL29 and has higher expression in roots. The analysis of all identified genes in RNA-seq data showed that they are expressed in roots and shoots under normal and abiotic stress. Our study offers valuable data on the functioning of PAL genes in wheat.

scholarly journals Genome-wide Survey of the Dehydrin Genes in Bread Wheat (Triticum Aestivum L.) and its Relatives: Identification, Evolution and Expression Profiling Under Various Abiotic Stresses

2021 ◽  
Author(s):  
Yongchao Hao ◽  
Ming Hao ◽  
Hongwei Wang
Keyword(s):  
Triticum Aestivum ◽  
Bread Wheat ◽  
Abiotic Stresses ◽  
Aegilops Tauschii ◽  
Protein Structures ◽  
Interaction Network ◽  
Wheat Breeding ◽  
Functional Study ◽  
Genome Wide ◽  
A Genome

Abstract Background: Bread wheat (Triticum aestivum) is an important and fundamental cereal worldwide. With increasingly severe environmental stress, it is very important to mine stress-resistant genes for wheat breeding. Dehydrin (DHN) genes are primary candidates because they are involved in the response to many stressors. Results: Here, a genome-wide analysis of this gene family was performed on the genomes of wheat and its three relatives. A total of 55 DHN genes in Triticum aestivum, 31 in Triticum dicoccoides, 15 in Triticum urartu, and 16 in Aegilops tauschii were identified. The phylogenetic, synteny, sequence and protein structure analyses showed that the DHN genes were divided into five groups, Genes in the same group share similar conserved motifs, protein structures, and potential functions. The tandem TaDHN genes responded strongly to drought, cold and high salinity stresses, while the non-tandem genes were responded weakly to all stress conditions. Further, multiple DHN proteins cooperation maybe an important way to prevent plants from abiotic stress according to the interaction network analysis. Conclusions: Conserved, duplicated DHN genes may have played an important role in the adaptation of wheat to a variety of conditions, hence, contributing to the distribution of bread wheat as a global staple food. This research illuminates the contributions of DHN genes to abiotic stresses in Triticeae species and offers helpful information for further functional study of DHN genes in these crops.

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.

A genome-wide identification of chromosomal regions determining nitrogen use efficiency components in wheat (Triticum aestivum L.)

2014 ◽  
Vol 127 (12) ◽  
pp. 2679-2693 ◽  
Author(s):  
Fabien Cormier ◽  
Jacques Le Gouis ◽  
Pierre Dubreuil ◽  
Stéphane Lafarge ◽  
Sébastien Praud
Keyword(s):  
Triticum Aestivum ◽  
Nitrogen Use Efficiency ◽  
Triticum Aestivum L ◽  
Nitrogen Use ◽  
Genome Wide ◽  
A Genome ◽  
Use Efficiency

scholarly journals Genome-Wide Analysis of Myeloblastosis-Related Genes in Brassica napus L. and Positive Modulation of Osmotic Tolerance by BnMRD107

2021 ◽  
Vol 12 ◽  
Author(s):  
Jian Li ◽  
Keyun Lin ◽  
Shuai Zhang ◽  
Jian Wu ◽  
Yujie Fang ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Brassica Napus ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Regulatory Elements ◽  
Functional Study ◽  
Evolutionary Analysis ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
A Genome

Myeloblastosis (MYB)-related transcription factors comprise a large subfamily of the MYB family. They play significant roles in plant development and in stress responses. However, MYB-related proteins have not been comprehensively investigated in rapeseed (Brassica napus L.). In the present study, a genome-wide analysis of MYB-related transcription factors was performed in rapeseed. We identified 251 Brassica napus MYB (BnMYB)-related members, which were divided phylogenetically into five clades. Evolutionary analysis suggested that whole genome duplication and segmental duplication events have played a significant role in the expansion of BnMYB-related gene family. Selective pressure of BnMYB-related genes was estimated using the Ka/Ks ratio, which indicated that BnMYB-related genes underwent strong purifying selection during evolution. In silico analysis showed that various development-associated, phytohormone-responsive, and stress-related cis-acting regulatory elements were enriched in the promoter regions of BnMYB-related genes. Furthermore, MYB-related genes with tissue or organ-specific, stress-responsive expression patterns were identified in B. napus based on temporospatial and abiotic stress expression profiles. Among the stress-responsive MYB-related genes, BnMRD107 was strongly induced by drought stress, and was therefore selected for functional study. Rapeseed seedlings overexpressing BnMRD107 showed improved resistance to osmotic stress. Our findings not only lay a foundation for further functional characterization of BnMYB-related genes, but also provide valuable clues to determine candidate genes for future genetic improvement of B. napus.

scholarly journals Genome-Wide Characterization of OFP Family Genes in Wheat (Triticum aestivum L.) Reveals That TaOPF29a-A Promotes Drought Tolerance

2020 ◽  
Vol 2020 ◽  
pp. 1-17
Author(s):  
Dezhou Wang ◽  
Zhichen Cao ◽  
Weiwei Wang ◽  
Wengen Zhu ◽  
Xiaocong Hao ◽  
...  
Keyword(s):  
Triticum Aestivum ◽  
Drought Tolerance ◽  
Expression Patterns ◽  
Triticum Aestivum L ◽  
Promoter Regions ◽  
Specific Expression ◽  
Genome Wide ◽  
A Genome ◽  
Starting Point ◽  
Genetically Engineer

OVATE family proteins (OFPs) are plant-specific transcription factors that play important roles in plant development. Although common wheat (Triticum aestivum L.) is a major staple food worldwide, OFPs have not been systematically analyzed in this important crop. Here, we performed a genome-wide survey of OFP genes in wheat and identified 100 genes belonging to 34 homoeologous groups. Arabidopsis thaliana, rice (Oryza sativa), and wheat OFP genes were divided into four subgroups based on their phylogenetic relationships. Structural analysis indicated that only four TaOFPs contain introns. We mapped the TaOFP genes onto the wheat chromosomes and determined that TaOFP17 was duplicated in this crop. A survey of cis-acting elements along the promoter regions of TaOFP genes suggested that subfunctionalization of homoeologous genes might have occurred during evolution. The TaOFPs were highly expressed in wheat, with tissue- or organ-specific expression patterns. In addition, these genes were induced by various hormone and stress treatments. For instance, TaOPF29a-A was highly expressed in roots in response to drought stress. Wheat plants overexpressing TaOPF29a-A had longer roots and higher dry weights than nontransgenic plants under drought conditions, suggesting that this gene improves drought tolerance. Our findings provide a starting point for further functional analysis of this important transcription factor family and highlight the potential of using TaOPF29a-A to genetically engineer drought-tolerant crops.

scholarly journals Genome-Wide Association Study Reveals the Genetic Architecture for Calcium Accumulation in Grains of Hexaploid Wheat (Triticum Aestivum L.)

2021 ◽  
Author(s):  
Xia Shi ◽  
Zhengfu Zhou ◽  
Wenxu Li ◽  
Maomao Qin ◽  
Pan Yang ◽  
...  
Keyword(s):  
Triticum Aestivum ◽  
Association Study ◽  
Hexaploid Wheat ◽  
Genetic Architecture ◽  
Genome Wide Association Study ◽  
Triticum Aestivum L ◽  
Genome Wide Association ◽  
Wheat Grain ◽  
Genome Wide ◽  
A Genome

Abstract Background: Hexaploid wheat (Triticum aestivum L.) is a leading cereal crop worldwide. Understanding the mechanism of calcium (Ca) accumulation in wheat is important to reduce the risk of human micronutrient deficiencies. However, the mechanisms of Ca accumulation in wheat grain are only partly understood. Results: Here, we performed a genome-wide association study to identify the genetic basis of Ca accumulation in wheat grain using an association population consisting of 207 varieties, with phenotypic data from three locations and the combined locations. In total, 18 non-redundant quantitative trait loci (QTLs) associated with Ca concentration were identified that explained, on average, 9.61%–26.93% of the phenotypic variation. Cultivars containing more superior alleles and fewer inferior alleles had increased grain Ca concentrations. Notably, six non-redundant loci were identified in at least two environments, indicating their stability across different environments. Searches of public databases revealed six putative candidate genes linked to Ca accumulation. Among them, two subunits of V-type Proton ATPase (TraesCS4A01G428900 and TraesCS3B01G241000) are encoded by genes associated with stable genetic loci on chromosomes 4A (AX-108912427) and 3B (AX-110922471), respectively, and they are typical generators of a proton gradient that might be involved in Ca homeostasis in wheat grain.Conclusion: This study could increases our understanding of the genetic architecture of grain Ca accumulation in wheat, and we plan to develop the identified superior alleles into molecular markers for wheat Ca biofortification pyramid breeding in the future.

scholarly journals A genome-wide map of regulatory elements in zebrafish

Lab Animal ◽  
2020 ◽  
Vol 50 (1) ◽  
pp. 17-17
Author(s):  
Alexandra Le Bras
Keyword(s):  
Regulatory Elements ◽  
Genome Wide ◽  
A Genome

scholarly journals A Genome-Wide Analysis of Pathogenesis-Related Protein-1 (PR-1) Genes from Piper nigrum Reveals Its Critical Role during Phytophthora capsici Infection

Genes ◽  
2021 ◽  
Vol 12 (7) ◽  
pp. 1007
Author(s):  
Divya Kattupalli ◽  
Asha Sreenivasan ◽  
Eppurathu Vasudevan Soniya
Keyword(s):  
Phytophthora Capsici ◽  
Regulatory Elements ◽  
Piper Nigrum ◽  
Binding Motif ◽  
Altered Expression ◽  
Genome Wide ◽  
A Genome ◽  
Pathogenesis Related Protein ◽  
Pathogenesis Related

Black pepper (Piper nigrum L.) is a prominent spice that is an indispensable ingredient in cuisine and traditional medicine. Phytophthora capsici, the causative agent of footrot disease, causes a drastic constraint in P. nigrum cultivation and productivity. To counterattack various biotic and abiotic stresses, plants employ a broad array of mechanisms that includes the accumulation of pathogenesis-related (PR) proteins. Through a genome-wide survey, eleven PR-1 genes that belong to a CAP superfamily protein with a caveolin-binding motif (CBM) and a CAP-derived peptide (CAPE) were identified from P. nigrum. Despite the critical functional domains, PnPR-1 homologs differ in their signal peptide motifs and core amino acid composition in the functional protein domains. The conserved motifs of PnPR-1 proteins were identified using MEME. Most of the PnPR-1 proteins were basic in nature. Secondary and 3D structure analyses of the PnPR-1 proteins were also predicted, which may be linked to a functional role in P. nigrum. The GO and KEGG functional annotations predicted their function in the defense responses of plant-pathogen interactions. Furthermore, a transcriptome-assisted FPKM analysis revealed PnPR-1 genes mapped to the P. nigrum-P. capsici interaction pathway. An altered expression pattern was detected for PnPR-1 transcripts among which a significant upregulation was noted for basic PnPR-1 genes such as CL10113.C1 and Unigene17664. The drastic variation in the transcript levels of CL10113.C1 was further validated through qRT-PCR and it showed a significant upregulation in infected leaf samples compared with the control. A subsequent analysis revealed the structural details, phylogenetic relationships, conserved sequence motifs and critical cis-regulatory elements of PnPR-1 genes. This is the first genome-wide study that identified the role of PR-1 genes during P. nigrum-P. capsici interactions. The detailed in silico experimental analysis revealed the vital role of PnPR-1 genes in regulating the first layer of defense towards a P. capsici infection in Panniyur-1 plants.

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