Dataset Information

Zinc Finger-Homeodomain Transcriptional Factors (ZF-HDs) in Wheat (Triticum aestivum L.): Identification, Evolution, Expression Analysis and Response to Abiotic Stresses.

ABSTRACT: Zinc finger-homeodomain transcriptional factors (ZF-HDs), a kind of plant-specific transcription factor, play important roles in plant growth, development and various stress responses. In this study, the genome-wide analysis of the ZF-HD gene family was performed in wheat. A total of 37 TaZF-HD genes were identified in T. aestivum and classified into six groups. The results of a synteny analysis showed that gene replication events contributed to the expansion of the TaZF-HD gene family. The TaZF-HD paralogous gene pairs with similar chromosomal locations in different subgenomes had similar expression patterns. TaZF-HDs were highly induced under PEG (polyethylene glycol), NaCl and cold stress but not induced under heat stress. Gene ontology (GO) annotation and protein-protein interactions suggested that TaZF-HD proteins may participate in various biological processes of plants. These results increase our understanding of ZF-HD genes and provide robust candidate genes for future functional investigations aimed at crop improvement.

SUBMITTER: Liu H

PROVIDER: S-EPMC8004245 | biostudies-literature | 2021 Mar

REPOSITORIES: biostudies-literature

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Zinc Finger-Homeodomain Transcriptional Factors (ZF-HDs) in Wheat (Triticum aestivum L.): Identification, Evolution, Expression Analysis and Response to Abiotic Stresses.

Liu Hao H Yang Ying Y Zhang Linsheng L

Plants (Basel, Switzerland) 20210322 3

Zinc finger-homeodomain transcriptional factors (ZF-HDs), a kind of plant-specific transcription factor, play important roles in plant growth, development and various stress responses. In this study, the genome-wide analysis of the ZF-HD gene family was performed in wheat. A total of 37 TaZF-HD genes were identified in T. aestivum and classified into six groups. The results of a synteny analysis showed that gene replication events contributed to the expansion of the TaZF- ...[more]

PMID: 33809871

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Project description:BackgroundZinc finger homeodomain (ZF-HD) belongs to the plant-specific transcription factor (TF) family and is widely involved in plant growth, development and stress responses. Despite their importance, a comprehensive identification and analysis of ZF-HD genes in the soybean (Glycine max) genome and their possible roles under abiotic stress remain unexplored.ResultsIn this study, 51 ZF-HD genes were identified in the soybean genome that were unevenly distributed on 17 chromosomes. All GmZF-HD genes contained a conserved ZF-HD_dimer domain and had diverse physicochemical features. Furthermore, the GmZF-HD gene structures exhibited 3 to 10 conserved motifs, and most of them showed intronless gene structures. Phylogenetic analysis categorized them into eight major groups with the highest closeness to dicots including Brassica rapa and Malus domestica. The cis-element analysis recognized plant growth and development (10%), phytohormones (31%) and stress-responsive (59%) elements. Synteny analysis identified 73 segmental and 1 tandem duplicated genes that underwent purifying selection. The collinearity analysis revealed that GmZF-HD genes showed higher homology with dicot species, indicating common ancestors with close evolutionary relationships. A total of 94 gma-miRNAs from 41 diverse miRNA families were identified, targeting 40 GmZF-HD genes, with GmZF-HD6 being most targeted by 7 miRNAs, and gma-miR4993 emerging as the dominant miRNA family. Different TFs including ERF, LBD, BBR-BPC and MYB, etc., were predicted in all 51 GmZF-HD genes upstream regions and visualized in the network. Expression profiling through RNA-Seq showed diverse expressions of GmZF-HD genes in different tissues including seeds, roots, shoots and leaves under diverse conditions. Further, the qRT-PCR analysis demonstrated that all tested GmZF-HD genes were significantly induced in soybean leaves, mainly the GmZF-HD5/6/13/39 and GmZF-HD45 genes were significantly upregulated (2.5 to 8.8 folds) under the tested stress treatments compared to control, highlighting their potential roles in response to stresses in soybean.ConclusionOverall, this study reveals comprehensive insights into the ZF-HD genes in soybeans and provides a valuable contribution towards functional studies for soybean improvement under stress conditions.

Project description:The GRAS transcription factors are multifunctional proteins involved in various biological processes, encompassing plant growth, metabolism, and responses to both abiotic and biotic stresses. Wheat is an important cereal crop cultivated worldwide. However, no systematic study of the GRAS gene family and their functions under heat, drought, and salt stress tolerance and molecular dynamics modeling in wheat has been reported. In the present study, we identified the GRAS gene in Triticum aestivum through systematically performing gene structure analysis, chromosomal location, conserved motif, phylogenetic relationship, and expression patterns. A total of 177 GRAS genes were identified within the wheat genome. Based on phylogenetic analysis, these genes were categorically placed into 14 distinct subfamilies. Detailed analysis of the genetic architecture revealed that the majority of TaGRAS genes had no intronic regions. The expansion of the wheat GRAS gene family was proven to be influenced by both segmental and tandem duplication events. The study of collinearity events between TaGRAS and analogous orthologs from other plant species provided valuable insights into the evolution of the GRAS gene family in wheat. It is noteworthy that the promoter regions of TaGRAS genes consistently displayed an array of cis-acting elements that are associated with stress responses and hormone regulation. Additionally, we discovered 14 miRNAs that target key genes involved in three stress-responsive pathways in our study. Moreover, an assessment of RNA-seq data and qRT-PCR results revealed a significant increase in the expression of TaGRAS genes during abiotic stress. These findings highlight the crucial role of TaGRAS genes in mediating responses to different environmental stresses. Our research delved into the molecular dynamics and structural aspects of GRAS domain-DNA interactions, marking the first instance of such information being generated. Overall, the current findings contribute to our understanding of the organization of the GRAS genes in the wheat genome. Furthermore, we identified TaGRAS27 as a candidate gene for functional research, and to improve abiotic stress tolerance in the wheat by molecular breeding.

Project description:Zinc finger-homeodomain (ZF-HDs) class IV transcriptional factors (TFs) is a plant-specific transcription factor and play a key role in stress responses, plant growth, development, and hormonal signaling. In this study, two new leaf rolling TFs genes, namely TaZHD1 and TaZHD10, were identified in wheat using comparative genomic analysis of the target region that carried a major QTL for leaf rolling identified through multi-environment phenotyping and high throughput genotyping of a RIL population. Structural and functional annotation of the candidate ZHD genes with its closest rice orthologs reflects the species-specific evolution and, undoubtedly, validates the notions of remote-distance homology concept. Meanwhile, the morphological analysis resulted in contrasting difference for leaf rolling in extreme RILs between parental lines HD2012 and NI5439 at booting and heading stages. Transcriptome-wide expression profiling revealed that TaZHD10 transcripts showed significantly higher expression levels than TaZHD1 in all leaf tissues upon drought stress. The relative expression of these genes was further validated by qRT-PCR analysis, which also showed consistent results across the studied genotypes at the booting and anthesis stage. The contrasting modulation of these genes under drought conditions and the available evidenced for its epigenetic behavior that might involve the regulation of metabolic and gene regulatory networks. Prediction of miRNAs resulted in five Tae-miRs that could be associated with RNAi mediated control of TaZHD1 and TaZHD10 putatively involved in the metabolic pathway controlling rolled leaf phenotype. Gene interaction network analysis indicated that TaZHD1 and TaZHD10 showed pleiotropic effects and might also involve other functions in wheat in addition to leaf rolling. Overall, the results increase our understanding of TaZHD genes and provide valuable information as robust candidate genes for future functional genomics research aiming for the breeding of wheat varieties tolerant to leaf rolling.

Project description:Root system architecture (RSA) plays a fundamental role in nutrient uptake, including zinc (Zn). Wheat grains are inheritably low in Zn. As Zn is an essential nutrient for plants, improving its uptake will not only improve their growth and yield but also the nutritional quality of staple grains. A rhizobox study followed by a pot study was conducted to evaluate Zn variability with respect to RSA and its impact on grain Zn concentration. The grain Zn content of one hundred wheat varieties was determined and grown in rhizoboxes with differential Zn (no Zn and 0.05 mg L-1 ZnSO4). Seedlings were harvested 12 days after sowing, and root images were taken and analyzed by SmartRoot software. Using principal component analysis, twelve varieties were screened out based on vigorous and weaker RSA with high and low grain Zn content. The screened varieties were grown in pots with (11 mg ZnSO4 kg-1 soil) and without Zn application to the soil. Zinc translocation, localization, and agronomic parameters were recorded after harvesting at maturity. In the rhizobox experiment, 4% and 8% varieties showed higher grain Zn content with vigorous and weaker RSA, respectively, while 45% and 43% varieties had lower grain Zn content with vigorous and weaker RSA. However, the pot experiment revealed that varieties with vigorous root system led to higher grain yield, though the grain Zn concentration were variable, while all varieties with weaker root system had lower yield as well as grain Zn concentration. Zincol-16 revealed the highest Zn concentration (28.07 mg kg-1) and grain weight (47.9 g). Comparatively higher level of Zn was localized in the aleurone layer than in the embryonic region and endosperm. It is concluded that genetic variability exists among wheat varieties for RSA and grain Zn content, with a significant correlation. Therefore, RSA attributes are promising targets for the Zn biofortification breeding program. However, Zn localization in endosperm needs to be further investigated to achieve the goal of reducing Zn malnutrition.

Dataset Information

Zinc Finger-Homeodomain Transcriptional Factors (ZF-HDs) in Wheat (Triticum aestivum L.): Identification, Evolution, Expression Analysis and Response to Abiotic Stresses.

Publications

Zinc Finger-Homeodomain Transcriptional Factors (ZF-HDs) in Wheat (<i>Triticum aestivum</i> L.): Identification, Evolution, Expression Analysis and Response to Abiotic Stresses.

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