Browse
Submit Data
Databases
API
Help

Dataset Information

16 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Characterization of Vascular plant One-Zinc finger (VOZ) in soybean (Glycine max and Glycine soja) and their expression analyses under drought condition.

ABSTRACT: Vascular plant one-zinc-finger (VOZ) transcription factors regulate plant growth and development under drought conditions. Six VOZ transcription factors encoding genes exist in soybean genome (both in Glycine max and Glycine soja). Herein, GmVOZs and GsVOZs were identified through in silico analysis and characterized with different bioinformatics tools and expression analysis. Phylogenetic analysis classified VOZ genes in four groups. Sequence logos analysis among G. max and G. soja amino acid residues revealed higher conservation. Presence of stress related cis-elements in the upstream regions of GmVOZs and GsVOZs highlights their role in tolerance against abiotic stresses. The collinearity analysis identified 14 paralogous/orthologous gene pairs within and between G. max and G. soja. The Ka/Ks values showed that soybean VOZ genes underwent selection pressure with limited functional deviation arising from whole genome and segmental duplication. The GmVOZs and GsVOZs were found to express in roots and leaves at seedling stage. The qRT-PCR revealed that GmVOZs and GsVOZs transcripts can be regulated by abiotic stresses such as polyethylene glycol (PEG). The findings of this study will provide a reference to decipher physiological and molecular functions of VOZ genes in soybean.

SUBMITTER: Rehman SU

PROVIDER: S-EPMC8253436 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Metabolomic Variability of Different Soybean Genotypes: β-Carotene-Enhanced (Glycine max), Wild (Glycine soja), and Hybrid (Glycine max × Glycine soja) Soybeans.

Project description:We obtained a new hybrid soybean (Hybrid) by hybridizing β-carotene-enhanced soybean (BCE; Glycine max L.) containing the phytoene synthase-2A-carotene desaturase gene and wild-type soybean (Wild; Glycine soja). To investigate metabolic changes between variants, we performed metabolic profiling of leaves (three growth stages) and seeds. Multivariate analyses revealed significant metabolic differences between genotypes in seeds and leaves, with seeds showing accumulation of phytosterols, tocopherols, and carotenoids (BCE only), indicating co-induction of the methylerythritol 4-phosphate and mevalonic acid pathways. Additionally, Hybrid produced intermediate levels of carotenoids and high levels of amino acids. Principal component analysis revealed metabolic discrimination between growth stages of soybean leaves and identified differences in leaf groups according to different genotypes at 8, 12, and 16 weeks, with Wild showing higher levels of environmental stress-related compounds relative to BCE and Hybrid leaves. The metabolic profiling approach could be a useful tool to identify metabolic links in various soybean cultivars.

| S-EPMC8535314 | biostudies-literature

The CCCH zinc finger family of soybean (Glycine max L.): genome-wide identification, expression, domestication, GWAS and haplotype analysis.

Project description:BackgroundThe CCCH zinc finger (zf_CCCH) is a unique subfamily featured one or more zinc finger motif(s) comprising of three Cys and one His residues. The zf_CCCH family have been reported involving in various processes of plant development and adaptation.ResultsIn this study, the zf_CCCH genes were identified via a genome-wide search and were systematically analyzed. 116 Gmzf_CCCHs were obtained and classified into seventeen subfamilies. Gene duplication and expansion analysis showed that tandem and segmental duplications contributed to the expansion of the Gmzf_CCCH gene family, and that segmental duplication play the main role. The expression patterns of Gmzf_CCCH genes were tissue-specific. Eleven domesticated genes were detected involved in the regulation of seed oil and protein synthesis as well as growth and development of soybean through GWAS and haplotype analysis for Gmzf_CCCH genes among the 164 of 302 soybeans resequencing data. Among which, 8 genes play an important role in the synthesis of seed oil or fatty acid, and the frequency of their elite haplotypes changes significantly among wild, landrace and improved cultivars, indicating that they have been strongly selected in the process of soybean domestication.ConclusionsThis study provides a scientific foundation for the comprehensive understanding, future cloning and functional studies of Gmzf_CCCH genes in soybean, meanwhile, it was also helpful for the improvement of soybean with high oil content.

| S-EPMC8261996 | biostudies-literature

Comparison of Phenolic and Flavonoid Compound Profiles and Antioxidant and α-Glucosidase Inhibition Properties of Cultivated Soybean (Glycine max) and Wild Soybean (Glycine soja).

Project description:Wild soybean (Glycine soja Sieb.et Zucc; WS) has been used as a traditional food in China for many years and contains significantly higher levels of isoflavones than cultivated soybean (Glycine max; CS), but the secondary metabolites, including flavonoids and the phenolic composition differences between them, remain unclear. The results showed that WS possessed significantly higher total phenolic and flavonoid content and exhibited better antioxidant and α-glucosidase inhibition activities as well as excellent protective effects against H2O2-induced oxidative injury in a human endothelial cell line. Through metabolomic analysis, 642 metabolites were identified, and 238 showed differential expression, with 151 upregulated and 87 downregulated. A total of 79 flavonoid compounds were identified, 42 of which were upregulated in WS. 2'-Hydroxygenistein, garbanzol, protocatechuic aldehyde, ligustilide, and resveratrol were the most discriminated compounds in WS. The metabolic pathway analysis of differential metabolites related to the biosynthesis of flavonoids and phenolic acids were the biosynthesis of phenylpropanoids, flavonoids, isoflavonoids, flavones, and flavonols. This study substantially elucidated differences in the content of flavonoids and biological activities between WS and CS, which is useful information for the effective utilization of these two black soybean species in food processing.

| S-EPMC8074397 | biostudies-literature

Vascular Plant One-Zinc-Finger (VOZ) Transcription Factors Are Positive Regulators of Salt Tolerance in Arabidopsis.

Project description:Soil salinity, a significant problem in agriculture, severely limits the productivity of crop plants. Plants respond to and cope with salt stress by reprogramming gene expression via multiple signaling pathways that converge on transcription factors. To develop strategies to generate salt-tolerant crops, it is necessary to identify transcription factors that modulate salt stress responses in plants. In this study, we investigated the role of VOZ (VASCULAR PLANT ONE-ZINC FINGER PROTEIN) transcription factors (VOZs) in salt stress response. Transcriptome analysis in WT (wild-type), voz1-1, voz2-1 double mutant and a VOZ2 complemented line revealed that many stress-responsive genes are regulated by VOZs. Enrichment analysis for gene ontology terms in misregulated genes in voz double mutant confirmed previously identified roles of VOZs and suggested a new role for them in salt stress. To confirm VOZs role in salt stress, we analyzed seed germination and seedling growth of WT, voz1, voz2-1, voz2-2 single mutants, voz1-1 voz2-1 double mutant and a complemented line under different concentrations of NaCl. Only the double mutant exhibited hypersensitivity to salt stress as compared to WT, single mutants, and a complemented line. Expression analysis showed that hypersensitivity of the double mutant was accompanied by reduced expression of salt-inducible genes. These results suggest that VOZ transcription factors act as positive regulators of several salt-responsive genes and that the two VOZs are functionally redundant in salt stress.

| S-EPMC6321167 | biostudies-literature

Transcriptomic study of soybean (Glycine max) in response to zinc deficiency

Project description:We conducted a genome-wide transcriptomic analysis in soybean leaves and roots treated with zinc (Zn) deficiency using RNA sequencing (RNA-seq) technology. Two biological replicates of RNA-seq were included for Zn-sufficient leaves (ZSL), Zn-deficient leaves (ZDL), Zn-sufficient roots (ZSR), and Zn-deficient roots (ZDR). Therefore a total of eight libraries were constructed. Using a 2-fold change and a P-value ≤0.05 as the cut-off for selecting the differentially expressed transcripts, we globally identified Zn-deficiency responsive genes. At least 20 genes that are potentially involved Zn homeostasis were significantly changed by Zn deficiency, including 7 ZIP (ZRT, IRT-related protein) transporter genes, 3 nicotianamine synthase genes, and 7 metallothionein genes. At least 48 genes encoding likely Zn-binding proteins were found to be responsive to Zn deficiency in leaves or roots. Eighty-five transcription factor genes were significantly changed by Zn deficiency in leaves or roots, including 5 bZIP members and 10 Golden 2-like members. In addition, some other groups of genes which are possibly related to reactive oxygen species scavenging, calcium and hormone signaling, and protein phosphorylation and dephosphorylation also differentially expressed under Zn deficiency.

2019-03-30 | GSE111799 | GEO

Identifications of QTLs and Candidate Genes Associated with Pseudomonas syringae Responses in Cultivated Soybean (Glycine max) and Wild Soybean (Glycine soja).

Project description:Soybeans (Glycine max) are a key food crop, serving as a valuable source of both oil and plant-derived protein. Pseudomonas syringae pv. glycinea (Psg) is among the most aggressive and prevalent pathogens affecting soybean production, causing a form of bacterial spot disease that impacts soybean leaves and thereby reduces crop yields. In this study, 310 natural soybean varieties were screened for Psg resistance and susceptibility. The identified susceptible and resistant varieties were then used for linkage mapping, BSA-seq, and whole genome sequencing (WGS) analyses aimed at identifying key QTLs associated with Psg responses. Candidate Psg-related genes were further confirmed through WGS and qPCR analyses. Candidate gene haplotype analyses were used to explore the associations between haplotypes and soybean Psg resistance. In addition, landrace and wild soybean plants were found to exhibit a higher degree of Psg resistance as compared to cultivated soybean varieties. In total, 10 QTLs were identified using chromosome segment substitution lines derived from Suinong14 (cultivated soybean) and ZYD00006 (wild soybean). Glyma.10g230200 was found to be induced in response to Psg, with the Glyma.10g230200 haplotype corresponding to soybean disease resistance. The QTLs identified herein can be leveraged to guide the marker-assisted breeding of soybean cultivars that exhibit partial resistance to Psg. Moreover, further functional and molecular studies of Glyma.10g230200 have the potential to offer insight into the mechanistic basis for soybean Psg resistance.

| S-EPMC10003559 | biostudies-literature

Integration of the Draft Sequence and Physical Map as a Framework for Genomic Research in Soybean (Glycine max (L.) Merr.) and Wild Soybean (Glycine soja Sieb. and Zucc.).

Project description:Soybean is a model for the legume research community because of its importance as a crop, densely populated genetic maps, and the availability of a genome sequence. Even though a whole-genome shotgun sequence and bacterial artificial chromosome (BAC) libraries are available, a high-resolution, chromosome-based physical map linked to the sequence assemblies is still needed for whole-genome alignments and to facilitate map-based gene cloning. Three independent G. max BAC libraries combined with genetic and gene-based markers were used to construct a minimum tiling path (MTP) of BAC clones. A total of 107,214 clones were assembled into 1355 FPC (FingerPrinted Contigs) contigs, incorporating 4628 markers and aligned to the G. max reference genome sequence using BAC end-sequence information. Four different MTPs were made for G. max that covered from 92.6% to 95.0% of the soybean draft genome sequence (gmax1.01). Because our purpose was to pick the most reliable and complete MTP, and not the MTP with the minimal number of clones, the FPC map and draft sequence were integrated and clones with unpaired BES were added to build a high-quality physical map with the fewest gaps possible (http://soybase.org). A physical map was also constructed for the undomesticated ancestor (G. soja) of soybean to explore genome variation between G. max and G. soja. 66,028 G. soja clones were assembled into 1053 FPC contigs covering approximately 547 Mbp of the G. max genome sequence. These physical maps for G. max and its undomesticated ancestor, G. soja, will serve as a framework for ordering sequence fragments, comparative genomics, cloning genes, and evolutionary analyses of legume genomes.

| S-EPMC3291501 | biostudies-literature

Comparison of Small RNA Profiles of Glycine max and Glycine soja at Early Developmental Stages.

Project description:Small RNAs, including microRNAs (miRNAs) and phased small interfering RNAs (phasiRNAs; from PHAS loci), play key roles in plant development. Cultivated soybean, Glycine max, contributes a great deal to food production, but, compared to its wild kin, Glycine soja, it may lose some genetic information during domestication. In this work, we analyzed the sRNA profiles of different tissues in both cultivated (C08) and wild soybeans (W05) at three stages of development. A total of 443 known miRNAs and 15 novel miRNAs showed varying abundances between different samples, but the miRNA profiles were generally similar in both accessions. Based on a sliding window analysis workflow that we developed, 50 PHAS loci generating 55 21-nucleotide phasiRNAs were identified in C08, and 46 phasiRNAs from 41 PHAS loci were identified in W05. In germinated seedlings, phasiRNAs were more abundant in C08 than in W05. Disease resistant TIR-NB-LRR genes constitute a very large family of PHAS loci. PhasiRNAs were also generated from several loci that encode for NAC transcription factors, Dicer-like 2 (DCL2), Pentatricopeptide Repeat (PPR), and Auxin Signaling F-box 3 (AFB3) proteins. To investigate the possible involvement of miRNAs in initiating the PHAS-phasiRNA pathway, miRNA target predictions were performed and 17 C08 miRNAs and 15 W05 miRNAs were predicted to trigger phasiRNAs biogenesis. In summary, we provide a comprehensive description of the sRNA profiles of wild versus cultivated soybeans, and discuss the possible roles of sRNAs during soybean germination.

| S-EPMC5187843 | biostudies-literature

Proteomic analysis of drought stress response mechanism in soybean (Glycine max L.) leaves.

Project description:Knowledge of the physiological and molecular mechanisms of drought responses is fundamental for developing genetically drought tolerant and high yielding crops. To understand molecular mechanism of drought tolerance of soybean (Glycine max L.), we compared leaf proteome patterns of in two genotypes GN-3074 (drought tolerant) and GN-2032 (drought-sensitive) under drought stress during vegetative stage. Proteins were extracted from leaves of well-watered and drought-treated plants by using the trichloroacetic acid (TCA)-acetone precipitation method and analyzed by two-dimensional polyacrylamide gel electrophoresis. Out 488 reproducibly detected and analyzed on two-dimensional electrophoresis gels, 26 proteins showed significant changes in at least one genotype. The identification of 20 differentially expressed proteins using mass spectrometry revealed a coordinated expression of proteins involved in cellular metabolisms including photosynthesis, oxidative stress defense, respiration, metabolism process, signal transduction, phosphorus transduction, and methyl transduction which enable plant to cope with drought conditions. The most identified proteins involved in photosynthesis and oxidative stress defense system. The up-regulation of several photosynthetic proteins and also high abundance of oxidative stress defense proteins in GN-3074 genotypes as compare to GN-2032 genotypes might reflect the fact that drought tolerance of GN-3074 is due to effective photosynthetic machinery and more defense against oxidative stress. Our results suggest that soybean plant might response to drought stress by applying efficiently stay-green mechanism through coordinated gene expression during vegetative stage.

| S-EPMC8020938 | biostudies-literature

Arabidopsis thaliana VOZ (Vascular plant One-Zinc finger) transcription factors are required for proper regulation of flowering time.

Project description:Transition to flowering in plants is tightly controlled by environmental cues, which regulate the photoperiod and vernalization pathways, and endogenous signals, which mediate the autonomous and gibberellin pathways. In this work, we investigated the role of two Zn(2+)-finger transcription factors, the paralogues AtVOZ1 and AtVOZ2, in Arabidopsis thaliana flowering. Single atvoz1-1 and atvoz2-1 mutants showed no significant phenotypes as compared to wild type. However, atvoz1-1 atvoz2-1 double mutant plants exhibited several phenotypes characteristic of flowering-time mutants. The double mutant displayed a severe delay in flowering, together with additional pleiotropic phenotypes. Late flowering correlated with elevated expression of FLOWERING LOCUS C (FLC), which encodes a potent floral repressor, and decreased expression of its target, the floral promoter FD. Vernalization rescued delayed flowering of atvoz1-1 atvoz2-1 and reversed elevated FLC levels. Accumulation of FLC transcripts in atvoz1-1 atvoz2-1 correlated with increased expression of several FLC activators, including components of the PAF1 and SWR1 chromatin-modifying complexes. Additionally, AtVOZs were shown to bind the promoter of MOS3/SAR3 and directly regulate expression of this nuclear pore protein, which is known to participate in the regulation of flowering time, suggesting that AtVOZs exert at least some of their flowering regulation by influencing the nuclear pore function. Complementation of atvoz1-1 atvoz2-1 with AtVOZ2 reversed all double mutant phenotypes, confirming that the observed morphological and molecular changes arise from the absence of functional AtVOZ proteins, and validating the functional redundancy between AtVOZ1 and AtVOZ2.

| S-EPMC3625871 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data