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Int J Mol Sci
2022 Sep 10;2318:. doi: 10.3390/ijms231810485.
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Genome-Wide Analysis of the Growth-Regulating Factor (GRF) Family in Aquatic Plants and Their Roles in the ABA-Induced Turion Formation of Spirodela polyrhiza.
Li G
,
Chen Y
,
Zhao X
,
Yang J
,
Wang X
,
Li X
,
Hu S
,
Hou H
.
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Growth-regulating factors (GRFs) are plant-specific transcription factors that play essential roles in regulating plant growth and stress response. The GRF gene families have been described in several terrestrial plants, but a comprehensive analysis of these genes in diverse aquatic species has not been reported yet. In this study, we identified 130 GRF genes in 13 aquatic plants, including floating plants (Azolla filiculoides, Wolffia australiana, Lemna minuta, Spirodela intermedia, and Spirodela polyrhiza), floating-leaved plants (Nymphaea colorata and Euryale ferox), submersed plants (Zostera marina, Ceratophyllum demersum, Aldrovanda vesiculosa, and Utricularia gibba), an emergent plant (Nelumbo nucifera), and an amphibious plant (Cladopus chinensis). The gene structures, motifs, and cis-acting regulatory elements of these genes were analyzed. Phylogenetic analysis divided these GRFs into five clusters, and ABRE cis-elements were highly enriched in the promoter region of the GRFs in floating plants. We found that abscisic acid (ABA) is efficient at inducing the turion of Spirodela polyrhiza (giant duckweed), accompanied by the fluctuated expression of SpGRF genes in their fronds. Our results provide information about the GRF gene family in aquatic species and lay the foundation for future studies on the functions of these genes.
2017YFE0128800 National Key Research and Development Program of China, 31870384 National Natural Science Foundation of China, 32101254 National Natural Science Foundation of China, 152342KYSB20200021 International Partnership Program of the Chinese Academy of Sciences
Figure 1. Calculations of the GRFs in A. thaliana and 13 aquatic plants.
Figure 2. Phylogenetic analysis of the GRFs in A. thaliana and 13 aquatic plants. The neighbor-joining (NJ) phylogenetic tree was generated by MEGA 7.0 with 1000 bootstrap replications on the JTT model. The 139 GRFs were divided into five groups (A–E named by numbers of genes and indicated by five different colors), and the GRFs from different species were labeled with different colored symbols. Tomato circles indicate genes from A. thaliana; Dark orange circles indicate genes from A. filiculoides; Maroon circles indicate genes from A. vesiculosa; Gold circles indicate genes from C. chinensis; Yellow circles indicate genes from C. demersum; Dark gold circles indicate genes from E. ferox; Blue circles indicate genes from U. gibba; Dodger blue circles indicate genes from N. colorata; Medium orchid circles indicate genes from N. nucifera; Cyan circles indicate genes from Z. marina; Deep sky blue triangles indicate genes from L. minuta; Purple triangles indicate genes from S. intermedia; Black triangles indicate genes from S. polyrhiza; Yellow triangles indicate genes from W. australiana.
Figure 3. Gene structures of the GRFs. The GRFs from different species were labeled with different colored symbols. Tomato circles indicate genes from A. thaliana; Dark orange circles indicate genes from A. filiculoides; Maroon circles indicate genes from A. vesiculosa; Gold circles indicate genes from C. chinensis; Yellow circles indicate genes from C. demersum; Dark gold circles indicate genes from E. ferox; Blue circles indicate genes from U. gibba; Dodger blue circles indicate genes from N. colorata; Medium orchid circles indicate genes from N. nucifera; Cyan circles indicate genes from Z. marina; Deep sky blue triangles indicate genes from L. minuta; Purple triangles indicate genes from S. intermedia; Black triangles indicate genes from S. polyrhiza; Yellow triangles indicate genes from W. australiana.
Figure 4. Conserved motifs of the GRFs. The GRFs from different species were labeled with different colored symbols. Tomato circles indicate genes from A. thaliana; Dark orange circles indicate genes from A. filiculoides; Maroon circles indicate genes from A. vesiculosa; Gold circles indicate genes from C. chinensis; Yellow circles indicate genes from C. demersum; Dark gold circles indicate genes from E. ferox; Blue circles indicate genes from U. gibba; Dodger blue circles indicate genes from N. colorata; Medium orchid circles indicate genes from N. nucifera; Cyan circles indicate genes from Z. marina; Deep sky blue triangles indicate genes from L. minuta; Purple triangles indicate genes from S. intermedia; Black triangles indicate genes from S. polyrhiza; Yellow triangles indicate genes from W. australiana.
Figure 5. Frequency of the main cis-elements in the 1.5 kb promoter of the 139 GRFs.
Figure 6. Chromosomal localization, gene collinearity, and synteny analysis of the SpGRFs. (A) Distribution of the SpGRF genes on the chromosomes of S. polyrhiza. The scale bar indicates chromosome length (Mb). (B) Gene collinearity of the SpGRF genes on the chromosomes of S. polyrhiza.
Figure 7. Synteny relationship of the GRF gene pairs between S. polyrhiza and four other plants. The red colour represents syntenic GRFs, and the gray lines show the collinear blocks of the plant genome. The chromosome number was labeled near each chromosome.
Figure 8. Phenotypes and expression of the SpGRFs in the frond and turion of S. polyrhiza. (A) Phenotypes of turion (left) and whole plant (right) of S. polyrhiza. Bar = 1 mm. Arrows indicate frond or roots of S. polyrhiza, separately. (B) Expression of the SpGRFs in the frond and turion. F1: SpGRF1 in the frond; F2: SpGRF2 in the frond; F3: SpGRF3 in the frond; F4: SpGRF4 in the frond; F5: SpGRF5 in the frond; F6: SpGRF6 in the frond; T1: SpGRF1 in the turion; T2: SpGRF2 in the turion; T3: SpGRF3 in the turion; T4: SpGRF4 in the turion; T5: SpGRF5 in the turion; T6: SpGRF6 in the turion. The different letters indicate statistically significant differences relative to F1, as determined by the Duncan test (p < 0.05).
Figure 9. Phenotypes and expression of the SpGRFs during the ABA-induced turion formation of S. polyrhiza. (A) Phenotypes of S. polyrhiza during the ABA-induced turion formation. Bars = 1 cm. (B) Expression of the SpGRFs in the fronds after the treatment. The different letters indicate statistically significant differences relative to 0 days, as determined by the Duncan test (p < 0.05).
Abid,
Genome-Wide Identification and Structural Characterization of Growth-Regulating Factors (GRFs) in Actinida eriantha and Actinidia chinensis.
2022, Pubmed
Abid,
Genome-Wide Identification and Structural Characterization of Growth-Regulating Factors (GRFs) in Actinida eriantha and Actinidia chinensis.
2022,
Pubmed
Brunetti,
Review: ABA, flavonols, and the evolvability of land plants.
2019,
Pubmed
Cao,
Genome-wide characterization of the GRF family and their roles in response to salt stress in Gossypium.
2020,
Pubmed
Chen,
Genome-wide identification of GRF transcription factors in soybean and expression analysis of GmGRF family under shade stress.
2019,
Pubmed
Chen,
TBtools: An Integrative Toolkit Developed for Interactive Analyses of Big Biological Data.
2020,
Pubmed
Chen,
Role of Nramp transporter genes of Spirodela polyrhiza in cadmium accumulation.
2021,
Pubmed
Choi,
Whole genome analysis of the OsGRF gene family encoding plant-specific putative transcription activators in rice (Oryza sativa L.).
2004,
Pubmed
Debernardi,
Post-transcriptional control of GRF transcription factors by microRNA miR396 and GIF co-activator affects leaf size and longevity.
2014,
Pubmed
Du,
Genome-Wide Identification and Characterization of Growth Regulatory Factor Family Genes in Medicago.
2022,
Pubmed
Engelhardt,
Effects of macrophyte species richness on wetland ecosystem functioning and services.
2001,
Pubmed
He,
Investigating the molecular basis for heterophylly in the aquatic plant Potamogeton octandrus (Potamogetonaceae) with comparative transcriptomics.
2018,
Pubmed
Hewezi,
The Arabidopsis microRNA396-GRF1/GRF3 regulatory module acts as a developmental regulator in the reprogramming of root cells during cyst nematode infection.
2012,
Pubmed
Iida,
Loss of heterophylly in aquatic plants: not ABA-mediated stress but exogenous ABA treatment induces stomatal leaves in Potamogeton perfoliatus.
2016,
Pubmed
Kim,
Regulation of plant growth and development by the GROWTH-REGULATING FACTOR and GRF-INTERACTING FACTOR duo.
2015,
Pubmed
Kim,
A transcriptional coactivator, AtGIF1, is involved in regulating leaf growth and morphology in Arabidopsis.
2004,
Pubmed
Kim,
The AtGRF family of putative transcription factors is involved in leaf and cotyledon growth in Arabidopsis.
2003,
Pubmed
Kim,
A molecular basis behind heterophylly in an amphibious plant, Ranunculus trichophyllus.
2018,
Pubmed
Kim,
Arabidopsis growth-regulating factor7 functions as a transcriptional repressor of abscisic acid- and osmotic stress-responsive genes, including DREB2A.
2012,
Pubmed
Kosugi,
Systematic identification of cell cycle-dependent yeast nucleocytoplasmic shuttling proteins by prediction of composite motifs.
2009,
Pubmed
Lantzouni,
GROWTH-REGULATING FACTORS Interact with DELLAs and Regulate Growth in Cold Stress.
2020,
Pubmed
Li,
Mechanisms of the Morphological Plasticity Induced by Phytohormones and the Environment in Plants.
2021,
Pubmed
Li,
The OsmiR396c-OsGRF4-OsGIF1 regulatory module determines grain size and yield in rice.
2016,
Pubmed
Li,
Genome-Wide Identification and Characterization of the Abiotic-Stress-Responsive GRF Gene Family in Diploid Woodland Strawberry (Fragaria vesca).
2021,
Pubmed
Li,
Heterophylly: Phenotypic Plasticity of Leaf Shape in Aquatic and Amphibious Plants.
2019,
Pubmed
Li,
Water-Wisteria as an ideal plant to study heterophylly in higher aquatic plants.
2017,
Pubmed
Lin,
Blue light and abscisic acid independently induce heterophyllous switch in marsilea quadrifolia.
1999,
Pubmed
Liu,
OsmiR396d-regulated OsGRFs function in floral organogenesis in rice through binding to their targets OsJMJ706 and OsCR4.
2014,
Pubmed
Nakashima,
ABA signaling in stress-response and seed development.
2013,
Pubmed
Omidbakhshfard,
Growth-Regulating Factors (GRFs): A Small Transcription Factor Family with Important Functions in Plant Biology.
2015,
Pubmed
Omidbakhshfard,
GROWTH-REGULATING FACTOR 9 negatively regulates arabidopsis leaf growth by controlling ORG3 and restricting cell proliferation in leaf primordia.
2018,
Pubmed
Rodriguez,
Control of cell proliferation in Arabidopsis thaliana by microRNA miR396.
2010,
Pubmed
Smart,
A plant gene with homology to D-myo-inositol-3-phosphate synthase is rapidly and spatially up-regulated during an abscisic-acid-induced morphogenic response in Spirodela polyrrhiza.
1993,
Pubmed
Smart,
The Physiological Role of Abscisic Acid in Eliciting Turion Morphogenesis.
1995,
Pubmed
Tang,
Genome-wide identification and expression analysis of the growth regulating factor (GRF) family in Jatropha curcas.
2021,
Pubmed
Treich,
SNF11, a new component of the yeast SNF-SWI complex that interacts with a conserved region of SNF2.
1995,
Pubmed
Vercruysse,
Molecular networks regulating cell division during Arabidopsis leaf growth.
2020,
Pubmed
Vercruyssen,
GROWTH REGULATING FACTOR5 stimulates Arabidopsis chloroplast division, photosynthesis, and leaf longevity.
2015,
Pubmed
Wang,
Analysis of ADP-glucose pyrophosphorylase expression during turion formation induced by abscisic acid in Spirodela polyrhiza (greater duckweed).
2012,
Pubmed
Wang,
MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity.
2012,
Pubmed
Wanke,
The ABA-mediated switch between submersed and emersed life-styles in aquatic macrophytes.
2011,
Pubmed
Xing,
Bioaccumulation of heavy metals by submerged macrophytes: looking for hyperaccumulators in eutrophic lakes.
2013,
Pubmed
Zan,
Genome-Wide Identification and Analysis of the Growth-Regulating Factor (GRF) Gene Family and GRF-Interacting Factor Family in Triticum aestivum L.
2020,
Pubmed
Zhang,
Genome-wide identification and analysis of the growth-regulating factor family in tobacco (Nicotiana tabacum).
2018,
Pubmed
Zhao,
Genome-Wide Analysis of the Growth-Regulating Factor Family in Peanut (Arachis hypogaea L.).
2019,
Pubmed
Zhao,
Genome-wide identification and comparative analysis of the WRKY gene family in aquatic plants and their response to abiotic stresses in giant duckweed (Spirodela polyrhiza).
2021,
Pubmed
van der Knaap,
A novel gibberellin-induced gene from rice and its potential regulatory role in stem growth.
2000,
Pubmed
