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Chang YL, Chang YC, Kurniawan A, Chang PC, Liou TY, Wang WD, Chuang HW. Employing Genomic Tools to Explore the Molecular Mechanisms behind the Enhancement of Plant Growth and Stress Resilience Facilitated by a Burkholderia Rhizobacterial Strain. Int J Mol Sci 2024; 25:6091. [PMID: 38892282 PMCID: PMC11172717 DOI: 10.3390/ijms25116091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 05/28/2024] [Accepted: 05/30/2024] [Indexed: 06/21/2024] Open
Abstract
The rhizobacterial strain BJ3 showed 16S rDNA sequence similarity to species within the Burkholderia genus. Its complete genome sequence revealed a 97% match with Burkholderia contaminans and uncovered gene clusters essential for plant-growth-promoting traits (PGPTs). These clusters include genes responsible for producing indole acetic acid (IAA), osmolytes, non-ribosomal peptides (NRPS), volatile organic compounds (VOCs), siderophores, lipopolysaccharides, hydrolytic enzymes, and spermidine. Additionally, the genome contains genes for nitrogen fixation and phosphate solubilization, as well as a gene encoding 1-aminocyclopropane-1-carboxylate (ACC) deaminase. The treatment with BJ3 enhanced root architecture, boosted vegetative growth, and accelerated early flowering in Arabidopsis. Treated seedlings also showed increased lignin production and antioxidant capabilities, as well as notably increased tolerance to water deficit and high salinity. An RNA-seq transcriptome analysis indicated that BJ3 treatment significantly activated genes related to immunity induction, hormone signaling, and vegetative growth. It specifically activated genes involved in the production of auxin, ethylene, and salicylic acid (SA), as well as genes involved in the synthesis of defense compounds like glucosinolates, camalexin, and terpenoids. The expression of AP2/ERF transcription factors was markedly increased. These findings highlight BJ3's potential to produce various bioactive metabolites and its ability to activate auxin, ethylene, and SA signaling in Arabidopsis, positioning it as a new Burkholderia strain that could significantly improve plant growth, stress resilience, and immune function.
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Affiliation(s)
- Yueh-Long Chang
- Department of Agricultural Biotechnology, National Chiayi University, Chiayi 600355, Taiwan
| | - Yu-Cheng Chang
- Department of Agricultural Biotechnology, National Chiayi University, Chiayi 600355, Taiwan
| | - Andi Kurniawan
- Department of Agricultural Biotechnology, National Chiayi University, Chiayi 600355, Taiwan
- Department of Agronomy, Brawijaya University, Malang 65145, Indonesia
| | - Po-Chun Chang
- Department of Agricultural Biotechnology, National Chiayi University, Chiayi 600355, Taiwan
| | - Ting-Yu Liou
- Department of Agricultural Biotechnology, National Chiayi University, Chiayi 600355, Taiwan
| | - Wen-Der Wang
- Department of Agricultural Biotechnology, National Chiayi University, Chiayi 600355, Taiwan
| | - Huey-wen Chuang
- Department of Agricultural Biotechnology, National Chiayi University, Chiayi 600355, Taiwan
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Bin J, Tan Q, Wen S, Huang L, Wang H, Imtiaz M, Zhang Z, Guo H, Xie L, Zeng R, Wei Q. Comprehensive Analyses of Four PhNF-YC Genes from Petunia hybrida and Impacts on Flowering Time. PLANTS (BASEL, SWITZERLAND) 2024; 13:742. [PMID: 38475587 DOI: 10.3390/plants13050742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 03/01/2024] [Accepted: 03/01/2024] [Indexed: 03/14/2024]
Abstract
Nuclear Factor Y (NF-Y) is a class of heterotrimeric transcription factors composed of three subunits: NF-A, NF-YB, and NF-YC. NF-YC family members play crucial roles in various developmental processes, particularly in the regulation of flowering time. However, their functions in petunia remain poorly understood. In this study, we isolated four PhNF-YC genes from petunia and confirmed their subcellular localization in both the nucleus and cytoplasm. We analyzed the transcript abundance of all four PhNF-YC genes and found that PhNF-YC2 and PhNF-YC4 were highly expressed in apical buds and leaves, with their transcript levels decreasing before flower bud differentiation. Silencing PhNF-YC2 using VIGS resulted in a delayed flowering time and reduced chlorophyll content, while PhNF-YC4-silenced plants only exhibited a delayed flowering time. Furthermore, we detected the transcript abundance of flowering-related genes involved in different signaling pathways and found that PhCO, PhGI, PhFBP21, PhGA20ox4, and PhSPL9b were regulated by both PhNF-YC2 and PhNF-YC4. Additionally, the transcript abundance of PhSPL2, PhSPL3, and PhSPL4 increased only in PhNF-YC2-silenced plants. Overall, these results provide evidence that PhNF-YC2 and PhNF-YC4 negatively regulate flowering time in petunia by modulating a series of flowering-related genes.
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Affiliation(s)
- Jing Bin
- Guangdong Province Key Laboratory of Plant Molecular Breeding, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
| | - Qinghua Tan
- College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Shiyun Wen
- Guangdong Province Key Laboratory of Plant Molecular Breeding, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Licheng Huang
- Guangdong Province Key Laboratory of Plant Molecular Breeding, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
| | - Huimin Wang
- College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Muhammad Imtiaz
- Department of Horticulture, Abdul Wali Khan University, Mardan 23200, Pakistan
| | - Zhisheng Zhang
- Guangdong Province Key Laboratory of Plant Molecular Breeding, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
| | - Herong Guo
- Guangdong Province Key Laboratory of Plant Molecular Breeding, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
| | - Li Xie
- Guangdong Province Key Laboratory of Plant Molecular Breeding, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
| | - Ruizhen Zeng
- Guangdong Province Key Laboratory of Plant Molecular Breeding, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
| | - Qian Wei
- Guangdong Province Key Laboratory of Plant Molecular Breeding, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
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Poethig RS, Fouracre J. Temporal regulation of vegetative phase change in plants. Dev Cell 2024; 59:4-19. [PMID: 38194910 PMCID: PMC10783531 DOI: 10.1016/j.devcel.2023.11.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 10/11/2023] [Accepted: 11/13/2023] [Indexed: 01/11/2024]
Abstract
During their vegetative growth, plants reiteratively produce leaves, buds, and internodes at the apical end of the shoot. The identity of these organs changes as the shoot develops. Some traits change gradually, but others change in a coordinated fashion, allowing shoot development to be divided into discrete juvenile and adult phases. The transition between these phases is called vegetative phase change. Historically, vegetative phase change has been studied because it is thought to be associated with an increase in reproductive competence. However, this is not true for all species; indeed, heterochronic variation in the timing of vegetative phase change and flowering has made important contributions to plant evolution. In this review, we describe the molecular mechanism of vegetative phase change, how the timing of this process is controlled by endogenous and environmental factors, and its ecological and evolutionary significance.
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Affiliation(s)
- R Scott Poethig
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Jim Fouracre
- School of Biological Sciences, University of Bristol, Bristol BS8 1TQ, UK
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Hamid R, Jacob F, Ghorbanzadeh Z, Jafari L, Alishah O. Dynamic roles of small RNAs and DNA methylation associated with heterosis in allotetraploid cotton (Gossypium hirsutum L.). BMC PLANT BIOLOGY 2023; 23:488. [PMID: 37828433 PMCID: PMC10571366 DOI: 10.1186/s12870-023-04495-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 09/28/2023] [Indexed: 10/14/2023]
Abstract
BACKGROUND Heterosis is a complex phenomenon wherein the hybrids outperform their parents. Understanding the underlying molecular mechanism by which hybridization leads to higher yields in allopolyploid cotton is critical for effective breeding programs. Here, we integrated DNA methylation, transcriptomes, and small RNA profiles to comprehend the genetic and molecular basis of heterosis in allopolyploid cotton at three developmental stages. RESULTS Transcriptome analysis revealed that numerous DEGs responsive to phytohormones (auxin and salicylic acid) were drastically altered in F1 hybrid compared to the parental lines. DEGs involved in energy metabolism and plant growth were upregulated, whereas DEGs related to basal defense were downregulated. Differences in homoeologous gene expression in F1 hybrid were greatly reduced after hybridization, suggesting that higher levels of parental expression have a vital role in heterosis. Small RNAome and methylome studies showed that the degree of DNA methylation in hybrid is higher when compared to the parents. A substantial number of allele-specific expression genes were found to be strongly regulated by CG allele-specific methylation levels. The hybrid exhibited higher 24-nt-small RNA (siRNA) expression levels than the parents. The regions in the genome with increased levels of 24-nt-siRNA were chiefly related to genes and their flanking regulatory regions, demonstrating a possible effect of these molecules on gene expression. The transposable elements correlated with siRNA clusters in the F1 hybrid had higher methylation levels but lower expression levels, which suggest that these non-additively expressed siRNA clusters, reduced the activity of transposable elements through DNA methylation in the hybrid. CONCLUSIONS These multi-omics data provide insights into how changes in epigenetic mechanisms and gene expression patterns can lead to heterosis in allopolyploid cotton. This makes heterosis a viable tool in cotton breeding.
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Affiliation(s)
- Rasmieh Hamid
- Department of Plant Breeding, Cotton Research Institute of Iran (CRII), Agricultural Research, Education and Extension Organization (AREEO), Gorgan, Iran.
| | - Feba Jacob
- Centre for Plant Biotechnology and Molecular Biology, Kerala Agricultural University, Thrissur, India
| | - Zahra Ghorbanzadeh
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Leila Jafari
- Horticultural Science Department, Faculty of Agriculture and Natural Resources, University of Hormozgan, Bandar Abbas, Iran
- Research Group of Agroecology in Dryland Areas, University of Hormozgan, Bandar Abbas, Iran
| | - Omran Alishah
- Department of Plant Breeding, Cotton Research Institute of Iran (CRII), Agricultural Research, Education and Extension Organization (AREEO), Gorgan, Iran
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Li Z, Yang Y, Chen B, Xia B, Li H, Zhou Y, He M. Genome-wide identification and expression analysis of SBP-box gene family reveal their involvement in hormone response and abiotic stresses in Chrysanthemum nankingense. PeerJ 2022; 10:e14241. [PMID: 36320567 PMCID: PMC9618261 DOI: 10.7717/peerj.14241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 09/23/2022] [Indexed: 01/24/2023] Open
Abstract
SQUAMOSA promoter-binding-protein (SBP)-box family proteins are a class of plant-specific transcription factors, and widely regulate the development of floral and leaf morphology in plant growth and involve in environment and hormone signal response. In this study, we isolated and identified 21 non-redundant SBP-box genes in Chrysanthemum nankingense with bioinformatics analysis. Sequence alignments of 21 CnSBP proteins discovered a highly conserved SBP domain including two zinc finger-like structures and a nuclear localization signal region. According to the amino acid sequence alignments, 67 SBP-box genes from Arabidopsis thaliana, rice, Artemisia annua and C. nankingense were clustered into eight groups, and the motif and gene structure analysis also sustained this classification. The gene evolution analysis indicated the CnSBP genes experienced a duplication event about 10 million years ago (Mya), and the CnSBP and AtSPL genes occurred a divergence at 24 Mya. Transcriptome data provided valuable information for tissue-specific expression profiles of the CnSBPs, which highly expressed in floral tissues and differentially expressed in leaf, root and stem organs. Quantitative Real-time Polymerase Chain Reaction data showed expression patterns of the CnSBPs under exogenous hormone and abiotic stress treatments, separately abscisic acid, salicylic acid, gibberellin A3, methyl jasmonate and ethylene spraying as well as salt and drought stresses, indicating that the candidate CnSBP genes showed differentiated spatiotemporal expression patterns in response to hormone and abiotic stresses. Our study provides a systematic genome-wide analysis of the SBP-box gene family in C. nankingense. In general, it provides a fundamental theoretical basis that SBP-box genes may regulate the resistance of stress physiology in chrysanthemum via exogenous hormone pathways.
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Affiliation(s)
- Ziwei Li
- College of Landscape Architecture, Northeast Forestry University, Harbin, Heilongjiang, China
| | - Yujia Yang
- College of Landscape Architecture, Northeast Forestry University, Harbin, Heilongjiang, China
| | - Bin Chen
- College of Landscape Architecture, Northeast Forestry University, Harbin, Heilongjiang, China
| | - Bin Xia
- College of Landscape Architecture, Northeast Forestry University, Harbin, Heilongjiang, China
| | - Hongyao Li
- College of Landscape Architecture, Northeast Forestry University, Harbin, Heilongjiang, China
| | - Yunwei Zhou
- College of Horticulture, Jilin Agricultural University, Jilin, China
| | - Miao He
- College of Landscape Architecture, Northeast Forestry University, Harbin, Heilongjiang, China
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Gao L, Lyu T, Lyu Y. Genome-Wide Analysis of the SPL Gene Family and Expression Analysis during Flowering Induction in Prunus × yedoensis 'Somei-yoshino'. Int J Mol Sci 2022; 23:ijms231710052. [PMID: 36077445 PMCID: PMC9456211 DOI: 10.3390/ijms231710052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 08/26/2022] [Accepted: 08/30/2022] [Indexed: 11/29/2022] Open
Abstract
SQUAMOSA Promoter-Binding Protein-Like (SPL) genes encode plant-specific transcription factors which bind to the SQUAMOSA promoter of the MADS-box genes to regulate its expression. It plays important regulatory roles in floral induction and development, fertility, light signals and hormonal transduction, and stress response in plants. In this study, 32 PySPL genes with complete SBP (squamosa promoter binding protein) conserved domain were identified from the genome of Prunus × yedoensis ‘Somei-yoshino’ and analyzed by bioinformatics. 32 PySPLs were distributed on 13 chromosomes, encoding 32 PySPL proteins with different physical and chemical properties. The phylogenetic tree constructed with Arabidopsis thaliana and Oryza sativa can be divided into 10 subtribes, indicating PySPLs of different clusters have different biological functions. The conserved motif prediction showed that the number and distribution of motifs on each PySPL is varied. The gene structure analysis revealed that PySPLs harbored exons ranging from 2 to 10. The predictive analysis of acting elements showed that the promoter of PySPLs contain a large number of light-responsive elements, as well as response elements related to hormone response, growth and development and stress response. The analysis of the PySPLs expressions in flower induction and flower organs based on qRT-PCR showed that PySPL06/22 may be the key genes of flower development, PySPL01/06 and PySPL22 may play a role in the development of sepal and pistil, respectively. The results provide a foundation for the study of SPL transcription factors of Prunus × yedoensis ‘Somei-yoshino’ and provide more reference information of the function of SPL gene in flowering.
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Affiliation(s)
- Lan Gao
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, China National Engineering Research Center for Floriculture, College of Landscape Architecture, Beijing Forestry University, Beijing 100083, China
| | - Tong Lyu
- Beijing Flower Engineering Technology Research Center, Plant Institute, China National Botanical Garden North Park, Beijing 100093, China
| | - Yingmin Lyu
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, China National Engineering Research Center for Floriculture, College of Landscape Architecture, Beijing Forestry University, Beijing 100083, China
- Correspondence:
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Lee YK, Kumari S, Olson A, Hauser F, Ware D. Role of a ZF-HD Transcription Factor in miR157-Mediated Feed-Forward Regulatory Module That Determines Plant Architecture in Arabidopsis. Int J Mol Sci 2022; 23:ijms23158665. [PMID: 35955798 PMCID: PMC9369202 DOI: 10.3390/ijms23158665] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/27/2022] [Accepted: 07/28/2022] [Indexed: 02/05/2023] Open
Abstract
In plants, vegetative and reproductive development are associated with agronomically important traits that contribute to grain yield and biomass. Zinc finger homeodomain (ZF-HD) transcription factors (TFs) constitute a relatively small gene family that has been studied in several model plants, including Arabidopsis thaliana L. and Oryza sativa L. The ZF-HD family members play important roles in plant growth and development, but their contribution to the regulation of plant architecture remains largely unknown due to their functional redundancy. To understand the gene regulatory network controlled by ZF-HD TFs, we analyzed multiple loss-of-function mutants of ZF-HD TFs in Arabidopsis that exhibited morphological abnormalities in branching and flowering architecture. We found that ZF-HD TFs, especially HB34, negatively regulate the expression of miR157 and positively regulate SQUAMOSA PROMOTER BINDING-LIKE 10 (SPL10), a target of miR157. Genome-wide chromatin immunoprecipitation sequencing (ChIP-Seq) analysis revealed that miR157D and SPL10 are direct targets of HB34, creating a feed-forward loop that constitutes a robust miRNA regulatory module. Network motif analysis contains overrepresented coherent type IV feedforward motifs in the amiR zf-HD and hbq mutant background. This finding indicates that miRNA-mediated ZF-HD feedforward modules modify branching and inflorescence architecture in Arabidopsis. Taken together, these findings reveal a guiding role of ZF-HD TFs in the regulatory network module and demonstrate its role in plant architecture in Arabidopsis.
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Affiliation(s)
- Young Koung Lee
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
- Institute of Plasma Technology, Korea Institute of Fusion Energy, 37, Dongjangsan-ro, Gunsan-si 54004, Korea
- Correspondence: (Y.K.L.); (D.W.)
| | - Sunita Kumari
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Andrew Olson
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Felix Hauser
- Division of Biological Sciences, University of California–San Diego, La Jolla, CA 92093, USA
| | - Doreen Ware
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
- USDA-ARS, Robert W. Holley Center, Ithaca, NY 14853, USA
- Correspondence: (Y.K.L.); (D.W.)
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Singer SD, Burton Hughes K, Subedi U, Dhariwal GK, Kader K, Acharya S, Chen G, Hannoufa A. The CRISPR/Cas9-Mediated Modulation of SQUAMOSA PROMOTER-BINDING PROTEIN-LIKE 8 in Alfalfa Leads to Distinct Phenotypic Outcomes. FRONTIERS IN PLANT SCIENCE 2022; 12:774146. [PMID: 35095953 PMCID: PMC8793889 DOI: 10.3389/fpls.2021.774146] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Accepted: 12/10/2021] [Indexed: 05/04/2023]
Abstract
Alfalfa (Medicago sativa L.) is the most widely grown perennial leguminous forage and is an essential component of the livestock industry. Previously, the RNAi-mediated down-regulation of alfalfa SQUAMOSA PROMOTER-BINDING PROTEIN-LIKE 8 (MsSPL8) was found to lead to increased branching, regrowth and biomass, as well as enhanced drought tolerance. In this study, we aimed to further characterize the function of MsSPL8 in alfalfa using CRISPR/Cas9-induced mutations in this gene. We successfully generated alfalfa genotypes with small insertions/deletions (indels) at the target site in up to three of four MsSPL8 alleles in the first generation. The efficiency of editing appeared to be tightly linked to the particular gRNA used. The resulting genotypes displayed consistent morphological alterations, even with the presence of up to two wild-type MsSPL8 alleles, including reduced leaf size and early flowering. Other phenotypic effects appeared to be dependent upon mutational dosage, with those plants with the highest number of mutated MsSPL8 alleles also exhibiting significant decreases in internode length, plant height, shoot and root biomass, and root length. Furthermore, MsSPL8 mutants displayed improvements in their ability to withstand water-deficit compared to empty vector control genotypes. Taken together, our findings suggest that allelic mutational dosage can elicit phenotypic gradients in alfalfa, and discrepancies may exist in terms of MsSPL8 function between alfalfa genotypes, growth conditions, or specific alleles. In addition, our results provide the foundation for further research exploring drought tolerance mechanisms in a forage crop.
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Affiliation(s)
- Stacy D. Singer
- Lethbridge Research and Development Center, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Kimberley Burton Hughes
- Lethbridge Research and Development Center, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Udaya Subedi
- Lethbridge Research and Development Center, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
- Department of Agricultural, Food and Nutritional Sciences, University of Alberta, Edmonton, AB, Canada
| | - Gaganpreet Kaur Dhariwal
- Lethbridge Research and Development Center, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Kazi Kader
- Lethbridge Research and Development Center, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Surya Acharya
- Lethbridge Research and Development Center, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Guanqun Chen
- Department of Agricultural, Food and Nutritional Sciences, University of Alberta, Edmonton, AB, Canada
| | - Abdelali Hannoufa
- London Research and Development Center, Agriculture and Agri-Food Canada, London, ON, Canada
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Zhou Q, Shi J, Li Z, Zhang S, Zhang S, Zhang J, Bao M, Liu G. miR156/157 Targets SPLs to Regulate Flowering Transition, Plant Architecture and Flower Organ Size in Petunia. PLANT & CELL PHYSIOLOGY 2021; 62:839-857. [PMID: 33768247 DOI: 10.1093/pcp/pcab041] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 03/19/2021] [Indexed: 05/15/2023]
Abstract
miR156/157 plays multiple pivotal roles during plant growth and development. In this study, we identified 11 miR156- and 5 miR157-encoding loci from the genome of Petunia axillaris and Petunia inflata, designated as PaMIR0156/157s and PiMIR0156/157s, respectively. Real-time quantitative reverse transcription PCR (qRT-PCR) analysis indicated that PhmiR156/157 was expressed predominantly in cotyledons, germinating seeds, flower buds, young fruits and seedlings. PhmiR156/157 levels declined in shoot apical buds and leaves of petunia before flowering as the plant ages; moreover, the temporal expression patterns of most miR156/157-targeted PhSPLs were complementary to that of PhmiR156/157. Ectopic expression of PhMIR0157a in Arabidopsis and petunia resulted in delayed flowering, dwarf plant stature, increased branches and reduced organ size. However, PhMIR0156f-overexpressing Arabidopsis and petunia plants showed only delayed flowering. In addition, downregulation of PhmiR156/157 level by overexpressing STTM156/157 led to taller plants with less branches, longer internodes and precocious flowering. qRT-PCR analysis indicated that PhmiR156/157 modulates these traits mainly by downregulating their PhSPL targets and subsequently decreasing the expression of flowering regulatory genes. Our results demonstrate that the PhmiR156/157-PhSPL module has conserved but also divergent functions in growth and development, which will help us decipher the genetic basis for the improvement of flower transition, plant architecture and organ development in petunia.
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Affiliation(s)
- Qin Zhou
- Key Laboratory of Horticultural Plant Biology, Ministry of Education; College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Jiewei Shi
- Key Laboratory of Horticultural Plant Biology, Ministry of Education; College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhineng Li
- Key Laboratory of Horticulture Science for Southern Mountains Regions, Ministry of Education; College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400715, China
| | - Sisi Zhang
- Wuhan Institute of Landscape Architecture, Peace Avenue No. 1240, Wuhan 430081, China
| | - Shuting Zhang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education; College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Jiaqi Zhang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education; College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Manzhu Bao
- Key Laboratory of Horticultural Plant Biology, Ministry of Education; College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Guofeng Liu
- Department of Botany, Guangzhou Institute of Forestry and Landscape Architecture, Guangzhou 510405, China
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10
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Xie X, Yue S, Shi B, Li H, Cui Y, Wang J, Yang P, Li S, Li X, Bian S. Comprehensive Analysis of the SBP Family in Blueberry and Their Regulatory Mechanism Controlling Chlorophyll Accumulation. FRONTIERS IN PLANT SCIENCE 2021; 12:703994. [PMID: 34276754 PMCID: PMC8281205 DOI: 10.3389/fpls.2021.703994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 06/09/2021] [Indexed: 06/13/2023]
Abstract
SQUAMOSA Promoter Binding Protein (SBP) family genes act as central players to regulate plant growth and development with functional redundancy and specificity. Addressing the diversity of the SBP family in crops is of great significance to precisely utilize them to improve agronomic traits. Blueberry is an important economic berry crop. However, the SBP family has not been described in blueberry. In the present study, twenty VcSBP genes were identified through data mining against blueberry transcriptome databases. These VcSBPs could be clustered into eight groups, and the gene structures and motif compositions are divergent among the groups and similar within each group. The VcSBPs were differentially expressed in various tissues. Intriguingly, 10 VcSBPs were highly expressed at green fruit stages and dramatically decreased at the onset of fruit ripening, implying that they are important regulators during early fruit development. Computational analysis showed that 10 VcSBPs were targeted by miR156, and four of them were further verified by degradome sequencing. Moreover, their functional diversity was studied in Arabidopsis. Noticeably, three VcSBPs significantly increased chlorophyll accumulation, and qRT-PCR analysis indicated that VcSBP13a in Arabidopsis enhanced the expression of chlorophyll biosynthetic genes such as AtDVR, AtPORA, AtPORB, AtPORC, and AtCAO. Finally, the targets of VcSBPs were computationally identified in blueberry, and the Y1H assay showed that VcSBP13a could physically bind to the promoter region of the chlorophyll-associated gene VcLHCB1. Our findings provided an overall framework for individually understanding the characteristics and functions of the SBP family in blueberry.
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Affiliation(s)
- Xin Xie
- College of Plant Science, Jilin University, Changchun, China
| | - Shaokang Yue
- College of Plant Science, Jilin University, Changchun, China
| | - Baosheng Shi
- College of Landscape Architecture and Tourism, Hebei Agricultural University, Baoding, China
| | - Hongxue Li
- College of Plant Science, Jilin University, Changchun, China
| | - Yuhai Cui
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON Canada
- Department of Biology, Western University, London, ON, Canada
| | - Jingying Wang
- College of Plant Science, Jilin University, Changchun, China
| | - Pengjie Yang
- College of Plant Science, Jilin University, Changchun, China
| | - Shuchun Li
- Department of Pain, Second Hospital of Jilin University, Changchun, China
| | - Xuyan Li
- College of Plant Science, Jilin University, Changchun, China
| | - Shaomin Bian
- College of Plant Science, Jilin University, Changchun, China
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Gioppato HA, Dornelas MC. Plant design gets its details: Modulating plant architecture by phase transitions. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 163:1-14. [PMID: 33799013 DOI: 10.1016/j.plaphy.2021.03.046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 03/20/2021] [Indexed: 06/12/2023]
Abstract
Plants evolved different strategies to better adapt to the environmental conditions in which they live: the control of their body architecture and the timing of phase change are two important processes that can improve their fitness. As they age, plants undergo two major phase changes (juvenile to adult and adult to reproductive) that are a response to environmental and endogenous signals. These phase transitions are accompanied by alterations in plant morphology and also by changes in physiology and the behavior of gene regulatory networks. Six main pathways involving environmental and endogenous cues that crosstalk with each other have been described as responsible for the control of plant phase transitions: the photoperiod pathway, the autonomous pathway, the vernalization pathway, the temperature pathway, the GA pathway, and the age pathway. However, studies have revealed that sugar is also involved in phase change and the control of branching behavior. In this review, we discuss recent advances in plant biology concerning the genetic and molecular mechanisms that allow plants to regulate phase transitions in response to the environment. We also propose connections between phase transition and plant architecture control.
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Affiliation(s)
- Helena Augusto Gioppato
- University of Campinas (UNICAMP), Biology Institute, Plant Biology Department, Rua Monteiro Lobato, 255 CEP 13, 083-862, Campinas, SP, Brazil
| | - Marcelo Carnier Dornelas
- University of Campinas (UNICAMP), Biology Institute, Plant Biology Department, Rua Monteiro Lobato, 255 CEP 13, 083-862, Campinas, SP, Brazil.
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Feyissa BA, Amyot L, Nasrollahi V, Papadopoulos Y, Kohalmi SE, Hannoufa A. Involvement of the miR156/SPL module in flooding response in Medicago sativa. Sci Rep 2021; 11:3243. [PMID: 33547346 PMCID: PMC7864954 DOI: 10.1038/s41598-021-82450-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 01/20/2021] [Indexed: 01/30/2023] Open
Abstract
The highly conserved plant microRNA, miR156, affects plant development, metabolite composition, and stress response. Our previous research revealed the role of miR156 in abiotic stress response in Medicago sativa exerted by downregulating SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE transcription factors. Here we investigated the involvement and possible mechanism of action of the miR156/SPL module in flooding tolerance in alfalfa. For that, we used miR156 overexpressing, SPL13RNAi, flood-tolerant (AAC-Trueman) and -sensitive (AC-Caribou) alfalfa cultivars exposed to flooding. We also used Arabidopsis ABA insensitive (abi1-2, abi5-8) mutants and transgenic lines with either overexpressed (KIN10-OX1, KIN10-OX2) or silenced (KIN10RNAi-1, KIN10RNAi-2) catalytic subunit of SnRK1 to investigate a possible role of ABA and SnRK1 in regulating miR156 expression under flooding. Physiological analysis, hormone profiling and global transcriptome changes revealed a role for miR156/SPL module in flooding tolerance. We also identified nine novel alfalfa SPLs (SPL1, SPL1a, SPL2a, SPL7, SPL7a, SPL8, SPL13a, SPL14, SPL16) responsive to flooding. Our results also showed a possible ABA-dependent SnRK1 upregulation to enhance miR156 expression, resulting in downregulation of SPL4, SPL7a, SPL8, SPL9, SPL13, and SPL13a. We conclude that these effects induce flooding adaptive responses in alfalfa and modulate stress physiology by affecting the transcriptome, ABA metabolites and secondary metabolism.
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Affiliation(s)
- Biruk A. Feyissa
- grid.55614.330000 0001 1302 4958Agriculture and Agri-Food Canada, 1391 Sandford Street, London, ON N5V 4T3 Canada ,grid.39381.300000 0004 1936 8884Department of Biology, University of Western Ontario, 1151 Richmond Street, London, ON N6A5B7 Canada
| | - Lisa Amyot
- grid.55614.330000 0001 1302 4958Agriculture and Agri-Food Canada, 1391 Sandford Street, London, ON N5V 4T3 Canada
| | - Vida Nasrollahi
- grid.55614.330000 0001 1302 4958Agriculture and Agri-Food Canada, 1391 Sandford Street, London, ON N5V 4T3 Canada ,grid.39381.300000 0004 1936 8884Department of Biology, University of Western Ontario, 1151 Richmond Street, London, ON N6A5B7 Canada
| | | | - Susanne E. Kohalmi
- grid.39381.300000 0004 1936 8884Department of Biology, University of Western Ontario, 1151 Richmond Street, London, ON N6A5B7 Canada
| | - Abdelali Hannoufa
- grid.55614.330000 0001 1302 4958Agriculture and Agri-Food Canada, 1391 Sandford Street, London, ON N5V 4T3 Canada ,grid.39381.300000 0004 1936 8884Department of Biology, University of Western Ontario, 1151 Richmond Street, London, ON N6A5B7 Canada
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Ma L, Liu X, Liu W, Wen H, Zhang Y, Pang Y, Wang X. Characterization of Squamosa-Promoter Binding Protein-Box Family Genes Reveals the Critical Role of MsSPL20 in Alfalfa Flowering Time Regulation. FRONTIERS IN PLANT SCIENCE 2021; 12:775690. [PMID: 35069631 PMCID: PMC8766856 DOI: 10.3389/fpls.2021.775690] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 12/14/2021] [Indexed: 05/22/2023]
Abstract
SQUAMOSA Promoter-binding protein-Like (SPL) genes affect a broad range of plant biological processes and show potential application in crop improvement by genetic modification. As the most widely planted forage crop in the world, biomass and abiotic stresses tolerance are important breeding targets for alfalfa (Medicago sativa L.). Nevertheless, the systematic analysis of SPL genes in alfalfa genome remains lacking. In the present study, we characterized 22 putative non-redundant SPL genes in alfalfa genome and uncovered the abundant structural variation among MsSPL genes. The phylogenetic analysis of plant SPL proteins separated them into 10 clades and clade J was an alfalfa-specific clade, suggesting SPL genes in alfalfa might have experienced gene duplication and functional differentiation within the genome. Meanwhile, 11 MsSPL genes with perfect matches to miRNA response elements (MREs) could be degraded by miR156, and the cleavage sites were gene specific. In addition, we investigated the temporal and spatial expression patterns of MsSPL genes and their expression patterns in response to multiple treatments, characterizing candidate SPL genes in alfalfa development and abiotic stress tolerant regulation. More importantly, overexpression of the alfalfa-specific SPL gene (MsSPL20) showed stable delayed flowering time, as well as increased biomass. Further studies indicated that MsSPL20 delayed flowering time by regulating the expression of genes involved in floret development, including HD3A, FTIP1, TEM1, and HST1. Together, our findings provide valuable information for future research and utilization of SPL genes in alfalfa and elucidate a possibly alfalfa-specific flowering time regulation, thereby supplying candidate genes for alfalfa molecular-assisted breeding.
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Affiliation(s)
- Lin Ma
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiqiang Liu
- College of Grassland Science and Technology, China Agricultural University, Beijing, China
| | - Wenhui Liu
- Key Laboratory of Superior Forage Germplasm in the Qinghai-Tibetan Plateau, Qinghai Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining, China
| | - Hongyu Wen
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yongchao Zhang
- Key Laboratory of Superior Forage Germplasm in the Qinghai-Tibetan Plateau, Qinghai Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining, China
| | - Yongzhen Pang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
- *Correspondence: Yongzhen Pang,
| | - Xuemin Wang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
- Xuemin Wang,
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14
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Wang H, Lu Z, Xu Y, Kong L, Shi J, Liu Y, Fu C, Wang X, Wang ZY, Zhou C, Han L. Genome-wide characterization of SPL family in Medicago truncatula reveals the novel roles of miR156/SPL module in spiky pod development. BMC Genomics 2019; 20:552. [PMID: 31277566 PMCID: PMC6612136 DOI: 10.1186/s12864-019-5937-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 06/26/2019] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND SQUAMOSA Promoter Binding Protein-Likes (SPLs) proteins are plant-specific transcription factors that play many crucial roles in plant growth and development. However, there is little information about SPL family in the model legume Medicago truncatula. RESULTS In this study, a total of 23 MtSPL genes were identified in M. truncatula genome, in which 17 of the MtSPLs contained the putative MtmiR156 binding site at the coding or 3' UTR regions. Tissue-specific expression pattern analysis showed that most MtmiR156-targeted MtSPLs were highly expressed in seed and pod. The observation of MtmiR156B-overexpressing plants reveals that MtmiR156/MtSPL modules are not only involved in the development of leaves and branches, but also in the seed pod development, especially the formation of spine on pod. CONCLUSION The spines on pods are developed in many plant species, which allow pods to adhere to the animals, and then be transported on the outside. This study sheds light on the new function of SPL family in seed dispersal by controlling the formation of spiky pod, and provides insights on understanding evolutionary divergence of the members of SPL gene family among plant species.
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Affiliation(s)
- Hongfeng Wang
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, 266101, China.,School of Life Science, Guangzhou University, Guangzhou, 510006, China
| | - Zhichao Lu
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, 266101, China
| | - Yiteng Xu
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, 266101, China
| | - Lingcui Kong
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, 266101, China
| | - Jianjun Shi
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, 266101, China
| | - Yafei Liu
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, 266101, China
| | - Chunxiang Fu
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
| | - Xiaoshan Wang
- Department of Grassland Science, College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
| | - Zeng-Yu Wang
- Noble Research Institute, LLC, Ardmore, OK, USA.,Present Address: Grassland Agri-Husbandry Research Center, Qingdao Agricultural University, Qingdao, People's Republic of China
| | - Chuanen Zhou
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, 266101, China.
| | - Lu Han
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, 266101, China.
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Selection pressure causes differentiation of the SPL gene family in the Juglandaceae. Mol Genet Genomics 2019; 294:1037-1048. [DOI: 10.1007/s00438-019-01562-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 04/03/2019] [Indexed: 10/27/2022]
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Cao R, Guo L, Ma M, Zhang W, Liu X, Zhao H. Identification and Functional Characterization of Squamosa Promoter Binding Protein-Like Gene TaSPL16 in Wheat ( Triticum aestivum L.). FRONTIERS IN PLANT SCIENCE 2019; 10:212. [PMID: 30873195 PMCID: PMC6401658 DOI: 10.3389/fpls.2019.00212] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 02/07/2019] [Indexed: 05/04/2023]
Abstract
Wheat (Triticum aestivum L.) is one of the most important crops in the world. Squamosa promoter binding protein-like (SPL) proteins are plant-specific transcript factors and play critical roles in plant growth and development. The functions of many SPL gene family members were well characterized in Arabidopsis and rice, in contrast, research on wheat SPL genes is lagging behind. In this study, we cloned and characterized TaSPL16, an orthologous gene of rice OsSPL16, in wheat. Three TaSPL16 homoeologs are located on the short arms of chromosome 7A, 7B, and 7D, and share more than 96% sequence identity with each other. All the TaSPL16 homoeologs have three exons and two introns, with a miR156 binding site in their last exons. They encode putative proteins of 407, 409, and 414 amino acid residues, respectively. Subcellular localization showed TaSPL16 distribution in the cell nucleus, and transcription activity of TaSPL16 was validated in yeast. Analysis of the spatiotemporal expression profile showed that TaSPL16 is highly expressed in young developing panicles, lowly expressed in developing seeds and almost undetectable in vegetative tissues. Ectopic expression of TaSPL16 in Arabidopsis causes a delay in the emergence of vegetative leaves (3-4 days late), promotes early flowering (5-7 days early), increases organ size, and affects yield-related traits. These results demonstrated the regulatory roles of TaSPL16 in plant growth and development as well as seed yield. Our findings enrich the existing knowledge on SPL genes in wheat and provide valuable information for further investigating the effects of TaSPL16 on plant architecture and yield-related traits of wheat.
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Affiliation(s)
- Rufei Cao
- College of Life Sciences, Northwest A&F University, Yangling, China
| | - Lijian Guo
- College of Life Sciences, Northwest A&F University, Yangling, China
| | - Meng Ma
- College of Life Sciences, Northwest A&F University, Yangling, China
| | - Wenjing Zhang
- College of Life Sciences, Northwest A&F University, Yangling, China
| | - Xiangli Liu
- College of Life Sciences, Northwest A&F University, Yangling, China
| | - Huixian Zhao
- College of Life Sciences, Northwest A&F University, Yangling, China
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronmy, Northwest A&F University, Yangling, China
- *Correspondence: Huixian Zhao,
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Constitutive Expression of Aechmea fasciata SPL14 (AfSPL14) Accelerates Flowering and Changes the Plant Architecture in Arabidopsis. Int J Mol Sci 2018; 19:ijms19072085. [PMID: 30021946 PMCID: PMC6073119 DOI: 10.3390/ijms19072085] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 07/10/2018] [Accepted: 07/14/2018] [Indexed: 11/16/2022] Open
Abstract
Variations in flowering time and plant architecture have a crucial impact on crop biomass and yield, as well as the aesthetic value of ornamental plants. Aechmea fasciata, a member of the Bromeliaceae family, is a bromeliad variety that is commonly cultivated worldwide. Here, we report the characterization of AfSPL14, a squamosa promoter binding protein-like gene in A. fasciata. AfSPL14 was predominantly expressed in the young vegetative organs of adult plants. The expression of AfSPL14 could be upregulated within 1 h by exogenous ethephon treatment. The constitutive expression of AfSPL14 in Arabidopsis thaliana caused early flowering and variations in plant architecture, including smaller rosette leaves and thicker and increased numbers of main inflorescences. Our findings suggest that AfSPL14 may help facilitate the molecular breeding of A. fasciata, other ornamental and edible bromeliads (e.g., pineapple), and even cereal crops.
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18
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Genome-wide analysis of the SPL/miR156 module and its interaction with the AP2/miR172 unit in barley. Sci Rep 2018; 8:7085. [PMID: 29728569 PMCID: PMC5935748 DOI: 10.1038/s41598-018-25349-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 04/11/2018] [Indexed: 12/20/2022] Open
Abstract
The SQUAMOSA-promoter binding like (SPL) gene family encodes transcription factors that have been shown in many species to influence plant growth and development, but information about these genes in barley (Hordeum vulgare L.) is limited. This study identified 17 barley SPL genes, within eight distinct groups, that are orthologs of SPL genes described in Arabidopsis, wheat, and rice. Sixteen barley SPLs undergo alternative splicing. Seven SPLs contain a putative miR156 target site and the transcript levels of the miR156-targeted HvSPLs (HvSPL3, 13 and 23) were lower in vegetative than in reproductive phase but this was true also for some SPL genes such as HvSPL6 that were not regulated by miR156. Because SPL gene products regulate miR172, which is also involved in floral development, the expression of miR172 was studied. An antagonistic expression pattern of miR156 and miR172b during the vegetative and the reproductive phases signifies their apparent function in barley growth phase transition. Characterization of a barley mir172 mutant having an abnormal, indeterminate spikelet phenotype suggests the possible feedback role of AP2/miR172 module on HvSPL genes. This is the first comprehensive analysis of the miR156/SPL/miR172 axis in barley that provides a basis to elucidate their roles in various biological processes.
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Zhou Q, Zhang S, Chen F, Liu B, Wu L, Li F, Zhang J, Bao M, Liu G. Genome-wide identification and characterization of the SBP-box gene family in Petunia. BMC Genomics 2018; 19:193. [PMID: 29703141 PMCID: PMC6389188 DOI: 10.1186/s12864-018-4537-9] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 02/08/2018] [Indexed: 11/29/2022] Open
Abstract
Background SQUAMOSA PROMOTER BINDING PROTEIN (SBP)-box genes encode a family of plant-specific transcription factors (TFs) that play important roles in many growth and development processes including phase transition, leaf initiation, shoot and inflorescence branching, fruit development and ripening etc. The SBP-box gene family has been identified and characterized in many species, but has not been well studied in Petunia, an important ornamental genus. Results We identified 21 putative SPL genes of Petunia axillaris and P. inflata from the reference genome of P. axillaris N and P. inflata S6, respectively, which were supported by the transcriptome data. For further confirmation, all the 21 genes were also cloned from P. hybrida line W115 (Mitchel diploid). Phylogenetic analysis based on the highly conserved SBP domains arranged PhSPLs in eight groups, analogous to those from Arabidopsis and tomato. Furthermore, the Petunia SPL genes had similar exon-intron structure and the deduced proteins contained very similar conserved motifs within the same subgroup. Out of 21 PhSPL genes, fourteen were predicted to be potential targets of PhmiR156/157, and the putative miR156/157 response elements (MREs) were located in the coding region of group IV, V, VII and VIII genes, but in the 3’-UTR regions of group VI genes. SPL genes were also identified from another two wild Petunia species, P. integrifolia and P. exserta, based on their transcriptome databases to investigate the origin of PhSPLs. Phylogenetic analysis and multiple alignments of the coding sequences of PhSPLs and their orthologs from wild species indicated that PhSPLs were originated mainly from P. axillaris. qRT-PCR analysis demonstrated differential spatiotemperal expression patterns of PhSPL genes in petunia and many were expressed predominantly in the axillary buds and/or inflorescences. In addition, overexpression of PhSPL9a and PhSPL9b in Arabidopsis suggested that these genes play a conserved role in promoting the vegetative-to-reproductive phase transition. Conclusion Petunia genome contains at least 21 SPL genes, and most of the genes are expressed in different tissues. The PhSPL genes may play conserved and diverse roles in plant growth and development, including flowering regulation, leaf initiation, axillary bud and inflorescence development. This work provides a comprehensive understanding of the SBP-box gene family in Petunia and lays a significant foundation for future studies on the function and evolution of SPL genes in petunia. Electronic supplementary material The online version of this article (10.1186/s12864-018-4537-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Qin Zhou
- Key Laboratory of Horticultural Plant Biology, Ministry of Education; Key Laboratory of Urban Agriculture in Central China, Ministry of Agriculture; College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Shizishan Street No. 1, Wuhan, 430070, China
| | - Sisi Zhang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education; Key Laboratory of Urban Agriculture in Central China, Ministry of Agriculture; College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Shizishan Street No. 1, Wuhan, 430070, China.,Wuhan Institute of Landscape Architecture, Peace Avenue No. 1240, Wuhan, 430081, China
| | - Feng Chen
- Key Laboratory of Horticultural Plant Biology, Ministry of Education; Key Laboratory of Urban Agriculture in Central China, Ministry of Agriculture; College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Shizishan Street No. 1, Wuhan, 430070, China
| | - Baojun Liu
- Key Laboratory of Horticultural Plant Biology, Ministry of Education; Key Laboratory of Urban Agriculture in Central China, Ministry of Agriculture; College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Shizishan Street No. 1, Wuhan, 430070, China
| | - Lan Wu
- Key Laboratory of Horticultural Plant Biology, Ministry of Education; Key Laboratory of Urban Agriculture in Central China, Ministry of Agriculture; College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Shizishan Street No. 1, Wuhan, 430070, China
| | - Fei Li
- Key Laboratory of Horticultural Plant Biology, Ministry of Education; Key Laboratory of Urban Agriculture in Central China, Ministry of Agriculture; College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Shizishan Street No. 1, Wuhan, 430070, China
| | - Jiaqi Zhang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education; Key Laboratory of Urban Agriculture in Central China, Ministry of Agriculture; College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Shizishan Street No. 1, Wuhan, 430070, China
| | - Manzhu Bao
- Key Laboratory of Horticultural Plant Biology, Ministry of Education; Key Laboratory of Urban Agriculture in Central China, Ministry of Agriculture; College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Shizishan Street No. 1, Wuhan, 430070, China
| | - Guofeng Liu
- Key Laboratory of Horticultural Plant Biology, Ministry of Education; Key Laboratory of Urban Agriculture in Central China, Ministry of Agriculture; College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Shizishan Street No. 1, Wuhan, 430070, China.
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20
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Hou H, Yan X, Sha T, Yan Q, Wang X. The SBP-Box Gene VpSBP11 from Chinese Wild Vitis Is Involved in Floral Transition and Affects Leaf Development. Int J Mol Sci 2017; 18:ijms18071493. [PMID: 28703739 PMCID: PMC5535983 DOI: 10.3390/ijms18071493] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 07/03/2017] [Accepted: 07/06/2017] [Indexed: 12/20/2022] Open
Abstract
Flowering occurs in angiosperms during a major developmental transition from vegetative growth to the reproductive phase. Squamosa promoter binding protein (SBP)-box genes have been found to play critical roles in regulating flower and fruit development, but their roles in grapevine have remained unclear. To better understand the functions of the grape SBP-box genes in both vegetative and reproductive growth phases, a full-length complementary DNA (cDNA) sequence of the putative SBP-box transcription factor gene, VpSBP11, was obtained from Chinese wild grapevine Vitis pseudoreticulata Wen Tsai Wang (W. T. Wang) clone ‘Baihe-35-1’. VpSBP11 encoded a putative polypeptide of 170 amino acids with a highly conserved SBP-domain with two zinc-binding sites of the Cx2C-x3-H-x11-C-x6-H (C2HCH) type and a nuclear localization signal. We confirmed that the VpSBP11 protein was targeted to the nucleus and possessed transcriptional activation activity by subcellular localization and trans-activation assay. Over-expression of VpSBP11 in Arabidopsis thaliana was shown to activate the FUL gene, and subsequently the AP1 and LFY genes, all of which were floral meristem identity genes, and to cause earlier flowering than in wild type (WT) plants. The pattern of vegetative growth was also different between the transgenic and WT plants. For example, in the VpSBP11 over-expressing transgenic plants, the number of rosette leaves was less than that of WT; the petiole was significantly elongated; and the rosette and cauline leaves curled upwards or downwards. These results were consistent with VpSBP11 acting as a transcription factor during the transition from the vegetative stage to the reproductive stage.
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Affiliation(s)
- Hongmin Hou
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, China.
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Yangling 712100, China.
- College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China.
| | - Xiaoxiao Yan
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, China.
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Yangling 712100, China.
| | - Ting Sha
- College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China.
| | - Qin Yan
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, China.
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Yangling 712100, China.
| | - Xiping Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, China.
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Yangling 712100, China.
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Pan F, Wang Y, Liu H, Wu M, Chu W, Chen D, Xiang Y. Genome-wide identification and expression analysis of SBP-like transcription factor genes in Moso Bamboo (Phyllostachys edulis). BMC Genomics 2017; 18:486. [PMID: 28655295 PMCID: PMC5488377 DOI: 10.1186/s12864-017-3882-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 06/20/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The SQUAMOSA promoter binding protein-like (SPL) proteins are plant-specific transcription factors (TFs) that function in a variety of developmental processes including growth, flower development, and signal transduction. SPL proteins are encoded by a gene family, and these genes have been characterized in two model grass species, Zea mays and Oryza sativa. The SPL gene family has not been well studied in moso bamboo (Phyllostachys edulis), a woody grass species. RESULTS We identified 32 putative PeSPL genes in the P. edulis genome. Phylogenetic analysis arranged the PeSPL protein sequences in eight groups. Similarly, phylogenetic analysis of the SBP-like and SBP proteins from rice and maize clustered them into eight groups analogous to those from P. edulis. Furthermore, the deduced PeSPL proteins in each group contained very similar conserved sequence motifs. Our analyses indicate that the PeSPL genes experienced a large-scale duplication event ~15 million years ago (MYA), and that divergence between the PeSPL and OsSPL genes occurred 34 MYA. The stress-response expression profiles and tissue-specificity of the putative PeSPL gene promoter regions showed that SPL genes in moso bamboo have potential biological functions in stress resistance as well as in growth and development. We therefore examined PeSPL gene expression in response to different plant hormone and drought (polyethylene glycol-6000; PEG) treatments to mimic biotic and abiotic stresses. Expression of three (PeSPL10, -12, -17), six (PeSPL1, -10, -12, -17, -20, -31), and nine (PeSPL5, -8, -9, -14, -15, -19, -20, -31, -32) genes remained relatively stable after treating with salicylic acid (SA), gibberellic acid (GA), and PEG, respectively, while the expression patterns of other genes changed. In addition, analysis of tissue-specific expression of the moso bamboo SPL genes during development showed differences in their spatiotemporal expression patterns, and many were expressed at high levels in flowers and leaves. CONCLUSIONS The PeSPL genes play important roles in plant growth and development, including responses to stresses, and most of the genes are expressed in different tissues. Our study provides a comprehensive understanding of the PeSPL gene family and may enable future studies on the function and evolution of SPL genes in moso bamboo.
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Affiliation(s)
- Feng Pan
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China
| | - Yue Wang
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China
| | - Huanglong Liu
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China
| | - Min Wu
- Key Laboratory of Crop Biology of Anhui Province, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Wenyuan Chu
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China
| | - Danmei Chen
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China
| | - Yan Xiang
- Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China. .,Key Laboratory of Crop Biology of Anhui Province, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China.
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22
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Genetic Determinants of Crop Timing and Quality Traits in Two Interspecific Petunia Recombinant Inbred Line Populations. Sci Rep 2017; 7:3200. [PMID: 28600539 PMCID: PMC5466624 DOI: 10.1038/s41598-017-03528-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 04/28/2017] [Indexed: 02/02/2023] Open
Abstract
The rate at which plants develop new nodes (development rate) is a major determinant of crop production time, yet the genetic control of this process, including genetic interactions with crop quality parameters, is poorly understood. We employed a modified genotyping-by-sequencing approach and generated genetic linkage maps with 6,291 and 3,297 single nucleotide polymorphisms (SNPs) for the interspecific Petunia recombinant inbred line (RIL) population - P. axillaris × P. exserta (AE) and P. integrifolia × P. axillaris (IA), respectively. Comparative mapping between the populations revealed perfect collinearity of marker order but different recombination frequency at the corresponding linkage groups (LGs). Quantitative trait loci (QTL) mapping conducted for development traits and other important quality traits indicated QTL clustered on chromosome 1, 2, 4 and 6 for the AE population and chromosome 1, 2, 5 and 6 for the IA population. Additionally, 209 differentially expressed unique transcripts were identified in shoot apex tissue between fast- and slow-developing RILs, 13 of which mapped to within 1 cM of a development rate QTL. These results will facilitate the identification of novel genes controlling crop timing and quality traits in Petunia and highlight the power of using multiple interspecific populations to elucidate genetic determinants of natural variation.
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23
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Kavas M, Kızıldoğan AK, Abanoz B. Comparative genome-wide phylogenetic and expression analysis of SBP genes from potato (Solanum tuberosum). Comput Biol Chem 2017; 67:131-140. [PMID: 28081487 DOI: 10.1016/j.compbiolchem.2017.01.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 07/27/2016] [Accepted: 01/03/2017] [Indexed: 11/28/2022]
Abstract
Flowering time is a very important phase in transition to reproductive stage of life in higher plants. SQUAMOSA promoter-binding protein (SBP) gene family encodes plant-specific transcription factors that are involved in regulation of several developmental processes, especially flowering. Although SBP-box genes have been identified in different plants, there have been no study indicating the regulatory effect of SBP box in potato flowering. Here, we report for the first time the identification and characterization of SBP-box transcription factors as well as determination of expression level of SBP-box genes in Solanum tuberosum L. an important crop worldwide. Fifteen different SBP-box transcription factor genes were identified in potato genome. They were found to be distributed in nine chromosomes and eight of them included miR156 and miRNA157 target sites. Characterization of amino acid sequences were performed and protein interactions were predicted. In addition, expression levels of five S. tuberosum SBP-box genes were analysed by both in silico and qRT-PCR. All these results provide a better understanding of functional role of SBP-box gene family members in flowering time in potato.
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Affiliation(s)
- Musa Kavas
- Ondokuz Mayıs University, Faculty of Agriculture, Department of Agricultural Biotechnology, Samsun, Turkey.
| | - Aslıhan Kurt Kızıldoğan
- Ondokuz Mayıs University, Faculty of Agriculture, Department of Agricultural Biotechnology, Samsun, Turkey
| | - Büşra Abanoz
- Ondokuz Mayıs University, Faculty of Agriculture, Department of Agricultural Biotechnology, Samsun, Turkey
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24
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Zhong J, Powell S, Preston JC. Organ boundary NAC-domain transcription factors are implicated in the evolution of petal fusion. PLANT BIOLOGY (STUTTGART, GERMANY) 2016; 18:893-902. [PMID: 27500862 DOI: 10.1111/plb.12493] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 08/05/2016] [Indexed: 05/25/2023]
Abstract
UNLABELLED Research rationale: Evolution of fused petals (sympetaly) is considered to be an important innovation that has repeatedly led to increased pollination efficiency, resulting in accelerated rates of plant diversification. Although little is known about the underlying regulation of sympetaly, genetic pathways ancestrally involved in organ boundary establishment (e.g. CUP SHAPED COTYLEDON [CUC] 1-3 genes) are strong candidates. In sympetalous petunia, mutations in the CUC1/2-like orthologue NO APICAL MERISTEM (NAM) inhibit shoot apical meristem formation. Despite this, occasional 'escape shoots' develop flowers with extra petals and fused inter-floral whorl organs. Central methods: To To determine if petunia CUC-like genes regulate additional floral patterning, we used virus-induced silencing (VIGS) following establishment of healthy shoot apices to re-examine the role of NAM in petunia petal development, and uniquely characterise the CUC3 orthologue NH16. KEY RESULTS Confirming previous results, we found that reduced floral NAM/NH16 expression caused increased petal-stamen and stamen-carpel fusion, and often produced extra petals. However, further to previous results, all VIGS plants infected with NAM or NH16 constructs exhibited reduced fusion in the petal whorl compared to control plants. MAIN CONCLUSIONS Together with previous data, our results demonstrate conservation of petunia CUC-like genes in establishing inter-floral whorl organ boundaries, as well as functional evolution to affect the fusion of petunia petals.
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Affiliation(s)
- J Zhong
- Department of Plant Biology, The University of Vermont, Burlington, VT, USA
| | - S Powell
- Department of Plant Biology, The University of Vermont, Burlington, VT, USA
| | - J C Preston
- Department of Plant Biology, The University of Vermont, Burlington, VT, USA.
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