scholarly journals Characterization of Squamosa-Promoter Binding Protein-Box Family Genes Reveals the Critical Role of MsSPL20 in Alfalfa Flowering Time Regulation

2022 ◽  
Vol 12 ◽  
Author(s):  
Lin Ma ◽  
Xiqiang Liu ◽  
Wenhui Liu ◽  
Hongyu Wen ◽  
Yongchao Zhang ◽  
...  
Keyword(s):  
Flowering Time ◽  
Binding Protein ◽  
Expression Patterns ◽  
Crop Improvement ◽  
Critical Role ◽  
Functional Differentiation ◽  
Future Research ◽  
Systematic Analysis ◽  
Squamosa Promoter Binding Protein ◽  
Delayed Flowering

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.

scholarly journals Roles of the GA-mediated SPL Gene Family and miR156 in the Floral Development of Chinese Chestnut (Castanea mollissima)

2019 ◽  
Vol 20 (7) ◽  
pp. 1577 ◽  
Author(s):  
Guosong Chen ◽  
Jingtong Li ◽  
Yang Liu ◽  
Qing Zhang ◽  
Yuerong Gao ◽  
...  
Keyword(s):  
Target Genes ◽  
Floral Development ◽  
Binding Protein ◽  
Expression Patterns ◽  
Evolutionary Relationship ◽  
Deciduous Tree ◽  
Main Function ◽  
Squamosa Promoter Binding Protein ◽  
Spl Genes ◽  
Castanea Mollissima

Chestnut (Castanea mollissima) is a deciduous tree species with major economic and ecological value that is widely used in the study of floral development in woody plants due its monoecious and out-of-proportion characteristics. Squamosa promoter-binding protein-like (SPL) is a plant-specific transcription factor that plays an important role in floral development. In this study, a total of 18 SPL genes were identified in the chestnut genome, of which 10 SPL genes have complementary regions of CmmiR156. An analysis of the phylogenetic tree of the squamosa promoter-binding protein (SBP) domains of the SPL genes of Arabidopsis thaliana, Populus trichocarpa, and C. mollissima divided these SPL genes into eight groups. The evolutionary relationship between poplar and chestnut in the same group was similar. A structural analysis of the protein-coding regions (CDSs) showed that the domains have the main function of SBP domains and that other domains also play an important role in determining gene function. The expression patterns of CmmiR156 and CmSPLs in different floral organs of chestnut were analyzed by real-time quantitative PCR. Some CmSPLs with similar structural patterns showed similar expression patterns, indicating that the gene structures determine the synergy of the gene functions. The application of gibberellin (GA) and its inhibitor (Paclobutrazol, PP333) to chestnut trees revealed that these exert a significant effect on the number and length of the male and female chestnut flowers. GA treatment significantly increased CmmiR156 expression and thus significantly decreased the expression of its target gene, CmSPL6/CmSPL9/CmSPL16, during floral bud development. This finding indicates that GA might indirectly affect the expression of some of the SPL target genes through miR156. In addition, RNA ligase-mediated rapid amplification of the 5′ cDNA ends (RLM-RACE) experiments revealed that CmmiR156 cleaves CmSPL9 and CmSPL16 at the 10th and 12th bases of the complementary region. These results laid an important foundation for further study of the biological function of CmSPLs in the floral development of C. mollissima.

scholarly journals SQUAMOSA Promoter Binding Protein-Like (SPL) Gene Family: TRANSCRIPTOME-Wide Identification, Phylogenetic Relationship, Expression Patterns and Network Interaction Analysis in Panax ginseng C. A. Meyer

Plants ◽  
2020 ◽  
Vol 9 (3) ◽  
pp. 354
Author(s):  
Shaokun Li ◽  
Li Li ◽  
Yang Jiang ◽  
Jun Wu ◽  
Honghua Sun ◽  
...  
Keyword(s):  
Gene Family ◽  
Panax Ginseng ◽  
Interaction Analysis ◽  
Binding Protein ◽  
Expression Patterns ◽  
Evolutionary Analysis ◽  
Main Function ◽  
Squamosa Promoter Binding Protein ◽  
Expression Characteristics ◽  
Spl Gene

SPL (SQUAMOSA promoter binding protein-like) gene family is specific transcription factor in the plant that have an important function for plant growth and development. Although the SPL gene family has been widely studied and reported in many various plant species from gymnosperm to angiosperm, there are no systematic studies and reports about the SPL gene family in Panax ginseng C. A. Meyer. In this study, we conducted transcriptome-wide identification, evolutionary analysis, structure analysis, and expression characteristics analysis of SPL gene family in Panax ginseng by bioinformatics. We annotated the PgSPL gene family and found that they might involve in multiple functions including encoding structural proteins, but the main function were still focused on the binding function. The result showed that 106 PgSPL transcripts were classified into two clades - A and B, both of which respectively consisted of three groups. Besides, we profiled PgSPL transcripts’ genotypic, temporal, and spatial expression characteristics. Furthermore, we calculated the correlation of PgSPL transcripts in the 14 tissues of a 4 years old ginseng and 42 farmers’ cultivars farmers’ cultivars of 4 years old ginsengs’ roots with both results showing that SPL transcripts formed a single network, which indicated that PgSPLs inter-coordinated when performing their functions. What’s more, we found that most PgSPL transcripts tended to express in older ginseng instead of younger ginseng, which was not only reflected in the expression of more types of SPL transcripts in older ginseng, but also in the higher expression of SPL transcripts in older ginseng. Additionally, we found that four PgSPL transcripts were only massively expressed in roots. According to PgSPL transcripts’ expression characteristics, we found that PgSPL23-35 and PgSPL24-09 were most proper two transcripts to further study as ginseng age’s molecular marker. These results provide the basis for further elucidation of the PgSPL transcripts’ biological function in ginseng and ginseng genetics improvement and gene breeding in the future.

scholarly journals Characterization and expression analysis of the SPL gene family during floral development and abiotic stress in pecan (Carya illinoinensis)

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12490
Author(s):  
Min Wang ◽  
Zhenghai Mo ◽  
Ruozhu Lin ◽  
Cancan Zhu
Keyword(s):  
Fruit Development ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Element Analysis ◽  
Systematic Analysis ◽  
Cis Element ◽  
Gene Pairs ◽  
Spatiotemporal Expression ◽  
Squamosa Promoter Binding Protein ◽  
Flower And Fruit Development

SQUAMOSA promoter binding protein-like (SPL) genes are a type of plant-specific transcription factors that play crucial roles in the regulation of phase transition, floral transformation, fruit development, and various stresses. Although SPLs have been characterized in several model species, no systematic analysis has been studied in pecans, an important woody oil tree species. In this study, a total of 32 SPL genes (CiSPLs) were identified in the pecan genome. After conducting phylogenetic analysis of the conserved SBP proteins from Arabidopsis, rice, and poplar, the CiSPLs were separated into eight subgroups. The CiSPL genes within the same subgroup contained very similar exon-intron structures and conserved motifs. Nine segmentally duplicated gene pairs in the pecan genome and 16 collinear gene pairs between the CiSPL and AtSPL genes were identified. Cis-element analysis showed that CiSPL genes may regulate plant meristem differentiation and seed development, participate in various biological processes, and respond to plant hormones and environmental stresses. Therefore, we focused our study on the expression profiles of CiSPL genes during flower and fruit development. Most of the CiSPL genes were predominantly expressed in buds and/or female flowers. Additionally, quantitative real time PCR (qRT-PCR) analyses confirmed that CiSPL genes showed distinct spatiotemporal expression patterns in response to drought and salt treatments. The study provides foundation for the further exploration of the function and evolution of SPL genes in pecan.

scholarly journals Multiplex CRISPR/Cas9 Mutagenesis of BrVRN1 Delays Flowering Time in Chinese Cabbage (Brassica rapa L. ssp. pekinensis)

Agriculture ◽  
2021 ◽  
Vol 11 (12) ◽  
pp. 1286
Author(s):  
Joon Ki Hong ◽  
Eun Jung Suh ◽  
Sang Ryeol Park ◽  
Jihee Park ◽  
Yeon-Hee Lee
Keyword(s):  
Flowering Time ◽  
Brassica Rapa ◽  
Chinese Cabbage ◽  
Crop Improvement ◽  
Sequencing Analysis ◽  
Vrn1 Gene ◽  
Floral Repressor ◽  
Dna Sequencing Analysis ◽  
Delayed Flowering ◽  
Golden Gate Cloning

The VERNALIZATION1 (VRN1) gene is a crucial transcriptional repressor involved in triggering the transition to flowering in response to prolonged cold. To develop Chinese cabbage (Brassica rapa L. ssp. pekinensis) plants with delayed flowering time, we designed a multiplex CRISPR/Cas9 platform that allows the co-expression of four sgRNAs targeting different regions of the endogenous BrVRN1 gene delivered via a single binary vector built using the Golden Gate cloning system. DNA sequencing analysis revealed site-directed mutations at two target sites: gRNA1 and gRNA2. T1 mutant plants with a 1-bp insertion in BrVRN1 exhibited late flowering after the vernalization. Additionally, we identified ‘transgene-free’ BrVRN1 mutant plants without any transgenic elements from the GE1 (gene-editing 1) and GE2 generations. All GE2 mutant plants contained successful edits in two out of three BrVRN1 orthologs and displayed delayed flowering time. In GE2 mutant plants, the floral repressor gene FLC1 was expressed during vernalization; but the floral integrator gene FT was not expressed after vernalization. Taken together, our data indicate that the BrVRN1 genes act as negative regulators of FLC1 expression during vernalization in Chinese cabbage, raising the possibility that the ‘transgene-free’ mutants of BrVRN1 developed in this study may serve as useful genetic resources for crop improvement with respect to flowering time regulation.

scholarly journals Genome-Wide Identification and Characterization of SQUAMOSA—Promoter-Binding Protein (SBP) Genes Involved in the Flowering Development of Citrus Clementina

Biomolecules ◽  
2019 ◽  
Vol 9 (2) ◽  
pp. 66 ◽  
Author(s):  
Ren-Fang Zeng ◽  
Jing-Jing Zhou ◽  
Sheng-Rui Liu ◽  
Zhi-Meng Gan ◽  
Jin-Zhi Zhang ◽  
...  
Keyword(s):  
Gene Family ◽  
Floral Induction ◽  
Binding Protein ◽  
Populus Trichocarpa ◽  
Expression Patterns ◽  
Specific Expression ◽  
Water Deficits ◽  
Citrus Clementina ◽  
Squamosa Promoter Binding Protein ◽  
Gene Structures

SQUAMOSA-promoter binding protein (SBP)-box genes encode a family of plant-specific transcription factors that play vital roles in plant growth and development. In this study, 15 SBP-box genes were identified and isolated from Citrus clementina (CclSBPs), where 10 of these genes were predicted to be putative targets of Citrus clementina microRNA156 (CclmiR156). The 15 CclSBP genes could be classified into six groups based on phylogenetic analysis, diverse intron–exon structure, and motif prediction, similar to the SQUAMOSA promoter binding protein-like (SPL) gene family of Populus trichocarpa and Arabidopsis thaliana. Furthermore, CclSBPs classified into a group/subgroup have similar gene structures and conserved motifs, implying their functional redundancy. Tissue-specific expression analysis of CclSBPs demonstrated their diversified expression patterns. To further explore the potential role of CclSBPs during floral inductive water deficits, the dynamic changes of the 15 CclSBPs were investigated during floral inductive water deficits, and the results showed that some CclSBPs were associated with floral induction. Among these genes, CclSBP6 was not homologous to the Arabidopsis SBP-box gene family, and CclSBP7 was regulated by being alternatively spliced. Therefore, CclSBP6 and CclSBP7 were genetically transformed in Arabidopsis. Overexpression of the two genes changed the flowering time of Arabidopsis.

scholarly journals Genome-Wide Characterization and Expression Profiling of Squamosa Promoter Binding Protein-like (SBP) Transcription Factors in Wheat (Triticum aestivum L.)

Agronomy ◽  
2019 ◽  
Vol 9 (9) ◽  
pp. 527 ◽  
Author(s):  
Song ◽  
Ma ◽  
Yin ◽  
Yang ◽  
He ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Hexaploid Wheat ◽  
Abiotic Stresses ◽  
Binding Protein ◽  
Expression Patterns ◽  
Local Alignment ◽  
Composition Analysis ◽  
Motif Analysis ◽  
Genome Wide ◽  
Squamosa Promoter Binding Protein

Transcription factors (TFs) play fundamental roles in the developmental processes of all living organisms. Squamosa Promoter Binding Protein-like (SBP/SBP-Box) is a major family of plant-specific TFs, which plays important roles in multiple processes involving plant growth and development. While some work has been done, there is a lot more that is yet to be discovered in the hexaploid wheat SBP (TaSBP) family. With the completion of whole genome sequencing, genome-wide analysis of SBPs in common hexaploid wheat is now possible. In this study, we used protein–protein Basic Local Alignment Search Tool (BLASTp) to hunt the newly released reference genome sequence of hexaploid wheat (Chinese spring). Seventy-four TaSBP proteins (belonging to 56 genes) were identified and clustered into five groups. Gene structure and motif analysis indicated that most TaSBPs have relatively conserved exon–intron arrangements and motif composition. Analysis of transcriptional data showed that many TaSBP genes responded to some biological and abiotic stresses with different expression patterns. Moreover, three TaSBP genes were generally expressed in the majority of tissues throughout the wheat growth and also responded to many environmental biotic and abiotic stresses. Collectively, the detailed analyses presented here will help in understanding the roles of the TaSBP and also provide a reference for the further study of its biological function in wheat.

scholarly journals Genome-wide identification of AP2/EREBP in Fragaria vesca and expression pattern analysis of the FvDREB subfamily under drought stress

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Chao Dong ◽  
Yue Xi ◽  
Xinlu Chen ◽  
Zong-Ming Cheng
Keyword(s):  
Drought Stress ◽  
Expression Pattern ◽  
Binding Protein ◽  
Abiotic Factors ◽  
Expression Patterns ◽  
Critical Role ◽  
Pcr Analysis ◽  
Fragaria Vesca ◽  
Element Binding Protein ◽  
Responsive Element

Abstract Background Drought is a common phenomenon worldwide. It is also one of the main abiotic factors that affect the growth and quality of strawberry. The dehydration-responsive element binding protein (DREB) members that belong to the APETALA2/ethylene-responsive element binding protein (AP2/EREBP) superfamily are unique transcription factors in plants that play important roles in the abiotic stress response. Results Here, a total of 119 AP2/EREBP genes were identified in Fragaria vesca, and the AP2/EREBP superfamily was divided into AP2, RAV, ERF, DREB, and soloist subfamilies, containing 18, 7, 61, 32, and one member(s), respectively. The DREB subfamily was further divided into six subgroups (A-1 to A-6) based on phylogenetic analysis. Gene structure, conserved motifs, chromosomal location, and synteny analysis were conducted to comprehensively investigate the characteristics of FvDREBs. Furthermore, transcriptome analysis revealed distinctive expression patterns among the FvDREB genes in strawberry plants exposed to drought stress. The expression of FvDREB6 of the A-2 subgroup was down-regulated in old leaves and up-regulated in young leaves in response to drought. Furthermore, qRT-PCR analysis found that FvDREB8 from the A-2 subgroup had the highest expression level under drought stress. Together, analyses with the expression pattern, phylogenetic relationship, motif, and promoter suggest that FvDREB18 may play a critical role in the regulation of FvDREB1 and FvDREB2 expression. Conclusions Our findings provide new insights into the characteristics and potential functions of FvDREBs. These FvDREB genes should be further studied as they appear to be excellent candidates for drought tolerance improvement of strawberry.

scholarly journals Overexpression of CpWRKY75 from Chimonanthus praecox Promotes Flowering Time in Transgenic Arabidopsis

Genes ◽  
2021 ◽  
Vol 13 (1) ◽  
pp. 68
Author(s):  
Renwei Huang ◽  
Shunzhao Sui ◽  
Huamin Liu ◽  
Mingyang Li ◽  
Daofeng Liu
Keyword(s):  
Flowering Time ◽  
Transcriptional Activation ◽  
Transgenic Arabidopsis ◽  
Binding Protein ◽  
Ectopic Expression ◽  
Physiological Processes ◽  
Open Time ◽  
Squamosa Promoter Binding Protein ◽  
New Gene ◽  
Chimonanthus Praecox

WRKY transcription factors play critical roles in the physiological processes of plants. Although the roles of WRKYs have been characterized in some model plants, their roles in woody plants, especially wintersweet (Chimonanthus praecox), are largely unclear. In this study, a wintersweet WRKY gene named CpWRKY75 belonging to group IIc was isolated and its characteristics were identified. CpWRKY75 is a nucleus-localized protein, and exhibited no transcriptional activation activity in yeast. CpWRKY75 was highly expressed in flowers at different bloom stages. Ectopic expression of CpWRKY75 significantly promoted the flowering time of transgenic Arabidopsis (Arabidopsis thaliana), as determined by the rosette leaf number and first flower open time. The expression levels of flowering-related genes were quantified by qRT-PCR, and the results suggested that CpWRKY75 had obvious influence on the expression level of MICRORNA156C (MIR156C), SQUAMOSA PROMOTER BINDING PROTEIN-LIKE3 (SPL3) and SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 9 (SPL9), FLOWERING LOCUS T (FT), LEAFY (LFY), SUPPRESSOR OF OVEREXPRESSION OF CO 1 (SOC1), APETALA1 (AP1), CAULIFLOWER (CAL), and FRUITFULL (FUL). These results suggest that CpWRKY75 might have a flowering time regulation function, and additionally provide a new gene resource for the genetic engineering of woody flowering plants.

scholarly journals Genome-Wide Identification of AP2/EREBP in Fragaria Vesca and Expression Pattern Analysis of The FvDREB Subfamily Under Drought Stress

2020 ◽  
Author(s):  
Chao Dong ◽  
Yue Xi ◽  
Xinlu Chen ◽  
Zong-Ming (Max) Cheng
Keyword(s):  
Drought Stress ◽  
Binding Protein ◽  
Abiotic Factors ◽  
Expression Patterns ◽  
Critical Role ◽  
Pcr Analysis ◽  
Abiotic Stress Response ◽  
Element Binding Protein ◽  
Young Leaves ◽  
Responsive Element

Abstract Background: Drought is a common phenomenon worldwide. It is also one of the main abiotic factors that affect the growth and quality of strawberry. The dehydration-responsive element binding protein (DREB) members that belong to the APETALA2/ethylene-responsive element binding protein (AP2/EREBP) superfamily are unique transcription factors in plants, which play an important role in the abiotic stress response. Results: Here, a total of 119 AP2/EREBP genes were identified in F. vesca, and the AP2/EREBP superfamily was divided into AP2, RAV, ERF, DREB, and soloist subfamilies, containing 18, 7, 61, 32, and 1 member(s), respectively. The DREB subfamily was further divided into six subgroups (A-1 to A-6) based on phylogenetic analysis. Gene structure, conserved motifs, chromosomal location, and synteny analysis were conducted to comprehensively investigate the gene characteristics of FvDREBs. Furthermore, transcriptome analysis revealed distinctive expression patterns among the FvDREB genes in strawberry plants exposed to drought stress. The expression of FvDREB6 of the A-2 subgroup was down-regulated in old leaves and up-regulated in young leaves in response to drought. Furthermore, qRT-PCR analysis found that FvDREB8 of the A-2 subgroup had the highest expression when plants were subjected to drought stress. Both analyses combined with promoter analysis suggested that FvDREB18 may play a critical role in regulating the expression of FvDREB1 and FvDREB2. Conclusions: Our findings provide new insights into the characteristics and potential functions of FvDREBs. And these FvDREB genes should be further studied as they appear to be excellent candidates for drought tolerance improvement of strawberry.

scholarly journals Isolation and Functional Characterization of Two SHORT VEGETATIVE PHASE Homologous Genes from Mango

2021 ◽  
Vol 22 (18) ◽  
pp. 9802
Author(s):  
Xiao Mo ◽  
Cong Luo ◽  
Haixia Yu ◽  
Jinwen Chen ◽  
Yuan Liu ◽  
...  
Keyword(s):  
Flowering Time ◽  
Expression Patterns ◽  
Functional Characterization ◽  
Bimolecular Fluorescence Complementation ◽  
Vegetative Phase ◽  
Expression Levels ◽  
Cdna Sequences ◽  
Short Vegetative Phase ◽  
Homologous Genes ◽  
Delayed Flowering

The SHORT VEGETATIVE PHASE (SVP) gene is a transcription factor that integrates flowering signals and plays an important role in the regulation of flowering time in many plants. In this study, two full-length cDNA sequences of SVP homologous genes—MiSVP1 and MiSVP2—were obtained from ‘SiJiMi’ mango. Sequence analysis showed that the MiSVPs had typical MADS-box domains and were highly conserved between each other. The analysis of expression patterns showed that the MiSVPs were expressed during flower development and highly expressed in vegetative tissues, with low expression in flowers/buds. The MiSVPs could responded to low temperature, NaCl, and PEG treatment. Subcellular localization revealed that MiSVP1 and MiSVP2 were localized in the nucleus. Transformation of Arabidopsis revealed that overexpression of MiSVP1 delayed flowering time, overexpression of MiSVP2 accelerated flowering time, and neither MiSVP1 nor MiSVP2 had an effect on the number of rosette leaves. Overexpression of MiSVP1 increased the expression of AtFLC and decreased the expression of AtFT and AtSOC1, and overexpression of MiSVP2 increased the expression levels of AtSOC1 and AtFT and decreased the expression levels of AtFLC. Point-to-point and bimolecular fluorescence complementation (BiFC) assays showed that MiSVP1 and MiSVP2 could interact with SEP1-1, SOC1D, and AP1-2. These results suggest that MiSVP1 and MiSVP2 may play a significant roles in the flowering process of mango.

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