MADS-box Genes Research Articles

Identification and Analysis of MADS-box, WRKY, NAC, and SBP-box Transcription Factor Families in Diospyros oleifera Cheng and Their Associations with Sex Differentiation

Transcription factors are crucial for plant growth and development. MADS-box, WRKY, NAC, and SBP-box, some of the most vital transcription factors, are not well identified in Diospyros spp., and their floral development and sex differentiation related functions remain unknown. We identified and analysed 53 MADS-box, 66 WRKY, 83 NAC, and 17 SBP-box transcription factors using the chromosomal D. oleifera genome. There were six DolSBPs identified as miR156 and miR157 targets. According to the multiple sequence alignments of Arabidopsis and D. oleifera proteins and their conserved domains and motifs, DolMADSs were divided into 23 type I and 30 type II. The DolWRKYs, DolNACs, and DolSBPs were divided into 7, 16, and 6 subgroups, respectively. It was found that one DolMADS, five DolWRKYs, one DolNAC, and four DolSBPs may promote unisexual female flowers development, while three DolMADSs, four DolWRKYs, and one DolNAC may enhance unisexual male flowers development. The functions among the different members of the same family may, thus, vary widely. The results will help to elucidate the evolution of the MADS-box, WRKY, NAC, and SBP-box genes families in D. oleifera and to determine their functions in flower development for Diospyros spp.

Genome-Wide Analysis of the SPL Gene Family and Expression Analysis during Flowering Induction in Prunus × yedoensis 'Somei-yoshino'.

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.

Identification of MADS-Box Transcription Factors in Iris laevigata and Functional Assessment of IlSEP3 and IlSVP during Flowering.

Iris laevigata is ideal for gardening and landscaping in northeast China because of its beautiful flowers and strong cold resistance. However, the short length of flowering time (2 days for individual flowers) greatly limits its applications. Molecular breeding and engineering hold high potential for producing I. laevigata of desirable flowering properties. A prerequisite is to identify and characterize key flowering control genes, the identity of which remains largely unknown in I. laevigata due to the lack of genome information. To fill this knowledge gap, we used sequencing data of the I. laevigata transcriptome to identify MADS-box gene-encoding transcription factors that have been shown to play key roles in developmental processes, including flowering. Our data revealed 41 putative MADS-box genes, which consisted of 8 type I (5 Mα and 3 Mβ, respectively) and 33 type II members (2 MIKC* and 31 MIKCC, respectively). We then selected IlSEP3 and IlSVP for functional studies and found that both are localized to the nucleus and that they interact physically in vitro. Ectopic expression of IlSEP3 in Arabidopsis resulted in early flowering (32 days) compared to that of control plants (36 days), which could be mediated by modulating the expression of FT, SOC1, AP1, SVP, SPL3, VRN1, and GA20OX. By contrast, plants overexpressing IlSVP were phenotypically similar to that of wild type. Our functional validation of IlSEP3 was consistent with the notion that SEP3 promotes flowering in multiple plant species and indicated that IlSEP3 regulates flowering in I. laevigata. Taken together, this work provided a systematic identification of MADS-box genes in I. laevigata and demonstrated that the flowering time of I. laevigata can be genetically controlled by altering the expression of key MADS-box genes.

FRUITFULL is involved in double fruit formation at high temperature in sweet cherry

Sweet cherry (Prunus avium L.) is sensitive to high temperature during pistil development, but the spatial and temporal variability of high temperature and the molecular mechanism of its impact on the formation of double pistils are little known. An analysis of historical and projected climate data was conducted to characterize the spatial and temporal variability of high temperature from June to September at 5 stations in main sweet cherry growing regions of China and a warmer reference site. Several high temperature indices were developed to quantify heat frequency, intensity and duration during pistil development based on observed and projected maximum temperatures. The risk of high temperature was projected to increase under two Representative Concentration Pathways for 2035–2065 and 2070–2100, and the increasing rate was higher in the south station than the north except for Yantai city. Furthermore, to explore the mechanism of double fruit formation at high temperature, we investigated the regulation of FRUITFULL (FUL) during the growth of floral buds in sweet cherry. We identified a AP1/ FUL family gene FUL from sweet cherry, which was grouped with PpCAL, PpMADS6 from Prunus persica, ParFUL from Prunus armeniaca, PyeCAL from Prunus yedoensis, and PdCAL, PdAGL8 from Prunus dulcis by phylogenetic tree analysis. The seasonal expression level of PavFUL was higher in the high multi-pistil rate cultivar during summer stage and enhanced by high temperature. Moreover, overexpression of PavFUL led to multi-silique formation and early flowering in Arabidopsis. In addition, Y2H and BiFC assays revealed that PavFUL interacted with other MADS-box proteins, including PavLFY, PavSOC1, PavAP1, and PavSEP, to co-regulate the flowering and multi-silique formation. Our findings will help decipher the possible mechanism of high temperature-mediated double fruit via affecting FUL and other MADS-box genes in molecular level for tree fruit species.

Mechanisms of Vernalization-Induced Flowering in Legumes.

Vernalization is the requirement for exposure to low temperatures to trigger flowering. The best knowledge about the mechanisms of vernalization response has been accumulated for Arabidopsis and cereals. In Arabidopsis thaliana, vernalization involves an epigenetic silencing of the MADS-box gene FLOWERING LOCUS C (FLC), which is a flowering repressor. FLC silencing releases the expression of the main flowering inductor FLOWERING LOCUS T (FT), resulting in a floral transition. Remarkably, no FLC homologues have been identified in the vernalization-responsive legumes, and the mechanisms of cold-mediated transition to flowering in these species remain elusive. Nevertheless, legume FT genes have been shown to retain the function of the main vernalization signal integrators. Unlike Arabidopsis, legumes have three subclades of FT genes, which demonstrate distinct patterns of regulation with respect to environmental cues and tissue specificity. This implies complex mechanisms of vernalization signal propagation in the flowering network, that remain largely elusive. Here, for the first time, we summarize the available information on the genetic basis of cold-induced flowering in legumes with a special focus on the role of FT genes.

A convergent mechanism of sex determination in dioecious plants: Distinct sex-determining genes display converged regulation on floral B-class genes.

Sex determination in dioecious plants has been broadly and progressively studied with the blooming of genome sequencing and editing techniques. This provides us with a great opportunity to explore the evolution and genetic mechanisms underlining the sex-determining system in dioecious plants. In this study, comprehensively reviewing advances in sex-chromosomes, sex-determining genes, and floral MADS-box genes in dioecious plants, we proposed a convergent model that governs plant dioecy across divergent species using a cascade regulation pathway connecting sex-determining genes and MADS-box genes e.g., B-class genes. We believe that this convergent mechanism of sex determination in dioecious plants will shed light on our understanding of gene regulation and evolution of plant dioecy. Perspectives concerning the evolutionary pathway of plant dioecy are also suggested.

De novo transcriptome assembly reveals characteristics of flower sex determination of Excoecaria agallocha

Key messageMADS-box genes family may play important roles in the flower sex determination in Excoecaria agallocha. A total of 73 MADS-box genes were identified in E. agallocha. De novo transcriptome assembly analysis suggested that AP1/FUL, AP3/PI, AGL104, and SOC1 plays potential roles in E. agallocha flower sex determination.ContextExcoecaria agallocha is a dioecious species containing both male and female individuals producing unisexual flowers. The underlying mechanisms regulating inflorescence differentiation in these species remains poorly understood.AimsFlower development influences reproduction and breeding in E.agallocha, which contributes to ecological restoration in the intertidal zone.MethodsWe performed de novo transcriptome assembly analysis on male and female flowers and leaves from E. agallocha.ResultsWe identified a total of 73 MADS-box genes in the E. agallocha genome, which we grouped into five distinct classes (MIKCc, Mα, Mβ, Mγ, MIKC*) after phylogenetic comparisons with J. curcas homologs. We analyzed expression profiles and suggested AP1/FUL, AP3/PI, AGL104, and SOC1 as candidate regulators of sex determination. In addition, several EaMADS genes were significantly upregulated in flowers compared to leaves.ConclusionOur study represents the first detailed, comprehensive evaluation of the regulation of MADS-box genes associated with sex determination in E. agallocha. The assembled transcriptomic profiles increase the genetic information available for this species and constitute an important contribution to functional studies of inflorescence genes. In turn, this will help exploring the molecular mechanisms underlying the evolution of E. agallocha.

Analysis of Floral Organ Development and Sex Determination in Schisandra chinensis by Scanning Electron Microscopy and RNA-Sequencing.

S. chinensis is a typical monoecious plant, and the number and development of female flowers determines the yield of S. chinensis. Due to a lack of genetic information, the molecular mechanism of sex differentiation in S. chinensis remains unclear. In this study, the combination of scanning electron microscopy (SEM) and RNA sequencing (RNA-seq) was used to understand the way of sex differentiation of S. chinensis and to mine the related genes of sex determination. The result shows the development of male and female S. chinensis flowers was completed at the same time, the unisexual S. chinensis flowers did not undergo a transition stage between sexes, and sex may have been determined at an early stage in flower development. The results of the gene function analysis of the plant hormone signaling pathway and sucrose metabolism pathway suggest that auxin and JA could be the key hormones for sex differentiation in S. chinensis, and sucrose may promote pollen maturation at the later stage of male flower development. Two AGAMOUS (GAG) genes, 10 AGAMOUS-like MADS-box (AGLs) genes, and the MYB, NAC, WRKY, bHLH, and Trihelix transcription factor families may play important roles in sex determination in S. chinensis. Taken together, the present findings provide valuable genetic information on flower development and sex determination in S. chinensis.

Role of grapevine SEPALLATA-related MADS-box gene VvMADS39 in flower and ovule development.

Seedlessness is one of the most important breeding goals for table grapes; thus, understanding the molecular genetic regulation of seed development and abortion is critical for the development of seedless cultivars. In the present study, we characterized VvMADS39, a class E MADS-box gene of grapevine (Vitis vinifera) orthologous to Arabidopsis SEP2. Heterologous overexpression of VvMADS39 in tomato reduced the fruit and seed size and seed number. Targeted mutagenesis of the homologous SlMADS39 in tomato induced various floral and fruit defects. It could reasonable to suppose that active VvMADS39 expression in "Thompson Seedless" may restrict cellular expansion, resulting in the development of smaller fruits and seeds, VvMADS39 may play a role in the regulation of ovule development in grapevine and contributes to seedless fruit formation. In contrast, VvMADS39 suppression in "Red Globe" was associated with enhanced histone H3 lysine 27 trimethylation in the promoter region of VvMADS39, allowing normal ovule and fruit development; Meanwhile, VvMADS39 interacts with VvAGAMOUS, and the activity of the VvMADS39-VvAGAMOUS dimer to induce integument development requires the activation and maintenance of VvINO expression. The synergistic cooperation between VvMADS39 and related proteins plays an important role in maintaining floral meristem characteristics, and fruit and ovule development.

SlMBP3 Knockout/down in Tomato: Normal-Sized Fruit with Increased Dry Matter Content through Non-Liquefied Locular Tissue by Altered Cell Wall Formation

The phenotypic effect of the knockdown/out of AGAMOUS clade MADS-box gene SlMBP3 in tomato was evaluated using a transferred DNA (T-DNA)-tagged mutant of SlMBP3 and SlMBP3-RNA interference lines. SlMBP3 was preferentially expressed in the locular tissue of fruit and the seed coat combined with the endoderm. Consistent with where SlMBP3 is expressed, the SlMBP3-knockout/down lines showed non-liquefied locular tissues and increased number of seed hairs than the wild type (WT). The early cell degradation of the locular tissue was not observed in the fruits of the SlMBP3-knockout/down lines, and the cells were elongated like placental cells resulting in non-liquefied locular tissues. As the result, the fruits of the SlMBP3-knockout/down lines exhibited higher dry matter contents and titratable acidity than those of the WT. During locular tissue cell development under the SlMBP3 knockout/down, the expression of cell-enlargement-related genes (beta-expansin gene SlEXPB1 and endo-beta-1,4-D-glucanase gene Cel8) and pectinase-inhibitor-related genes (pectin esterase inhibitor gene PE inhibitor and polygalacturonase inhibitor gene PG inhibitor) was upregulated and that of pectinase-encoding genes (polygalacturonase gene QRT3-like and pectin lyase gene PL2) was downregulated. In the seed coat of the SlMBP3-knockout/down lines, tomato trichome-formation-related genes such as MYB genes containing R2 and R3 repeats (R2R3-MYB) transcription factor SlMYB75, B-type cyclin SlCycB2 and Homeodomain Leucine Zipper (HD-Zip) IV transcription factor Woolly were downregulated. Our results demonstrate that SlMBP3 is involved in the liquefaction of the locular tissue through the modification of cell development and degradation processes and seed hair formation in tomato fruits, and the SlMBP3 knockout/down results in normal-sized fruit with increased dry matter content.

Characterization of the MADS-Box Gene CmFL3 in chrysanthemum

Chrysanthemummorifolium is one of the four major cut flowers in the world, with high ornamental and economic value. Flowering time is an important ornamental characteristic of chrysanthemum that affects its value in the market. In Arabidopsis, the FRUITFULL (FUL) gene plays a key role in inducing flowering. Here, we isolated an FUL clade MADS-box gene, CmFL3, from chrysanthemum inflorescence buds. CmFL3 localized in the cellular membrane and nucleus, and showed no transcriptional activity in yeast. The qRT-PCR assay showed that CmFL3 was strongly expressed in the leaves, receptacles, and disc floret petals. Furthermore, CmFL3 was mainly detected in the inflorescence meristem and bract primordia using in situ hybridization. Similar to Arabidopsis, overexpression of CmFL3 in chrysanthemum induced early flowering. Particularly, the expression level of CmAFT was downregulated, whereas that of CmFTL3 was upregulated in the leaves of transgenic chrysanthemum lines. Meanwhile, the overexpression of CmFL3 in Arabidopsis also led to earlier flowering. Furthermore, the expression of AtFT, AtAP1, AtLFY, and AtFUL was significantly increased in CmFL3 transgenic Arabidopsis. The present study verified the function of CmFL3 in regulating flowering time and further revealed that it could affect the expression of other flowering-related genes—CmAFT and CmFTL3. Therefore, the CmFL3 gene may be an important candidate for genetic breeding aimed at regulating flowering.

Diverse function of the PISTILLATA, APETALA 3, and AGAMOUS-like MADS-box genes involved in the floral development in Alpinia hainanensis (Zingiberaceae)

Zingiberaceae is the vital clue and key node in the decreased process of fertile stamens in Zingiberales, helping to understand the evolution of the ginger families. This study focuses on Alpinia hainanensis to investigate the function of B- and C-class MADS-box genes in floral development. The introns size of two B-class genes AhPI and AhAP3, and one C-class gene AhAG are quite variable. By contrast, the positions of the corresponding introns are conserved, resulting in a similar exon size in homologs. The typical region 70 bp-CCAATCA element was not found in the second intron of AhAG compared to AG homologs. The subcellular localization showed that AhAP3 was in both intranuclear and extranuclear. The heterodimer was formed between APETALA3 and PISTILLATA but not between the B- and C-class proteins using Y2H and BiFC. The 35S::AhAG heterologous transformed Arabidopsis had curly and smaller rosette leaves with early flowering. Floral organs had no homeotic conversion, albeit sepals and petals reduced in size. Siliques development was affected and displayed wrinkled and shorter. By contrast, 35S::AhAP3 and 35S::AhPI did not show any modified phenotype in transgenic Arabidopsis thaliana. We first proposed the model for Alpinia flower development. MADS-box transcription factor binding at particular genomic locations and interaction with partners may be crucial for the development of the floral organ.

Transcriptomic comparison sheds new light on regulatory networks for dimorphic flower development in response to photoperiod in Viola prionantha

BackgroundChasmogamous (CH)–cleistogamous (CL) dimorphic flowers are developed in Viola prionantha. However, the environmental and genetic factors necessary for the CH–CL transition are unknown.ResultsIn the present work, short-day (SD) conditions induced CH flowers, whereas long days (LDs) triggered CL flowers in V. prionantha. Compared to fully developed CH flowers, CL flowers had less mature stamens, no nectar glands, and immature petals. Comparative transcriptomics revealed differentially expressed genes (DEGs) during CL and CH development. Core genes in the photoperiod pathway, such as V. prionantha orthologs of GIGANTEA (GI), CONSTANS (CO), and SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1), which promote floral induction, were highly expressed in CL flowers, whereas UNUSUAL FLORAL ORGANS (UFO) and B-class MADS-box genes for floral organ identity and development showed an opposite alteration. Moreover, genes in the glycolytic process, sucrose metabolic process, and fatty acid biosynthetic process were all highly expressed in CH flowers. Interestingly, V. prionantha orthologs of the B-class MADS-box genes APETALA3 (AP3) and PISTILLATA (PI) might relate to these sugar–fatty acid processes and were co-expressed with GAIP-B-like and YABBY5 (YAB5), which regulate the development of the petal, stamen, and nectary. Compared to CH flowers, DEGs and hub genes in the most significantly correlated modules of the gene co-expression network, which are involved in abiotic and biotic responses, were upregulated in CL flowers.ConclusionsWe proposed an integrative model for transcription regulation of genes in the photoperiod pathway, floral organ development, stress response, and sugar–fatty acid processes to determine CH–CL flower development in V. prionantha. Particularly, under LDs, activated GI may induce genes involved in the stress-response pathways, and then downregulated AP3 and PI or UFO to inhibit the sugar–fatty acid metabolic processes, together forming CL flowers. In contrast, CH flowers were produced under SDs. This work provides novel insights into the developmental evolution of dimorphic flowers in Viola.

Mechanism of fertilization-induced auxin synthesis in the endosperm for seed and fruit development

The dominance of flowering plants on earth is owed largely to the evolution of maternal tissues such as fruit and seedcoat that protect and disseminate the seeds. The mechanism of how fertilization triggers the development of these specialized maternal tissues is not well understood. A key event is the induction of auxin synthesis in the endosperm, and the mobile auxin subsequently stimulates seedcoat and fruit development. However, the regulatory mechanism of auxin synthesis in the endosperm remains unknown. Here, we show that a type I MADS box gene AGL62 is required for the activation of auxin synthesis in the endosperm in both Fragaria vesca, a diploid strawberry, and in Arabidopsis. Several strawberry FveATHB genes were identified as downstream targets of FveAGL62 and act to repress auxin biosynthesis. In this work, we identify a key mechanism for auxin induction to mediate fertilization success, a finding broadly relevant to flowering plants.

The Mechanism of MADS-box Gene SlMBP3 Modulating Tomato Fruit Size

The Mechanism of MADS-box Gene SlMBP3 Modulating Tomato Fruit Size

Analysis and Characterization of MADS-box Genes from Davidia involucrata Baill. and Regulation of Flowering Time in Arabidopsis

Analysis and Characterization of MADS-box Genes from Davidia involucrata Baill. and Regulation of Flowering Time in Arabidopsis

H3K4me3 plays a key role in establishing permissive chromatin states during bud dormancy and bud break in apple.

Bud dormancy helps woody perennials survive winter and activate robust plant development in the spring. For apple (Malus × domestica), short-term chilling induces bud dormancy in autumn, then prolonged chilling leads to dormancy release and a shift to a quiescent state in winter, with subsequent warm periods promoting bud break in spring. Epigenetic regulation contributes to seasonal responses such as vernalization. However, how histone modifications integrate seasonal cues and internal signals during bud dormancy in woody perennials remains largely unknown. Here, we show that H3K4me3 plays a key role in establishing permissive chromatin states during bud dormancy and bud break in apple. The global changes in gene expression strongly correlated with changes in H3K4me3, but not H3K27me3. High expression of DORMANCY-ASSOCIATED MADS-box (DAM) genes, key regulators of dormancy, in autumn was associated with high H3K4me3 levels. In addition, known DAM/SHORT VEGETATIVE PHASE (SVP) target genes significantly overlapped with H3K4me3-modified genes as bud dormancy progressed. These data suggest that H3K4me3 contributes to the central dormancy circuit, consisting of DAM/SVP and abscisic acid (ABA), in autumn. In winter, the lower expression and H3K4me3 levels at DAMs and gibberellin metabolism genes control chilling-induced release of dormancy. Warming conditions in spring facilitate the expression of genes related to phytohormones, the cell cycle, and cell wall modification by increasing H3K4me3 toward bud break. Our study also revealed that activation of auxin and repression of ABA sensitivity in spring are conditioned at least partly through temperature-mediated epigenetic regulation in winter.

Identification and expression analysis of the MADS-box genes of Kentucky bluegrass during inflorescence development.

The online version contains supplementary material available at 10.1007/s12298-022-01216-1.

Differentially Expressed Transcription Factors during Male and Female Cone Development in Pinus halepensis

The molecular regulation of induction and development of reproductive organs is well established in angiosperms, while it is slowly accumulating in gymnosperms. Here, we conducted comparative transcriptomic profiles at different stages of male and female cone development in Pinus halepensis. Our aim was to reveal transcription factor encoding genes involved in reproductive induction and development. For accurate developmental stage identification, histological analysis preceded the molecular analysis. The flowering induction genes FT/TFL were expressed mainly at the late developmental stages of the male cone, suggesting involvement in vegetative bud dormancy instead of flowering induction. The male cone development was associated with the expression of the C-class PhMADS2, and the B-class genes PhDAL11 and PhDAL13, while the female cone development was associated with the expression of the C-class MADS1 and DAL14 genes. This study adds valuable knowledge to the profile of transcription factors and MADS-box genes regulating cone development in gymnosperms.

Functional analysis of flower development related gene SvGLOBOSA from Senecio vulgaris.

The unique capitulum of Asteraceae has important ornamental and research value. Few studies have described the complex molecular mechanism of flower development. In this study, SvGLOBOSA(SvGLO), the MADS-box gene of Senecio vulgaris, was identified by screening the transcriptome data, and its function was examined. The gene structure was analyzed and its function was predicted through bioinformatics. The relative expression levels in different tissues of wild-type S. vulgaris were analyzed by qRT-PCR. SvGLO was overexpressed in Solanum nigrum and morphological observations were made. Histological staining was used in analyzing the histological changes in the ovary of transgenic S. nigrum. The results showed that the open reading frame of SvGLO was 591 bp long, encoding 196 amino acids. It has typical MADS-box and K-box domains and contains a PI motif at the C-terminal. SvGLO belongs to the PI/GLO subfamily of class B MADS-box genes. qRT-PCR results showed that SvGLO was highly expressed in inflorescence tissues but not in vegetative organs. In SvGLO-overexpressed S. nigrum, the sepals showed some characteristics of petals, carpels transformed into stamen-like organs, and fruit development was abnormal. Histological staining revealed that the morphology of ovary wall cells of transgenic S. nigrum was similar to that of anther wall cells of the stamen of wild-type S. vulgaris. Therefore, SvGLO may be involved in the regulation of petal and stamen development in S. vulgaris.