Search Results (107)

Chimonanthus praecox, a traditional ornamental plant in China, is admired for its ability to bloom during the cold winter season and is recognized as an outstanding woody cut flower. MADS-box genes encode transcription factors essential for plant growth and development, with key functions in regulating flowering time and the formation of floral organs. In this study, 74 MADS-box genes (CpMADS1–CpMADS74) were identified and mapped across 11 chromosomes, with chromosome 1 harboring the highest number (13 genes) and chromosome 3 the fewest (3 genes). Physicochemical property analysis revealed that all CpMADS proteins are hydrophilic and predominantly nuclear-localized. Phylogenetic analysis classified these genes into Type I and Type II subfamilies, highlighting a clear divergence in domain structure. Eighty simple sequence repeat (SSR) loci were detected, with dinucleotide repeats being the most abundant, and the majority located in Type II MADS genes. From 23 C. praecox samples, 10 polymorphic SSR markers were successfully developed and PCR-validated, enabling a cluster analysis that grouped these cultivars into three distinct clusters. This study offers significant insights into the regulation of flowering, floral organ development, genetic linkage map construction, and the application of marker-assisted selection in C. praecox. Full article

Pear (Pyrus pyrifolia) is an important deciduous fruit tree that requires a specific period of low-temperature accumulation to trigger spring flowering. The warmer winter caused by global warming has led to insufficient winter chilling, disrupting floral initiation and significantly reducing pear yields in Southern China. In this study, we integrated targeted phytohormone metabolomics, full-length transcriptomics, and proteomics to explore the regulatory mechanisms of dormancy in ‘Mixue’, a pear cultivar with an extremely low chilling requirement. Comparative analyses across the multi-omics datasets revealed 30 differentially abundant phytohormone metabolites (DPMs), 2597 differentially expressed proteins (DEPs), and 7722 differentially expressed genes (DEGs). Integrated proteomic and transcriptomic expression clustering analysis identified five members of the dormancy-associated MADS-box (DAM) gene family among dormancy-specific differentially expressed proteins (DEPs) and differentially expressed genes (DEGs). Phytohormone correlation analysis and cis-regulatory element analysis suggest that DAM genes may mediate dormancy progression by responding to abscisic acid (ABA), gibberellin (GA), and salicylic acid (SA). A dormancy-associated transcriptional regulatory network centered on DAM genes and phytohormone signaling revealed 35 transcription factors (TFs): 19 TFs appear to directly regulate the expression of DAM genes, 18 TFs are transcriptionally regulated by DAM genes, and two TFs exhibit bidirectional regulatory interactions with DAM. Within this regulatory network, we identified a novel pathway involving REVEILLE 6 (RVE6), DAM, and CONSTANS-LIKE 8 (COL8), which might play a critical role in regulating bud dormancy in the ‘Mixue’ low-chilling pear cultivar. Furthermore, lncRNAs ONT.19912.1 and ONT.20662.7 exhibit potential cis-regulatory interactions with DAM1/2/3. This study expands the DAM-mediated transcriptional regulatory network associated with bud dormancy, providing new insights into its molecular regulatory mechanisms in pear and establishing a theoretical framework for future investigations into bud dormancy control. Full article

MIKC-type MADS-box transcription factors constitute one of the largest gene families in plants, playing pivotal roles in regulating plant growth and development, hormone signaling transduction, and responses to biotic and abiotic stresses. However, there have been no reports on the systematic identification and characterization of MIKC-type MADS-box proteins in walnuts. In this study, we identified 52 JrMADS genes in the walnut genome and transcriptome, and categorized them into 14 subfamilies through structural domain and phylogenetic tree analysis. It was found that these genes were unevenly distributed across 16 chromosomes. Within the MIKC-type MADS-box gene family, we identified three pairs of tandem-duplicated genes and 40 pairs of segmental duplicated genes, indicating that segmental duplication was the primary mechanism of gene amplification in walnut. Ka/Ks analysis showed that the family genes have undergone purifying selection during evolutionary processes. The promoter was predicted to contain cis-acting elements related to growth, development, plant hormones, and stress response. Expression profile analysis showed that JrMADS genes have different expression patterns in various tissues and developmental stages of male and female flower buds. Notably, an ancient clade of TM8 (JrMADS43) genes was found, which is absent in Arabidopsis but present in other flowering plants. Another gene, TM6 gene (JrMADS4), belongs to the AP3 subfamily and is a clade that has diverged from tomatoes. Through qPCR analysis, we verified the differential expression of JrMADS genes at different developmental stages (MB-1/2/3 and FB-1/2/3), with JrMADS5, JrMADS8, JrMADS14, JrMADS24, JrMADS40, JrMADS46, JrMADS47, JrGA3ox1, and JrGA3ox3 showing significantly higher expression in male than in female flower buds. In summary, our results provide valuable information for further biological functions research on MIKC-type MADS-box genes in walnut, such as flower organ development, and lays a solid foundation for future studies. Full article

The SEPALLATA3 (SEP3)-like MADS-box genes play crucial roles in determining petal identity and development in the petunia and tomato of Solanaceae. Solanum nigrum is a self-pollinating plant in the Solanaceae family, and produces white flowers. However, the mechanisms controlling the transition from green to white petals during flower development remain poorly understood. In this study, we isolated a flower-specific SEP3-like gene, SnMADS37, from S. nigrum, and investigated its potential role in chlorophyll metabolism during petal development. Our results show that quantitative RT-PCR analysis demonstrates that SnMADS37 is exclusively expressed in petals and stamens during early floral bud development. Overexpression of SnMADS37 clearly enhanced the number of petals, promoting the formation of additional petal-like tissues in stamens and extra organs in some fruits. Moreover, fully opened transformed petals exhibited notable chlorophyll accumulation at their tips and veins, whereas silencing of Snmads37 clearly inhibited petal expansion and reduced green pigmentation in early flower buds. Additionally, the transformed green petals exhibited distinct conical epidermal cells in the green regions, similar to wild type (WT) petals. Our results demonstrate that SnMADS37 plays a critical role in regulating petal identity, expansion, and chlorophyll metabolism during petal development. These findings provide new insights into the functional diversification of SEP3-like MADS-box genes in angiosperms. Full article

Primulina huaijiensis is a promising candidate for eco-bottle flowers, yet the genes related to flowering remain unexplored despite the availability of genomic data for several years. MADS-box genes constitute a large family of transcription factors that play crucial roles in plant growth and development, particularly in flower development. In this study, we identified 84 MADS-box genes (PhuMADS) in P. huaijiensis genome and analyzed their evolution and expression profiles to gain insights into the flowering mechanism. The 84 genes constitute 29 type I and 55 type II MADS-box genes. Phylogenetic analysis further classified them into 17 subfamilies, which were randomly distributed across 18 chromosomes and four scaffolds. PhuMADS genes exhibit a range of 1 to 12 exons and share conserved motifs. Segmental duplication was found to be the primary driver of PhuMADS gene family expansion, with duplicated gene pairs undergoing purifying selection. Cis-acting elements analysis revealed PhuMADS promoters harbor abiotic stress-, hormone-, light-, and growth-related motifs, implicating roles in development and environmental adaptation in P. huaijiensis. RNA-seq showed distinct expression patterns of PhuMADS genes among different tissues or developmental stages. The results of qRT-PCR analysis of selected genes further validated the RNA-seq findings, suggesting these genes may exert distinct functional roles during floral development. This study laid a theoretical foundation for further functional studies of the MADS-box genes in P. huaijiensis. Full article

The APETALA2/Ethylene-Responsive Factor (AP2/ERF) superfamily is one of the largest transcription factor families in plants, playing diverse roles in development, stress response, and metabolic regulation. Despite their ecological and economic importance, AP2/ERF genes remain uncharacterized in marigold (Tagetes erecta), a valuable ornamental and medicinal plant in the Asteraceae family known for its unique capitulum-type inflorescence with distinct ray and disc florets. Here, we conducted a comprehensive genome-wide analysis of the AP2/ERF superfamily in marigold and identified 177 AP2/ERF genes distributed across 11 of the 12 chromosomes. Phylogenetic analysis revealed their classification into the AP2 (28 genes), ERF (143 genes), RAV (4 genes), and Soloist (2 genes) families based on domain architecture. Gene structure and motif composition analyses demonstrated group-specific patterns that correlated with their evolutionary relationships. Chromosome mapping and synteny analyses revealed that segmental duplications significantly contributed to AP2/ERF superfamily gene expansion in marigold, with extensive collinearity observed between marigold and other species. Expression profiling across different tissues and developmental stages indicated distinct spatio-temporal expression patterns, with several genes exhibiting tissue-specific expression in Asteraceae-specific structures. In floral organs, TeAP2/ERF145 exhibited significantly higher expression in ray floret corollas compared to disc florets, while TeAP2/ERF103 showed stamen-specific expression in disc florets. Protein interaction network analysis revealed AP2 as a central hub with extensive predicted interactions with MADS-box and TCP family proteins. These findings suggest that AP2 family genes may collaborate with MADS-box and CYC2 genes in regulating the characteristic floral architecture of marigold, establishing a foundation for future functional studies and molecular breeding efforts to enhance ornamental and agricultural traits in this economically important plant. Full article

Background/Objectives: In perennial plants, developing floral buds survive winter through entering a dormant state, which is induced by low temperature and abscisic acid (ABA). ABA performs vital functions in the dormancy process. ABA-insensitive 5 (ABI5) transcription factor is a key regulator in the ABA signaling pathway. However, little is known about the regulation of ABI5 in the winter dormancy of sweet cherries. Methods: We identified the sweet cherry ABI5 gene and its expression changes using gene cloning and qRT-PCR. Additionally, we validated the interaction between PavABI5 and PavCIG1/2 using Yeast One-Hybrid and Dual-Luciferase Assays. Results: In this study, we identified a basic leucine zipper (bZIP) family gene ABI5 from the sweet cherry, which was closely related to PduABI5 from Prunus dulcis, PpABI5 from Prunus persica, PmABI5 from Prunus mume, and ParABI5 from Prunus armeniaca, through phylogenetic tree analysis. The seasonal expression pattern showed that the PavABI5 level was increased during the winter dormancy stage and induced by exogenous ABA. Specifically, we found that the expression of cherry cold-induced genes (PavCIG1/2) was positively correlated with PavABI5 expression. Furthermore, PavABI5 directly bound to the ABRE elements in the PavCIG1/2 promoters to activate their expression. We further confirmed that the dormancy-associated MADS-box (DAM) genes DAM4 and DAM5 function downstream of the ABA signaling pathway to regulate bud dormancy in sweet cherries. Conclusions: Our findings suggest a putative regulatory model of ABA-mediated bud-dormancy with PavABI5. Full article

MADS-box transcription factors play a crucial role in plant growth and development. Although previous genome-wide analyses have investigated the MADS-box family in cucumber, this study provides the first comprehensive reannotation of the MADS-box gene family in Cucumis sativus using updated Cucurbitaceae genome data, offering novel insights into the gene family’s evolution and functional diversity. The results show that a total of 48 CsMADS-box genes were identified in the V3 version of cucumber, while 3 of the 43 genes identified in the V1 version were duplicated. The V1 version actually has only 40 genes. Additionally, we analyzed the variability in protein sequences and found that the amino acid sequences of 14 genes showed no differences between the two versions of the database, while the amino acid sequences of 29 genes exhibited significant differences. The further analysis of conserved motifs revealed that although the amino acid lengths of 15 genes had changed, their conserved motifs remained unchanged; however, the conserved motifs of 12 genes had altered. Furthermore we found that motif1 and motif2 were present in most proteins, indicating that they are highly conserved. Gene structure analysis revealed that most type I (Mα, Mβ) MADS-box genes lack introns, whereas type II (MIKC) genes exhibit a similar structure with a higher number of introns. Chromosomal localization analysis indicated that CsMADS-box genes are unevenly distributed across the seven chromosomes of cucumber. Promoter region analysis showed that the promoter regions of CsMADS-box genes contain response elements related to plant growth and development, suggesting that CsMADS-box genes may be extensively involved in plant growth and development. Different CsMADS-box genes exhibit specific high expression in roots, stems, leaves, tendrils, male flowers, female flowers, and ovaries, suggesting that these genes play crucial roles in the growth, development, reproduction and morphogenesis of cucumber. Moreover, 26, 18, 8, and 10 CsMADS-box genes were differentially expressed under high temperature, NaCl and/or silicon, downy mildew, and powdery mildew treatments, respectively. Interestingly, CsMADS07 and CsMADS16 responded to all tested stress conditions. These findings provide a reference and basis for further investigation into the function and mechanisms of the MADS-box genes for resistance breeding in cucumber. Full article

Stem internode length determines height to first pod (HFP), an important trait for mechanical harvesting in legume crops. In the present study, this trait in lentil was (Lens culinaris Medik.) examined using scanning electron microscopy (SEM) of epidermal cells in stem internodes of two parents, Flip92-36L and ILL-1552, with long and short HFP, respectively. No significant differences in cell length, but differences in cell width were seen. This indicates that HFP was determined by cell number rather than cell length. The candidate gene family for HFP, Suppressor of Overexpression of Constans 1 (SOC1), a member of the MADS-box transcription factor family, controls both flowering time (FT) and HFP traits. Six LcSOC1 genes were identified in this study, and their expression was analysed. Most of the genes studied showed constitutive expression during vegetative growth, flowering, and seed development stages. Expression of LcSOC1-a seems to be involved in the transition to flowering and FT, whereas expression of LcSOC1-b2 was strongly associated with HFP but not FT. Two haplotypes with two SNP each were identified in LcSOC1-b2 among eight sequenced lentil accessions, and an SNP-based ASQ marker was developed and used for genotyping of a lentil germplasm collection. Significant association between LcSOC1-b2 haplotypes and HFP was found in this study, indicating a primary role for this gene in internode length, potentially by regulating cell number. Full article

The MIKC-type MADS-box (MIKC) gene family is essential for controlling various plant developmental processes, including flowering time and dormancy transitions. Although the MIKC gene family has been widely studied across different plants, its characterization and functional study in herbaceous peony remain limited. In this study, 19 Paeonia lactiflora Pall. MIKC-type (PlMIKC) genes were identified from the transcriptome of a low-chilling requirement Paeonia lactiflora Pall. cultivar ‘Hang Baishao’. These MIKC genes were categorized into seven clades: six were classified as MIKC^C-type, including FUL/AP1, DAM, PI, AGL18, AGL12, AG, and SOC1, and one, AGL30, was classified as MIKC*-type. Notably, the FLC clade genes were absent in Paeonia lactiflora Pall. The PlMIKC genes were predominantly localized to the nucleus, and their sequences contained highly conserved MADS and K-domains. Phylogenetic analysis demonstrated that PlMIKC genes share a strong evolutionary affinity with the MIKC genes from grapevine (Vitis vinifera) and poplar (Populus trichocarpa). A low-temperature-induced bud dormancy transition (BDT) experiment revealed that PlMIKC genes, such as PlFUL and PlDAM, were highly expressed during dormancy maintenance, while PlSOC1, PlAGL12, and PlAGL30 were upregulated during BDT. Additionally, the transient overexpression of PlSOC1 in ‘Hang Baishao’ significantly accelerated BDT and promoted bud break, suggesting that SOC1, traditionally linked to flowering regulation, also plays a key role in dormancy transition. Since limited literature on the MIKC gene family is currently available in herbaceous peony, this study expands the knowledge of the MIKC genes in Paeonia lactiflora Pall. and offers valuable insights into the molecular regulation of bud dormancy in response to low temperatures. Full article

Chinese cabbage (Brassica rapa L. ssp. pekinensis) is a key vegetable crop in Asia, but its commercial value is often reduced by premature flowering triggered by vernalization. The molecular mechanisms behind this process are not fully understood. MADS-box genes, as crucial transcriptional regulators, play vital roles in plant development, including flowering. In this study, 102 MADS-box genes were identified in Chinese cabbage through bioinformatics analyses, covering phylogeny, chromosomal localization, and gene structure. Real-time quantitative PCR and RNA-seq data analysis revealed that the expression level of AGL27 declined as vernalization time increased. To determine BrAGL27′s functions, we obtained BrAGL27-overexpressed (OE) Arabidopsis thaliana lines that showed significantly later flowering compared with the wild type (WT). The expression levels of flowering suppressor genes AtFLC and AtTEM1 were significantly high-regulated in the BrAGL27-OE lines compared to WT plants, while the expression levels of the floral genes AtSPL15, AtSOC1, AtFT, and AtAP3 were significantly lower in the BrAGL27-overexpressed lines than in the wild type. These findings enhance understanding of MADS-box genes in vernalization and flowering regulation, offering a basis for further research on bolting resistance and flowering control in Chinese cabbage. Full article

Lumnitzera littorea (Jack) Voigt is an endangered mangrove species in China. Low fecundity and environmental pressure are supposed to be key factors limiting the population expansion of L. littorea. Transcription factors with the MADS-box domain are crucial regulators of plant flower development, reproduction, and stress response. In this study, we performed a comprehensive investigation into the features and functions of MADS-box genes of L. littorea. Sixty-three LlMADS genes with similar structure and motif composition were identified in the L. littorea genome, and these genes were unevenly distributed on the 11 chromosomes. Segmental duplication was suggested to make a main contribution to the expansion of the LlMADS gene family. Some LIMADS genes exhibited differential expression in different flower types or in response to cold stress. Overexpression of the B-class gene LlMADS37 had substantial effects on the flower morphology and flowering time of transgenic Arabidopsis plants, demonstrating its key role in regulating flower morphogenesis and inflorescence. These findings largely enrich our understanding of the functional importance of MADS-box genes in the inflorescence and stress acclimation of L. littorea and provide valuable resources for future genetic research to improve the conservation of this species. Full article

The MADS-box transcription factor gene family is essential for the differentiation and development of floral organs. Genome-wide and transcriptome data from Phoebe bournei provide the foundation for studying its floral development. In this study, phylogenetic relationships, protein characteristics, conserved domains, gene structures, and cis-acting elements in promoter regions of P. bournei MADS-box genes were systematically analyzed through bioinformatics methodologies. A total of 69 PbMADS genes were identified and classified into 15 subfamilies based on their phylogenetic relationships. The potential functions of these genes were inferred based on transcriptomic data and GO classification. In addition, we selected genes from the ABCDE model to analyze protein interactions and performed RT-qPCR to analyze their expression in each floral organ whorl (outer tepals, inner tepals, stamens, and carpel). Based on these analyses, we rationally constructed a model for the floral organ development in P. bournei. This study, thus, provides a theoretical reference for germplasm innovation in P. bournei and offers insights into the floral development in other Lauraceae species. Full article

To investigate the evolutionary trajectory during the recent speciation of AA-genome Oryza species, we conducted a comprehensive analysis of the MADS-box gene family across eight Oryza species. We identified 1093 MADS-box genes in total and systematically examined their evolutionary history, gene family expansion, and expression divergence. Our results revealed that extensive lineage-specific expansions occurred in AA-genome Oryza species, which were primarily generated by proximal and tandem duplications, with a particularly notable episode in Type-I genes. Despite the significant expansion, Type-I genes were generally expressed at low levels or not expressed across various organs. In contrast, the expansion of Type-II genes was primarily observed in the AG, AGL12, SOC1, GGM13, and MIKC* subfamilies, which exhibited high levels of expression in reproductive organs such as panicles and stigmas. Additionally, we found species-specific gene expression in the two out-crossing wild rice species, Oryza rufipogon and Oryza longistaminata. Notably, a unique MADS-box gene in O. longistaminata exhibited high expression levels in rhizomes and stems, which may be associated with the species’ distinctive rhizomatous growth habit. Full article

Korean pine (Pinus koraiensis Siebold & Zucc.) is an important timber and economic tree species in northeast China. Its seeds serve as both a primary means of propagation and a significant economic product. In this study, we identified 12 full-length MADS-box genes based on the Korean pine flower-induced transcriptome data available in our laboratory. These genes were identified through multiple sequence alignment and screening for conserved structural domains. We analyzed the genetic relationships of these genes and predicted their physicochemical properties. Additionally, we examined the expression patterns of three SHORT VEGETATIVE PHASE (SVP) genes across different tissues and developmental stages of Korean pine. The results indicate that the amino acid composition, molecular weight, isoelectric point, and other physicochemical properties of the MADS-box gene family in Pinus koraiensis are generally similar, though some individual variations are observed. A total of 12 MADS-box family genes were identified from the Korean pine transcriptome, distributed across five subfamilies. Conserved motif analysis revealed that these genes share similar conserved sequences. Structural and physicochemical analyses showed that genes with similar sequences exhibited comparable characteristics. Expression levels of the SVP genes varied significantly across different developmental stages and tissues, with the expression of the three SVP genes in leaves being markedly higher than in buds (approximately 200-fold). The expression levels of these genes in leaves were not only higher than in buds but also exceeded those in other tissues. Based on these findings, we conclude that these three SVP genes primarily play a suppressive role in the process of flower bud formation, helping Korean pine maintain a juvenile state under certain conditions, and are also involved in the growth and development of its leaves. This research provides a basis for future studies on the flowering induction mechanism in Korean pine. Full article