Search Results (131)

Fruit-specific promoters (FSPs) are a class of regulatory DNA sequences that direct transgene expression exclusively in fruit tissues or during specific stages of fruit development. They are indispensable molecular tools in modern agricultural biotechnology, with broad applications in fruit quality improvement, nutritional enhancement, and shelf-life extension. By functioning as precise molecular switches that regulate fruit-specific gene expression, FSPs overcome the limitations of constitutive promoters and facilitate precision molecular breeding for fruit quality improvement. This review systematically summarizes recent advances in FSP research. First, based on their spatiotemporal expression patterns, FSPs are classified into four categories: immature fruit-specific, fruit ripening-specific, whole fruit development stage-specific, and dual-stage (immature fruit/ripening) promoters. Their origins, expression characteristics, and key cis-regulatory elements are comprehensively summarized. Second, the complex transcriptional regulatory network governing FSP activity is discussed from the perspectives of cis-regulatory elements, major transcription factor families (such as MADS-box and NAC proteins), and epigenetic regulation, including DNA methylation and histone modifications. Furthermore, recent advances in key methodologies, including promoter cloning, functional characterization, and CRISPR/Cas9-mediated precise editing of cis-regulatory elements, are reviewed, together with their applications in crop genetic improvement, plant molecular farming, and fundamental molecular biology research. Finally, this review highlights the major challenges limiting the application of FSPs, including the relatively weak transcriptional activity of natural promoters, insufficient tissue specificity, and limited cross-species applicability. Future perspectives are discussed, emphasizing the integration of artificial intelligence-assisted promoter design, high-throughput screening, and single-cell omics technologies to develop finely tunable synthetic promoters. These advances are expected to provide both a theoretical foundation and technical support for precision molecular breeding in fruit crops. Full article

Fruit endocarp and seed coat are essential protective structures that influence key agronomic and mechanical traits in species with lignified protective tissues, yet their regulatory mechanisms remain incompletely understood. Here, we conducted a comprehensive genome-wide analysis of the MADS-box gene family in four angiosperm species: Juglans sigillata, Carya illinoinensis, Macadamia integrifolia, and Ricinus communis. A total of 58, 55, 57, and 57 MADS-box genes were identified, respectively, and systematically characterized through phylogenetic, structural, and evolutionary analyses. Comparative results revealed that MIKCc-type genes are highly conserved and primarily expanded via segmental duplication under strong purifying selection. Co-expression network analysis identified MADS-box genes as high-connectivity hub candidates that are strongly associated with genes involved in tissue specification, hormone signaling, and secondary cell wall biosynthesis. Promoters analysis indicated that these genes contain diverse cis-regulatory elements; however, these results are based on sequence prediction and do not demonstrate functional regulatory interactions. Across species, MADS-box genes exhibited analogous temporal expression dynamics during lignified endocarp and seed coat development, consistent with a potentially conserved transcriptional framework. Collectively, this study provides new insights into the evolutionary diversification and putative functions of MADS-box genes, and proposes a putative hierarchical regulatory framework for lignified endocarp and seed coat development. These findings supply valuable candidate target genes for future molecular breeding aimed at improving shell thickness, hardness, and related agronomic traits in woody nut and oilseed species. Full article

The MADS-box family is a multifunctional family of transcription factors characterized by the presence of a unique MADS domain, which plays an important part in regulating essential biological processes, including metabolic synthesis and the stress response. In this review, we analyze the structural features and classification of MADS-box proteins, then summarize the functions of the MADS-box family in the stress response. The MADS-box family can directly regulate downstream functional genes by binding to the CArG-box in the promoters of target genes, thereby influencing growth, development, and stress responses. Also, MADS-box transcription factors can form protein complexes with both MADS-box proteins and other types of transcription factors and chromatin regulatory proteins to modulate the chromatin state or transcriptional activation. Furthermore, they can regulate plant physiological responses by facilitating the synthesis of essential signaling molecules, including hormones and non-coding RNA. Finally, we discuss the potential of the MADS-box family in crop molecular breeding, offering a novel approach for developing high-yield and stress-resistant cultivars for solving global food security and climate change challenges. Full article

AGL6 genes are critical floral regulators in diverse angiosperms, yet their roles in legumes remain poorly understood. This study aimed to characterize GmAGL6 genes in soybean (Glycine max [L.] Merr. cv. Williams 82). We identified four homologs (GmAGL6a–d) featuring conserved MADS-box and K-box domains that cluster within the AGL6 lineage. Tissue-specific expression profiling revealed significant transcript enrichment during flower bud differentiation and maturation. Using CRISPR/Cas9, we generated quadruple knockout lines to evaluate gene function. Phenotypic analysis showed that, unlike the homeotic transformations typical of AGL6 loss in monocots, Gmagl6 quadruple mutants retained a standard papilionaceous floral structure without keel petal aberrations. However, the mutants did not show significant changes in floral height or width, but exhibited a significantly increased floral height-to-width ratio and smaller mature seeds, while vegetative architecture and podding capacity remained unaffected. These results suggest that GmAGL6 genes in soybean may function primarily in the regulation of floral proportion and seed development rather than floral organ identity. This research provides insights into the evolution of specialized legume flowers and suggests candidate genes for seed size improvement. Full article

The MADS-box transcription factor (TF) family constitutes a critical class of transcriptional regulators in plants, playing pivotal roles in diverse developmental processes. MIKC-type proteins represent Type II MADS-box TFs that widely function in regulating floral organ development and reproductive growth in plants. In this study, a total of 38 MIKC-type MADS TFs were identified from the sorghum genome, distributed across nine chromosomes. Based on sequence alignments and phylogenetic analysis, these 38 SbMIKC genes (SbMIKCs) were further classified into 10 distinct subfamilies. The expression profiling of these SbMIKCs across multiple tissues revealed five major patterns, among which SbMIKC17 exhibited relatively abundant transcript levels during grain development in sorghum. Further assays confirmed that the protein encoded by SbMIKC17 localizes to the nucleus without self-transactivation activity in yeast. Integrated results from DNA affinity purification sequencing (DAP-seq), dual-luciferase assays, and yeast one-hybrid experiments demonstrate that SbMIKC17 binds to the promoter of SbAGPS1 and activates its activity, as well as enhance the promoter activities of SbBt1, SbGBSSI, SbSSIIa, and SbISA1 simultaneously. Collectively, these findings suggest that the MIKC-type MADS member of SbMIKC17 serves as a potential transcriptional regulator in starch biosynthesis in sorghum. Full article

The MADS-box gene family encodes a critical class of transcription factors that regulate diverse developmental processes in plants. However, its role in abiotic stress responses remains poorly characterized in Lilium davidii var. unicolor (Lanzhou lily). In this study, we identified 62 LdMADS genes in the Lanzhou lily genome, classifying them into 17 Type I and 45 Type II members. Notably, the SOC1 subfamily exhibited a pronounced expansion. These LdMADS members were distributed across all twelve chromosomes and displayed considerable structural variation, with some genes harboring exceptionally long introns. Tissue-specific expression profiling revealed that M-type and MIKC* genes were predominantly and specifically expressed in ovaries and anthers, whereas MIKC^C members exhibited complex and diverse expression patterns across multiple tissues. The selection of candidate LdMADS genes for abiotic stress response was based on their transcript abundance in leaf and root tissues, together with the enrichment of their cis-acting elements. The expression of these LdMADS genes under drought, heat, and cold stresses was further examined by qRT-PCR. Among them, LdMADS4 and LdMADS14 from the SEP subfamily, as well as LdMADS25 and LdMADS26 from the SOC1 subfamily, responded to multiple stress conditions. This study provides functional clues for the roles of MADS-box genes in the development and stress responses of Lanzhou Lily. Full article

Deciphering the molecular regulatory networks of panicle development is essential for the genetic improvement of crop yield. However, to date, no systematic studies of gene expression across different panicle developmental stages have been performed in foxtail millet. In this study, a transcriptome analysis of foxtail millet panicle was conducted in four stages of development spanning from the initiation of primary branches to floral organ differentiation. A total of 20,377 expressed genes were identified, including 10,647 differentially expressed genes. Fuzzy C-means clustering detected stage-specific expressed homologs of key transcription regulators, which may be involved in plant organ morphogenesis. Moreover, 1215 transcription factors of 55 families were identified. Members of the MADS-box and GRAS transcription factors showed stage-specific expression patterns, whose conservation was useful in discovering genes related to foxtail millet panicle development. Our analysis was further substantiated by the functional characterization of SiSOC1, whose expression exhibited a gradual upregulation across the four developmental stages. SiSOC1 was identified and validated, which revised the annotation of the reference genome. Overexpression of SiSOC1 markedly accelerated the heading of foxtail millet under long-day and short-day conditions, validating its function in regulating the heading date. In summary, this study systematically identified the transcriptomic landscape of foxtail millet panicle development, and elucidated key regulatory genes. These results provide a theoretical foundation and gene resources for facilitating the molecular breeding of foxtail millet. Full article

Korean pine (Pinus koraiensis) is a vital woody oil tree species native to Northeast Asia, with its pine nuts serving as the primary global source of edible pine nuts globally due to their rich nutritional content. Currently, seed yield from Korean pine is low and unstable, failing to meet the market demand. The limited number of female cones is the primary factor restricting its yield. MADS-box family members are crucial in regulating the initiation, differentiation, and morphogenesis of floral organs. However, systematic identification and characterization of MADS-box proteins in Korean pine have not been reported. This study utilized transcriptome data from reproductive and vegetative buds during the flower bud differentiation stage of Korean pine to comprehensively identify MADS-box family members through bioinformatics analysis and molecular biology approaches. A total of 37 PkMADS-box genes were identified, including 6 type I and 31 type II (MIKC) genes, which were classified into 8 subfamilies. The physicochemical properties, conserved domains, conserved motifs, protein structures, gene expression profiles, and protein–protein interaction networks of these genes were analyzed. Key genes associated with physiological differentiation (flower induction) and sexual organogenesis were identified based on expression patterns during flower bud differentiation and flower organ development. Among these, PkMADS4 and PkMADS26 are likely involved in positively regulating flower induction, while PkMADS9 plays a role in the morphological differentiation of sexual organs in a dose-dependent manner and overexpression of PkMADS9 promoting early flowering in transgenic Arabidopsis. These genes were also identified as key candidates for regulating reproductive phase changes and strobilus development. This study provides a theoretical foundation for further investigation of MADS-box genes in reproduction and offers insights into genetic improvements aimed at enhancing the seed yield of Korean pine. Full article

MADS-box transcription factors are key regulators of plant development and environmental responses. Here, we performed an integrated phylogenomic and expression analysis of the MADS-box gene family in Capsicum annuum, identifying 97 members that fall into 52 Type I and 45 Type II genes. Comparative phylogeny, exon–intron organization, conserved motifs, and chromosomal mapping allowed classification into 15 subfamilies. Gene duplication analysis revealed that segmental duplication has been a major driver of family expansion. Expression profiling across multiple tissues, together with promoter cis-element prediction and stress-responsive transcriptome data, demonstrated that Type II genes exhibit broad and dynamic expression patterns, particularly under ABA treatment and temperature stress. A key finding of this study is the complete absence of the Mβ lineage, a Type I subfamily typically associated with gametophyte and endosperm development in other angiosperms. No Mβ-like sequences were detected in the pepper genome, and Type I genes overall showed extremely low expression, suggesting that the Mβ lineage has undergone lineage-specific evolutionary loss and that its functions may be compensated by other Type I members or by expanded Type II regulatory modules. Together, this study provides the first evidence for the evolutionary disappearance of the Mβ subfamily in Capsicum and offers a comprehensive resource for dissecting the developmental and stress-responsive roles of MADS-box genes in pepper. Full article

Background/Objectives: This study was based on the joint analysis of transcriptome and metabolome to explore the key genes and metabolic pathways of gardenia single flower petal number variation and to explore the possible mechanism of floral organ variation. Methods: Five, six, and seven petals of single-flower gardenia were selected as test materials for transcriptome and metabolome determination to excavate the key genes in regulating petal number in gardenia. Results: Metabolomic analysis identified triethylamine, succinic acid, succinylaldehyde, 2-phenylethanol, and o-xylene as the top five differentially expressed metabolites affecting petal number variation in gardenia. In the KEGG enrichment analysis, gardenia five, six, and seven DEGs were mainly enriched in amphetamine biosynthesis, the biosynthesis of plant secondary metabolites; transcriptome results showed that the identified differential transcription factors mainly come from NAC, ERF, C2H2, MYB, and MADS-box gene families; the expression of GjMADS50, GjMADS59, and GjERF28 changed with the increase in petal number. The commonality between gardenia five, six, and seven flowers exceeded the difference, and the expression pattern of MADS-box and ERF gene family members was the upregulation of GjERF28, GjERF39, and GjMADS67 and downregulation of GjMADS50, GjMADS59, and GjMADS60. Conclusions: We propose that ERF transcription factors may determine the initial number of petal primordia by mediating gibberellin biosynthesis or signaling, thereby coordinately regulating floral meristem activity and specific metabolic states. Full article

Pearl millet, an African-origin crop with exceptional heat tolerance, maintains normal flowering and seed production even under extremely high temperatures. The MADS-box transcription factor family plays a central role not only in floral organs, but also in abiotic stress responses. However, its specific function in pearl millet’s heat stress response remains unclear. In this study, a total of 63 MADS-box genes were identified. These genes were classified into five subfamilies and distributed across seven chromosomes, with chromosome 6 containing the highest number (12 genes). Additionally, expression analysis revealed that 53 MADS-box genes exhibited increased expression levels following heat stress under high-temperature conditions. Differential expression analysis identified five key MADS-box genes responding to heat stress. Further analysis of their expression trends using qRT-PCR revealed that the expression levels of these genes first increased and then decreased after heat stress treatment, with differences in the timing of peak expression among different genes. PMA1G07218.1 was selected for further functional characterization, which exhibited a significant response to heat stress treatment and reached a peak at 6 h. Subcellular localization analysis confirmed that the encoded protein is exclusively nuclear-localized. Through the yeast one-hybrid method (Y1H), we found that PMA1G07218.1 interacts by binding to the AG cis-acting element of F-box gene PMA1G04890.1. These findings provide valuable insight into the role of MADS-box genes in the high-temperature stress response of pearl millet, highlighting PMA1G07218.1 as a promising candidate for enhancing thermotolerance in this species. Full article

Background: In plants, members of the MADS-box gene family encode transcription factors that regulate a wide range of developmental processes, including cell differentiation, organ identity, floral induction, and responses to environmental stimuli. Moreover, MADS-box genes play central roles in the well-known ABCDE model of floral development. Teak (Tectona grandis), a woody species belonging to the Lamiaceae family, is recognized for its medicinal and agricultural significance. The recent availability of a chromosome-level genome assembly for T. grandis has enabled the genome-wide identification of 87 MADS-box genes, which are distributed across 18 pseudo-chromosomes. Methods: The amino acid sequences of these genes were compared with orthologous proteins from Arabidopsis thaliana, Sesamum indicum, and Amborella trichopoda to infer the phylogenetic relationships. The structures of key floral quartets in the MADS-box proteins were predicted, and the stability of these predicted tetramers were analyzed via molecular dynamics simulations. Results: The phylogenetic analysis classified the genes into 33 Type I and 54 Type II MADS-box members, forming four major clades (MIKC^C, MIKC*, Mα, and Mγ), while the Mβ-type clade was absent. A conserved motif analysis revealed that the Type II genes exhibited greater motif diversity than the Type I, suggesting that T. grandis Type II MADS-box genes possess more complex structures and potentially broader functions. The transcriptomic data from different tissues showed that the MIKC-type genes were particularly active during flower development. Although stable over the simulation time, the T. grandis AP3 ortholog had shorter I and K domains and had an odd mode of protein–protein interaction. Conclusion: Overall, the presented genome-wide analysis provides a comprehensive base for understanding the evolutionary diversification of the MADS-box gene family in T. grandis and identifies candidate genes for future structural and functional characterization. Full article

Brachiaria decumbens is a high-yielding forage grass of major economic value in tropical regions. The root endophytic fungus Piriformospora indica is widely recognized for promoting plant growth and stress tolerance, yet its effects on B. decumbens remain poorly characterized. Here, we profiled root responses to P. indica colonization at 10 days after inoculation (dais; early stage) and 20 dais (late stage) during symbiosis establishment. Colonization was confirmed by phenotypic and physiological assessments, with inoculated plants showing enhanced root growth; colonized roots exhibited higher activities of catalase (CAT), superoxide dismutase (SOD), and peroxidase (POD), along with increased indole-3-acetic acid (IAA) levels, whereas malondialdehyde (MDA), jasmonic acid (JA), and the ethylene precursor 1-aminocyclopropane-1-carboxylic acid (ACC) were reduced. Transcriptome and metabolomic profiling identified 1884 and 1077 differentially expressed genes (DEGs) and 2098 and 1509 differentially accumulated metabolites (DAMs) at 10 dais (Pi10d vs. CK10d) and 20 dais (Pi20d vs. CK20d), respectively, and 3355 DEGs and 2314 DAMs between stages (Pi20d vs. Pi10d). Functional enrichment highlighted key pathways related to secondary metabolism, carbohydrate metabolism, and lipid biosynthesis. Differentially expressed transcription factors spanned multiple families, including MYB, AP2/ERF, MADS-box, and bZIP, consistent with broad transcriptional reprogramming during symbiosis establishment. Integrative multi-omics analysis further highlighted phenylpropanoid biosynthesis and α-linolenic acid metabolism as consistently co-enriched pathways, suggesting coordinated shifts in gene expression and metabolite accumulation across colonization stages. Collectively, these results provide a multi-layered resource and a framework for mechanistic dissection of the P. indica–B. decumbens interaction. Full article

Soluble sugars are key determinants of fruit quality, directly influencing sensory attributes such as sweetness and flavor, as well as nutritional value and texture. Their content and composition are precisely regulated by sugar-metabolizing enzymes. Key enzymes, including invertase (INV), sucrose phosphate synthase (SPS), sucrose synthase (SUS), fructokinase (FRK), and hexokinase (HXK), play pivotal roles in these processes. However, a systematic and in-depth analysis of their regulatory mechanisms is currently lacking, which hinders a comprehensive understanding of the regulatory network governing fruit sugar metabolism. This review employs bibliometric analysis to systematically examine research trends in fruit sugar metabolism. Furthermore, it synthesizes recent advances in the coordinated regulatory mechanisms from the perspectives of transcriptional regulation, epigenetic modifications, and signal transduction, aiming to provide a clearer framework for future research. At the transcriptional level, transcription factor families such as MYB, WRKY, NAC, and MADS-box achieve precise regulation of sugar metabolism-related genes by specifically binding to the promoters of their target genes. Regarding epigenetic regulation, mechanisms including histone modifications, non-coding RNAs, and DNA methylation influence the expression of sugar-metabolizing enzymes at the post-transcriptional level by modulating chromatin accessibility or mRNA stability. Signaling pathways integrate hormonal signals (e.g., ABA, ethylene), environmental signals (e.g., temperature, light), and sugar-derived signals into the regulatory network, forming complex feedback mechanisms. These regulatory mechanisms not only directly affect sugar accumulation in fruits but also participate in fruit quality formation by modulating processes such as cell turgor pressure and carbon allocation. By integrating recent findings on transcriptional regulation, epigenetics, and signaling pathways, this review provides a theoretical foundation for fruit quality improvement and targeted breeding. Full article

The floral morphology of Rosa chinensis significantly influences its ornamental value. However, the molecular mechanisms underlying specific floral types remain poorly understood. Viridiflora, a stable genetic variant of R. chinensis, exhibits homeotic transformation of floral organs into sepal-like structures, providing a valuable model for studying floral organ identity and development. In this study, Viridiflora was compared with Old Blush to elucidate floral development through morphological observation, transcriptomic profiling, and functional genetics. Four distinct developmental stages were defined, encompassing the formation of sepal, petal, stamen, and pistil primordia. Transcriptome analysis identified candidate genes associated with the Viridiflora phenotype, among which RcAGAMOUS2 (RcAG2) and RcFRUITFULL (RcFUL) were selected for in-depth functional characterization. The proteins encoded by these two genes are hydrophilic, lack signal peptides and transmembrane domains, and contain multiple phosphorylation sites. They feature typical MADS-box family domains and show close phylogenetic affinity to Rosa rugosa. Subcellular localization showed their nuclear presence. Heterologous overexpression of RcAG2 and RcFUL in Arabidopsis resulted in notable phenotypic alterations: RcAG2 caused petal reduction and stamen exposure, while RcFUL led to greenish, leaf-like petals with pigmentation gradients, increased sepal number, and failed seed set. Conclusion: These results suggest that RcAG2 and RcFUL play key roles in floral organ development through genetic regulation, providing a theoretical foundation for further research on floral development in R. chinensis. Full article