The evolution of the MADS-box gene family is essential for the rapid differentiation of floral organs and fruit types in angiosperms. Two key processes drive the evolution of gene families: gene duplication and functional differentiation. Duplicated copies provide the material for variation, while advantageous mutations can confer new functions on gene copies. In this study, we selected the Rosaceae family, which includes a variety of fruit types and flower organs, as well as species that existed before and after whole-genome duplication (WGD). The results indicate that different fruit types are associated with different copies of MADS-box gene family duplications and WGD events. While most gene copies derived from WGD have been lost, MADS-box genes not only retain copies derived from WGD but also undergo further gene duplication. The sequences, protein structures, and expression patterns of these gene copies have undergone significant differentiation. This work provides a clear example of MADS-box genes in the context of gene duplication and functional differentiation, offering new insights into the evolution of fruit types and floral organs.

Evolution of unisexual flowers involves extreme changes in floral development. Spinach is one of the species to discern the formation and evolution of dioecy. MADS-box gene family is involved in regulation of floral organ identity and development and in many other plant developmental processes. However, there is no systematic analysis of MADS-box family genes in spinach. A comprehensive genome-wide analysis and transcriptome profiling of MADS-box genes were undertaken to understand their involvement in unisexual flower development at different stages in spinach. In total, 54 MADS-box genes found to be unevenly located across 6 chromosomes and can be divided into type I and type II genes. Twenty type I MADS-box genes are subdivided into Mα, Mβ and Mγ subgroups. While thirty-four type II SoMADSs consist of 3 MIKC*, and 31 MIKCC -type genes including sixteen floral homeotic MADS-box genes that are orthologous to the proposed Arabidopsis ABCDE model of floral organ identity determination, were identified in spinach. Gene structure, motif distribution, physiochemical properties, gene duplication and collinearity analyses for these genes are performed in detail. Promoters of both types of SoMADS genes contain mainly MeJA and ABA response elements. Expression profiling indicated that MIKCc genes exhibited more dynamic and intricate expression patterns compared to M-type genes and the majority of type-II genes AP1, SVP, and SOC1 sub-groups showed female flower-biased expression profiles, suggesting their role in carpel development, while PI showed male-biased expression throughout flower developmental stages, suggesting their role in stamen development. These results provide genomic resources and insights into spinach dioecious flower development and expedite spinach improvement.

High temperature (HT) is an environmental factor that considerably affects plant physiology, development, crop yield, and economic value. HT can cause diseases and early bolting of leaf lettuce, thereby reducing the yield and quality of leaf lettuce. Herein, we used two leaf lettuce (Lactuca sativa L.) cultivars (bolting-resistant \'S24\' and bolting-sensitive \'S39\') to investigate the key factors and molecular mechanism impacting bolting. We found that 14 MADS-box genes implicated in bolting and flowering, LsMADS54 (also referred to as L. sativa FRUITFULL, LsFUL), was significantly up-regulated 1000 times after 5-d HT treatment and that HT-induced up-regulation of LsFUL was higher in bolting-sensitive than in resistant cultivars. The overexpression lines of LsFUL exhibited an earlier bolting time than that in the non-transformed \'S39\'(CK). However, the RNA interference, and CRISPR-Cas9-mediated knockout lines of LsFUL exhibited a later bolting time than that in CK. In addition, we found that L. sativa SUPPRESSORS OF MEC-8 AND UNC-52 PROTEIN 2 (LsSMU2) and L. sativa CONSTANS-LIKE PROTEIN 5 (LsCOL5) interact with LsFUL, and these interactions could stimulate or prevent bolting. We observed that elevated temperature stimulated the abundance of LsSMU2 in the stem, which collaborated with LsFUL to accelerate bolting. Conversely, room temperature (RT) condition led to relatively more stable LsCOL5, which worked with LsFUL to postpone bolting. In summary, our findings demonstrate a molecular regulatory module of LsSMU2-LsFUL associated with HT-induced premature bolting, which serves as a reference for understanding HT-induced premature bolting phenomenon in leaf lettuce.

The development of floral organs, crucial for the establishment of floral symmetry and morphology in higher plants, is regulated by MADS-box genes. In sunflower, the capitulum is comprised of ray and disc florets with various floral organs. In the sunflower long petal mutant (lpm), the abnormal disc (ray-like) floret possesses prolongated petals and degenerated stamens, resulting in a transformation from zygomorphic to actinomorphic symmetry. In this study, we investigated the effect of MADS-box genes on floral organs, particularly on petals, using WT and lpm plants as materials. Based on our RNA-seq data, 29 MADS-box candidate genes were identified, and their roles on floral organ development, especially in petals, were explored, by analyzing the expression levels in various tissues in WT and lpm plants through RNA-sequencing and qPCR. The results suggested that HaMADS3, HaMADS7, and HaMADS8 could regulate petal development in sunflower. High levels of HaMADS3 that relieved the inhibition of cell proliferation, together with low levels of HaMADS7 and HaMADS8, promoted petal prolongation and maintained the morphology of ray florets. In contrast, low levels of HaMADS3 and high levels of HaMADS7 and HaMADS8 repressed petal extension and maintained the morphology of disc florets. Their coordination may contribute to the differentiation of disc and ray florets in sunflower and maintain the balance between attracting pollinators and producing offspring. Meanwhile, Pearson correlation analysis between petal length and expression levels of MADS-box genes further indicated their involvement in petal prolongation. Additionally, the analysis of cis-acting elements indicated that these three MADS-box genes may regulate petal development and floral symmetry establishment by regulating the expression activity of HaCYC2c. Our findings can provide some new understanding of the molecular regulatory network of petal development and floral morphology formation, as well as the differentiation of disc and ray florets in sunflower.

BACKGROUND: The MADS-box gene family is widely distributed in the plant kingdom, and its members typically encoding transcription factors to regulate various aspects of plant growth and development. In particular, the MIKC-type MADS-box genes play a crucial role in the determination of floral organ development and identity recognition. As a type of androdioecy plant, Chionanthus retusus have unique gender differentiation. Manifested as male individuals with only male flowers and female individuals with only bisexual flowers. However, due to the lack of reference genome information, the characteristics of MIKC-type MADS-box genes in C. retusus and its role in gender differentiation of C. retusus remain largely unknown. Therefore, it is necessary to identify and characterize the MADS-box gene family within the genome of the C. retusus.
RESULTS: In this study, we performed a genome-wide identification and analysis of MIKC-type MADS-box genes in C. retusus (2n = 2x = 46), utilizing the latest reference genome, and studied its expression pattern in individuals of different genders. As a result, we identified a total of 61 MIKC-type MADS-box genes in C. retusus. 61 MIKC-type MADS-box genes can be divided into 12 subfamilies and distributed on 18 chromosomes. Genome collinearity analysis revealed their conservation in evolution, while gene structure, domains and motif analysis indicated their conservation in structure. Finally, based on their expression patterns in floral organs of different sexes, we have identified that CrMADS45 and CrMADS60 may potentially be involved in the gender differentiation of C. retusus.
CONCLUSIONS: Our studies have provided a general understanding of the conservation and characteristics of the MIKC-type MADS-box genes family in C. retusus. And it has been demonstrated that members of the AG subfamily, CrMADS45 and CrMADS60, may play important roles in the gender differentiation of C. retusus. This provides a reference for future breeding efforts to improve flower types in C. retusus and further investigate the role of MIKC-type MADS-box genes in gender differentiation.

The plant MADS-box transcription factor family is a major regulator of plant flower development and reproduction, and the AGAMOUS-LIKE11/SEEDSTICK (AGL11/STK) subfamily plays conserved functions in the seed development of flowering plants. Camellia japonica is a world-famous ornamental flower, and its seed kernels are rich in highly valuable fatty acids. Seed abortion has been found to be common in C. japonica, but little is known about how it is regulated during seed development. In this study, we performed a genome-wide analysis of the MADS-box gene the in C. japonica genome and identified 126 MADS-box genes. Through gene expression profiling in various tissue types, we revealed the C/D-class MADS-box genes were preferentially expressed in seed-related tissues. We identified the AGL11/STK-like gene, CjSTK, and showed that it contained a typical STK motif and exclusively expressed during seed development. We found a significant increase in the CjSTK expression level in aborted seeds compared with normally developing seeds. Furthermore, overexpression of CjSTK in Arabidopsis thaliana caused shorter pods and smaller seeds. Taken together, we concluded that the fine regulation of the CjSTK expression at different stages of seed development is critical for ovule formation and seed abortion in C. japonica. The present study provides evidence revealing the regulation of seed development in Camellia.

Grain weight, grain number per panicle, and the number of panicles are the three factors that determine rice (Oryza sativa L.) yield. Of these, grain weight, which not only directly determines rice yield but also influences appearance and quality, is often considered the most important for rice production. Here, we describe OsNF-YC1, a member of the NF-Y transcription factor family that regulates rice grain size. OsNF-YC1 knockout plants (osnf-yc1), obtained using CRISPR-Cas9 technology, showed reduced grain weight due to reduced width and thickness, with no change in grain length, leading to a slenderer grain shape. Downregulation of OsNF-YC1 using RNA interference resulted in similar grain phenotypes as osnf-yc1. OsNF-YC1 affects grain formation by regulating both cell proliferation and cell expansion. OsNF-YC1 localizes in both the nucleus and cytoplasm, has transcriptional activation activity at both the N-terminus and C-terminus, and is highly expressed in young panicles. OsNF-YC1 interacts with OsMADS1 both in vivo and in vitro. Further analysis showed that the histone-like structural CBFD-NFYB-HMF domain of OsNF-YC1 conserved in the OsNF-YC transcription factor family can directly interact with the MADS-box domain of OsMADS1 to enhance its transcriptional activation activity. This interaction positively regulates the expression of OsMADS55, the direct downstream target of OsMADS1. Therefore, this paper reveals a potential grain size regulation pathway controlled by an OsNF-YC1-OsMADS1-OsMADS55 module in rice.

Epigenetic modifications, such as histone alterations, play crucial roles in regulating the flowering process in Arabidopsis, a typical long-day model plant. Histone modifications are notably involved in the intricate regulation of FLC, a key inhibitor of flowering. Although sirtuin-like protein and NAD+-dependent deacetylases play an important role in regulating energy metabolism, plant stress responses, and hormonal signal transduction, the mechanisms underlying their developmental transitions remain unclear. Thus, this study aimed to reveal how Arabidopsis NAD + -dependent deacetylase AtSRT1 affects flowering by regulating the expression of flowering integrators. Genetic and molecular evidence demonstrated that AtSRT1 mediates histone deacetylation by directly binding near the transcriptional start sites (TSS) of the flowering integrator genes FT and SOC1 and negatively regulating their expression by modulating the expression of the downstream gene LFY to inhibit flowering. Additionally, AtSRT1 directly down-regulates the expression of TOR, a glucose-driven central hub of energy signaling, which controls cell metabolism and growth in response to nutritional and environmental factors. This down-regulation occurs through binding near the TSS of TOR, facilitating the addition of H3K27me3 marks on FLC via the TOR-FIE-PRC2 pathway, further repressing flowering. These results uncover a multi-pathway regulatory network involving deacetylase AtSRT1 during the flowering process, highlighting its interaction with TOR as a hub for the coordinated regulation of energy metabolism and flowering initiation. These findings significantly enhance understanding of the complexity of histone modifications in the regulation of flowering.

Flowering time and maturity are crucial agronomic traits that affect the regional adaptability of soybean plants. The development of soybean cultivars with early maturity adapted to longer days and colder climates of high latitudes is very important for ensuring normal ripening before frost begins. FUL belongs to the MADS-box transcription factor family and has several duplicated members in soybeans. In this study, we observed that overexpression of GmFULc in the Dongnong 50 cultivar promoted soybean maturity, while GmFULc knockout mutants exhibited late maturity. Chromatin immunoprecipitation sequencing (ChIP-seq) and RNA sequencing (RNA-seq) revealed that GmFULc could bind to the CArG, bHLH and homeobox motifs. Further investigation revealed that GmFULc could directly bind to the CArG motif in the promoters of the GmZTL3 and GmZTL4 genes. Overexpression of GmZTL4 promoted soybean maturity, whereas the ztl4 mutants exhibited delayed maturity. Moreover, we found that the cis element box 4 motif of the GmZTL4 promoter, a motif of light response elements, played an important role in controlling the growth period. Deletion of this motif shortened the growth period by increasing the expression levels of GmZTL4. Functional investigations revealed that short-day treatment promoted the binding of GmFULc to the promoter of GmZTL4 and inhibited the expression of E1 and E1Lb, ultimately resulting in the promotion of flowering and early maturation. Taken together, these findings suggest a novel photoperiod regulatory pathway in which GmFULc directly activates GmZTL4 to promote earlier maturity in soybean.

The mechanisms and timescales controlling de novo establishment of chromatin-mediated transcriptional silencing by Polycomb repressive complex 2 (PRC2) are unclear. Here, we investigate PRC2 silencing at Arabidopsis FLOWERING LOCUS C (FLC), known to involve co-transcriptional RNA processing, histone demethylation activity, and PRC2 function, but so far not mechanistically connected. We develop and test a computational model describing proximal polyadenylation/termination mediated by the RNA-binding protein FCA that induces H3K4me1 removal by the histone demethylase FLD. H3K4me1 removal feeds back to reduce RNA polymerase II (RNA Pol II) processivity and thus enhance early termination, thereby repressing productive transcription. The model predicts that this transcription-coupled repression controls the level of transcriptional antagonism to PRC2 action. Thus, the effectiveness of this repression dictates the timescale for establishment of PRC2/H3K27me3 silencing. We experimentally validate these mechanistic model predictions, revealing that co-transcriptional processing sets the level of productive transcription at the locus, which then determines the rate of the ON-to-OFF switch to PRC2 silencing.