Molecular Basis of Natural Variation in Photoperiodic Flowering Responses

Overexpression of two DELLA subfamily genes MiSLR1 and MiSLR2 from mango promotes early flowering and enhances abiotic stress tolerance in Arabidopsis

Gibberellic acids (GAs) are a group of endogenous phytohormones that play important roles in plant growth and development. SLENDER RICE (SLR) serves as a vital component of the DELLA gene family, which plays an irreplaceable role in regulating plant flowering and height, as well as stress responses. SLR gene has not been reported in mango, and its function is unknown. In present study, two DELLA subfamily genes MiSLR1 and MiSLR2 were identified from mango. MiSLR1 and MiSLR2 were highly expressed in the stems of the juvenile stage, but were expressed at a low level in flower buds and flowers. Gibberellin treatment could up-regulate the expression of MiSLR1 and MiSLR2 genes, but gibberellin biosynthesis inhibitor prohexadione-calcium (Pro-Ca) and paclobutrazol (PAC) treatments significantly down-regulated the expression of MiSLR1, while MiSLR2 was up-regulated. The expression levels of MiSLR1 and MiSLR2 were up-regulated under both salt and drought treatments. Overexpression of MiSLR1 and MiSLR2 genes significantly resulted early flowering in transgenic Arabidopsis and significantly up-regulated the expression levels of endogenous flower-related genes, such as SUPPRESSOR OF CONSTANS1 (SOC1), APETALA1 (AP1), and FRUITFULL (FUL). Interestingly, MiSLR1 significantly reduced the height of transgenic plants, while MiSLR2 gene increased. Overexpression of MiSLR1 and MiSLR2 increased seed germination rate, root length and survival rate of transgenic plants under salt and drought stress. Physiological and biochemical detection showed that the contents of proline (Pro) and superoxide dismutase (SOD) were significantly increased, while the contents of malondialdehyde (MDA) and H2O2 were significantly decreased. Additionally, protein interaction analysis revealed that MiSLR1 and MiSLR2 interacted with several flowering-related and GA-related proteins. The interaction between MiSLR with MiGF14 and MiSOC1 proteins was found for the first time. Taken together, the data showed that MiSLR1 and MiSLR2 in transgenic Arabidopsis both regulated the flowering time and plant height, while also acting as positive regulators of abiotic stress responses.

Advances in functional studies of plant MYC transcription factors

Myelocytomatosis (MYC) transcription factors (TFs) belong to the basic helix-loop-helix (bHLH) family in plants and play a central role in governing a wide range of physiological processes. These processes encompass plant growth, development, adaptation to biotic and abiotic stresses, as well as secondary metabolism. In recent decades, significant strides have been made in comprehending the multifaceted regulatory functions of MYCs. This advancement has been achieved through the cloning of MYCs and the characterization of plants with MYC deficiencies or overexpression, employing comprehensive genome-wide 'omics' and protein-protein interaction technologies. MYCs act as pivotal components in integrating signals from various phytohormones' transcriptional regulators to orchestrate genome-wide transcriptional reprogramming. In this review, we have compiled current research on the role of MYCs as molecular switches that modulate signal transduction pathways mediated by phytohormones and phytochromes. This comprehensive overview allows us to address lingering questions regarding the interplay of signals in response to environmental cues and developmental shift. It also sheds light on the potential implications for enhancing plant resistance to diverse biotic and abiotic stresses through genetic improvements achieved by plant breeding and synthetic biology efforts.

Multilayered regulation and implication of flowering time in plants

Initiation of flowering is a key switch for plants to shift from the vegetative growth to the phase of reproductive growth. This critical phase is essential not only for achieving successful reproduction, but also for facilitating environmental adaptation and maximizing yield potential. In the past decades, the environmental factors and genetic pathways that control flowering time have undergone extensive investigation in both model plant Arabidopsis and various crop species. The impact of environmental factors on plant flowering time is well documented. This paper focuses on the multilayered modulation of flowering time. Recent multi-omics approaches, and genetic screens have revealed additional components that modulate flowering time across various levels, encompassing chromatin modification, transcriptional and post-transcriptional control, as well as translational and post-translational regulation. The interplay between these various layers of regulation creates a finely-tuned system that can respond to a wide variety of inputs and allows plants to adjust flowering time in response to changing environmental conditions. In this review, we present a comprehensive overview of the recent progress made in understanding the intricate regulation of flowering time in plants, emphasizing the pivotal molecular components and their intricate interactions. Additionally, we provide an exhaustive list of key genes implicated in the intricate modulation of flowering time and offer a detailed summary of regulators of FLOWERING LOCUS T (FT) and FLOWERING LOCUS (FLC). We also discuss the implications of this knowledge for crop improvement and adaptation to changing environments.

Arabidopsis thaliana MYC2 and MYC3 Are Involved in Ethylene-Regulated Hypocotyl Growth as Negative Regulators

The ethylene-regulated hypocotyl elongation of Arabidopsis thaliana involves many transcription factors. The specific role of MYC transcription factors in ethylene signal transduction is not completely understood. The results here revealed that two MYCs, MYC2 and MYC3, act as negative regulators in ethylene-suppressed hypocotyl elongation. Etiolated seedlings of the loss-of-function mutant of MYC2 or MYC3 were significantly longer than wild-type seedlings. Single- or double-null mutants of MYC2 and MYC3 displayed remarkably enhanced response to ACC(1-aminocyclopropane-1-carboxylate), the ethylene precursor, compared to wild-type seedlings. MYC2 and MYC3 directly bind to the promoter zone of ERF1, strongly suppressing its expression. Additionally, EIN3, a key component in ethylene signaling, interacts with MYC2 or MYC3 and significantly suppresses their binding to ERF1's promoter. MYC2 and MYC3 play crucial roles in the ethylene-regulated expression of functional genes. The results revealed the novel role and functional mechanism of these transcription factors in ethylene signal transduction. The findings provide valuable information for deepening our understanding of their role in regulating plant growth and responding to stress.

Genetic and epigenetic basis of phytohormonal control of floral transition in plants

The timing of the developmental transition from the vegetative to the reproductive stage is critical for angiosperms, and is fine-tuned by the integration of endogenous factors and external environmental cues to ensure successful reproduction. Plants have evolved sophisticated mechanisms to response to diverse environmental or stress signals, and these can be mediated by hormones to coordinate flowering time. Phytohormones such as gibberellin, auxin, cytokinin, jasmonate, abscisic acid, ethylene, and brassinosteroids and the cross-talk among them are critical for the precise regulation of flowering time. Recent studies of the model flowering plant Arabidopsis have revealed that diverse transcription factors and epigenetic regulators play key roles in relation to the phytohormones that regulate floral transition. This review aims to summarize our current knowledge of the genetic and epigenetic mechanisms that underlie the phytohormonal control of floral transition in Arabidopsis, offering insights into how these processes are regulated and their implications for plant biology.

Inhibition of flowering by gibberellins in the woody plant Jatropha curcas is restored by overexpression of JcFT

Jatropha curcas (J. curcas) is a perennial oil-seed plant with vigorous vegetative growth but relatively poor reproductive growth and low seed yield. Gibberellins (GAs) promotes flowering in most annual plants but inhibits flowering in many woody plants, including J. curcas. However, the underlying mechanisms of GA inhibits flowering in perennial woody plants remain unclear. Here, we found that overexpression of the GA biosynthesis gene JcGA20ox1 inhibits flowering in J. curcas and in J. curcas × J. integerrima hybrids. Consistent with this finding, overexpression of the GA catabolic gene JcGA2ox6 promotes flowering in J. curcas. qRTPCR revealed that inhibits floral transition by overexpressing JcGA20ox1 resulted from a decrease in the expression of JcFT and other flowering-related genes, which was restored by overexpressing JcFT in J. curcas. Overexpression of JcGA20ox1 or JcGA2ox6 reduced seed yield, but overexpression of JcFT significantly increased seed yield. Furthermore, hybridization experiments showed that the reduction in seed yield caused by overexpression of JcGA20ox1 or JcGA2ox6 was partially restored by the overexpression of JcFT. In addition, JcGA20ox1, JcGA2ox6 and JcFT were also found to be involved in the regulation of seed oil content and endosperm development. In conclusion, our study revealed that the inhibitory effect of GA on flowering is mediated through JcFT and demonstrated the effects of JcGA20ox1, JcGA2ox6 and JcFT on agronomic traits in J. curcas. This study also indicates the potential value of GA metabolism genes and JcFT in the breeding of new varieties of woody oil-seed plants.

Gibberellins regulate masculinization through the SpGAI-SpSTM module in dioecious spinach

The sex of dioecious plants is mainly determined by genetic factors, but it can also be converted by environmental cues such as exogenous phytohormones. Gibberellic acids (GAs) are well-known inducers of flowering and sexual development, yet the pathway of gibberellin-induced sex conversion in dioecious spinach (Spinacia oleracea L.) remains elusive. Based on sex detection before and after GA3 application using T11A and SSR19 molecular markers, we confirmed and elevated the masculinization effect of GA on a single female plant through exogenous applications of GA3, showing complete conversion and functional stamens. Silencing of GIBBERELLIC ACID INSENSITIVE (SpGAI), a single DELLA family protein that is a central GA signaling repressor, results in similar masculinization. We also show that SpGAI can physically interact with the spinach KNOX transcription factor SHOOT MERISTEMLESS (SpSTM), which is a homolog of the flower meristem identity regulator STM in Arabidopsis. The silencing of SpSTM also masculinized female flowers in spinach. Furthermore, SpSTM could directly bind the intron of SpPI to repress SpPI expression in developing female flowers. Overall, our results suggest that GA induces a female masculinization process through the SpGAI-SpSTM-SpPI regulatory module in spinach. These insights may help to clarify the molecular mechanism underlying the sex conversion system in dioecious plants while also elucidating the physiological basis for the generation of unisexual flowers so as to establish dioecy in plants.

Flowering time: From physiology, through genetics to mechanism

Plant species have evolved different requirements for environmental/endogenous cues to induce flowering. Originally, these varying requirements were thought to reflect the action of different molecular mechanisms. Thinking changed when genetic and molecular analysis in Arabidopsis thaliana revealed that a network of environmental and endogenous signaling input pathways converge to regulate a common set of "floral pathway integrators." Variation in the predominance of the different input pathways within a network can generate the diversity of requirements observed in different species. Many genes identified by flowering time mutants were found to encode general developmental and gene regulators, with their targets having a specific flowering function. Studies of natural variation in flowering were more successful at identifying genes acting as nodes in the network central to adaptation and domestication. Attention has now turned to mechanistic dissection of flowering time gene function and how that has changed during adaptation. This will inform breeding strategies for climate-proof crops and help define which genes act as critical flowering nodes in many other species.

Genome-Wide Identification of MYC Transcription Factors and Their Potential Functions in the Growth and Development Regulation of Tree Peony (Paeonia suffruticosa)

Tree peony (Paeonia suffruticosa Andr.) is a traditional Chinese flower with significant ornamental and medicinal value. Its growth and development process is regulated by some internal and external factors, and the related regulatory mechanism is largely unknown. Myelocytomatosis transcription factors (MYCs) play significant roles in various processes such as plant growth and development, the phytohormone response, and the stress response. As the identification and understanding of the MYC family in tree peony remains limited, this study aimed to address this gap by identifying a total of 15 PsMYCs in tree peony and categorizing them into six subgroups based on bioinformatics methods. Furthermore, the gene structure, conservative domains, cis-elements, and expression patterns of the PsMYCs were thoroughly analyzed to provide a comprehensive overview of their characteristics. An analysis in terms of gene structure and conserved motif composition suggested that each subtribe had similarities in function. An analysis of the promoter sequence revealed the presence of numerous cis-elements associated with plant growth and development, the hormone response, and the stress response. qRT-PCR results and the protein interaction network further demonstrated the potential functions of PsMYCs in the growth and development process. While in comparison to the control, only PsMYC2 exhibited a statistically significant variation in expression levels in response to exogenous hormone treatments and abiotic stress. A promoter activity analysis of PsMYC2 revealed its sensitivity to Flu and high temperatures, but exhibited no discernible difference under exogenous GA treatment. These findings help establish a basis for comprehending the molecular mechanism by which PsMYCs regulate the growth and development of tree peony.

Jasmonate inhibits plant growth and reduces gibberellin levels via microRNA5998 and transcription factor MYC2

Jasmonate (JA) and gibberellins (GAs) exert antagonistic effects on plant growth and development in response to environmental and endogenous stimuli. Although the crosstalk between JA and GA has been elucidated, the role of JA in GA biosynthesis remains unclear. Therefore, in this study, we investigated the mechanism underlying JA-mediated regulation of endogenous GA levels in Arabidopsis (Arabidopsis thaliana). Transient and electrophoretic mobility shift assays showed that transcription factor MYC2 regulates GA inactivation genes. Using transgenic plants, we further evaluated the contribution of MYC2 in regulating GA inactivation genes. JA treatment increased DELLA accumulation but did not inhibit DELLA protein degradation. Additionally, JA treatment decreased bioactive GA content, including GA4, significantly decreased the expression of GA biosynthesis genes, including ent-kaurene synthase (AtKS), GA 3β-hydroxylase (AtGA3ox1), and AtGA3ox2, and increased the expression of GA inactivation genes, including GA 2 oxidase (AtGA2ox4), AtGA2ox7, and AtGA2ox9. Conversely, JA treatment did not significantly affect gene expression in the myc2 myc3 myc4 triple mutant, demonstrating the MYC2-4-dependent effects of JA in GA biosynthesis. Additionally, JA post-transcriptionally regulated AtGA3ox1 expression. We identified microRNA miR5998 as an AtGA3ox1-associated miRNA; its overexpression inhibited plant growth by suppressing AtGA3ox1 expression. Overall, our findings indicate that JA treatment inhibits endogenous GA levels and plant growth by decreasing the expression of GA biosynthesis genes and increasing the expression of GA inactivation genes via miR5998 and MYC2 activities.

Gibberellin signaling modulates flowering via the DELLA-BRAHMA-NF-YC module in Arabidopsis

Gibberellin (GA) plays a key role in floral induction by activating the expression of floral integrator genes in plants, but the epigenetic regulatory mechanisms underlying this process remain unclear. Here, we show that BRAHMA (BRM), a core subunit of the chromatin-remodeling SWItch/sucrose nonfermentable (SWI/SNF) complex that functions in various biological processes by regulating gene expression, is involved in GA-signaling-mediated flowering via the formation of the DELLA-BRM-NF-YC module in Arabidopsis (Arabidopsis thaliana). DELLA, BRM, and NF-YC transcription factors interact with one another, and DELLA proteins promote the physical interaction between BRM and NF-YC proteins. This impairs the binding of NF-YCs to SOC1, a major floral integrator gene, to inhibit flowering. On the other hand, DELLA proteins also facilitate the binding of BRM to SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1). The GA-induced degradation of DELLA proteins disturbs the DELLA-BRM-NF-YC module, prevents BRM from inhibiting NF-YCs, and decreases the DNA-binding ability of BRM, which promote the deposition of H3K4me3 on SOC1 chromatin, leading to early flowering. Collectively, our findings show that BRM is a key epigenetic partner of DELLA proteins during the floral transition. Moreover, they provide molecular insights into how GA signaling coordinates an epigenetic factor with a transcription factor to regulate the expression of a flowering gene and flowering in plants.

Ectopic expression of Camellia oleifera Abel. gibberellin 20-oxidase gene increased plant height and promoted secondary cell walls deposition in Arabidopsis

MAIN CONCLUSION

Ectopic expression of Camellia oleifera Abel. gibberellin 20-oxidase 1 caused a taller phenotype, promoted secondary cell wall deposition, leaf enlargement, and early flowering, and reduced chlorophyll and anthocyanin accumulation and seed enlargement phenotype in Arabidopsis. Plant height and secondary cell wall (SCW) deposition are important plant traits. Gibberellins (GAs) play important roles in regulating plant height and SCWs deposition. Gibberellin 20-oxidase (GA20ox) is an important enzyme involved in GA biosynthesis. In the present study, we identified a GA synthesis gene in Camellia oleifera. The total length of the CoGA20ox1 gene sequence was 1146 bp, encoding 381 amino acids. Transgenic plants with CoGA20ox1 had a taller phenotype; a seed enlargement phenotype; promoted SCWs deposition, leaf enlargement, and early flowering; and reduced chlorophyll and anthocyanin accumulation. Genetic analysis showed that the mutant ga20ox1-3 Arabidopsis partially rescued the phenotype of CoGA20ox1 overexpression plants. The results showed that CoGA20ox1 participates in the growth and development of C. oleifera. The morphological changes in CoGA20ox1 overexpressed plants provide a theoretical basis for further exploration of GA biosynthesis and analysis of the molecular mechanism in C. oleifera.

Photoperiodic flowering in Arabidopsis: Multilayered regulatory mechanisms of CONSTANS and the florigen FLOWERING LOCUS T

The timing of flowering affects the success of sexual reproduction. This developmental event also determines crop yield, biomass, and longevity. Therefore, this mechanism has been targeted for improvement along with crop domestication. The underlying mechanisms of flowering are highly conserved in angiosperms. Central to these mechanisms is how environmental and endogenous conditions control transcriptional regulation of the FLOWERING LOCUS T (FT) gene, which initiates floral development under long-day conditions in Arabidopsis. Since the identification of FT as florigen, efforts have been made to understand the regulatory mechanisms of FT expression. Although many transcriptional regulators have been shown to directly influence FT, the question of how they coordinately control the spatiotemporal expression patterns of FT still requires further investigation. Among FT regulators, CONSTANS (CO) is the primary one whose protein stability is tightly controlled by phosphorylation and ubiquitination/proteasome-mediated mechanisms. In addition, various CO interaction partners, some of them previously identified as FT transcriptional regulators, positively or negatively modulate CO protein activity. The FT promoter possesses several transcriptional regulatory "blocks," highly conserved regions among Brassicaceae plants. Different transcription factors bind to specific blocks and affect FT expression, often causing topological changes in FT chromatin structure, such as the formation of DNA loops. We discuss the current understanding of the regulation of FT expression mainly in Arabidopsis and propose future directions related to this topic.

Arabidopsis AGAMOUS-LIKE16 and SUPPRESSOR OF CONSTANS1 regulate the genome-wide expression and flowering time

Flowering transition is tightly coordinated by complex gene regulatory networks, in which AGAMOUS-LIKE 16 (AGL16) plays important roles. Here, we identified the molecular function and binding properties of AGL16 and demonstrated its partial dependency on the SUPPRESSOR OF CONSTANS 1 (SOC1) function in regulating flowering. AGL16 bound to promoters of more than 2,000 genes via CArG-box motifs with high similarity to that of SOC1 in Arabidopsis (Arabidopsis thaliana). Approximately 70 flowering genes involved in multiple pathways were potential targets of AGL16. AGL16 formed a protein complex with SOC1 and shared a common set of targets. Intriguingly, only a limited number of genes were differentially expressed in the agl16-1 loss-of-function mutant. However, in the soc1-2 knockout background, AGL16 repressed and activated the expression of 375 and 182 genes, respectively, with more than a quarter bound by AGL16. Corroborating these findings, AGL16 repressed the flowering time more strongly in soc1-2 than in the Col-0 background. These data identify a partial inter-dependency between AGL16 and SOC1 in regulating genome-wide gene expression and flowering time, while AGL16 provides a feedback regulation on SOC1 expression. Our study sheds light on the complex background dependency of AGL16 in flowering regulation, thus providing additional insights into the molecular coordination of development and environmental adaptation.

Indoor Vegetable Production: An Alternative Approach to Increasing Cultivation

As the world's population is increasing exponentially, human diets have changed to less healthy foods resulting in detrimental health complications. Increasing vegetable intake by both rural and urban dwellers can help address this issue. However, these communities often face the challenge of limited vegetable supply and accessibility. More so, open field vegetable production cannot supply all the vegetable needs because biotic and abiotic stress factors often hinder production. Alternative approaches such as vegetable production in greenhouses, indoor farms, high tunnels, and screenhouses can help fill the gap in the supply chain. These alternative production methods provide opportunities to use less resources such as land space, pesticide, and water. They also make possible the control of production factors such as temperature, relative humidity, and carbon dioxide, as well as extension of the growing season. Some of these production systems also make the supply and distribution of nutrients to crops easier and more uniform to enhance crop growth and yield. This paper reviews these alternative vegetable production approaches which include hydroponics, aeroponics, aquaponics and soilless mixes to reveal the need for exploring them further to increase crop production. The paper also discusses facilities used, plant growth factors, current challenges including energy costs and prospects.

Transcriptome analysis reveals the roles of phytohormone signaling in tea plant (Camellia sinensis L.) flower development

BACKGROUND

Tea plant (Camellia sinensis (L.) O. Kuntze) is an important economic tea crop, but flowering will consume a lot of nutrients of C. sinensis, which will seriously affect the nutritional growth of C. sinensis. However, there are few studies on the development mechanism of C. sinensis flower, and most studies focus on a single C. sinensis cultivar.

RESULTS

Here, we identified a 92-genes' C. sinensis flower development core transcriptome from the transcriptome of three C. sinensis cultivars ('BaiYe1', 'HuangJinYa' and 'SuChaZao') in three developmental stages (bud stage, white bud stage and blooming stage). In addition, we also reveal the changes in endogenous hormone contents and the expression of genes related to synthesis and signal transduction during the development of C. sinensis flower. The results showed that most genes of the core transcriptome were involved in circadian rhythm and autonomous pathways. Moreover, there were only a few flowering time integrators, only 1 HD3A, 1 SOC1 and 1 LFY, and SOC1 played a dominant role in the development of C. sinensis flower. Furthermore, we screened out 217 differentially expressed genes related to plant hormone synthesis and 199 differentially expressed genes related to plant hormone signal transduction in C. sinensis flower development stage.

CONCLUSIONS

By constructing a complex hormone regulation network of C. sinensis flowering, we speculate that MYC, FT, SOC1 and LFY play key roles in the process of endogenous hormones regulating C. sinensis flowering development. The results of this study can a provide reference for the further study of C. sinensis flowering mechanism.

JAZ1-3 and MYC2-1 Synergistically Regulate the Transformation from Completely Mixed Flower Buds to Female Flower Buds in Castanea mollisima

Chestnut (Castanea mollisima) is an important woody food crop, but its yield has been low in cultivation, mainly due to the problems of fewer female flowers and more male flowers. Therefore, regulating the transition of chestnut flowers and effectively balancing the proportion of male and female to improve the yield are key factor to be solved in production. In this study, the chestnut floral buds in pre- and post-winter were used as materials. The data of metabolites, hormones, and gene expression during flower bud differentiation of chestnut were analyzed by transcriptomics and metabolomics to preliminarily reveal the possible reason of male and female flower bud transformation in pre- and post-winter. The analysis of Differentially Expressed Genes (DEGs) showed that there were 6323 DEGs in the Complete mixed flower bud (CMF) group in pre- and post-winter, of which 3448 genes were up-regulated and 2875 genes were down-regulated. There were 8037 DEGs in the Incomplete mixed flower bud (IMF) in pre- and post-winter, of which 4546 genes were up-regulated and 3491 genes were down-regulated. A total of 726 genes from the two flower buds were enriched into 251 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways in post winter, of which plant hormone signal transduction accounted for 4.13%. The analysis results of differential metabolites showed that the differential metabolites of the two flower buds were mainly concentrated in the secondary metabolic synthesis pathway. The difference of hormone content showed that the content of Gibberellin 9 (GA9) and GA19 in CMF was higher than that in IMF in pre-winter, but the opposite in post-winter. Methyl jasmonate (MeJA) content was only very high in CMF in pre-winter, while Jasmonoyl-(l)-Isoleucine (JA-ILE) showed high content in CMF in post-winter. In post-winter, higher concentration of JA-ILE was positively correlated with the expression of Flowering Locus T (CmFT), and CmFT gene was significantly positively correlated with the expression levels of MYC2-1, MYC2-2 and LFY 3 (LEAFY 3). The higher concentration of JA-ILE was negatively correlated with the transcription level of JAZ1-3. In vitro experiments further verified that Jasmonate-Zim 1–3 (JAZ 1–3) combined with MYC2-1 inhibited the transcription of CmFT gene, while MYC2-1 alone promoted the expression of FT. The results suggested that a higher concentration of GA is conducive to breaking the dormancy of flower buds and promoting the development of male flower buds, while a lower concentration of GA and a higher concentration of JA-ILE are conducive to the differentiation and formation of female flower buds in post-winter, in which JAZ1-3 and MYC2-1 play a key role in the differentiation of female flower buds of chestnut.

CONSTANS Polymorphism Modulates Flowering Time and Maturity in Soybean

CONSTANS (CO) plays a critical role in the photoperiodic flowering pathway. However, the function of soybean CO orthologs and the molecular mechanisms in regulating flowering remain largely unknown. This study characterized the natural variations in CO family genes and their association with flowering time and maturity in soybeans. A total of 21 soybean CO family genes (GmCOLs) were cloned and sequenced in 128 varieties covering 14 known maturity groups (MG 0000-MG X from earliest to latest maturity). Regarding the whole genomic region involving these genes, GmCOL1, GmCOL3, GmCOL8, GmCOL9, GmCOL10, and GmCOL13 were conserved, and the remaining 15 genes showed genetic variation that was brought about by mutation, namely, all single-nucleotide polymorphisms (SNPs) and insertions-deletions (InDels). In addition, a few genes showed some strong linkage disequilibrium. Point mutations were found in 15 GmCOL genes, which can lead to changes in the potential protein structure. Early flowering and maturation were related to eight genes (GmCOL1/3/4/8/13/15/16/19). For flowering and maturation, 11 genes (GmCOL2/5/6/14/20/22/23/24/25/26/28) expressed divergent physiognomy. Haplotype analysis indicated that the haplotypes of GmCOL5-Hap2, GmCOL13-Hap2/3, and GmCOL28-Hap2 were associated with flowering dates and soybean maturity. This study helps address the role of GmCOL family genes in adapting to diverse environments, particularly when it is necessary to regulate soybean flowering dates and maturity.

LsRGL1 controls the bolting and flowering times of lettuce by modulating the gibberellin pathway

Bolting, which is a serious problem during lettuce (Lactuca sativa L.) production, is responsible for substantial annual yield and quality losses. Gibberellin plays a critical role in the regulation of lettuce bolting. Additionally, DELLA proteins negatively regulate the gibberellin signaling pathway. However, it is unclear if DELLA proteins are involved in the regulation of lettuce bolting. Therefore, in this study, we identified four DELLA-encoding genes in lettuce, including LsRGL1, which was highly expressed in the stem and negatively correlated with bolting. Knocking down this gene in lettuce promoted bolting, whereas its overexpression inhibited bolting and the biosynthesis of gibberellin and auxin. A transcriptome analysis revealed that genes involved in gibberellin and auxin biosynthesis and flowering were affected in the LsRGL1-overexpressing lines. The yeast two-hybrid and yeast one-hybrid assay results indicated that LsRGL1 can interact with LsGA3ox and the LsYUC4 promoter region. Considered together, the results of this study suggest LsRGL1 negatively regulates lettuce bolting. Furthermore, its function may depend on modifications to gibberellin and auxin levels mediated at the transcript and protein levels.

Photoperiod Control of Plant Growth: Flowering Time Genes Beyond Flowering

Fluctuations in environmental conditions greatly influence life on earth. Plants, as sessile organisms, have developed molecular mechanisms to adapt their development to changes in daylength, or photoperiod. One of the first plant features that comes to mind as affected by the duration of the day is flowering time; we all bring up a clear image of spring blossom. However, for many plants flowering happens at other times of the year, and many other developmental aspects are also affected by changes in daylength, which range from hypocotyl elongation in Arabidopsis thaliana to tuberization in potato or autumn growth cessation in trees. Strikingly, many of the processes affected by photoperiod employ similar gene networks to respond to changes in the length of light/dark cycles. In this review, we have focused on developmental processes affected by photoperiod that share similar genes and gene regulatory networks.

The emerging role of jasmonate in the control of flowering time

Plants dynamically synchronize their flowering time with changes in the internal and external environments through a variety of signaling pathways to maximize fitness. In the last two decades, the major pathways associated with flowering, including the photoperiod, vernalization, age, autonomous, gibberellin, and ambient temperature pathways, have been extensively analyzed. In recent years, an increasing number of signals, such as sugar, thermosensory, stress, and certain hormones, have been shown to be involved in fine-tuning flowering time. Among these signals, the jasmonate signaling pathway has a function in the determination of flowering time that has not been systematically summarized. In this review, we present an overview of current knowledge of jasmonate control of flowering and discuss jasmonate crosstalk with other signals (such as gibberellin, defense, and touch) during floral transition.

Efficiency of graft-transmitted JcFT for floral induction in woody perennial species of the Jatropha genus depends on transport distance

FLOWERING LOCUS T (FT) promotes flowering by integrating six genetic pathways. In Arabidopsis, the FT protein is transported from leaves to shoot apices and induces flowering. However, contradictory conclusions about floral induction via graft-transmitted FT in trees were reported in previous studies. We obtained extremely early-flowering transgenic woody Jatropha curcas L. by overexpression of J. curcas FT using Arabidopsis thaliana SUCROSE TRANSPORTER 2 (SUC2) promoter (SUC2:JcFT) and non-flowering transgenic J. curcas by RNA interference (RNAi), which were used to investigate the function of graft-transmitted JcFT in floral induction in woody perennials. Scions from five wild-type species of the Jatropha genus and from JcFT-RNAi transgenic J. curcas were grafted onto SUC2:JcFT rootstocks. Most grafted plants produced flowers in 1-2 months, and the flowering percentage and frequency of various grafted plants decreased with increasing scion length. Consistently, FT protein abundance in scions also decreased with increasing distance from graft junctions to the buds. These findings suggest that FT proteins can be transmitted by grafting and can induce the floral transition in woody perennials, and the efficiency of graft-transmitted JcFT for floral induction depends on the scion length, which may help explain previous seemingly contradictory observations regarding floral induction via graft-transmitted FT in trees.

RID1 sets rice heading date by balancing its binding with SLR1 and SDG722

Rice (Oryza sativa) is a major crop that feeds billions of people, and its yield is strongly influenced by flowering time (heading date). Loss of RICE INDETERMINATE1 (RID1) function causes plants not to flower; thus, RID1 is considered a master switch among flowering-related genes. However, it remains unclear whether other proteins function together with RID1 to regulate rice floral transition. Here, we revealed that the chromatin accessibility and H3K9ac, H3K4me3, and H3K36me3 levels at Heading date 3a (Hd3a) and RICE FLOWERING LOCUS T1 (RFT1) loci were significantly reduced in rid1 mutants. Notably, RID1 interacted with SET DOMAIN GROUP PROTEIN 722 (SDG722), a methyltransferase. We determined that SDG722 affects the global level of H3K4me2/3 and H3K36me2/3, and promotes flowering primarily through the Early heading date1-Hd3a/RFT1 pathway. We further established that rice DELLA protein SLENDER RICE1 (SLR1) interacted with RID1 to inhibit its transactivation activity, that SLR1 suppresses rice flowering, and that messenger RNA and protein levels of SLR1 gradually decrease with plant growth. Furthermore, SLR1 competed with SDG722 for interaction with RID1. Overall, our results establish that interplay between RID1, SLR1, and SDG722 feeds into rice flowering-time control.

Genome-wide identification and expression analysis of the MYC transcription factor family and its response to sulfur stress in cabbage (Brassica oleracea L.)

MYC transcriptional factors are members of the bHLH (basic helix-loop-helix) superfamily, and play important roles in plant growth, biological and abiotic stress. Recent studies have revealed that some MYCs are involved in the synthesis of sulfur-containing secondary metabolites. Cabbage, as a typical sulfur-loving crop and rich in sulfur-containing secondary metabolites, the regulatory relationship between sulfur stress and MYC gene family, related reports are relatively rare. In this study, we conducted the first genome-wide analysis of the MYC transcription factor family of cabbage and identified 17 BoMYC genes. Homology of the 17 BoMYC genes, 12 Arabidopsis, 12 Chinese cabbage, 8 wheat and 21 maize MYC were analyzed using the phylogenetic analysis. Meanwhile, chromosome locations, physical and chemical characteristics, gene structures, conserved motif, cis-element, specific expression in different tissues were studied. Finally, we analyzed the expression of the BoMYC gene under sulfur stress and its GO annotation and KEGG enrichment analysis, determined the expression of the BoMYC gene under hormone treatment and the growth index, photosynthetic capacity and hormone content in the leaves. This study is of great significance for functional identification and revealed the effect of S on BoMYC transcription factors.

Regulation of Flowering Time: When and Where?

In seasonal flowering, plants need to monitor environmental variables. A combination of photoreceptors and the circadian clock initiate signals that regulate a network of genes in the leaf vascular system which communicates through mobile FLOWERING LOCUS T (FT) proteins, with the shoot apical meristem (SAM). At the SAM, a second network of genes is turned on specifically in certain cell domains, established by a second mobile protein, TERMINAL FLOWER 1 (TFL1), to ensure that flowering signals are translated into floral meristems at the flanks of the SAM but without compromising the nature of the SAM itself. Here, we provide an update on recent findings about the integration of light signals upstream of FT and tissue-specific events that occur in the SAM to balance flower production with SAM endurance.

Gibberellin Induced Transcriptome Profiles Reveal Gene Regulation of Loquat Flowering

Flowering is an integral part of the life cycle of flowering plants, which is essential for plant survival and crop production. Most woody fruit trees such as apples and pears bloom in spring, but loquat blooms in autumn and winter. Gibberellin (GA) plays a key role in the regulation of plant flower formation. In this study, we sprayed loquat plants with exogenous GA₃, which resulted in vigorous vegetative growth rather than floral bud formation. We then performed a comprehensive RNA-seq analysis on GA₃-treated and control-treated leaves and buds over three time periods to observe the effects of exogenous GA₃ application on floral initiation and development. The results showed that 111 differentially expressed genes (DEGs) and 563 DEGs were down-regulated, and 151 DEGs and 506 DEGs were up-regulated in buds and leaves, respectively, upon treatment with GA₃. Among those that are homologs of the DELLA-mediated GA signal pathway genes, some may be involved in the positive regulation of flower development, including EjWRKY75, EjFT, EjSOC1, EjAGL24, EjSPL, EjLFY, EjFUL, and EjAP1; while some may be involved in the negative regulation of flower development, including EjDELLA, EjMYC3, EjWRKY12, and EjWRKY13. Finally, by analyzing the co-expression of DEGs and key floral genes EjSOC1s, EjLFYs, EjFULs, EjAP1s, 330 candidate genes that may be involved in the regulation of loquat flowering were screened. These genes belong to 74 gene families, including Cyclin_C, Histone, Kinesin, Lipase_GDSL, MYB, P450, Pkinase, Tubulin, and ZF-HD_dimer gene families. These findings provide new insights into the regulation mechanism of loquat flowering.

Beyond the Genetic Pathways, Flowering Regulation Complexity in Arabidopsis thaliana

Flowering is one of the most critical developmental transitions in plants’ life. The irreversible change from the vegetative to the reproductive stage is strictly controlled to ensure the progeny’s success. In Arabidopsis thaliana, seven flowering genetic pathways have been described under specific growth conditions. However, the evidence condensed here suggest that these pathways are tightly interconnected in a complex multilevel regulatory network. In this review, we pursue an integrative approach emphasizing the molecular interactions among the flowering regulatory network components. We also consider that the same regulatory network prevents or induces flowering phase change in response to internal cues modulated by environmental signals. In this sense, we describe how during the vegetative phase of development it is essential to prevent the expression of flowering promoting genes until they are required. Then, we mention flowering regulation under suboptimal growing temperatures, such as those in autumn and winter. We next expose the requirement of endogenous signals in flowering, and finally, the acceleration of this transition by long-day photoperiod and temperature rise signals allowing A. thaliana to bloom in spring and summer seasons. With this approach, we aim to provide an initial systemic view to help the reader integrate this complex developmental process.

Molecular regulation of plant developmental transitions and plant architecture via PEPB family proteins: an update on mechanism of action

This year marks the 100th anniversary of the experiments by Garner and Allard that showed that plants measure the duration of the night and day (the photoperiod) to time flowering. This discovery led to the identification of Flowering Locus T (FT) in Arabidopsis and Heading Date 3a (Hd3a) in rice as a mobile signal that promotes flowering in tissues distal to the site of cue perception. FT/Hd3a belong to the family of phosphatidylethanolamine-binding proteins (PEBPs). Collectively, these proteins control plant developmental transitions and plant architecture. Several excellent recent reviews have focused on the roles of PEBPs in diverse plant species; here we will primarily highlight recent advances that enhance our understanding of the mechanism of action of PEBPs and discuss critical open questions.

Isoprenoid-Derived Metabolites and Sugars in the Regulation of Flowering Time: Does Day Length Matter?

In plants, a diverse set of pathways regulate the transition to flowering, leading to remarkable developmental flexibility. Although the importance of photoperiod in the regulation of flowering time is well known, increasing evidence suggests the existence of crosstalk among the flowering pathways regulated by photoperiod and metabolic pathways. For example, isoprenoid-derived phytohormones (abscisic acid, gibberellins, brassinosteroids, and cytokinins) play important roles in regulating flowering time. Moreover, emerging evidence reveals that other metabolites, such as chlorophylls and carotenoids, as well as sugar metabolism and sugar accumulation, also affect flowering time. In this review, we summarize recent findings on the roles of isoprenoid-derived metabolites and sugars in the regulation of flowering time and how day length affects these factors.

Improved Plant Nitrate Status Involves in Flowering Induction by Extended Photoperiod

The floral transition stage is pivotal for sustaining plant populations and is affected by several environmental factors, including photoperiod. However, the mechanisms underlying photoperiodic flowering responses are not fully understood. Herein, we have shown that exposure to an extended photoperiod effectively induced early flowering in Arabidopsis plants, at a range of different nitrate concentrations. However, these photoperiodic flowering responses were attenuated when the nitrate levels were suboptimal for flowering. An extended photoperiod also improved the root nitrate uptake of by NITRATE TRANSPORTER 1.1 (NRT1.1) and NITRATE TRANSPORTER 2.1 (NRT2.1), whereas the loss of function of NRT1.1/NRT2.1 in the nrt1.1-1/2.1-2 mutants suppressed the expression of the key flowering genes CONSTANS (CO) and FLOWERING LOCUS T (FT), and reduced the sensitivity of the photoperiodic flowering responses to elevated levels of nitrate. These results suggest that the upregulation of root nitrate uptake during extended photoperiods, contributed to the observed early flowering. The results also showed that the sensitivity of photoperiodic flowering responses to elevated levels of nitrate, were also reduced by either the replacement of nitrate with its assimilation intermediate product, ammonium, or by the dysfunction of the nitrate assimilation pathway. This indicates that nitrate serves as both a nutrient source for plant growth and as a signaling molecule for floral induction during extended photoperiods.

Photoperiodic Signaling and Senescence, an Ancient Solution to a Modern Problem?

The length of the day (photoperiod) is a robust seasonal signal originated by earth orbital and translational movements, a resilient external cue to the global climate change, and a predictable hint to initiate or complete different developmental programs. In eukaryotic algae, the gene expression network that controls the cellular response to photoperiod also regulates other basic physiological functions such as starch synthesis or redox homeostasis. Land plants, evolving in a novel and demanding environment, imbued these external signals within the regulatory networks controlling organogenesis and developmental programs. Unlike algae that largely have to deal with cellular physical cues, within the course of evolution land plants had to transfer this external information from the receiving organs to the target tissues, and mobile signals such as hormones were recruited and incorporated in the regulomes. Control of senescence by photoperiod, as suggested in this perspective, would be an accurate way to feed seasonal information into a newly developed function (senescence) using an ancient route (photoperiodic signaling). This way, the plant would assure that two coordinated aspects of development such as flowering and organ senescence were sequentially controlled. As in the case of senescence, there is growing evidence to support the idea that harnessing the reliability of photoperiod regulation over other, more labile signaling pathways could be used as a robust breeding tool to enhance plants against the harmful effects of climate change.

The Crosstalk between MicroRNAs and Gibberellin Signaling in Plants

Gibberellin (GA) is an integral phytohormone that plays prominent roles in controlling seed germination, stem elongation, leaf development and floral induction. It has been shown that GA regulates these diverse biological processes mainly through overcoming the suppressive effects of the DELLA proteins, a family of nuclear repressors of GA response. MicroRNAs (miRNAs), which have been identified as master regulators of gene expression in eukaryotes, are also involved in a wide range of plant developmental events through the repression of their target genes. The pathways of GA biosynthesis and signaling, as well as the pathways of miRNA biogenesis and regulation, have been profoundly delineated in the past several decades. Growing evidence has shown that miRNAs and GAs are coordinated in regulating plant development, as several components in GA pathways are targeted by miRNAs, and GAs also regulate the expression of miRNAs or their target genes vice versa. Here, we review the recent advances in our understanding of the molecular connections between miRNAs and GA, with an emphasis on the two miRNAs, miR156 and miR159.

Genome-wide study of pineapple (Ananas comosus L.) bHLH transcription factors indicates that cryptochrome-interacting bHLH2 (AcCIB2) participates in flowering time regulation and abiotic stress response

BACKGROUND

Transcription factors (TFs) are essential regulators of growth and development in eukaryotes. Basic-helix-loop-helix (bHLHs) is one of the most significant TFs families involved in several critical regulatory functions. Cryptochrome-interacting bHLH (CIB) and cryptochromes form an extensive regulatory network to mediate a plethora of pathways. Although bHLHs regulate critical biological processes in plants, the information about pineapple bHLHs remains unexplored.

RESULTS

Here, we identified a total of 121 bHLH proteins in the pineapple genome. The identified genes were renamed based on the ascending order of their gene ID and classified into 18 subgroups by phylogenetic analysis. We found that bHLH genes are expressed in different organs and stages of pineapple development. Furthermore, by the ectopic expression of AcCIB2 in Arabidopsis and complementation of Atcib2 mutant, we verified the involvement of AcCIB2 in photomorphogenesis and abiotic stress response.

CONCLUSIONS

Our findings revealed that AcCIB2 plays an essential role in flowering time regulation and abiotic stress response. The present study provides additional insights into the current knowledge of bHLH genes and suggests their potential role in various biological processes during pineapple development.

Florigen trafficking integrates photoperiod and temperature signals in Arabidopsis

The transition to flowering is the most dramatic phase change in flowering plants and is crucial for reproductive success. A complex regulatory network in plants has evolved to perceive and integrate the endogenous and environmental signals. These signals perceived, including day length and temperature, converge to regulate FLOWERING LOCUS T (FT), which encodes a mobile stimulus required for floral induction in Arabidopsis. Despite the discovery of modulation of FT messenger RNA (mRNA) expression by ambient temperature, whether the trafficking of FT protein is controlled in response to changes in growth temperature is so far unknown. Here, we show that FT transport from companion cells to sieve elements is controlled in a temperature-dependent manner. This process is mediated by multiple C2 domain and transmembrane region proteins (MCTPs) and a soluble N-ethylmaleimide-sensitive factor protein attachment protein receptor (SNARE). Our findings suggest that ambient temperatures regulate both FT mRNA expression and FT protein trafficking to prevent precocious flowering at low temperatures and ensure plant reproductive success under favorable environmental conditions.

Genetic and molecular basis of floral induction in Arabidopsis thaliana

Many plants synchronize their life cycles in response to changing seasons and initiate flowering under favourable environmental conditions to ensure reproductive success. To confer a robust seasonal response, plants use diverse genetic programmes that integrate environmental and endogenous cues and converge on central floral regulatory hubs. Technological advances have allowed us to understand these complex processes more completely. Here, we review recent progress in our understanding of genetic and molecular mechanisms that control flowering in Arabidopsis thaliana.

Integrated multi-omics framework of the plant response to jasmonic acid

Understanding the systems-level actions of transcriptional responses to hormones provides insight into how the genome is reprogrammed in response to environmental stimuli. Here, we investigated the signalling pathway of the hormone jasmonic acid (JA), which controls a plethora of critically important processes in plants and is orchestrated by the transcription factor MYC2 and its closest relatives in Arabidopsis thaliana. We generated an integrated framework of the response to JA, which spans from the activity of master and secondary regulatory transcription factors, through gene expression outputs and alternative splicing, to protein abundance changes, protein phosphorylation and chromatin remodelling. We integrated time-series transcriptome analysis with (phospho)proteomic data to reconstruct gene regulatory network models. These enabled us to predict previously unknown points of crosstalk of JA to other signalling pathways and to identify new components of the JA regulatory mechanism, which we validated through targeted mutant analysis. These results provide a comprehensive understanding of how a plant hormone remodels cellular functions and plant behaviour, the general principles of which provide a framework for analyses of cross-regulation between other hormone and stress signalling pathways.

Evolutionary processes from the perspective of flowering time diversity

Although it is well appreciated that genetic studies of flowering time regulation have led to fundamental advances in the fields of molecular and developmental biology, the ways in which genetic studies of flowering time diversity have enriched the field of evolutionary biology have received less attention despite often being equally profound. Because flowering time is a complex, environmentally responsive trait that has critical impacts on plant fitness, crop yield, and reproductive isolation, research into the genetic architecture and molecular basis of its evolution continues to yield novel insights into our understanding of domestication, adaptation, and speciation. For instance, recent studies of flowering time variation have reconstructed how, when, and where polygenic evolution of phenotypic plasticity proceeded from standing variation and de novo mutations; shown how antagonistic pleiotropy and temporally varying selection maintain polymorphisms in natural populations; and provided important case studies of how assortative mating can evolve and facilitate speciation with gene flow. In addition, functional studies have built detailed regulatory networks for this trait in diverse taxa, leading to new knowledge about how and why developmental pathways are rewired and elaborated through evolutionary time.

Genome-wide association study reveals new genes involved in leaf trichome formation in polyploid oilseed rape (Brassica napus L.)

Leaf trichomes protect against various biotic and abiotic stresses in plants. However, there is little knowledge about this trait in oilseed rape (Brassica napus). Here, we demonstrated that hairy leaves were less attractive to Plutella xylostella larvae than glabrous leaves. We established a core germplasm collection with 290 accessions for a genome-wide association study (GWAS) of the leaf trichome trait in oilseed rape. We compared the transcriptomes of the shoot apical meristem (SAM) between hairy- and glabrous-leaf genotypes to narrow down the candidate genes identified by GWAS. The single nucleotide polymorphisms and the different transcript levels of BnaA.GL1.a, BnaC.SWEET4.a, BnaC.WAT1.a and BnaC.WAT1.b corresponded to the divergence of the hairy- and glabrous-leaf phenotypes, indicating the role of sugar and/or auxin signalling in leaf trichome initiation. The hairy-leaf SAMs had lower glucose and sucrose contents but higher expression of putative auxin responsive factors than the glabrous-leaf SAMs. Spraying of exogenous auxin (8 μm) increased leaf trichome number in certain genotypes, whereas spraying of sucrose (1%) plus glucose (6%) slightly repressed leaf trichome initiation. These data contribute to the existing knowledge about the genetic control of leaf trichomes and would assist breeding towards the desired leaf surface type in oilseed rape.

New insights into gibberellin signaling in regulating flowering in Arabidopsis

In angiosperms, floral transition is a key developmental transition from the vegetative to reproductive growth, and requires precise regulation to maximize the reproductive success. A complex regulatory network governs this transition through integrating flowering pathways in response to multiple exogenous and endogenous cues. Phytohormones are essential for proper plant developmental regulation and have been extensively studied for their involvement in the floral transition. Among various phytohormones, gibberellin (GA) plays a major role in affecting flowering in the model plant Arabidopsis thaliana. The GA pathway interact with other flowering genetic pathways and phytohormone signaling pathways through either DELLA proteins or mediating GA homeostasis. In this review, we summarize the recent advances in understanding the mechanisms of DELLA-mediated GA pathway in flowering time control in Arabidopsis, and discuss its possible link with other phytohormone pathways during the floral transition.