The CONSTANS gene of Arabidopsis promotes flowering and encodes a protein showing similarities to zinc finger transcription factors

TANDEM ZINC-FINGER/PLUS3 integrates light signaling and flowering regulatory pathways at the chromatin level

Environmental and endogenous stimuli determine plant developmental transitions including flowering through multiple signaling cascades. Although the key activators and repressors of flowering initiation are defined, the components and mechanisms integrating light signaling and flowering pathways are not fully established. This study investigates the role of TANDEM ZINC-FINGER/PLUS3 (TZP), a light-integrating transcriptional regulator, to elucidate how light cues influence the epigenetic regulation of flowering in Arabidopsis thaliana. To dissect the molecular function of TZP, this study employed a combination of genetics, RNA sequencing, chromatin immunoprecipitation sequencing and phenotypic assays. These approaches were used to determine TZP's genomic binding sites, its downstream gene targets and its influence on flowering time and chromatin modifications. TANDEM ZINC-FINGER/PLUS3 was found to directly associate with the promoter regions of chromatin-modifying genes, including FLOWERING LOCUS D (a histone H3K4 demethylase) and histone deacetylase 6 (a histone deacetylase). This regulation promotes a chromatin environment that represses FLOWERING LOCUS C (FLC) transcription, thereby accelerating flowering. TANDEM ZINC-FINGER/PLUS3 thus functions upstream of multiple pathways integrating photoperiodic and autonomous floral cues. TANDEM ZINC-FINGER/PLUS3 mediates crosstalk between light signaling and flowering pathways by modulating chromatin structure at the FLC locus. This provides a mechanistic framework for understanding how environmental signals dynamically influence epigenetic regulation of developmental transitions.

CONSTANS-like 13 homologs MiCOL13 A and MiCOL13B orchestrate flowering time and salt-drought tolerance in mango

The CO/COL gene family serves as a central regulator of photoperiod-dependent floral transition and exhibits functional diversification in plant adaptation to abiotic stress conditions. Through comprehensive analysis of the genomic data from the mango cultivar Guire 82 (Mangifera indica L.), two COL13 homologs, designated MiCOL13 A and MiCOL13B, were successfully characterized. Phylogenetic categorization revealed that MiCOL13 A and MiCOL13B cluster within evolutionary clade III of the CONSTANS-like superfamily. These two homologous genes displayed a circadian rhythm and were strongly expressed in the leaves throughout the flowering induction phase. Under short-day (SD) conditions, the flowering time of Arabidopsis strains overexpressing MiCOL13 A and MiCOL13B was significantly delayed. However, overexpression of MiCOL13 A promoted early flowering in Arabidopsis, and MiCOL13B delayed flowering under long-day (LD) conditions. Subcellular localization demonstrated that the nucleus was the location of MiCOL13 A and MiCOL13B. The study also revealed that the overexpression of MiCOL13 A and MiCOL13B enhances Arabidopsis resistance to salt and drought stresses, resulting in overexpressing lines with longer roots and higher survival rates. Investigations of physiological and biochemical parameters revealed that elevated expression of MiCOL13 A/B significantly upregulated the expression of stress-responsive endogenous genes in A. thaliana under saline and drought conditions. Moreover, yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) analyses revealed that the MiCOL13A and MiCOL13B proteins interact with two stress-related proteins, zinc finger protein 4 (MiZFP4) and MYB30-INTERACTING E3 LIGASE 1 (MiMIEL1). Together, our findings indicate that MiCOL13 A and MiCOL13B have dual functions in controlling flowering and responding to abiotic stress in plants.

CONSTANS-Like and SHORT VEGETATIVE PHASE-Like Genes Coordinately Modulate TERMINAL FLOWER 2 to Control Dormancy Transitions in Pinus tabuliformis

With global climate change, understanding how conifers manage seasonal dormancy is increasingly important. This study explores the physiological and molecular processes controlling dormancy transitions in P. tabuliformis, a key species in northern China. Using dormancy simulations and Time-Ordered Gene Co-Expression Network (TO-GCN) analysis, we identified low temperature, rather than photoperiod, as the primary trigger for dormancy release. The PtTFL2 gene functions as both an environmental sensor and dormancy marker, regulated by cold-dependent and independent pathways involving the photoperiod-responsive PtCOL1 and PtSVP-like (SVL) genes. During the autumn-to-winter transition, PtSVL controls PtTFL2 transcription, forming a regulatory complex to fine-tune dormancy. PtCOL1 also directly regulates PtTFL2 and indirectly modulates it by affecting PtSVL expression. The CO-TFL module controls fall dormancy (ecodormancy), while the SVP-TFL module manages the shift to endodormancy in winter. These findings reveal dual regulatory pathways governing dormancy in conifers, offering insights into their adaptation to cold environments and laying the foundation for further research into dormancy mechanisms in gymnosperms.

Genome-wide identification of GmEDS1 gene family members in soybean and expression analysis in response to biotic and abiotic stresses

Enhanced Disease Susceptibility 1 (EDS1), a key regulator in plant defense responses, plays central roles in resistance to stresses. Therefore, the identification and characterization of soybean GmEDS1 family genes and verification of how these genes are associated with stresses are the focus of this study. We identified 11 GmEDS1 genes, which all have lipase-like and EP (EDS1-PAD4-specific) conserved domains, they are unevenly distributed across six chromosomes, including tandem repetitions. Whole-genome duplication and segmental duplication events were the main reason for GmEDS1 family expansion, and the family underwent purification selection during evolution. We detected 25 types of cis-regulatory elements, which enable GmEDS1s to respond to multiple signals. GmEDS1s are rapidly and strongly induced by drought, salt, the common cutworm, and soybean mosaic virus, indicating that they have important biological functions in coping with both abiotic and biological stresses. Furthermore, the expression levels of GmEDS1s differed between long-day and short-day conditions: it was very low under short-day conditions, which may increase the sensitivity of soybean to pathogens under short-day conditions. Overall, this study identified and characterized the members of the GmEDS1 gene family in the soybean genome, and determined that GmEDS1s respond to both abiotic and biotic stresses, providing new key genes for soybean breeders.

The GhWRKY46-GhGAI Module Mediates Cotton Flowering by Regulating the Expression of Flowering Promotion Factors

Flowering represents a pivotal developmental transition stage in the life cycle of a plant, and the occurrence of flowering at the optimal time is critical for reproductive success. WRKY transcription factors play a vital role in a signaling network that governs a multitude of plant processes. Here, a gene, GhWRKY46, that was differentially expressed in early and late maturing materials was identified via association analysis, and it was specifically expressed in flower buds. Under natural light and temperature conditions, compared to Jin668, the flowering time of OE-GhWRKY46 plants was advanced by approximately 6 days, while the flowering time of CR-GhWRKY46 plants was delayed by approximately 8 days. Transcriptomic data indicated that overexpression or knockout of GhWRKY46 resulted in the activation or repression, respectively, of the photoperiod gene CO-Like and genes related to bud differentiation. Combined RNA-seq and DAP-seq analysis revealed that three genes, namely, GhCOL4, GhCOL2 and GhFPF1-like, may be expressed downstream of GhWRKY46. Dual-luciferase assays and electrophoretic mobility shift assays (EMSAs) demonstrated that GhWRKY46 could directly bind to the W-box and promote the expression of these genes. Similarly, GhFT was also found to be activated by GhWRKY46. Both in vivo and in vitro biochemical analyses demonstrated that GhWRKY46 interacted with GhGAI, and GhGAI could interfere with the transcriptional activation of GhWRKY46, which in turn inhibited the expression of GhCOL4, GhCOL2, GhFPF1-like, and GhFT. In conclusion, this study accurately predicted the GhWRKY46 binding motif, which is important for the construction of regulatory networks of the WRKY family in other crops and introduces a novel regulatory module for the flowering regulation pathway in cotton.

Genome-Wide Analysis and Expression Profiles of AhCOLs Family in Peanut (Arachis hypogaea L.)

The CONSTANS-like (COL) gene family plays critical roles in plant growth, development, stress responses, and light signal transduction. However, its functions in peanut (Arachis hypogaea) remain poorly understood. In this study, we identified 18 AhCOL genes in the peanut genome, all localized in the nucleus. Phylogenetic analysis classified these genes into three subfamilies, with Group I containing eight members and Groups II and III each comprising five. Conserved domain analysis revealed that all AhCOL proteins possess at least one B-box and one CCT domain. Most of the AhCOL members in peanuts contain a large number of ABA and MeJA elements. Additionally, some members have low-temperature response elements, anaerobic induction, circadian control, and defense stress elements. Expression profiling indicated that most AhCOL genes are abundantly expressed in leaves, flowers, and fruit needles. Notably, genes such as AhCOL4, AhCOL8, AhCOL13, and AhCOL14 were upregulated under light induction and mechanical stress, highlighting their involvement in pod development. AhCOL1 interacts with AhNF-YC1, while AhCOL3 interacts with both AhNF-YC1 and AhCOP1 proteins. This study identifies key AhCOL genes implicated in light and mechanical stress responses, offering insights into their potential roles in peanut flowering and abiotic stress tolerance.

Overexpressing OsCCT23 Delays Heading Date and Increases Grain Yield by Activating Ghd7 in Rice

Heading date and panicle architecture are pivotal traits that significantly influence rice yield. Here, we identified a gene OsCCT23 encoding a CCT domain-containing protein that delays heading by over 40 days and increases grain yield by 60-104% through overexpressing. Two types transcripts OsCCT23L and OsCCT23S were isolated by 5'RACE, and transgenic events demonstrated that the effect of the predominant transcript OsCCT23S, encoding an 81-aa protein without the B-box domain, is comparable to OsCCT23. OsCCT23 is predominantly expressed in leaves and follows a diurnal expression pattern with a peak at dawn. Overexpressing OsCCT23 upregulated the floral repressor Ghd7 and downregulated the floral inducer RID1, consequently led to the downregulation of Ehd1, Hd3a and RFT1. Additionally, it regulates the expression of certain circadian clock-related genes, including OsGI and OsTOC1. RNA in situ hybridisation analysis confirmed that OsCCT23 activates the expression of Ghd7 in the panicle branch meristem. OsCCT23 suppresses the expression of four OsCKX genes including Gn1a, which associate with cytokinin accumulation in panicles. Natural variation in OsCCT23 promoter identified by eGWAS associates its mRNA abundance and rice heading date. Consequently, OsCCT23 substantially delays heading and significantly increases grain yield, making it highly valuable for rice breeding.

Innovations and threats facing the storage of sugar in sugar beet

Sugar beet has great economic impact, particularly in the Northern Hemisphere. Classical breeding has increased the plants' taproot sugar contents to 20 %, but further improvements require the identification of factors limiting sucrose accumulation. Recent research uncovered key elements for sucrose storage, including the identification of the transporter pumping sucrose into taproot vacuoles and regulatory proteins controlling its activity. As with other crops, sugar beet breeding led to undesirable trait-offs, like increased frost sensitivity. However, studies of the plants' metabolic reprogramming upon cold temperatures suggest potential strategies for i) improving cold/frost tolerance and ii) stabilizing yield. In addition, a rapidly evolving bacterial infection has emerged, causing "Syndrome basses richesses". Our understanding of this disease is limited, so research is needed to prevent its spread and secure sugar beet production. Accordingly, managing the effects of environmental stresses on genetically optimized plants and minimizing disease threats is critical for maintaining and improving yield.

Canalization of flower production across thermal environments requires Florigen and CLAVATA signaling

The ability to maintain invariant developmental phenotypes across disparate environments is termed canalization, but few examples of canalization mechanisms are described. In plants, robust flower production across environmental gradients contributes to reproductive success and agricultural yields. Flowers are produced by the shoot apical meristem (SAM) in an auxin-dependent manner following the switch from vegetative growth to the reproductive phase. While the timing of this phase change, called the floral transition, is sensitized to numerous environmental and endogenous signals, flower formation itself is remarkably invariant across environmental conditions. Previously we found that CLAVATA peptide signaling promotes auxin-dependent flower primordia formation in cool environments, but that high temperatures can restore primordia formation through unknown mechanisms. Here, we show that heat promotes floral primordia patterning and formation in SAMs not by increased auxin production, but through the production of the mobile flowering signal, florigen, in leaves. Florigen, which includes FLOWERING LOCUS T (FT) and its paralog TWIN SISTER OF FT (TSF) in Arabidopsis thaliana, is necessary and sufficient to buffer flower production against the loss of CLAVATA signaling and promotes heat-mediated primordia formation through specific SAM expressed transcriptional regulators. We find that sustained florigen production is necessary for continuous flower primordia production at warmer temperatures, contrasting florigen's switch-like control of floral transition. Lastly, we show that CLAVATA signaling and florigen synergize to canalize flower production across broad temperature ranges. This work sheds light on the mechanisms governing the canalization of plant development and provides potential targets for engineering crop plants with improved thermal tolerances.

Transcript-Wide Identification and Characterization of the BBX Gene Family in Trichosanthes kirilowii and Its Potential Roles in Development and Abiotic Stress

The B-box (BBX) protein has an impact on flowering physiology, photomorphogenesis, shade effects, and responses to both biotic and abiotic stresses. Although recent research described the BBX gene family in numerous plants, knowledge of the BBX gene in Trichosanthes kirilowii was sparse. In this study, we identified a total of 25 TkBBX genes, and phylogenetic analysis showed that these genes were divided into five subfamilies. Analyses of gene structure and motifs for each group found relative conservation. Ka/Ks values showed that most TkBBX genes have undergone negative selection. qRT-PCR analyses revealed that TkBBX1, TkBB4, TkBBX5, TkBBX7, TkBBX15, TkBBX16, TkBBX17, TkBBX19, and TkBBX21 genes respond to salt and drought treatment. Furthermore, we cloned TkBBX7 and TkBBX17 genes and performed a subcellular localization experiment, which revealed that these two genes were both located in the nucleus. Transgenic yeast experiments demonstrated that TkBBX7 and TkBBX17 enhanced yeast tolerance to both salt and drought stresses. These findings provide a theoretical foundation for further investigation on the functions of TkBBX genes in Trichosanthes kirilowii.

Function diversification of CONSTANS-like genes in Pyrus and regulatory mechanisms in response to different light quality

Pear (Pyrus L.) is a significant commercial fruit globally, with diverse species exhibiting variations in their flowering periods due to environmental factors. CONSTANS-like (COL) genes, known from previous studies in Arabidopsis, are key regulators of flowering time by sensing photoperiod. However, the evolutionary history and functions of COL genes in different pear species remain unclear. In this study, we identified a total of 79 COL genes in different pear species, including 12 COL genes in Pyrus bretschneideri 'DangshanSuli', 9 in Pyrus ussuriensis × hybrid 'Zhongai 1', 11 in Pyrus communis 'Bartlett', 13 in Pyrus betulifolia, 18 in Pyrus pyrifolia 'Cuiguan', 16 in Pyrus pyrifolia 'Nijisseiki'. Analysis of gene structure, phylogenetic tree, and multiple sequences provided valuable insights into the fundamental understanding of COL genes in pear. The impact of selection pressure on the PbrCOLs in Chinese white pear was assessed using Ka/Ks, revealing that the evolution rate of PbrCOLs was influenced by purification selection factors. The study also revealed different tissue-specific expression patterns of PbrCOLs under varying light quality. Real-time quantitative PCR revealed that under natural light conditions, the expression patterns of PbrCOL2, PbrCOL3, and PbrCOL4 are similar to previous studies on CONSTANS gene in Arabidopsis, with increased expression levels during the day and decreased levels at night. However, PbrCOL1, PbrCOL6, and PbrCOL9 exhibit different expression patterns, with decreased expression levels both during the day and at night. After red light treatment, high expression of PbrCOL3 and PbrCOL4 was observed at night, while the expression patterns of the other four genes did not show significant changes. Following blue light treatment, the expression peaks of PbrCOL1 and PbrCOL6 occurred during the night, showing opposite expression patterns compared to the study in Arabidopsis. The overexpression of PbrCOL3 significantly increase the chlorophyll content in pear seedlings, and its expression significantly affected the expression of other key flowering-related genes. Also, overexpression of PbrCOL3 resulted in a late-flowering phenotype in Arabidopsis. These findings indicate diverse responsive mechanisms and functions of PbrCOL genes on flowering time in pear. In conclusion, this study established a foundation for a deeper understanding of the specific roles of PbrCOLs in regulating the reproductive development of pear, particularly in the context of the photoperiodic flowering process.

Research progress on delayed flowering under short-day condition in Arabidopsis thaliana

Flowering represents a pivotal phase in the reproductive and survival processes of plants, with the photoperiod serving as a pivotal regulator of plant-flowering timing. An investigation of the mechanism of flowering inhibition in the model plant Arabidopsis thaliana under short-day (SD) conditions will facilitate a comprehensive approach to crop breeding for flowering time, reducing or removing flowering inhibition, for example, can extend the range of adaptation of soybean to high-latitude environments. In A. thaliana, CONSTANS (CO) is the most important component for promoting flowering under long-day (LD) conditions. However, CO inhibited flowering under the SD conditions. Furthermore, the current studies revealed that A. thaliana delayed flowering through multiple pathways that inhibit the transcription and sensitivity of FLOWERING LOCUS T (FT) and suppresses the response to, or synthesis of, gibberellins (GA) at different times, for potential crop breeding resources that can be explored in both aspects. However, the underlying mechanism remains poorly understood. In this review, we summarized the current understanding of delayed flowering under SD conditions and discussed future directions for related topics.

More than flowering: CONSTANS plays multifaceted roles in plant development and stress responses

Plants have evolved a remarkable ability to sense and respond to changes in photoperiod, allowing adjustments to their growth and development based on seasonal and environmental cues. The floral transition is a pivotal stage in plant growth and development, signifying a shift from vegetative to reproductive growth. CONSTANS (CO), a central photoperiodic response factor conserved in various plants, mediates day-length signals to control the floral transition, although its mechanisms of action vary among plants with different day-length requirements. In addition, recent studies have uncovered roles for CO in organ development and stress responses. These pleiotropic roles in model plants and crops make CO a potentially fruitful target for molecular breeding aimed at modifying crop agronomic traits. This review systematically traces research on CO, from its discovery and functional studies to the exploration of its regulatory mechanisms and newly discovered functions, providing important insight into the roles of CO and laying a foundation for future research.

Combined transcriptional and metabolomic analysis of flavonoids in the regulation of female flower bud differentiation in Juglans sigillata Dode

Juglans sigillata Dode is rich in flavonoids, but the low ratio of female to male flower buds limits the development of the J. sigillata industry. While the abundance of flavonoids in J. sigillata is known, whether flavonoids influence female flower bud differentiation has not been reported. In this study, we explored the regulatory mechanisms of gene expression and metabolite accumulation during female flower bud differentiation through integrated transcriptomic and metabolomic analyses. Our findings revealed that flavonoid biosynthesis is a key pathway influencing female flower bud differentiation, with metabolites primarily shifting towards the isoflavonoid, flavone, and flavonol branches. Structural genes such as chalcone synthase, dihydroflavonol 4-reductase, flavonol synthase, and flavonoid 3',5'-hydroxylase were identified as playing crucial regulatory roles. The expression of these genes promoted the accumulation of flavonoids, which in turn influenced female flower bud differentiation by modulating key regulatory genes including Suppressor of Overexpression of Constans1, Constans, Flowering Locus T, and APETALA1. Furthermore, transcription factors (TFs) highly expressed during the physiological differentiation of female flower buds, particularly M-type MADS, WRKY, and MYB, were positively correlated with flavonoid biosynthesis genes, indicating their significant role in the regulation of flavonoid production. These results offer valuable insights into the mechanisms of female flower bud differentiation in J. sigillata and highlight the regulatory role of flavonoids in plant bud differentiation.

Photoperiodic control of growth and reproduction in non-flowering plants

Photoperiodic responses shape plant fitness to the changing environment and are important regulators of growth, development, and productivity. Photoperiod sensing is one of the most important cues to track seasonal variations. It is also a major cue for reproductive success. The photoperiodic information conveyed through the combined action of photoreceptors and the circadian clock orchestrates an output response in plants. Multiple responses such as hypocotyl elongation, induction of dormancy, and flowering are photoperiodically regulated in seed plants (eg. angiosperms). Flowering plants such as Arabidopsis or rice have served as important model systems to understand the molecular players involved in photoperiodic signalling. However, photoperiodic responses in non-angiosperm plants have not been investigated and documented in detail. Genomic and transcriptomic studies have provided evidence on the conserved and distinct molecular mechanisms across the plant kingdom. In this review, we have attempted to compile and compare photoperiodic responses in the plant kingdom with a special focus on non-angiosperms.

A combination of upstream alleles involved in rice heading hastens natural long-day responses

BACKGROUND

The female parental line Jinbuol (JBO, early heading) and two recombinant isogenic lines, JSRIL1 and JSRIL2, have been shown to flower 44, 34 and 16 days earlier, respectively, than the male parental line Samgwang (SG, late heading) in paddy fields.

OBJECTIVE

To explore how photoperiodicity-related genes are involved in differential heading among these lines.

METHODS

Deep sequencing was conducted for these lines, photoperiodicity-related genes (71) were categorized, and qRT-PCR was performed for some key genes.

RESULTS

Deep sequencing revealed a nearly even contribution of parental groups, with 48.5% and 45% of the chromosomes in JSRIL1 and JSRIL2, respectively, inherited from the female parent JBO; however, Chr6 contained the most biased parental contribution, with 99.4% inherited from the female parent. The variation in single-nucleotide polymorphisms (SNPs) among many known flower-inducing genes, including rice GIGANTEA (OsGI); grain number, plant height and heading date 7 (Ghd7); and EARLY HEADING DATE 1 (Ehd1), was minimal. In the JSRILs, HEADING DATE 1 (Hd1) and VERNALIZATION INSENSITIVE 3-LIKE 1 (OsVIL2) originated from JBO, whereas FLAVIN-BINDING, KELCH REPEAT, F BOX 1 (OsFKF1) originated from SG. Interestingly, HEN1 suppressor 1 (OsHESO1) originated from SG in JSRIL1 and JBO in JSRIL2. RNA sequencing and qRT‒PCR analyses of plants at the floral meristem stage revealed that transcriptional regulation through chromosomal restructuring and posttranscriptional regulation might control minute gene regulation, resulting in delayed heading in JSRILs.

CONCLUSION

Our gene expression and SNP analyses of elite recombinant isogenic lines could be helpful in understanding how photoperiodicity-related genes in rice are modulated.

The HISTONE ACETYLTRANSFERASE 1 interacts with CONSTANS to promote flowering in Arabidopsis

Chromatin modifications, including histone acetylation, play essential roles in regulating flowering. The CBP/p300 family HISTONE ACETYLTRANSFERASE 1 (HAC1), which mediates histone acetylation, promotes the process of floral transition; however, the precise mechanism remains largely unclear. Specifically, how HAC1 is involved in the flowering regulatory network and which genes are the direct targets of HAC1 during flowering regulation are still unknown. In this study, we elucidated the critical function of HAC1 in promoting flowering via exerting active epigenetic markers at two key floral integrators, FT and SOC1, thereby regulating their expression to trigger the flowering process. We show that HAC1 physically interacts with CONSTANS (CO) in vivo and in vitro. Chromatin immunoprecipitation results indicate that HAC1 directly binds to the FT and SOC1 loci. Loss of HAC1 impairs CO-mediated transcriptional activation of FT and SOC1 in promoting flowering. Moreover, CO mutation leads to the decreased enrichment of HAC1 at FT and SOC1, indicating that CO recruits HAC1 to FT and SOC1. Finally, HAC1, as well as CO, is required for the elevated histone acetylation level at FT and SOC1. Taken together, our finding reveals that HAC1-mediated histone acetylation boots flowering via a CO-dependent activation of FT and SOC1.

Circadian clock regulation in soybean senescence: a transcriptome analysis of early and late senescence types

BACKGROUND

Plant senescence is the process of physiological maturation of plants and is important for crop yield and quality. Senescence is controlled by several factors, such as temperature and photoperiod. However, the molecular basis by which these genes promote senescence in soybeans is not well understood. We identified senescence-related genes via transcriptome analysis of early-senescence (ES)- and late-senescence (LS)-type plants to elucidate the molecular mechanisms of senescence in soybeans.

RESULTS

We obtained early-senescence (ES)- and late-senescence (LS)-type F7 plants from a cross between a hybrid (Glycine max × Glycine soja) and the Glycine max cultivar. The ES-type plants presented the reproductive (R2) growth stage at 50 days after sowing (DAS) and the R7 growth stage at 95 DAS, whereas the LS-type plants presented the beginning of the R1 and R6 growth stages at 50 and 95 DAS, respectively. To understand the molecular mechanisms underlying this senescence, we performed transcriptome analysis of leaves from 50 to 95 DAS of ES- and LS-type plants. A total of 2,414 and 2,471 genes at 50 and 95 DAS, respectively, were differentially expressed between ES-type and LS-type plants. Twenty-three candidate genes associated with the circadian clock, chlorophyll biosynthesis, phytohormones, and senescence-associated protein kinases were identified, and their expression levels were analyzed. In addition, to understand interaction between circadian clock and senescence, we analyzed expression patterns of seven circadian clock-related genes during the time period (light and dark condition): CIRCADIAN CLOCK ASSOCIATED 1 (CCA1), LATE ELONGATED HYPOCOTYL (LHY), CONSTANS-LIKE 9 (COL9), LUX ARRHYTHMO (LUX) EARLY FLOWERING 3 (ELF3), PSEUDO-RESPONSE REGULATOR5 (PRR5) and GIGANTEA (GI). The expression patterns of circadian clock-related genes were similar in the ES- and LS-type plants. However, the transcription levels of these genes were compared between ES- and LS-type plants, and the expression of these genes was greater than that in LS-type plants during the period when expression increased. Therefore, each set of candidate genes regulated senescence in each plant by regulating their expression level.

CONCLUSIONS

These findings provide novel insights into the regulation of senescence in soybean plants, which could lead to the development of new strategies to improve agriculture.

Proline and ROS: A Unified Mechanism in Plant Development and Stress Response?

The proteinogenic amino acid proline plays crucial roles in both plant development and stress responses, far exceeding its role in protein synthesis. However, the molecular mechanisms and the relative importance of these additional functions of proline remain under study. It is well documented that both stress responses and developmental processes are associated with proline accumulation. Under stress conditions, proline is believed to confer stress tolerance, while under physiological conditions, it assists in developmental processes, particularly during the reproductive phase. Due to proline's properties as a compatible osmolyte and potential reactive oxygen species (ROS) scavenger, most of its beneficial effects have historically been attributed to the physicochemical consequences of its accumulation in plants. However, emerging evidence points to proline metabolism as the primary driver of these beneficial effects. Recent reports have shown that proline metabolism, in addition to supporting reproductive development, can modulate root meristem size by controlling ROS accumulation and distribution in the root meristem. The dynamic interplay between proline and ROS highlights a sophisticated regulatory network essential for plant resilience and survival. This fine-tuning mechanism, enabled by the pro-oxidant and antioxidant properties of compartmentalized proline metabolism, can modulate redox balance and ROS homeostasis, potentially explaining many of the multiple roles attributed to proline. This review uniquely integrates recent findings on the dual role of proline in both ROS scavenging and signaling, provides an updated overview of the most recent research published to date, and proposes a unified mechanism that could account for many of the multiple roles assigned to proline in plant development and stress defense. By focusing on the interplay between proline and ROS, we aim to provide a comprehensive understanding of this proposed mechanism and highlight the potential applications in improving crop resilience to environmental stress. Additionally, we address current gaps in understanding and suggest future research directions to further elucidate the complex roles of proline in plant biology.

The B-box protein BBX13/COL15 suppresses photoperiodic flowering by attenuating the action of CONSTANS in Arabidopsis

The optimal timing of transition from vegetative to floral reproductive phase is critical for plant productivity and agricultural yields. Light plays a decisive role in regulating this transition. The B-box (BBX) family of transcription factors regulates several light-mediated developmental processes in plants, including flowering. Here, we identify a previously uncharacterized group II BBX family member, BBX13/COL15, as a negative regulator of flowering under long-day conditions. BBX13 is primarily expressed in the leaf vasculature, buds, and flowers, showing a similar spatial expression pattern to the major flowering time regulators CO and FT. bbx13 mutants flower early, while BBX13-overexpressors exhibit delayed flowering under long days. Genetic analyses showed that BBX13 acts upstream to CO and FT and negatively regulates their expression. BBX13 physically interacts with CO and inhibits the CO-mediated transcriptional activation of FT. In addition, BBX13 directly binds to the CORE2 motif on the FT promoter, where CO also binds. Chromatin immunoprecipitation data indicates that BBX13 reduces the in vivo binding of CO on the FT promoter. Through luciferase assay, we found that BBX13 inhibits the CO-mediated transcriptional activation of FT. Together, these findings suggest that BBX13/COL15 represses flowering in Arabidopsis by attenuating the binding of CO on the FT promoter.

Short day promotes gall swelling by a CONSTANS-FLOWERING LOCUS T pathway in Zizania latifolia

"Jiaobai" is a symbiont of Zizania latifolia and Ustilago esculenta, producing fleshy galls as a popular vegetable in South and East Asia. Current "Jiaobai" cultivars exhibit abundant variation in their gall formation date; however, the underlying mechanism is not clear. In this study, a strict short-day (SD) "Jiaobai" line "YD-3" was used. Plants were treated with two day-length regimes [14 h/10 h (day/night) (control) and 8 h/16 h (day/night) (SD)] from 100 to 130 days after planting. The gall swelling rate of the two treatments and another early SD treatment (from 60 to 90 days after planting), together with the contingent flowering plants in the experiment population, revealed that SD can improve both gall enlargement and flowering of "Jiaobai" plants. Comparison of RNA sequencing data among control, SD swelling, and SD flowering treatments of leaves and meristems indicated that SD promotion of "Jiaobai" swelling is conducted by the CONSTANS (CO)-FLOWERING LOCUS T (FT) pathway, similar but not identical to the SD-induced flowering pathway in Z latifolia and rice. "Virus-induced gene silencing", "Yeast one-hybrid assay" and "Dual-luciferase assay" showed that a FT gene, ZlGsd1, is critical in SD promotion of gall formation and is positively regulated by a CO gene, ZlCOL1. Our study elucidated how photoperiod affects the formation of a unique organ produced by plant-fungus symbiosis. The difference in SD response between "Jiaobai" and rice, as well as their potential applications in breeding of "Jiaobai" and rice, were also discussed.

A molecular module connects abscisic acid with auxin signals to facilitate seasonal wood formation in Populus

Perennial trees have a recurring annual cycle of wood formation in response to environmental fluctuations. However, the precise molecular mechanisms that regulate the seasonal formation of wood remain poorly understood. Our prior study indicates that VCM1 and VCM2 play a vital role in regulating the activity of the vascular cambium by controlling the auxin homoeostasis of the cambium zone in Populus. This study indicates that abscisic acid (ABA) affects the expression of VCM1 and VCM2, which display seasonal fluctuations in relation to photoperiod changes. ABA-responsive transcription factors AREB4 and AREB13, which are predominantly expressed in stem secondary vascular tissue, bind to VCM1 and VCM2 promoters to induce their expression. Seasonal changes in the photoperiod affect the ABA amount, which is linked to auxin-regulated cambium activity via the functions of VCM1 and VCM2. Thus, the study reveals that AREB4/AREB13-VCM1/VCM2-PIN5b acts as a molecular module connecting ABA and auxin signals to control vascular cambium activity in seasonal wood formation.

ChBBX6 and ChBBX18 are positive regulators of anthocyanins biosynthesis and carotenoids degradation in Cerasus humilis

B-box zinc-finger transcription factor (BBX) plays important regulatory roles in plant secondary metabolism. Here, we identified 21 BBXs that could be further categorized into five subfamilies from Cerasus humilis. Two segmentally duplicated Subfamily IV members, ChBBX6 and ChBBX18, were found to share high homology with reported anthocyanin-related BBXs and express highly in fruits with high anthocyanins but low carotenoids contents. Their transient overexpression in apple and C. humilis fruits both led to significantly increased anthocyanins accumulation and significantly upregulated expression of anthocyanins-related genes. However, their overexpression resulted in decreased carotenoids accumulation and greatly upregulated the expression of carotenoids-related genes especially degradation-related genes. Additionally, their overexpression both greatly improved the ABA content in C. humilis fruits. Through yeast one-hybrid and dual-luciferase reporter assays, we found that both ChBBX6 and ChBBX18 could bind to and activate the promoters of chalcone synthase (ChCHS), flavanone 3-hydroxylase (ChF3H), and 9-cis-epoxycarotenoid dioxygenase 5 (ChNCED5). Our study demonstrates that ChBBX6 and ChBBX18 are positive regulators of anthocyanins biosynthesis and carotenoids degradation and can provide basis for understanding the roles of BBX genes in C. humilis.

Genome-Wide Identification and Expression Profiling Analysis of the CCT Gene Family in Solanum lycopersicum and Solanum melongena

CCT family genes play crucial roles in photoperiodic flowering and environmental stress response; however, there are limited reports in Solanum species with considerable edible and medicinal value. In this study, we conducted genome-wide characterization and expression profiling analysis of the CCT gene family in two Solanum species: tomato (Solanum lycopersicum L.) and eggplant (Solanum melongena L.). A total of 27 SlCCT and 29 SmCCT genes were identified in the tomato and eggplant genomes, respectively. Phylogenetic analysis showed that the CCT gene family could be divided into six subgroups (COL I, COL II, COL III, PRR, CMF I, and CMF II) in Oryza sativa and Arabidopsis thaliana. The similarity in the distribution of exon-intron structures and conserved motifs within the same subgroup indicated the conservation of SlCCT and SmCCT genes during evolution. Intraspecies collinearity analysis revealed that six pairs of SlCCT genes and seven pairs of SmCCT genes showed collinear relationships, suggesting that segmental duplication played a vital role in the expansion of the SlCCT and SmCCT family genes. Cis-acting element prediction indicated that SlCCT and SmCCT were likely to be involved in multiple responses stimulated by light, phytohormones, and abiotic stress. RT-qPCR analysis revealed that SmCCT15, SlCCT6/SlCCT14, and SlCCT23/SmCCT9 responded significantly to salt, drought, and cold stress, respectively. Our comprehensive analysis of the CCT gene family in tomato and eggplant provides a basis for further studies on its molecular role in regulating flowering and resistance to abiotic stress, and provides valuable candidate gene resources for tomato and eggplant molecular breeding.

Genome-wide exploration of the CONSTANS-like (COL) gene family and its potential role in regulating plant flowering time in foxtail millet (Setaria italica)

In photoperiod-sensitive plants, the CO-like gene (CONSTANS-like, COL) has a crucial function in regulating the timing of flowering. The blooming period in foxtail millet is greatly influenced by the duration of daylight; however, there is a scarcity of data regarding the molecular properties of the COL genes in the foxtail millet. In this study, we conducted a comprehensive analysis of the COL gene family in foxtail millet at the genome-wide level. We identified 11 SiCOL genes and performed gene structure analysis, which showed pronounced variation in gene length and intron number among the genes. The examination of COL proteins in foxtail millet and other plant species using phylogenetic analysis revealed that they could be clustered into three distinct groups. Cis-element analysis identified elements related to light-responsiveness, hormones, and abiotic stress in the promoter region of the SiCOL gene. Furthermore, tissue-specific expression analysis showed widespread expression of all 11 SiCOL genes in various foxtail millet tissues and organs, particularly in leaves and panicles. Collinearity analysis identified 14 syntenic gene pairs in both foxtail millet and rice. The results also revealed diurnal oscillations in the transcription levels of SiCOL genes under different light conditions. Moreover, among the 11 genes, SiCO, SiCOL1, and SiCOL6 expression levels were negatively correlated with flowering time variation in two foxtail cultivars. Additionally, upon constructing a network of predicted molecular interactions, FLOWER LOCUS-like (FTL) and Phytochromea A (PHY A) were suggested to potentially interact with SiCO, SiCOL1, and SiCOL6. SiCO, SiCOL1, and SiCOL6 have the potential for flowering and heading in foxtail millet. This research enhances our comprehension of the role and control of the SiCOL gene family constituents in foxtail millet, establishing a basis for future investigations.

Assessment and the regulation of adaptive phenotypic plasticity

Organisms can react to environmental variation by altering their phenotype, and such phenotypic plasticity is often adaptive. This plasticity contributes to the diversity of phenotypes across the tree of life. Generally, the production of these phenotypes must be preceded by assessment, where the individual acquires information about its environment and phenotype relative to that environment, and then determines if and how to respond with an alternative phenotype. The role of assessment in adaptive plasticity is, therefore, crucial. In this Review, we (1) highlight the need for explicitly considering the role of assessment in plasticity; (2) present two different models for how assessment and the facultative production of phenotypes are related; and (3) describe an overarching framework for how assessment evolves. In doing so, we articulate avenues of future work and suggest that explicitly considering the role of assessment in the evolution of plasticity is key to explaining how and when plasticity occurs. Moreover, we emphasize the need to understand the role of assessment in adaptive versus maladaptive plasticity, which is an issue that will become increasingly important in a rapidly changing world.

Transcription factors LvBBX24 and LvbZIP44 coordinated anthocyanin accumulation in response to light in lily petals

Lily (Lilium spp.), a horticultural crop serving both ornamental and edible functions, derives its coloration primarily from anthocyanins. However, limited studies have been conducted on the accumulation of anthocyanins within lilies. In this study, we cloned a light-induced transcription factor named as LvBBX24 in lilies. Through genetic and biochemical analysis, we determined that LvBBX24 could upregulate the transcription of LvMYB5 and facilitate anthocyanin synthesis. Moreover, we identified that darkness promoted the degradation of LvBBX24 protein. Through screening a yeast library, we identified LvbZIP44 acts as its interacting partner. Genetic testing confirmed that LvbZIP44 also plays a role in promoting lily anthocyanin synthesis. This indicates a potential synergistic regulatory effect between LvBBX24 and LvbZIP44. Our study indicates that LvBBX24 and LvbZIP44 cooperate to regulate anthocyanin accumulation in lily petals. These findings provide compelling evidence supporting the idea that LvBBX24 and LvbZIP44 may form a looped helix surrounding the LvMYB5 promoter region to regulate anthocyanin biosynthesis.

THYLAKOID FORMATION 1 interacts with FLOWERING LOCUS T and modulates temperature-responsive flowering in Arabidopsis

The intracellular localization of the florigen FLOWERING LOCUS T (FT) is important for its long-distance transport toward the shoot apical meristem. However, the mechanisms regulating the FT localization remain poorly understood. Here, we discovered that in Arabidopsis thaliana, the chloroplast-localized protein THYLAKOID FORMATION 1 (THF1) physically interacts with FT, sequestering FT in the outer chloroplast envelope. Loss of THF1 function led to temperature-insensitive flowering, resulting in early flowering, especially under low ambient temperatures. THF1 mainly acts in the leaf vasculature and shoot apex to prevent flowering. Mutation of CONSTANS or FT completely suppressed the early flowering of thf1-1 mutants. FT and THF1 interact via their anion binding pocket and coiled-coil domain (CCD), respectively. Deletion of the CCD in THF1 by gene editing caused temperature-insensitive early flowering similar to that observed in the thf1-1 mutant. FT levels in the outer chloroplast envelope decreased in the thf1-1 mutant, suggesting that THF1 is important for sequestering FT. Furthermore, THF1 protein levels decreased in seedlings grown at high ambient temperature, suggesting an explanation for its role in plant responses to ambient temperature. A thf1-1 phosphatidylglycerolphosphate synthase 1 (pgp1) double mutant exhibited additive acceleration of flowering at 23 and 16°C, compared to the single mutants, indicating that THF1 and phosphatidylglycerol (PG) act as independent but synergistic regulators of temperature-responsive flowering. Collectively, our results provide an understanding of the genetic pathway involving THF1 and its role in temperature-responsive flowering and reveal a previously unappreciated additive interplay between THF1 and PG in temperature-responsive flowering.

Genome-wide analysis of the CCT gene family and functional characterization of SlCCT6 in response to drought stress in tomato

CCT transcription factors are important for photoperiod and abiotic stress regulation in Arabidopsis and rice. However, the CCT gene family has not been reported in tomato. Here, we systematically analyzed this. Thirty-one SlCCT genes were identified and divided into five groups (CMF, TIFY, PRR, S8, and COL), with members unevenly distributed across 12 chromosomes and the third chromosome exhibiting the most distribution. SlCCT was found to interact with an interacting protein (SlGI), transcription factor (MYB), and non-coding RNA (sly-miR156-5p) to jointly regulate the tomato stress response. cis-Acting element analysis of the SlCCT promoter region indicated large stress- and hormone-response elements in this family. Real-time PCR results indicated that SlPRR subfamily genes respond to various abiotic stresses and hormones. Tissue expression analysis revealed that several PRR subfamily genes are highly expressed in flowers, and subcellular localization analysis indicated an SlCCT6 nuclear location. Notably, SlCCT6 expression was significantly induced by drought, and its silencing reduced drought stress tolerance. Moreover, SlCCT6 overexpression enhanced tomato drought resistance by increasing antioxidant enzyme activity and activating stress-related genes, whereas SlCCT6 knockout decreased drought resistance. In conclusion, this provides valuable insights for future research on SlCCT functions.

A reduced vernalization requirement is a key component of the early-bolting trait in globe artichoke (Cynara cardunculus var. scolymus)

Early bolting is a major breeding objective for globe artichoke (Cynara cardunculus var. scolymus L.). It has been suggested that globe artichoke bolting time is linked to a vernalization requirement, although environmental conditions under which vernalized plants and controls have been grown may not always allow for proper comparison. Here, we defined morphological markers to monitor the vegetative-to-reproductive phase transition at the shoot apex and linked these to expression changes of homologs of key Arabidopsis flowering regulators SOC1, FUL, and AP1. Importantly, we developed an experimental setup where control and vernalized plants grow under comparable conditions. These tools together allowed for comparison of the vegetative-to-reproductive phase transition between early- and late-bolting genotypes and how they respond to vernalization. Our results show that vernalization requirement is significantly lower in early-bolting genotypes, supporting the hypothesis that the early-bolting trait is at least partly underlain by alterations in the network controlling vernalization response.

Research Progress on Photoperiod Gene Regulation of Heading Date in Rice

Heading date is a critical physiological process in rice that is influenced by both genetic and environmental factors. The photoperiodic pathway is a primary regulatory mechanism for rice heading, with key florigen genes Hd3a (Heading date 3a) and RFT1 (RICE FLOWERING LOCUS T1) playing central roles. Upstream regulatory pathways, including Hd1 and Ehd1, also significantly impact this process. This review aims to provide a comprehensive examination of the localization, cloning, and functional roles of photoperiodic pathway-related genes in rice, and to explore the interactions among these genes as well as their pleiotropic effects on heading date. We systematically review recent advancements in the identification and functional analysis of genes involved in the photoperiodic pathway. We also discuss the molecular mechanisms underlying rice heading date variation and highlight the intricate interactions between key regulatory genes. Significant progress has been made in understanding the molecular mechanisms of heading date regulation through the cloning and functional analysis of photoperiod-regulating genes. However, the regulation of heading date remains complex, and many underlying mechanisms are not yet fully elucidated. This review consolidates current knowledge on the photoperiodic regulation of heading date in rice, emphasizing novel findings and gaps in the research. It highlights the need for further exploration of the interactions among flowering-related genes and their response to environmental signals. Despite advances, the full regulatory network of heading date remains unclear. Further research is needed to elucidate the intricate gene interactions, transcriptional and post-transcriptional regulatory mechanisms, and the role of epigenetic factors such as histone methylation in flowering time regulation. This review provides a detailed overview of the current understanding of photoperiodic pathway genes in rice, setting the stage for future research to address existing gaps and improve our knowledge of rice flowering regulation.

A truncated B-box zinc finger transcription factor confers drought sensitivity in modern cultivated tomatoes

Enhancing drought tolerance in crops and understanding the underlying mechanisms have been subject of intense research. The precise function and molecular mechanisms of B-box zinc finger proteins (BBX) remain elusive. Here, we report a natural allele of BBX18 (BBX18TT) that encodes a C-terminal truncated protein. While most wild tomato germplasms contain the BBX18CC allele and show more drought tolerant, modern cultivated tomatoes mostly carry BBX18TT allele and are more drought sensitive. Knockout of BBX18 leads to improved drought tolerance in transgenic plants of cultivated tomato. Ascorbate peroxidase 1 (APX1) is identified as a BBX18-interacting protein that acts as a positive regulator of drought resistance in tomato. Chromatin immunoprecipitation sequencing analyses reveal that BBX18 binds to a unique cis-acting element of the APX1 promoter and represses its gene expression. This study provides insights into the molecular mechanism underlying drought resistance mediated by the BBX18-APX1 module in plants.

ABI5 binding proteins: key players in coordinating plant growth and development

During the course of terrestrial evolution, plants have developed complex networks that involve the coordination of phytohormone signalling pathways in order to adapt to an ever-changing environment. Transcription factors coordinate these responses by engaging in different protein complexes and exerting both positive and negative effects. ABA INSENSITIVE 5 (ABI5) binding proteins (AFPs), which are closely related to NOVEL INTERACTOR OF JAZ (NINJA)-like proteins, are known for their fundamental role in plants' morphological and physiological growth. Recent studies have shown that AFPs regulate several hormone-signalling pathways, including abscisic acid (ABA) and gibberellic acid (GA). Here, we review the genetic control of AFPs and their crosstalk with plant hormone signalling, and discuss the contributions of AFPs to plants' growth and development.

Biological macromolecules mediated by environmental signals affect flowering regulation in plants: A comprehensive review

Flowering time is a crucial developmental stage in the life cycle of plants, as it determines the reproductive success and overall fitness of the organism. The precise regulation of flowering time is influenced by various internal and external factors, including genetic, environmental, and hormonal cues. This review provided a comprehensive overview of the molecular mechanisms and regulatory pathways of biological macromolecules (e.g. proteins and phytohormone) and environmental factors (e.g. light and temperature) involved in the control of flowering time in plants. We discussed the key proteins and signaling pathways that govern the transition from vegetative growth to reproductive development, highlighting the intricate interplay between genetic networks, environmental cues, and phytohormone signaling. Additionally, we explored the impact of flowering time regulation on plant adaptation, crop productivity, and agricultural practices. Moreover, we summarized the similarities and differences of flowering mechanisms between annual and perennial plants. Understanding the mechanisms underlying flowering time control is not only essential for fundamental plant biology research but also holds great potential for crop improvement and sustainable agriculture.

BBX9 forms feedback loops with PIFs and BBX21 to promote photomorphogenic development

Light is one of the most essential environmental factors that tightly and precisely control various physiological and developmental processes in plants. B-box CONTAINING PROTEINs (BBXs) play central roles in the regulation of light-dependent development. In this study, we report that BBX9 is a positive regulator of light signaling. BBX9 interacts with the red light photoreceptor PHYTOCHROME B (phyB) and transcription factors PHYTOCHROME-INTERACTING FACTORs (PIFs). phyB promotes the stabilization of BBX9 in light, while BBX9 inhibits the transcriptional activation activity of PIFs. In turn, PIFs directly bind to the promoter of BBX9 to repress its transcription. On the other hand, BBX9 associates with the positive regulator of light signaling, BBX21, and enhances its biochemical activity. BBX21 associates with the promoter regions of BBX9 and transcriptionally up-regulates its expression. Collectively, this study unveiled that BBX9 forms a negative feedback loop with PIFs and a positive one with BBX21 to ensure that plants adapt to fluctuating light conditions.

BBX Genes of Cymbidium ensifolium Exhibited Intense Response to Blue Light in Meristem Induction through Artificial Control

Cymbidium ensifolium, a prominent orchid species, is both highly valued for its ornamental qualities and commercially cultivated. However, the species has a considerable challenge in its breeding efforts due to the lengthy period of 7-8 years required for it to transition from seed germination to flowering. BBXs are multifunctional proteins that modulate the actions of critical regulators including HY5 and COP1 in response to blue light, ultimately impacting photomorphogenic processes. In this study, BBX proteins, known for their essential roles in regulating developmental processes under various light conditions, were chosen as the main subject of investigation. The outcome reveals the presence of 19 BBX genes in their genome. The genes are classified into four separate clades and dispersed among 12 out of the 20 chromosomes. Located in the nuclear, physicochemical properties of proteins, analysis of the promoter region reveals the existence of almost 800 cis-acting elements, highlighting the complex regulatory mechanisms that control the expression of the CeBBXs in various organs, as well as their response to light and hormone inputs. Moreover, the examination of differential expression under blue light therapy reveals their involvement in photomorphogenic reactions. The expression of CeBBXs exhibits substantial alterations as the duration of exposure to blue light increases. These findings contribute to a deeper understanding of the roles that BBX genes serve in C. ensifolium, providing a basis for future studies on the functions and regulatory mechanisms of BBX members in the context of floral initiation and development within this species.

Genome-Wide Identification of B-Box Family Genes and Their Potential Roles in Seed Development under Shading Conditions in Rapeseed

B-box (BBX) proteins, a subfamily of zinc-finger transcription factors, are involved in various environmental signaling pathways. In this study, we conducted a comprehensive analysis of BBX family members in Brassica crops. The 482 BBX proteins were divided into five groups based on gene structure, conserved domains, and phylogenetic analysis. An analysis of nonsynonymous substitutions and (Ka)/synonymous substitutions (Ks) revealed that most BBX genes have undergone purifying selection during evolution. An analysis of transcriptome data from rapeseed (Brassica napus) organs suggested that BnaBBX3d might be involved in the development of floral tissue-specific RNA-seq expression. We identified numerous light-responsive elements in the promoter regions of BnaBBX genes, which were suggestive of participation in light signaling pathways. Transcriptomic analysis under shade treatment revealed 77 BnaBBX genes with significant changes in expression before and after shading treatment. Of these, BnaBBX22e showed distinct expression patterns in yellow- vs. black-seeded materials in response to shading. UPLC-HESI-MS/MS analysis revealed that shading influences the accumulation of 54 metabolites, with light response BnaBBX22f expression correlating with the accumulation of the flavonoid metabolites M46 and M51. Additionally, BnaBBX22e and BnaBBX22f interact with BnaA10.HY5. These results suggest that BnaBBXs might function in light-induced pigment accumulation. Overall, our findings elucidate the characteristics of BBX proteins in six Brassica species and reveal a possible connection between light and seed coat color, laying the foundation for further exploring the roles of BnaBBX genes in seed development.

Genome-Wide Identification and Expression Analysis of the COL Gene Family in Hemerocallis citrina Baroni

Hemerocallis citrina Baroni (H. citrina) is an important specialty vegetable that is not only edible and medicinal but also has ornamental value. However, much remains unknown about the regulatory mechanisms associated with the growth, development, and flowering rhythm of this plant. CO, as a core regulatory factor in the photoperiod pathway, coordinates light and circadian clock inputs to transmit flowering signals. We identified 18 COL genes (HcCOL1-HcCOL18) in the H. citrina cultivar 'Mengzihua' and studied their chromosomal distribution, phylogenetic relationships, gene and protein structures, collinearity, and expression levels in the floral organs at four developmental stages. The results indicate that these genes can be classified into three groups based on phylogenetic analysis. The major expansion of the HcCOL gene family occurred via segmental duplication, and the Ka/Ks ratio indicated that the COL genes of Arabidopsis thaliana, Oryza sativa, Phalaenopsis equestris, and H. citrina were under purifying selection. Many cis-elements, including light response elements, abiotic stress elements, and plant hormone-inducible elements, were distributed in the promoter sequences of the HcCOL genes. Expression analysis of HcCOL genes at four floral developmental stages revealed that most of the HcCOL genes were expressed in floral organs and might be involved in the growth, development, and senescence of the floral organs of H. citrina. This study lays a foundation for the further elucidation of the function of the HcCOL gene in H. citrina and provides a theoretical basis for the molecular design breeding of H. citrina.

CONSTANS alters the circadian clock in Arabidopsis thaliana

Plants are sessile organisms that have acquired highly plastic developmental strategies to adapt to the environment. Among these processes, the floral transition is essential to ensure reproductive success and is finely regulated by several internal and external genetic networks. The photoperiodic pathway, which controls plant response to day length, is one of the most important pathways controlling flowering. In Arabidopsis photoperiodic flowering, CONSTANS (CO) is the central gene activating the expression of the florigen FLOWERING LOCUS T (FT) in the leaves at the end of a long day. The circadian clock strongly regulates CO expression. However, to date, no evidence has been reported regarding a feedback loop from the photoperiod pathway back to the circadian clock. Using transcriptional networks, we have identified relevant network motifs regulating the interplay between the circadian clock and the photoperiod pathway. Gene expression, chromatin immunoprecipitation experiments, and phenotypic analysis allowed us to elucidate the role of CO over the circadian clock. Plants with altered CO expression showed a different internal clock period, measured by daily leaf rhythmic movements. We showed that CO upregulates the expression of key genes related to the circadian clock, such as CCA1, LHY, PRR5, and GI, at the end of a long day by binding to specific sites on their promoters. Moreover, a high number of PRR5-repressed target genes are upregulated by CO, and this could explain the phase transition promoted by CO. The CO-PRR5 complex interacts with the bZIP transcription factor HY5 and helps to localize the complex in the promoters of clock genes. Taken together, our results indicate that there may be a feedback loop in which CO communicates back to the circadian clock, providing seasonal information to the circadian system.

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.

B-BOX proteins:Multi-layered roles of molecular cogs in light-mediated growth and development in plants

B-box containing proteins (BBXs) are a class of zinc-ligating transcription factors or regulators that play essential roles in various physiological and developmental processes in plants. They not only directly associate with target genes to regulate their transcription, but also interact with other transcription factors to mediate target genes' expression, thus forming a complex transcriptional network ensuring plants' adaptation to dynamically changing light environments. This review summarizes and highlights the molecular and biochemical properties of BBXs, as well as recent advances with a focus on their critical regulatory functions in photomorphogenesis (de-etiolation), shade avoidance, photoperiodic-mediated flowering, and secondary metabolite biosynthesis and accumulation in plants.

The CONSTANS-LIKE gene PeCOL13 regulates flowering through intron-retained alternative splicing in Phyllostachys edulis

Woody bamboo exhibits a unique flowering characteristic with a lengthy flowering cycle, often followed by death. In many plant species, alternative splicing (AS) is a common phenomenon involved in controlling flowering. In this study, a PeCOL13 gene in moso bamboo (Phyllostachys edulis) was characterized. It produced two isoforms: PeCOL13α and PeCOL13β, due to an intron-retained AS. The PeCOL13α expressed in the vegetative phase and the reproductive phase, but the PeCOL13β didn't express during the vegetative phase and showed only a weak expression from F1 to F3 during the reproductive phase. Overexpression of PeCOL13α in rice (Oryza sativa) resulted in a delayed heading time through inhibiting the expressions of Hd3a, OsFTL1, and Ehd1 and activating the expressions of Ghd7 and RCN1. However, the PeCOL13β-overexpressed rice didn't show any significant differences in flowering compared with wild-type (WT), and the expressions of downstream flowering genes had no notable changes. Further analysis revealed that both PeCOL13α and PeCOL13β can bind to the PeFT promoter. Meanwhile, PeCOL13α can inhibit the transcription of PeFT, but PeCOL13β showed no effect. When PeCOL13α and PeCOL13β coexist, the inhibitory effect of PeCOL13α on PeFT transcription was weakened by PeCOL13β. This study provides new insights into the mechanism of bamboo flowering research.

Genome-Wide Identification and Characterization of CCT Gene Family from Microalgae to Legumes

The CCT (CO, COL and TOC1) gene family has been elucidated to be involved in the functional differentiation of the products in various plant species, but their specific mechanisms are poorly understood. In the present investigation, we conducted a genome-wide identification and phylogenetic analysis of CCT genes from microalgae to legumes. A total of 700 non-redundant members of the CCT gene family from 30 species were identified through a homology search. Phylogenetic clustering with Arabidopsis and domain conservation analysis categorized the CCT genes into three families. Multiple sequence alignment showed that the CCT domain contains important amino acid residues, and each CCT protein contains 24 conserved motifs, as demonstrated by the motif analysis. Whole-genome/segment duplication, as well as tandem duplication, are considered to be the driving forces in the evolutionary trajectory of plant species. This comprehensive investigation into the proliferation of the CCT gene family unveils the evolutionary dynamics whereby WGD/segment duplication is the predominant mechanism contributing to the expansion of the CCT genes. Meanwhile, the examination of the gene expression patterns revealed that the expression patterns of CCT genes vary in different tissues and at different developmental stages of plants, with high expression in leaves, which is consistent with the molecular regulation of flowering in photosynthesis by CCT. Based on the protein-protein interaction analysis of CCT genes in model plants, we propose that the CCT gene family synergistically regulates plant development and flowering with light-signaling factors (PHYs and PIFs) and MYB family transcription factors. Understanding the CCT gene family's molecular evolution enables targeted gene manipulation for enhanced plant traits, including optimized flowering and stress resistance.

The PHYB-FOF2-VOZ2 module functions to fine-tune flowering in response to changes in light quality by modulating FLC expression in Arabidopsis

Proper timing of flowering under different environmental conditions is critical for plant propagation. Light quality is a pivotal environmental cue that plays a critical role in flowering regulation. Plants tend to flower late under light with a high red (R)/far-red (FR) light ratio but early under light with a low R/FR light ratio. However, how plants fine-tune flowering in response to changes in light quality is not well understood. Here, we demonstrate that F-box of Flowering 2 (FOF2), an autonomous pathway-related regulator, physically interacts with VASCULAR PLANT ONE-ZINC FINGER 1 and 2 (VOZ1 and VOZ2), which are direct downstream factors of the R/FR light receptor phytochrome B (PHYB). We show that PHYB physically interacts with FOF2, mediates stabilization of the FOF2 protein under FR light and end-of-day FR light, and enhances FOF2 binding to VOZ2, which leads to degradation of VOZ2 by SCFFOF2 E3 ligase. By contrast, PHYB mediates degradation of FOF2 protein under R light and end-of-day R light. Genetic interaction studies demonstrated that FOF2 functions downstream of PHYB to promote FLC expression and inhibit flowering under both high R/FR light and simulated shade conditions, processes that are partially dependent on VOZ proteins. Taken together, our findings suggest a novel mechanism whereby plants fine-tune flowering time through a PHYB-FOF2-VOZ2 module that modulates FLC expression in response to changes in light quality.

A CAM-Related NF-YB Transcription Factor Enhances Multiple Abiotic Stress Tolerance in Arabidopsis

Abiotic stresses often occur simultaneously, and the tolerance mechanisms of plants to combined multiple abiotic stresses remain poorly studied. Extremophytes, adapted to abiotic stressors, might possess stress-adaptive or -responsive regulators that could enhance multiple abiotic stress resistance in crop plants. We identified an NF-YB transcription factor (TF) from the heat-tolerant obligate Crassulacean acid metabolism (CAM) plant, Kalanchoe fedtschenkoi, as a potential regulator of multiple abiotic stresses. The KfNF-YB3 gene was overexpressed in Arabidopsis to determine its role in multiple abiotic stress responses. Transgenic lines exhibited accelerated flowering time, increased biomass, larger rosette size, higher seed yield, and more leaves. Transgenic lines had higher germination rates under combined NaCl, osmotic, and water-deficit stress treatments compared to control plants. They also showed enhanced root growth and survival under simultaneous NaCl, osmotic, water-deficit, and heat stress conditions in vitro. Interestingly, potted transgenic lines had higher survival rates, yield, and biomass under simultaneous heat, water-deficit, and light stresses compared to control plants. Altogether, these results provide initial insights into the functions of a CAM-related TF and its potential roles in regulating multiple abiotic stress responses. The CAM abiotic stress-responsive TF-based approach appears to be an ideal strategy to enhance multi-stress resilience in crop plants.

A tomato B-box protein regulates plant development and fruit quality through the interaction with PIF4, HY5, and RIN transcription factors

During the last decade, knowledge about BBX proteins has greatly increased. Genome-wide studies identified the BBX gene family in several ornamental, industry, and food crops; however, reports regarding the role of these genes as regulators of agronomically important traits are scarce. Here, by phenotyping a knockout mutant, we performed a comprehensive functional characterization of the tomato locus Solyc12g089240, hereafter called SlBBX20. The data revealed the encoded protein as a positive regulator of light signaling affecting several physiological processes during the life span of plants. Through inhibition of PHYTOCHROME INTERACTING FACTOR 4 (SlPIF4)-auxin crosstalk, SlBBX20 regulates photomorphogenesis. Later in development, it controls the balance between cell division and expansion to guarantee correct vegetative and reproductive development. In fruits, SlBBX20 is transcriptionally induced by the master transcription factor RIPENING INHIBITOR (SlRIN) and, together with ELONGATED HYPOCOTYL 5 (SlHY5), up-regulates flavonoid biosynthetic genes. Finally, SlBBX20 promotes the accumulation of steroidal glycoalkaloids and attenuates Botrytis cinerea infection. This work clearly demonstrates that BBX proteins are multilayer regulators of plant physiology because they affect not only multiple processes during plant development but they also regulate other genes at the transcriptional and post-translational levels.

Circadian and photoperiodic regulation of the vegetative to reproductive transition in plants

As sessile organisms, plants must respond constantly to ever-changing environments to complete their life cycle; this includes the transition from vegetative growth to reproductive development. This process is mediated by photoperiodic response to sensing the length of night or day through circadian regulation of light-signaling molecules, such as phytochromes, to measure the length of night to initiate flowering. Flowering time is the most important trait to optimize crop performance in adaptive regions. In this review, we focus on interplays between circadian and light signaling pathways that allow plants to optimize timing for flowering and seed production in Arabidopsis, rice, soybean, and cotton. Many crops are polyploids and domesticated under natural selection and breeding. In response to adaptation and polyploidization, circadian and flowering pathway genes are epigenetically reprogrammed. Understanding the genetic and epigenetic bases for photoperiodic flowering will help improve crop yield and resilience in response to climate change.

Genome-Wide Identification and Characterization of the CCT Gene Family in Rapeseed (Brassica napus L.)

The CCT gene family is present in plants and is involved in biological processes such as flowering, circadian rhythm regulation, plant growth and development, and stress resistance. We identified 87, 62, 46, and 40 CCTs at the whole-genome level in B. napus, B. rapa, B. oleracea, and A. thaliana, respectively. The CCTs can be classified into five groups based on evolutionary relationships, and each of these groups can be further subdivided into three subfamilies (COL, CMF, and PRR) based on function. Our analysis of chromosome localization, gene structure, collinearity, cis-acting elements, and expression patterns in B. napus revealed that the distribution of the 87 BnaCCTs on the chromosomes of B. napus was uneven. Analysis of gene structure and conserved motifs revealed that, with the exception of a few genes that may have lost structural domains, the majority of genes within the same group exhibited similar structures and conserved domains. The gene collinearity analysis identified 72 orthologous genes, indicating gene duplication and expansion during the evolution of BnaCCTs. Analysis of cis-acting elements identified several elements related to abiotic and biotic stress, plant hormone response, and plant growth and development in the promoter regions of BnaCCTs. Expression pattern and protein interaction network analysis showed that BnaCCTs are differentially expressed in various tissues and under stress conditions. The PRR subfamily genes have the highest number of interacting proteins, indicating their significant role in the growth, development, and response to abiotic stress of B. napus.

Overexpression of the Chrysanthemum lavandulifolium ROS1 gene promotes flowering in Arabidopsis thaliana by reducing the methylation level of CONSTANS

DNA demethylation is involved in the regulation of flowering in plants, yet the underlying molecular mechanisms remain largely unexplored. The RELEASE OF SILENCING 1 (ROS1) gene, encoding a DNA demethyltransferase, plays key roles in many developmental processes. In this study, the ROS1 gene was isolated from Chrysanthemum lavandulifolium, where it was strongly expressed in the leaves, buds and flowers. Overexpression of the ClROS1 gene caused an early flowering phenotype in Arabidopsis thaliana. RNA-seq analysis of the transgenic plants revealed that differentially expressed genes (DEGs) were significantly enriched in the circadian rhythm pathway and that the positive regulator of flowering, CONSTANS (CO), was up-regulated. Additionally, whole-genome bisulphite sequencing (WGBS), PCR following methylation-dependent digestion with the enzyme McrBC, and bisulfite sequencing PCR (BSP) confirmed that the methylation level of the AtCO promoter was reduced, specifically in CG context. Overall, our results demonstrated that ClROS1 accelerates flowering by reducing the methylation level of the AtCO promoter. These findings clarify the epigenetic mechanism by which ClROS1-mediated DNA demethylation regulates flowering.