Functional divergence of the TFL1-like gene family in Arabidopsis revealed by characterization of a novel homologue

Flowering time regulation through the lens of evolution

Flowering, the onset of reproductive development, marks a critical transition in the angiosperm life cycle. In the model plant Arabidopsis thaliana, the process is tightly regulated by a complex network of approximately 300 genes organized into distinct pathways. This mini-review examines the genetic and molecular mechanisms regulating flowering time from an evolutionary perspective. Our analysis reveals that genes involved in the age and photoperiod pathways are evolutionarily ancient and highly conserved across bryophytes and vascular plants. In contrast, other regulatory modules appear to have evolved more recently, likely through the repurposing of existing genes or adaptations to environmental changes. We propose that future research should shift away from studying flowering regulation mechanisms in individual model plants to exploring the evolution of flowering time pathways and their underlying drivers. Adopting an evolutionary perspective may ultimately illuminate the fundamental principles governing the timing of reproductive development in plants.

Antagonizing cis-regulatory elements of a conserved flowering gene mediate developmental robustness

Developmental transitions require precise temporal and spatial control of gene expression. In plants, such regulation is critical for flower formation, which involves the progressive maturation of stem cell populations within shoot meristems to floral meristems, followed by rapid sequential differentiation into floral organs. Across plant taxa, these transitions are orchestrated by the F-box transcriptional cofactor gene UNUSUAL FLORAL ORGANS (UFO). The conserved and pleiotropic functions of UFO offer a useful framework for investigating how evolutionary processes have shaped the intricate cis-regulation of key developmental genes. By pinpointing a conserved promoter sequence in an accessible chromatin region of the tomato ortholog of UFO, we engineered in vivo a series of cis-regulatory alleles that caused both loss- and gain-of-function floral defects. These mutant phenotypes were linked to disruptions in predicted transcription factor binding sites for known transcriptional activators and repressors. Allelic combinations revealed dosage-dependent interactions between opposing alleles, influencing the penetrance and expressivity of gain-of-function phenotypes. These phenotypic differences support that robustness in tomato flower development requires precise temporal control of UFO expression dosage. Bridging our analysis to Arabidopsis, we found that although homologous sequences to the tomato regulatory region are dispersed within the UFO promoter, they maintain similar control over floral development. However, phenotypes from disrupting these sequences differ due to the differing expression patterns of UFO. Our study underscores the complex cis-regulatory control of dynamic developmental genes and demonstrates that critical short stretches of regulatory sequences that recruit both activating and repressing machinery are conserved to maintain developmental robustness.

The transition from vegetative growth to flowering is associated with suppression of the MUSA CENTRORADIALIS (MCN) gene family in day neutral banana

Control over flowering time is essential for reproductive success and survival of plants. The TERMINAL FLOWER1/CENTRORADIALIS/BROTHER OF FT AND TFL1 (TFL1/CEN/BFT) genes are key suppressor of flowering time that prevents premature conversion of the apical meristem into a floral meristem thereby allowing indeterminate vegetative growth. We have identified and characterized seven members of banana TFL1/CEN/BFT gene family (MCN1-7). All genes except MCN6 show overlapping expression in the shoot apical meristem as well as leaves from the initial to mid-vegetative phases. Their expression is collectively reduced to their lowest just prior to flowering initiation at around 171 days, 226 days and 297 days, respectively, in three differently flowering varieties. Thereafter, there is steady increase in their transcript levels in the apical meristem as well as leaves that correlates with the development and growth of the inflorescence. The ability of three of the genes, MCNs1-3, to functionally complement the tfl1-14 mutant of Arabidopsis provides additional evidence for structural and functional similarities of the MCN proteins to TFL1 even in a distantly related plant. Together, these results suggest that the MCN family in banana is associated with vegetative growth and suppression of flowering time initiation as well as indeterminate growth of inflorescence.

Florigen and antiflorigen gene expression correlates with reproductive state in a marine angiosperm, Zostera marina

• Florigen and antiflorigen genes within the phosphatidylethanolamine-binding protein (PEBP) family regulate flowering in angiosperms. In eelgrass (Zostera marina), a marine foundation species threatened by climate change, flowering and seed production are crucial for population resilience. Yet, the molecular mechanism underpinning flowering remains unknown. • Using phylogenetic analysis and functional assays in Arabidopsis, we identified thirteen PEBP genes in Z. marina (ZmaPEBP) and showed that four genes altered flowering phenotypes when overexpressed. We used quantitative RT-PCR on Z. marina shoots from perennial and annual populations in Willapa Bay, USA to assess expression of these four genes in different tissue and expression changes throughout the growth season. • We demonstrated that ZmaFT2 and ZmaFT4 promote flowering, and ZmaFT9 and ZmaTFL1a repress flowering in Arabidopsis. Across five natural sites exhibiting different degrees of population genetic structure, ZmaFT2 and ZmaFT4 were expressed in leaves of vegetative and reproductive shoots and in stems and rhizomes of reproductive shoots. ZmaFT9 was distinctively expressed in leaves of vegetative and juvenile shoots, while ZmaTFL1a levels increased after flowering shoots emerged. • Our results suggest that ZmaFT2 and ZmaFT4 may promote flowering, while ZmaFT9 may inhibit a floral transition in eelgrass. We speculate that ZmaTFL1a may be involved in flowering shoot architecture.

Both the Positioned Supplemental or Night-Interruptional Blue Light and the Age of Leaves (or Tissues) Are Important for Flowering and Vegetative Growth in Chrysanthemum

In this study, the effects of supplemental or night interruptional blue light (S-BL or NI-BL) positioning on morphological growth, photoperiodic flowering, and expression of floral genes in Chrysanthemum morifolium were investigated. Blue light-emitting diodes (LEDs) at an intensity of 30 μmol·m-2·s-1 photosynthetic photon flux density (PPFD) were used for 4 h either (1) to supplement the white LEDs at the end of the 10 h short-day (SD10 + S-BL4) and 13 h long-day conditions (LD13 + S-BL4), or (2) to provide night interruption in the SD10 (SD10 + NI-BL4) and LD13 (LD13 + NI-BL4). The S-BL4 or NI-BL4 was positioned to illuminate either the shoot tip, the youngest leaf (vigorously growing the third leaf from the shoot tip), or the old leaf (the third leaf from the stem base). In the text, they will be denoted as follows: SD10 + S-BL4-S, -Y, or -O; SD10 + NI-BL4-S, -Y, or -O; LD13 + S-BL4-S, -Y, or -O; LD13 + NI-BL4-S, -Y, or -O. Normally, the LD13 conditions enhanced more vegetative growth than the SD10 periods. The growth of leaves, stems, and branches strongly responded to the S-BL4 or NI-BL4 when it was targeted onto the shoot tip, followed by the youngest leaf. The SD10 + S-BL4 or +NI-BL4 on the old leaf obviously suppressed plant extension growth, resulting in the smallest plant height. Under LD13 conditions, the flowering-related traits were significantly affected when the S-BL4 or NI-BL4 was shed onto the youngest leaf. However, these differences do not exist in the SD10 environments. At the harvest stage, other than the non-flowered LD13 treatment, the LD13 + S-BL4 irradiating the youngest leaf induced the most flowers, followed by the shoot tip and old leaf. Moreover, LD13 + NI-BL4 resulted in the latest flowering, especially when applied to the shoot tip and old leaf. However, the SD10 + S-BL4 or + NI-BL4 irradiated the shoot tip, youngest leaf, or old leaf all significantly earlier and increased flowering compared to the SD10 treatment. Overall: (1) Generally, vegetative growth was more sensitive to photoperiod rather than lighting position, while, during the same photoperiod, the promotion of growth was stronger when the light position of S-BL4 or NI-BL4 was applied to the shoot tip or the youngest leaf. (2) The photoperiodic flowering of these short-day plants (SDPs) comprehensively responded to the photoperiod combined with blue light positioning. Peculiarly, when they were exposed to the LD13 flowering-inhibited environments, the S-BL4 or NI-BL4 shed onto the leaves, especially the youngest leaves, significantly affecting flowering.

Evolution of FLOWERING LOCUS T-like genes in angiosperms: a core Lamiales-specific diversification

Plant life history is determined by two transitions, germination and flowering time, in which the phosphatidylethanolamine-binding proteins (PEBPs) FLOWERING LOCUS T (FT) and TERMINAL FLOWER1 (TFL1) play key regulatory roles. Compared with the highly conserved TFL1-like genes, FT-like genes vary significantly in copy numbers in gymnosperms, and monocots within the angiosperms, while sporadic duplications can be observed in eudicots. Here, via a systematic analysis of the PEBPs in angiosperms with a special focus on 12 representative species featuring high-quality genomes in the order Lamiales, we identified a successive lineage-specific but systematic expansion of FT-like genes in the families of core Lamiales. The first expansion event generated FT1-like genes mainly via a core Lamiales-specific whole-genome duplication (cL-WGD), while a likely random duplication produced the FT2-like genes in the lineages containing Scrophulariaceae and the rest of the core Lamiales. Both FT1- and FT2-like genes were further amplified tandemly in some families. These expanded FT-like genes featured highly diverged expression patterns and structural variation, indicating functional diversification. Intriguingly, some core Lamiales contained the relict MOTHER OF FT AND TFL1 like 2 (MFT2) that probably expanded in the common ancestor of angiosperms. Our data showcase the highly dynamic lineage-specific expansion of the FT-like genes, and thus provide important and fresh evolutionary insights into the gene regulatory network underpinning flowering time diversity in Lamiales and, more generally, in angiosperms.

BdRCN4, a Brachypodium distachyon TFL1 homologue, is involved in regulation of apical meristem fate

In higher plants, the shift from vegetative to reproductive development is governed by complex interplay of internal and external signals. TERMINALFLOWER1 (TFL1) plays a crucial role in the regulation of flowering time and inflorescence architecture in Arabidopsis thaliana. This study aimed to explore the function of BdRCN4, a homolog of TFL1 in Brachypodium distachyon, through functional analyses in mutant and transgenic plants. The results revealed that overexpression of BdRCN4 in B. distachyon leads to an extended vegetative phase and reduced production of spikelets. Similar results were found in A. thaliana, where constitutive expression of BdRCN4 promoted a delay in flowering time, followed by the development of hypervegetative shoots, with no flowers or siliques produced. Our results suggest that BdRCN4 acts as a flowering repressor analogous to TFL1, negatively regulating AP1, but no LFY expression. To further validate this hypothesis, a 35S::LFY-GR co-transformation approach on 35::BdRCN4 lines was performed. Remarkably, AP1 expression levels and flower formation were restored to normal in co-transformed plants when treated with dexamethasone. Although further molecular studies will be necessary, the evidence in B. distachyon support the idea that a balance between LFY and BdRCN4/TFL1 seems to be essential for activating AP1 expression and initiating floral organ identity gene expression. This study also demonstrates interesting conservation through the molecular pathways that regulate flowering meristem transition and identity across the evolution of monocot and dicot plants.

MsTFL1A delays flowering and regulates shoot architecture and root development in Medicago sativa

KEY MESSAGE

MsTFL1A is an important gene involved in flowering repression in alfalfa (Medicago sativa) which conditions not only above-ground plant shoot architecture but also root development and growth. Delayed flowering is an important trait for forage species, as it allows harvesting of high-quality forage for a longer time before nutritional values decline due to plant architecture changes related to flowering onset. Despite the relevance of delayed flowering, this trait has not yet been thoroughly exploited in alfalfa. This is mainly due to its complex genetics, sensitivity to inbreeding and to the fact that delayed flowering would be only advantageous if it allowed increased forage quality without compromising seed production. To develop new delayed-flowering varieties, we have characterized the three TERMINAL FLOWERING 1 (TFL1) family of genes in alfalfa: MsTFL1A, MsTFL1B and MsTFL1C. Constitutive expression of MsTFL1A in Arabidopsis caused late flowering and changes in inflorescence architecture, indicating that MsTFL1A is the ortholog of Arabidopsis TFL1. Overexpression of MsTFL1A in alfalfa consistently led to delayed flowering in both controlled and natural field conditions, coupled to an increase in leaf/stem ratio, a common indicator of forage quality. Additionally, overexpression of MsTFL1A reduced root development, reinforcing the role of MsTFL1A not only as a flowering repressor but also as a regulator of root development.We conclude that the precise manipulation of MsTFL1A gene expression may represent a powerful tool to improve alfalfa forage quality.

Genome-Wide Characterization of PEBP Gene Family and Functional Analysis of TERMINAL FLOWER 1 Homologs in Macadamia integrifolia

Edible Macadamia is one of the most important commercial nut trees cultivated in many countries, but its large tree size and long juvenile period pose barriers to commercial cultivation. The short domestication period and well-annotated genome of Macadamia integrifolia create great opportunities to breed commercial varieties with superior traits. Recent studies have shown that members of the phosphatidylethanolamine binding protein (PEBP) family play pivotal roles in regulating plant architecture and flowering time in various plants. In this study, thirteen members of MiPEBP were identified in the genome of M. integrifolia, and they are highly similarity in both motif and gene structure. A phylogenetic analysis divided the MiPEBP genes into three subfamilies: MFT-like, FT-like and TFL1-like. We subsequently identified two TERMINAL FLOWER 1 homologues from the TFL1-like subfamily, MiTFL1 and MiTFL1-like, both of which were highly expressed in stems and vegetative shoots, while MiTFL1-like was highly expressed in young leaves and early flowers. A subcellular location analysis revealed that both MiTFL1 and MiTFL1-like are localized in the cytoplasm and nucleus. The ectopic expression of MiTFL1 can rescue the early-flowering and terminal-flower phenotypes in the tfl1-14 mutant of Arabidopsis thaliana, and it indicates the conserved functions in controlling the inflorescence architecture and flowering time. This study will provide insight into the isolation of PEBP family members and the key targets for breeding M. integrifolia with improved traits in plant architecture and flowering time.

Functional characterization of three TERMINAL FLOWER 1-like genes from Platanus acerifolia

KEY MESSAGE

TFL1-like genes of the basal eudicot Platanus acerifolia have conserved roles in maintaining vegetative growth and inhibiting flowering, but may act through distinct regulatory mechanism. Three TERMINAL FLOWER 1 (TFL1)-like genes were isolated and characterized from London plane tree (Platanus acerifolia). All genes have conserved genomic organization and characteristic of the phosphatidylethanolamine-binding protein (PEBP) family. Sequence alignment and phylogenetic analysis indicated that two genes belong to the TFL1 clade, designated as PlacTFL1a and PlacTFL1b, while another one was grouped in the BFT clade, named as PlacBFT. qRT-PCR analysis showed that all three genes primarily expressed in vegetative phase, but the expression of PlacTFL1a was much higher and wider than that of PlacTFL1b, with the latter only detected at relatively low expression levels in apical and lateral buds in April. PlacBFT was mainly expressed in young stems of adult trees followed by juvenile tissues. Ectopic expression of any TFL1-like gene in Arabidopsis showed phenotypes of delayed or repressed flowering. Furthermore, overexpression of PlacTFL1a gene in petunia also resulted in extremely delayed flowering. In non-flowering 35:PlacTFL1a transgenic petunia plants, the FT-like gene (PhFT) gene was significantly upregulated and AP1 homologues PFG, FBP26 and FBP29 were significantly down-regulated in leaves. Yeast two-hybrid analysis indicated that only weak interactions were detected between PlacTFL1a and PlacFDL, and PlacTFL1a showed no interaction with PhFDL1/2. These results indicated that the TFL1-like genes of Platanus have conserved roles in repressing flowering, but probably via a distinct regulatory mechanism.

Identification, evolution and expression analyses of the whole genome-wide PEBP gene family in Brassica napus L

BACKGROUND

With the release of genomic data for B.rapa, B.oleracea, and B.napus, research on the genetic and molecular functions of Brassica spp. has entered a new stage. PEBP genes in plants play an important role in the transition to flowering as well as seed development and germination. Molecular evolutionary and functional analyses of the PEBP gene family in B.napus based on molecular biology methods can provide a theoretical basis for subsequent investigations of related regulators.

RESULTS

In this paper, we identified a total of 29 PEBP genes from B.napus that were located on 14 chromosomes and 3 random locations. Most members contained 4 exons and 3 introns; motif 1 and motif 2 were the characteristic motifs of PEBP members. On the basis of intraspecific and interspecific collinearity analyses, it is speculated that fragment replication and genomic replication are the main drivers of for the amplification and evolution of the PEBP gene in the B.napus genome. The results of promoter cis-elements prediction suggest that BnPEBP family genes are inducible promoters, which may directly or indirectly participate in multiple regulatory pathways of plant growth cycle. Furthermore, the tissue-specific expression results show that the expression levels of BnPEBP family genes in different tissues were quite different, but the gene expression organization and patterns of the same subgroup were basically the same. qRT‒PCR revealed certain spatiotemporal patterns in the expression of the PEBP subgroups in roots, stems, leaves, buds, and siliques, was tissue-specific, and related to function.

CONCLUSIONS

A systematic comparative analysis of the B.napus PEBP gene family was carried out at here. The results of gene identification, phylogenetic tree construction, structural analysis, gene duplication analysis, prediction of promoter cis-elements and interacting proteins, and expression analysis provide a reference for exploring the molecular mechanisms of BnPEBP family genes in future research.

The Cm14-3-3μ protein and CCT transcription factor CmNRRa delay flowering in chrysanthemum

Floral transition from vegetative to reproductive growth is pivotal in the plant life cycle. NUTRITION RESPONSE AND ROOT GROWTH (OsNRRa) as a CONSTANS, CONSTANS-LIKE, TOC1 (CCT) domain protein delays flowering in rice and an orthologous gene CmNRRa inhibits flowering in chrysanthemum; however, the mechanism remains unknown. In this study, using yeast two-hybrid screening, we identified the 14-3-3 family member Cm14-3-3µ as a CmNRRa-interacting protein. Biochemical assays using a combination of bimolecular fluorescence complementation (BiFC), pull-down, and Co-immunoprecipitation (Co-IP) were performed to confirm the physical interaction between CmNRRa and Cm14-3-3µ in chrysanthemum. In addition, expression analysis showed that CmNRRa, but not Cm14-3-3µ, responded to the diurnal rhythm, whereas both genes were highly expressed in the leaves. Moreover, the function in flowering time regulation of Cm14-3-3µ is similar to that of CmNRRa. Furthermore, CmNRRa repressed chrysanthemum FLOWERING LOCUS T-like 3 (CmFTL3) and APETALA 1 (AP1)/FRUITFULL (FUL)-like gene (CmAFL1), but induced TERMINAL FLOWER1 (CmTFL1) directly by binding to their promoters. Cm14-3-3µ enhanced the ability of CmNRRa to regulate the expression of these genes. These findings suggest that there is a synergistic relationship between CmNRRa and Cm14-3-3µ in flowering repression in chrysanthemum.

Genome-wide identification and characterization profile of phosphatidy ethanolamine-binding protein family genes in carrot

Members of the family of Phosphatidy Ethanolamine-Binding Protein (PEBP) have been shown to be key regulators of the transition of plants from vegetative to reproductive phases. Here, a total of 12 PEBP proteins were identified in the carrot (Daucus carota L.) genome and classified into FT-like (4), TFL1-like (6), and MFT-like 2) subfamilies, that had different lengths (110-267 aa) and were distributed unevenly across seven chromosomes. Moreover, 13 and 31 PEBP proteins were identified in other two Apiaceae species, celery (Apium graveolens L.) and coriander (Coriandrum sativum L.). The phylogenetic and evolutionary results of these PEBP family proteins were obtained based on the protein sequences. In the three Apiaceae species, purifying selection was the main evolutionary force, and WGD, segmental duplication, and dispersed duplication have played key roles in the PEBP family expansion. The expression analysis showed that carrot PEBP genes exhibited relatively broad expression patterns across various tissues. In the period of bolting to flowering, the carrot FT-like subfamily genes were upregulated as positive regulators, and TFL1-like subfamily genes remained at lower expression levels as inhibitors. More interestingly, the members of carrot FT-like genes had different temporal-spatial expression characteristics, suggesting that they have different regulatory functions in the carrot reproductive phase. In summary, this study contributes to our understanding of the PEBP family proteins and provides a foundation for exploring the mechanism of carrot bolting and flowering for the breeding of cultivars with bolting resistance.

The flowering of SDP chrysanthemum in response to intensity of supplemental or night-interruptional blue light is modulated by both photosynthetic carbon assimilation and photoreceptor-mediated regulation

The photoreceptor-mediated photoperiodic sensitivity determines the obligate short-day flowering in chrysanthemum (Chrysanthemum morifolium Ramat.) when the night length is longer than a critical minimum, otherwise, flowering is effectively inhibited. The reversal of this inhibition by subsequent exposure to a short period of supplemental (S) or night-interruptional (NI) blue (B) light (S-B; NI-B) indicates the involvement of B light-received photoreceptors in the flowering response. Flowering is mainly powered by sugars produced through photosynthetic carbon assimilation. Thus, the light intensity can be involved in flowering regulation by affecting photosynthesis. Here, it is elucidated that the intensity of S-B or NI-B in photoperiodic flowering regulation of chrysanthemums by applying 4-h of S-B or NI-B with either 0, 10, 20, 30, or 40 μmol·m-2·s-1 photosynthetic photon flux density (PPFD) in a 10-h short-day (SD10) [SD10 + 4B or + NI-4B (0, 10, 20, 30, or 40)] or 13-h long-day (LD13) condition [LD13 + 4B or + NI-4B (0, 10, 20, 30, or 40)] provided by 300 ± 5 μmol·m-2·s-1 PPFD white (W) LEDs. After 60 days of photoperiodic light treatments other than the LD13 and LD13 + NI-4B (40), flowering with varying degrees was observed, although the SD10 gave the earliest flowering. And the LD13 + 4B (30) produced the greatest number of flowers. The flowering pattern in response to the intensity of S-B or NI-B was consistent as it was gradually promoted from 10 to 30 μmol m-2 s-1 PPFD and inhibited by 40B regardless of the photoperiod. In SD conditions, the same intensity of S-B and NI-B did not significantly affect flowering, while differential flowering inhibition was observed with any intensity of NI-B in LDs. Furthermore, the 30 μmol·m-2·s-1 PPFD of S-B or NI-B up-regulated the expression of floral meristem identity or florigen genes, as well as the chlorophyll content, photosynthetic efficiency, and carbohydrate accumulation. The 40B also promoted these physiological traits but led to the unbalanced expression of florigen or anti-florigen genes. Overall, the photoperiodic flowering in response to the intensity of S-B or NI-B of the SDP chrysanthemum suggests the co-regulation of photosynthetic carbon assimilation and differential photoreceptor-mediated control.

Expression Profiling of Four Mango FT/TFL1-Encoding Genes under Different Fruit Load Conditions, and Their Involvement in Flowering Regulation

Plant flowering is antagonistically modulated by similar FLOWERING LOCUS T (FT) and TERMINAL FLOWER 1 (TFL1) proteins. In mango (Mangifera indica L.), flowering is induced by cold temperatures, unless the tree is juvenile or the adult tree had a high fruit load (HFL) in the summer. Here, we studied the effects of juvenility and fruit load on the expression of four MiFT/TFL1 genes cloned from the mango ‘Shelly’ cultivar. Ectopic expression of MiFT1 in Arabidopsis resulted in early flowering, whereas over-expression of MiFT2 and the two cloned MiTFL1 genes repressed flowering. Moreover, juvenility was positively correlated with higher transcript levels of MiFT2 and both MiTFL1s. In trees with a low fruit load, leaf MiFT1 expression increased in winter, whereas HFL delayed its upregulation. MiFT2 expression was upregulated in both leaves and buds under both fruit load conditions. Downregulation of both MITFL1s in buds was associated with a decrease in regional temperatures under both conditions; nevertheless, HFL delayed the decrease in their accumulation. Our results suggest that cold temperature has opposite effects on the expression of MiFT1 and the MiTFL1s, thereby inducing flowering, whereas HFL represses flowering by both suppressing MiFT1 upregulation and delaying MiTFL1s downregulation. The apparent flowering-inhibitory functions of MiFT2 are discussed.

Expression Patterns of Key Genes in the Photoperiod and Vernalization Flowering Pathways in Lilium longiflorum with Different Bulb Sizes

Lilium longiflorum is a wild Lilium, and its flowering transition requires a long period of cold exposure to meet the demand of vernalization. The responses of different sized bulbs to cold exposure and photoperiod are different, and the floral transition pathways of small and large bulbs are different. In this study, small and large bulbs were placed in cold storage for different weeks and then cultured at a constant ambient temperature of 25 °C under long day (LD) and short day (SD) conditions. Then, the flowering characteristics and expression patterns of key genes related to the vernalization and photoperiod pathways in different groups were calculated and analyzed. The results showed that the floral transition of Lilium longiflorum was influenced by both vernalization and photoperiod, that vernalization and LD conditions can significantly improve the flowering rate of Lilium longiflorum, and that the time from planting to visible flowering buds’ appearance was decreased. The flowering time and rate of large bulbs were greatly influenced by cold exposure, and the vernalization pathway acted more actively at the floral transition stage. The floral transition of small bulbs was affected more by the photoperiod pathway. Moreover, it was speculated that cold exposure may promote greater sensitivity of the small bulbs to LD conditions. In addition, the expression of LlVRN1, LlFKF1, LlGI, LlCO5, LlCO7, LlCO16, LlFT1, LlFT3 and LlSOC1 was high during the process of floral transition, and LlCO13, LlCO14 and LlCO15 were highly expressed in the vegetative stage. The expression of LlCO13 and LlCO14 was different under different lighting conditions, and the flowering induction function of LlCO9 and LlFT3 was related to vernalization. Moreover, LlFKF1, LlGI, LlCO5, LlCO16, LlSOC1 and LlFT2 were involved in the entire growth process of plants, while LlCO6, LlCO16 and LlFT1 are involved in the differentiation and formation of small bulblets of plants after the inflorescence stage, and this process is also closely related to LD conditions. This study has great significance for understanding the molecular mechanisms of the vernalization and photoperiod flowering pathways of Lilium longiflorum.

Fine mapping and analysis of candidate genes for qFT7.1, a major quantitative trait locus controlling flowering time in Brassica rapa L

qFT7.1, a major QTL for flowering time in Brassica rapa was fine-mapped to chromosome A07 in a 56.4-kb interval, in which the most likely candidate gene is BraA07g018240.3C. In Brassica rapa, flowering time (FT) is an important agronomic trait that affects the yield, quality, and adaption. FT is a complicated trait that is regulated by many genes and is affected greatly by the environment. In this study, a chromosome segment substitution line (CSSL), CSSL16, was selected that showed later flowering than the recurrent parent, a rapid-cycling inbred line of B. rapa (RcBr). Using Bulked Segregant RNA sequencing, we identified a late flowering quantitative trait locus (QTL), designated as qFT7.1, on chromosome A07, based on a secondary-F₂ population derived from the cross between CSSL16 and RcBr. qFT7.1 was further validated by conventional QTL mapping. This QTL explained 39.9% (logarithm of odds = 32.2) of the phenotypic variations and was fine mapped to a 56.4-kb interval using recombinant analysis. Expression analysis suggested that BraA07g018240.3C, which is homologous to ATC (encoding Arabidopsis thaliana CENTRORADIALIS homologue), a gene for delayed flowering in Arabidopsis, as the most promising candidate gene. Sequence analysis demonstrated that two synonymous mutations existed in the coding region and numerous bases replacements existed in promoter region between BraA07g018240.3C from CSSL16 and RcBr. The results will increase our knowledge related to the molecular mechanism of late flowering in B. rapa and lays a solid foundation for the breeding of late bolting B. rapa.

Asymmetric expansions of FT and TFL1 lineages characterize differential evolution of the EuPEBP family in the major angiosperm lineages

Background

In flowering plants, precise timing of the floral transition is crucial to maximize chances of reproductive success, and as such, this process has been intensively studied. FLOWERING LOCUS T (FT) and TERMINAL FLOWER1 (TFL1) have been identified as closely related eukaryotic phosphatidylethanolamine-binding proteins (‘EuPEBPs’) that integrate multiple environmental stimuli, and act antagonistically to determine the optimal timing of the floral transition. Extensive research has demonstrated that FT acts similar to hormonal signals, being transported in the phloem from its primary site of expression in leaves to its primary site of action in the shoot meristem; TFL1 also appears to act as a mobile signal. Recent work implicates FT, TFL1, and the other members of the EuPEBP family, in the control of other important processes, suggesting that the EuPEBP family may be key general regulators of developmental transitions in flowering plants. In eudicots, there are a small number of EuPEBP proteins, but in monocots, and particularly grasses, there has been a large, but uncharacterized expansion of EuPEBP copy number, with unknown consequences for the EuPEBP function.

Results

To systematically characterize the evolution of EuPEBP proteins in flowering plants, and in land plants more generally, we performed a high-resolution phylogenetic analysis of 701 PEBP sequences from 208 species. We refine previous models of EuPEBP evolution in early land plants, demonstrating the algal origin of the family, and pin-pointing the origin of the FT/TFL1 clade at the base of monilophytes. We demonstrate how a core set of genes (MFT1, MFT2, FT, and TCB) at the base of flowering plants has undergone differential evolution in the major angiosperm lineages. This includes the radical expansion of the FT family in monocots into 5 core lineages, further re-duplicated in the grass family to 12 conserved clades.

Conclusions

We show that many grass FT proteins are strongly divergent from other FTs and are likely neo-functional regulators of development. Our analysis shows that monocots and eudicots have strongly divergent patterns of EuPEBP evolution.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12915-021-01128-8.

Linkage mapping and QTL analysis of flowering time in faba bean

Flowering time marks the transition from vegetative to reproductive growth and is key for optimal yield in any crop. The molecular mechanisms controlling this trait have been extensively studied in model plants such as Arabidopsis thaliana and rice. While knowledge on the molecular regulation of this trait is rapidly increasing in sequenced galegoid legume crops, understanding in faba bean remains limited. Here we exploited translational genomics from model legume crops to identify and fine map QTLs linked to flowering time in faba bean. Among the 31 candidate genes relevant for flowering control in A. thaliana and Cicer arietinum assayed, 25 could be mapped in a segregating faba bean RIL population. While most of the genes showed conserved synteny among related legume species, none of them co-localized with the 9 significant QTL regions identified. The FT gene, previously implicated in the control of flowering time in numerous members of the temperate legume clade, mapped close to the most relevant stable and conserved QTL in chromosome V. Interestingly, QTL analysis suggests an important role of epigenetic modifications in faba bean flowering control. The new QTLs and candidate genes assayed here provide a robust framework for further genetic studies and will contribute to the elucidation of the molecular mechanisms controlling this trait.

Linkage mapping and QTL analysis of flowering time in faba bean

Flowering time marks the transition from vegetative to reproductive growth and is key for optimal yield in any crop. The molecular mechanisms controlling this trait have been extensively studied in model plants such as Arabidopsis thaliana and rice. While knowledge on the molecular regulation of this trait is rapidly increasing in sequenced galegoid legume crops, understanding in faba bean remains limited. Here we exploited translational genomics from model legume crops to identify and fine map QTLs linked to flowering time in faba bean. Among the 31 candidate genes relevant for flowering control in A. thaliana and Cicer arietinum assayed, 25 could be mapped in a segregating faba bean RIL population. While most of the genes showed conserved synteny among related legume species, none of them co-localized with the 9 significant QTL regions identified. The FT gene, previously implicated in the control of flowering time in numerous members of the temperate legume clade, mapped close to the most relevant stable and conserved QTL in chromosome V. Interestingly, QTL analysis suggests an important role of epigenetic modifications in faba bean flowering control. The new QTLs and candidate genes assayed here provide a robust framework for further genetic studies and will contribute to the elucidation of the molecular mechanisms controlling this trait.

Functional analysis and expression patterns of members of the FLOWERING LOCUS T (FT) gene family in Lilium

Lilium is an important commercial flowering species, and there are many varieties and more than 100 species of wild Lilium. Lilium × formolongi is usually propagated from seedlings, and the flowering of these plants is driven mainly by the photoperiodic pathway. Most of the other lily plants are propagated via bulblets and need to be vernalized; these plants can be simply divided into pretransplantation types and posttransplantation types according to the time at which the floral transition occurs. We identified three Lilium FLOWERING LOCUS T (LFT) family members in 7 Lilium varieties, and for each gene, the coding sequence of the different varieties was identical. Among these genes, the LFT1 gene of Lilium was most homologous to the AtFT gene, which promotes flowering in Arabidopsis. We analyzed the expression patterns of LFT genes in Lilium × formolongi seedlings and in different Lilium varieties, and the results showed that LFT1 and LFT3 may promote floral induction. Compared with LFT3, LFT1 may have a greater effect on floral induction in Lilium, which is photoperiod sensitive, while LFT3 may play a more important role in the floral transition of lily plants, which have a high requirement for vernalization. LFT2 may be involved in the differentiation of bulblets, which was verified by tissue culture experiments, and LFT1 may have other functions involved in promoting bulblet growth. The functions of LFT genes were verified by the use of transgenic Arabidopsis thaliana plants, which showed that both the LFT1 and LFT3 genes can promote early flowering in Arabidopsis. Compared with LFT3, LFT1 promoted flowering more obviously, and thus, this gene could be an important promoter of floral induction in Lilium.

FT5a interferes with the Dt1-AP1 feedback loop to control flowering time and shoot determinacy in soybean

Flowering time and stem growth habit determine inflorescence architecture in soybean, which in turn influences seed yield. Dt1, a homolog of Arabidopsis TERMINAL FLOWER 1 (TFL1), is a major controller of stem growth habit, but its underlying molecular mechanisms remain unclear. Here, we demonstrate that Dt1 affects node number and plant height, as well as flowering time, in soybean under long-day conditions. The bZIP transcription factor FDc1 physically interacts with Dt1, and the FDc1-Dt1 complex directly represses the expression of APETALA1 (AP1). We propose that FT5a inhibits Dt1 activity via a competitive interaction with FDc1 and directly upregulates AP1. Moreover, AP1 represses Dt1 expression by directly binding to the Dt1 promoter, suggesting that AP1 and Dt1 form a suppressive regulatory feedback loop to determine the fate of the shoot apical meristem. These findings provide novel insights into the roles of Dt1 and FT5a in controlling the stem growth habit and flowering time in soybean, which determine the adaptability and grain yield of this important crop.

Genome-wide member identification, phylogeny and expression analysis of PEBP gene family in wheat and its progenitors

The phosphatidylethanolamine binding protein (PEBP) family comprises ancient proteins found throughout the biosphere that play an important role in plant growth and development, flowering, seed development and dormancy. However, not all PEBP genes have been identified or analyzed in common wheat (Triticum aestivum L.) and its progenitors. In this study, we identified the PEBP genes in common wheat, Triticum dicoccoides, Triticum urartu and Aegilops tauschii by searching whole genome sequences, and characterized these genes by phylogenetic and transcriptome analyses. A total of 76, 38, 16 and 22 PEBP genes were identified in common wheat, T. dicoccoides, T. urartu and Ae. tauschii, respectively. Phylogenetic analysis classified the PEBP genes into four subfamilies (PEBP-like, MFT-like, TFL-like and FT-like); the PEBP-like subfamily was identified as a new subfamily with genes in this subfamily were conserved in plants. Group 2, 3 and 5 chromosomes of common wheat and its progenitors contained more PEBP genes than other chromosomes. The PEBP genes were conserved in wheat during evolution, and tandem duplication played a more important role in the amplification of PEBP genes than segmental duplication. Furthermore, transcriptome analysis revealed that PEBP genes showed tissue/organ-specific expression profiles and some PEBP genes were induced to express by biotic stresses. Quantitative real-time PCR (qRT-PCR) analysis revealed that seven randomly selected PEBP genes expressed differently during seed germination under cold, drought, flood, heat and salt stress treatments, and five of these genes (TaPEBP1, TaPEBP5, TaPEBP9, TaPEBP66 and TaPEBP69) showed significantly higher expression under different stress treatments, indicating that these genes play important roles during seed germination under stress conditions.

Evolution and functional diversification of FLOWERING LOCUS T/TERMINAL FLOWER 1 family genes in plants

Plant growth and development, particularly the induction of flowering, are tightly controlled by key regulators in response to endogenous and environmental cues. The FLOWERING LOCUS T (FT)/TERMINAL FLOWER 1 (TFL1) family of phosphatidylethanolamine-binding protein (PEBP) genes is central to plant development, especially the regulation of flowering time and plant architecture. FT, the long-sought florigen, promotes flowering and TFL1 represses flowering. The balance between FT and TFL1 modulates plant architecture by switching the meristem from indeterminate to determinate growth, or vice versa. Recent studies in a broad range of plant species demonstrated that, in addition to their roles in flowering time and plant architecture, FT/TFL1 family genes participate in diverse aspects of plant development, such as bamboo seed germination and potato tuber formation. In this review, we briefly summarize the evolution of the FT/TFL1 family and highlight recent findings on their conserved and divergent functions in different species.

Identification and Characterization of the PEBP Family Genes in Moso Bamboo (Phyllostachys heterocycla)

Moso bamboo is one of the economically most important plants in China. Moso bamboo is a monocarpic perennial that exhibits poor and slow germination. Thus, the flowering often causes destruction of moso bamboo forestry. However, how control of flowering and seed germination are regulated in moso bamboo is largely unclear. In this study, we identified 5 members (PhFT1-5) of the phosphatidyl ethanolamine-binding proteins (PEBP) family from moso bamboo genome that regulate flowering, flower architecture and germination, and characterized the function of these PEBP family genes further in Arabidopsis. Phylogenetic analysis revealed that 3 (PhFT1, PhFT2 and PhFT3), 1 (PhFT4) and 1 (PhFT5) members belong to the TFL1-like clade, FT-like clade, and MFT-like clade, respectively. These PEBP family genes possess all structure necessary for PEBP gene function. The ectopic overexpression of PhFT4 and PhFT5 promotes flowering time in Arabidopsis, and that of PhFT1, PhFT2 and PhFT3 suppresses it. In addition, the overexpression of PhFT5 promotes seed germination rate. Interestingly, the overexpression of PhFT1 suppressed seed germination rate in Arabidopsis. The expression of PhFT1 and PhFT5 is significantly higher in seed than in tissues including leaf and shoot apical meristem, implying their function in seed germination. Taken together, our results suggested that the PEBP family genes play important roles as regulators of flowering and seed germination in moso bamboo and thereby are necessary for the sustainability of moso bamboo forest.

Genetic insights into the modification of the pre-fertilization mechanisms during plant domestication

Plant domestication is the process of adapting plants to human use by selecting specific traits. The selection process often involves the modification of some components of the plant reproductive mechanisms. Allelic variants of genes associated with flowering time, vernalization, and the circadian clock are responsible for the adaptation of crops, such as rice, maize, barley, wheat, and tomato, to non-native latitudes. Modifications in the plant architecture and branching have been selected for higher yields and easier harvests. These phenotypes are often produced by alterations in the regulation of the transition of shoot apical meristems to inflorescences, and then to floral meristems. Floral homeotic mutants are responsible for popular double-flower phenotypes in Japanese cherries, roses, camellias, and lilies. The rise of peloric flowers in ornamentals such as snapdragon and florists' gloxinia is associated with non-functional alleles that control the relative expansion of lateral and ventral petals. Mechanisms to force outcrossing such as self-incompatibility have been removed in some tree crops cultivars such as almonds and peaches. In this review, we revisit some of these important concepts from the plant domestication perspective, focusing on four topics related to the pre-fertilization mechanisms: flowering time, inflorescence architecture, flower development, and pre-fertilization self-incompatibility mechanisms.

Highly multiplexed AmpliSeq technology identifies novel variation of flowering time-related genes in soybean (Glycine max)

Whole-genome re-sequencing is a powerful approach to detect gene variants, but it is expensive to analyse only the target genes. To circumvent this problem, we attempted to detect novel variants of flowering time-related genes and their homologues in soybean mini-core collection by target re-sequencing using AmpliSeq technology. The average depth of 382 amplicons targeting 29 genes was 1,237 with 99.85% of the sequence data mapped to the reference genome. Totally, 461 variants were detected, of which 150 sites were novel and not registered in dbSNP. Known and novel variants were detected in the classical maturity loci-E1, E2, E3, and E4. Additionally, large indel alleles, E1-nl and E3-tr, were successfully identified. Novel loss-of-function and missense variants were found in FT2a, MADS-box, WDR61, phytochromes, and two-component response regulators. The multiple regression analysis showed that four genes-E2, E3, Dt1, and two-component response regulator-can explain 51.1-52.3% of the variation in flowering time of the mini-core collection. Among them, the two-component response regulator with a premature stop codon is a novel gene that has not been reported as a soybean flowering time-related gene. These data suggest that the AmpliSeq technology is a powerful tool to identify novel alleles.

Functional characterization of Terminal Flower1 homolog in Cornus canadensis by genetic transformation

TFL1homologCorcanTFL1suppresses the initiation of inflorescence development and regulates the inflorescence morphology inCornus canadensis. In flowering plants, there is a wide range of variation of inflorescence morphology. Despite the ecological and evolutionary importance, efforts devoted to the evolutionary study of the genetic basis of inflorescence morphology are far fewer compared to those on flower development. Our previous study on gene expression patterns suggested a CorTFL1-CorAP1 based model for the evolution of determinate umbels, heads, and mini dichasia from elongated inflorescences in Cornus. Here, we tested the function of CorcanTFL1 in regulating inflorescence development in Cornus canadensis through Agrobacterium-mediated transformation. We showed that transgenic plants overexpressing CorcanTFL1 displayed delayed or suppressed inflorescence initiation and development and extended periods of vegetative growth. Transgenic plants within which CorcanTFL1 had been down-regulated displayed earlier emergence of inflorescence and a reduction of bract and inflorescence sizes, conversions of leaves to bracts and axillary leaf buds to small inflorescences at the uppermost node bearing the inflorescence, or phyllotaxy changes of inflorescence branches and leaves from decussate opposite to spirally alternate. These observations support an important role of CorcanTFL1 in determining flowering time and the morphological destinies of leaves and buds at the node bearing the inflorescence. The evidence is in agreement with the predicted function of CorTFL1 from the gene expression model, supporting a key role of CorTFL1 in the evolutionary divergence of inflorescence forms in Cornus.

Flax latitudinal adaptation at LuTFL1 altered architecture and promoted fiber production

After domestication in the Near East around 10,000 years ago several founder crops, flax included, spread to European latitudes. On reaching northerly latitudes the architecture of domesticated flax became more suitable to fiber production over oil, with longer stems, smaller seeds and fewer axillary branches. Latitudinal adaptations in crops typically result in changes in flowering time, often involving the PEBP family of genes that also have the potential to influence plant architecture. Two PEBP family genes in the flax genome, LuTFL1 and LuTFL2, vary in wild and cultivated flax over latitudinal range with cultivated flax receiving LuTFL1 alleles from northerly wild flax populations. Compared to a background of population structure of flaxes over latitude, the LuTFL1 alleles display a level of differentiation that is consistent with selection for an allele III in the north. We demonstrate through heterologous expression in Arabidopsis thaliana that LuTFL1 is a functional homolog of TFL1 in A. thaliana capable of changing both flowering time and plant architecture. We conclude that specialized fiber flax types could have formed as a consequence of a natural adaptation of cultivated flax to higher latitudes.

Nulliplex-branch, a TERMINAL FLOWER 1 ortholog, controls plant growth habit in cotton

Nulliplex-branch (nb) mutants in cotton display a specific architecture. The gene responsible for the nb phenotype was identified, and its modulation mode was further studied. Plant architecture is an important agronomic factor influencing various traits such as yield and variety adaptability in crop plants. Cotton (Gossypium) simultaneously displays monopodial and sympodial growth. Nulliplex-branch (nb) mutants showing determinate sympodial shoots have been reported in both G. hirsutum (Ghnb) and G. barbadense (Gbnb). In this study, the gene responsible for the nb phenotype was identified. GhNB and GbNB were found to be allelic loci and are TERMINAL FLOWER 1 orthologs on the Dt subgenome, though the At copies remain native. Sequencing and association analyses identified four (Gh-nb1-Gh-nb4) and one (Gb-nb1) type of point mutation in the coding sequences of Ghnb and Gbnb, respectively. The NB gene was mainly expressed in the root and shoot apex, and expression rhythms were also observed in these tissues, suggesting that the expression of the NB gene could be regulated by photoperiod. Constitutive overexpression of GhNB suppresses the differentiation of the reproductive shoots. Knockout of both copies of GhNB caused the main and lateral shoots to terminate in flowers, which is a more determinate architecture than that of the nb mutants and implies that its function might be dosage dependent. A protein lipid overlay assay indicated that the amino acid substitutions in Gh-nb1 and Gb-nb1 weaken the ligand-binding activity of the NB protein in vitro. These findings suggest that the NB gene plays crucial roles in regulating the determinacy of shoots, and the modulation of this gene should constitute an effective crop improvement approach through adjusting the growth habit of cotton.

Cotton CENTRORADIALIS/TERMINAL FLOWER 1/SELF-PRUNING genes functionally diverged to differentially impact plant architecture

Genes of the CENTRORADIALIS/TERMINAL FLOWER 1/SELF-PRUNING (CETS) family influence meristem identity by controlling the balance between indeterminate and determinate growth, thereby profoundly impacting plant architecture. Artificial selection during cotton (Gossypium hirsutum) domestication converted photoperiodic trees to the day-neutral shrubs widely cultivated today. To understand the regulation of cotton architecture and exploit these principles to enhance crop productivity, we characterized the CETS gene family from tetraploid cotton. We demonstrate that genes of the TERMINAL FLOWER 1 (TFL1)-like clade show different roles in regulating growth patterns. Cotton has five TFL1-like genes: SELF-PRUNING (GhSP) is a single gene whereas there are two TFL1-like and BROTHER OF FT (BFT)-like genes, and these duplications are specific to the cotton lineage. All genes of the cotton TFL1-like clade delay flowering when ectopically expressed in transgenic Arabidopsis, with the strongest phenotypes failing to produce functional flowers. GhSP, GhTFL1-L2, and GhBFT-L2 rescue the early flowering Attfl1-14 mutant phenotype, and the encoded polypeptides interact with a cotton FD protein. Heterologous promoter::GUS fusions illustrate differences in the regulation of these genes, suggesting that genes of the GhTFL1-like clade may not act redundantly. Characterizations of the GhCETS family provide strategies for nuanced control of plant growth.

Characterization of two TERMINAL FLOWER1 homologs PgTFL1 and PgCENa from pomegranate (Punica granatum L.)

FLOWERING LOCUS T (FT) and TERMINAL FLOWER1/CENTRORADIALIS (TFL1/CEN) are the key regulators of flowering time in plants with FT promoting flowering and TFL1 repressing flowering. TFL1 also controls floral meristem identity and its maintenance. In this study we have characterized two pomegranate (Punica granatum L.) TFL1/CEN-like genes designated as PgTFL1 and PgCENa. The expression of PgTFL1 and PgCENa fluctuated through alternate pruning and flowering cycles, being highly expressed during the vegetative phase (immediately after pruning) and decreasing gradually in the months thereafter such that their lowest levels, especially for PgCENa coincided with the flowering phase. Both the genes are able to functionally suppress the Arabidopsis tfl1-14 mutant flowering defect. Their expression in Arabidopsis resulted in delayed flowering time, increased plant height and leaf number, branches and shoot buds as compared with wild type, suggesting that PgTFL1 and PgCENa are bonafide homologs of TFL1. However, both the genes show distinct expression patterns, being expressed differentially in vegetative shoot apex and floral bud samples. While PgTFL1 expression was low in vegetative shoot apex and high in flower bud, PgCENa expression showed the opposite trend. These results suggest that the two TFL1s in pomegranate may be utilized to control distinct developmental processes, namely repression of flowering by PgCENa and development and growth of the reproductive tissues by PgTFL1 via distinct temporal and developmental regulation of their expression.

Florigen and anti-florigen: flowering regulation in horticultural crops

Flowering time regulation has significant effects on the agricultural and horticultural industries. Plants respond to changing environments and produce appropriate floral inducers (florigens) or inhibitors (anti-florigens) that determine flowering time. Recent studies have demonstrated that members of two homologous proteins, FLOWERING LOCUS T (FT) and TERMINAL FLOWER 1 (TFL1), act as florigen and anti-florigen, respectively. Studies in diverse plant species have revealed universal but diverse roles of the FT/TFL1 gene family in many developmental processes. Recent studies in several crop species have revealed that modification of flowering responses, either due to mutations in the florigen/anti-florigen gene itself, or by modulation of the regulatory pathway, is crucial for crop domestication. The FT/TFL1 gene family could be an important potential breeding target in many crop species.

Functional divergence and intron variability during evolution of angiosperm TERMINAL FLOWER1 (TFL1) genes

The protein encoded by the TERMINAL FLOWER1 (TFL1) gene maintains indeterminacy in inflorescence meristem to repress flowering, and has undergone multiple duplications. However, basal angiosperms have one copy of a TFL1-like gene, which clusters with eudicot TFL1/CEN paralogs. Functional conservation has been reported in the paralogs CENTRORADIALIS (CEN) in eudicots, and ROOTS CURL IN NPA (RCNs) genes in monocots. In this study, long-term functional conservation and selective constraints were found between angiosperms, while the relaxation of selective constraints led to subfunctionalisation between paralogs. Long intron lengths of magnoliid TFL1-like gene contain more conserved motifs that potentially regulate TFL1/CEN/RCNs expression. These might be relevant to the functional flexibility of the non-duplicate TFL1-like gene in the basal angiosperms in comparison with the short, lower frequency intron lengths in eudicot and monocot TFL1/CEN/RCNs paralogs. The functionally conserved duplicates of eudicots and monocots evolved according to the duplication-degeneration-complementation model, avoiding redundancy by relaxation of selective constraints on exon 1 and exon 4. These data suggest that strong purifying selection has maintained the relevant functions of TFL1/CEN/RCNs paralogs on flowering regulation throughout the evolution of angiosperms, and the shorter introns with radical amino acid changes are important for the retention of paralogous duplicates.

TET3-mediated demethylation in tomato activates expression of a CETS gene that stimulates vegetative growth

Expression of the mammalian DNA demethylase enzyme TET3 in plants can be used to induce hypomethylation of DNA. In tomato lines that express a TET3 transgene, we observed distinct phenotypes including an increase in the length and number of leaves of primary shoots. As these changes resemble phenotypes observed in plants with strong expression of SELF PRUNING (SP), a member of the PEBP/CETS family, we investigated in TET3 lines the expression levels of members of the PEBP/CETS gene family, which affect shoot architecture and growth of sympodial units in tomato. We did not detect any changes in SP expression in TET3 lines, but for CEN1.1, a putative family member that has not been functionally characterized, we identified changes in gene expression that corresponded to hypomethylation in the upstream region. In tomato wild type, CEN1.1 is expressed in roots, petals, and shoot apices but not in mature leaves. In contrast, in TET3 transformants, the CEN1.1 gene became hypomethylated and activated in leaves. Ectopic expression of CEN1.1 in tomato caused similar phenotypes to those seen in TET3 transformants. Vegetative growth was increased, resulting both in a delay in inflorescence development and in an instability of the inflorescences, which frequently reverted to a vegetative state. Ectopic expression of CEN1.1 in Arabidopsis thaliana also caused floral repression. Our data suggest that the phenotypes observed in TET3 lines are a consequence of ectopic activation of CEN1.1, which promotes vegetative growth, and that CEN1.1 expression is sensitive to DNA methylation changes.

Alterations of CorTFL1 and CorAP1 expression correlate with major evolutionary shifts of inflorescence architecture in Cornus (Cornaceae) - a proposed model for variation of closed inflorescence forms

TFL1-, AP1- and LFY-like genes are known to be key regulators of inflorescence development. However, it remains to be tested whether the evolutionary modifications of inflorescence morphology result from shifts in their expression patterns. We compared the spatiotemporal expression patterns of CorTFL1, CorAP1 and CorLFY in six closely related Cornus species that display four types of closed inflorescence morphology using quantitative real-time polymerase chain reaction (qRT-PCR) and RNA in situ hybridization. Character mapping on the phylogeny was conducted to identify evolutionary changes and to assess the correlation between changes in gene expression and inflorescence morphology. Results demonstrated variation of gene expression patterns among species and a strong correlation between CorTFL1 expression and the branch index of the inflorescence type. Evolutionary changes in CorTFL1 and CorAP1 expression co-occurred on the phylogeny with the morphological changes underpinning inflorescence divergence. The study found a clear correlation between the expression patterns of CorTFL1 and CorAP1 and the inflorescence architecture in a natural system displaying closed inflorescences. The results suggest a role for the alteration in CorTFL1 and CorAP1 expression during the evolutionary modification of inflorescences in Cornus. We propose that a TFL1-like and AP1-like gene-based model may explain variation of closed inflorescences in Cornus and other lineages.

Three FT and multiple CEN and BFT genes regulate maturity, flowering, and vegetative phenology in kiwifruit

Kiwifruit is a woody perennial horticultural crop, characterized by excessive vegetative vigor, prolonged juvenility, and low productivity. To understand the molecular factors controlling flowering and winter dormancy, here we identify and characterize the kiwifruit PEBP (phosphatidylethanolamine-binding protein) gene family. Five CEN-like and three BFT-like genes are differentially expressed and act as functionally conserved floral repressors, while two MFT-like genes have no impact on flowering time. FT-like genes are differentially expressed, with AcFT1 confined to shoot tip and AcFT2 to mature leaves. Both act as potent activators of flowering, but expression of AcFT2 in Arabidopsis resulted in a greater impact on plant morphology than that of AcFT1. Constitutive expression of either construct in kiwifruit promoted in vitro flowering, but AcFT2 displayed a greater flowering activation efficiency than AcFT1, leading to immediate floral transition and restriction of leaf development. Both leaf and flower differentiation were observed in AcFT1 kiwifruit lines. Sequential activation of specific PEBP genes in axillary shoot buds during growth and dormancy cycles indicated specific roles in regulation of kiwifruit vegetative and reproductive phenologies. AcCEN and AcCEN4 marked active growth, AcBFT2 was associated with suppression of latent bud growth during winter, and only AcFT was activated after cold accumulation and dormancy release.

CmFTL2 is involved in the photoperiod- and sucrose-mediated control of flowering time in chrysanthemum

The chrysanthemum genome harbors three FT-like genes: CmFTL1 and CmFTL3 are thought to act as regulators of floral induction under long-day (LD) and short-day (SD) conditions, respectively, whereas the function of CmFTL2 is currently unclear. The objective of the present research was to explore the function of CmFTL2 in the determination of flowering time of the photo-insensitive chrysanthemum cultivar 'Floral Yuuka', both in response to variation in the photoperiod and to the exogenous provision of sucrose. Spraying leaves of 'Floral Yuuka' plants with 50 mM sucrose accelerated flowering and increased the level of CmFTL2 transcription in the leaf more strongly than either CmFTL1 or FTL3 under both long and SD conditions. Transcription profiling indicated that all three CmFTL genes were upregulated during floral induction. The relationship of the CmFTL2 sequence with that of other members of the PEBP family suggested that its product contributes to the florigen rather than to the anti-florigen complex. The heterologous expression of CmFTL2 in the Arabidopsis thaliana ft-10 mutant rescued the mutant phenotype, showing that CmFTL2 could compensate for the absence of FT. These results suggest that CmFTL2 acts as a regulator of floral transition and responds to both the photoperiod and sucrose.

Possible Role of MADS AFFECTING FLOWERING 3 and B-BOX DOMAIN PROTEIN 19 in Flowering Time Regulation of Arabidopsis Mutants with Defects in Nonsense-Mediated mRNA Decay

Eukaryotic cells use nonsense-mediated mRNA decay (NMD) to clear aberrant mRNAs from the cell, thus preventing the accumulation of truncated proteins. In Arabidopsis, two UP-Frameshift (UPF) proteins, UPF1 and UPF3, play a critical role in NMD. Although deficiency of UPF1 and UPF3 leads to various developmental defects, little is known about the mechanism underlying the regulation of flowering time by NMD. Here, we showed that the upf1-5 and upf3-1 mutants had a late-flowering phenotype under long-day conditions and the upf1-5 upf3-1 double mutants had an additive effect in delaying flowering time. RNA sequencing of the upf mutants revealed that UPF3 exerted a stronger effect than UPF1 in the UPF-mediated regulation of flowering time. Among genes known to regulate flowering time, FLOWERING LOCUS C (FLC) mRNA levels increased (up to 8-fold) in upf mutants, as confirmed by qPCR. The upf1-5, upf3-1, and upf1-5 upf3-1 mutants responded to vernalization, suggesting a role of FLC in delayed flowering of upf mutants. Consistent with the high FLC transcript levels and delayed flowering in upf mutants, levels of FLOWERING LOCUS T (FT) and SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1) mRNAs were reduced in the upf mutants. However, RNA-seq did not identify an aberrant FLC transcript containing a premature termination codon (PTC), suggesting that FLC is not a direct target in the regulation of flowering time by NMD. Among flowering time regulators that act in an FLC-dependent manner, we found that MAF3, NF-YA2, NF-YA5, and TAF14 showed increased transcript levels in upf mutants. We also found that BBX19 and ATC, which act in an FLC-independent manner, showed increased transcript levels in upf mutants. An aberrant transcript containing a PTC was identified from MAF3 and BBX19 and the levels of the aberrant transcripts increased in upf mutants. Taking these results together, we propose that the late-flowering phenotype of upf mutants is mediated by at least two different pathways, namely, by MAF3 in an FLC-dependent manner and by BBX19 in an FLC-independent manner.

Ultra-dense SNP genetic map construction and identification of SiDt gene controlling the determinate growth habit in Sesamum indicum L

Sesame (Sesamum indicum L.) is an important oilseed crop and has an indeterminate growth habit. Here we resequenced the genomes of the parents and 120 progeny of an F2 population derived from crossing Yuzhi 11 (indeterminate, Dt) and Yuzhi DS899 (determinate, dt1), and constructed an ultra-dense SNP map for sesame comprised of 3,041 bins including 30,193 SNPs in 13 linkage groups (LGs) with an average marker density of 0.10 cM. Results indicated that the same recessive gene controls the determinacy trait in dt1 and a second determinate line, dt2 (08TP092). The QDt1 locus for the determinacy trait was located in the 18.0 cM-19.2 cM interval of LG8. The target SNP, SiDt27-1, and the determinacy gene, DS899s00170.023 (named here as SiDt), were identified in Scaffold 00170 of the Yuzhi 11 reference genome, based on genetic mapping and genomic association analysis. Unlike the G397A SNP change in the dt1 genotype, the SiDt allele in dt2 line was lost from the genome. This example of map-based gene cloning in sesame provides proof-of-concept of the utility of ultra-dense SNP maps for accurate genome research in sesame.

Comparative analysis of the pteridophyte Adiantum MFT ortholog reveals the specificity of combined FT/MFT C and N terminal interaction with FD for the regulation of the downstream gene AP1

To study the evolution of phosphatidylethanolamine-binding protein (PEBP) gene families in non-flowering plants, we performed a functional analysis of the PEBP gene AcMFT of the MFT clade in the pteridophyte Adiantum capillus-veneris. The expression of AcMFT was regulated by photoperiod similar to that for FT under both long day and short day conditions. Ectopic expression of AcMFT in Arabidopsis promotes the floral transition and partially complements the late flowering defect in transgenic Arabidopsis ft-1 mutants, suggesting that AcMFT functions similarly to FT in flowering plants. Interestingly, a similar partial compensation of the ft-1 late flowering phenotype was observed in Arabidopsis ectopically expressing only exon 4 of the C terminus of AcMFT and FT. This result indicated that the fourth exon of AcMFT and FT plays a similar and important role in promoting flowering. Further analysis indicated that exons 1-3 in the N terminus specifically enhanced the function of FT exon 4 in controlling flowering in Arabidopsis. Protein pull-down assays indicated that Arabidopsis FD proteins interact with full-length FT and AcMFT, as well as peptides encoded by 1-3 exon fragments or the 4th exon alone. Furthermore, similar FRET efficiencies for FT-FD and AcMFT-FD heterodimer in nucleus were observed. These results indicated that FD could form the similar complex with FT and AcMFT. Further analysis indicated that the expression of AP1, a gene downstream of FT, was up-regulated more strongly by FT than AcMFT in transgenic Arabidopsis. Our results revealed that AcMFT from a non-flowering plant could interact with FD to regulate the floral transition and that this function was reduced due to the weakened ability of AcMFT-FD to activate the downstream gene AP1.

Genetic analysis of developmental and adaptive traits in three doubled haploid populations of barley (Hordeum vulgare L.)

Study of three interconnected populations identified 13 maturity QTL of which eight collocate with phenology genes, and 18 QTL for traits associated with adaptation to drought-prone environments. QTL for maturity and other adaptive traits affecting barley adaptation were mapped in a drought-prone environment. Three interconnected doubled haploid (DH) populations were developed from inter-crossing three Australian elite genotypes (Commander, Fleet and WI4304). High-density genetic maps were constructed using genotyping by sequencing and single nucleotide polymorphisms (SNP) for major phenology genes controlling photoperiod response and vernalization requirement. Field trials were conducted on the three DH populations in six environments at three sites in southern Australia and over two cropping seasons. Phenotypic evaluations were done for maturity, early vigour, normalized difference vegetation index (NDVI) and leaf chlorophyll content (SPAD), leaf waxiness and leaf rolling. Thirteen maturity QTL were identified, all with significant QTL × environment interaction with one exception. Eighteen QTL were detected for other adaptive traits across the three populations, including three QTL for leaf rolling, six for leaf waxiness, three for early vigour, four for NDVI, and two QTL for SPAD. The three interlinked populations with high-density linkage maps described in this study are a significant resource for examining the genetic basis for barley adaptation in low-to-medium rainfall Mediterranean type environments.

Analysis of two TFL1 homologs of dogwood species (Cornus L.) indicates functional conservation in control of transition to flowering

Two TFL1 -like genes, CorfloTFL1 and CorcanTFL1 cloned from Cornus florida and C. canadensis, function in regulating the transition to reproductive development in Arabidopsis. TERMINAL FLOWER 1 (TFL1) is known to regulate inflorescence development in Arabidopsis thaliana and to inhibit the transition from a vegetative to reproductive phase within the shoot apical meristem. Despite the importance, TFL1 homologs have been functionally characterized in only a handful eudicots. Here we report the role of TFL1 homologs of Cornus L. in asterid clade of eudicots. Two TFL1-like genes, CorfloTFL1 and CorcanTFL1, were cloned from Cornus florida (a tree) and C. canadensis (a subshrub), respectively. Both are deduced to encode proteins of 175 amino acids. The amino acid sequences of these two Cornus TFL1 homologs share a high similarity to Arabidopsis TFL1 and phylogenetically more close to TFL1 paralogous copy ATC (Arabidopsis thaliana CENTRORADIALIS homologue). Two genes are overexpressed in wild-type and tfl1 mutant plants of A. thaliana. The over-expression of each gene in wild-type Arabidopsis plants results in delaying flowering time, increase of plant height and cauline and rosette leaf numbers, excessive shoot buds, and secondary inflorescence branches. The over-expression of each gene in the tfl1 mutant rescued developmental defects, such as the early determinate inflorescence development, early flowering time, and other vegetative growth defects, to normal phenotypes of wild-type plants. These transgenic phenotypes are inherited in progenies. All data indicate that CorfloTFL1 and CorcanTFL1 have conserved the ancestral function of TFL1 and CEN regulating flowering time and inflorescence determinacy.

Factorial combinations of protein interactions generate a multiplicity of florigen activation complexes in wheat and barley

The FLOWERING LOCUS T (FT) protein is a central component of a mobile flowering signal (florigen) that is transported from leaves to the shoot apical meristem (SAM). Two FT monomers and two DNA-binding bZIP transcription factors interact with a dimeric 14-3-3 protein bridge to form a hexameric protein complex. This complex, designated as the 'florigen activation complex' (FAC), plays a critical role in flowering. The wheat homologue of FT, designated FT1 (= VRN3), activates expression of VRN1 in the leaves and the SAM, promoting flowering under inductive long days. In this study, we show that FT1, other FT-like proteins, and different FD-like proteins, can interact with multiple wheat and barley 14-3-3 proteins. We also identify the critical amino acid residues in FT1 and FD-like proteins required for their interactions, and demonstrate that 14-3-3 proteins are necessary bridges to mediate the FT1-TaFDL2 interaction. Using in vivo bimolecular fluorescent complementation (BiFC) assays, we demonstrate that the interaction between FT1 and 14-3-3 occurs in the cytoplasm, and that this complex is then translocated to the nucleus, where it interacts with TaFDL2 to form a FAC. We also demonstrate that a FAC including FT1, TaFDL2 and Ta14-3-3C can bind to the VRN1 promoter in vitro. Finally, we show that relative transcript levels of FD-like and 14-3-3 genes vary among tissues and developmental stages. Since FD-like proteins determine the DNA specificity of the FACs, variation in FD-like gene expression can result in spatial and temporal modulation of the effects of mobile FT-like signals.

FLOWERING LOCUS T has higher protein mobility than TWIN SISTER OF FT

In plants, successful reproduction requires the proper timing of flowering under changing environmental conditions. Arabidopsis FLOWERING LOCUS T (FT), which encodes a proposed phloem-mobile florigen, has a close homologue, TWIN SISTER OF FT (TSF). During the vegetative phase, TSF shows high levels of expression in the hypocotyl before FT induction, but the tsf mutation does not have an apparent flowering-time phenotype on its own under long-day conditions. This study compared the protein mobility of FT and TSF. With TSF-overexpressing plants as the rootstock, the flowering time of ft tsf scion plants was only slightly accelerated. Previous work has shown that FT is graft-transmissible; by contrast, this study did not detect movement of TSF from the roots into the shoot of the scion plants. This study used plants overexpressing FT/TSF chimeric proteins to map a region responsible for FT movement. A chimeric TSF with region II of FT (L28 to G98) expressed in the rootstock caused early flowering in ft tsf scion plants; movement of the chimeric protein from the rootstocks into the shoot apical region of the ft tsf scion plants was also detected. Misexpression of TSF in the leaf under the control of the FT promoter or grafting of 35S::TSF cotyledons accelerated flowering of ft-10 plants. FT was more stable than TSF. Taking these results together, we propose that protein mobility of FT is higher than that of TSF, possibly due to a protein domain that confers mobility and/or protein stability.

CsTFL1, a constitutive local repressor of flowering, modulates floral initiation by antagonising florigen complex activity in chrysanthemum

Chrysanthemums require repeated cycles of short-day (SD) photoperiod for successful anthesis, but their vegetative state is strictly maintained under long-day (LD) or night-break (NB) conditions. We have previously demonstrated that photoperiodic flowering of a wild diploid chrysanthemum (Chrysanthemum seticuspe f. boreale) is controlled by a pair of systemic floral regulators, florigen (CsFTL3) and anti-florigen (CsAFT), produced in the leaves. Here, we report the functional characterisation of a local floral regulator, CsTFL1, a chrysanthemum orthologue of TERMINAL FLOWER 1 gene in Arabidopsis. Constitutive expression of CsTFL1 in C. seticuspe (CsTFL1-ox) resulted in extremely late flowering under SD and prevented up-regulation of floral meristem identity genes in shoot tips and leaves. Bimolecular fluorescence complementation assay showed that both CsTFL1 and CsFTL3 interacted with CsFDL1, a bZIP transcription factor FD homologue, in the nucleus. The transient gene expression assay indicated that CsTFL1 suppresses flowering by directly antagonising the flower inductive activity of the CsFTL3-CsFDL1 complex. Our results suggest that strict maintenance of vegetative state under non-inductive photoperiod is achieved by the coordinated action of both the systemic floral inhibitor and local floral inhibitor CsTFL1, which is constitutively expressed in shoot tips.

Changing the spatial pattern of TFL1 expression reveals its key role in the shoot meristem in controlling Arabidopsis flowering architecture

Models for the control of above-ground plant architectures show how meristems can be programmed to be either shoots or flowers. Molecular, genetic, transgenic, and mathematical studies have greatly refined these models, suggesting that the phase of the shoot reflects different genes contributing to its repression of flowering, its vegetativeness ('veg'), before activators promote flower development. Key elements of how the repressor of flowering and shoot meristem gene TFL1 acts have now been tested, by changing its spatiotemporal pattern. It is shown that TFL1 can act outside of its normal expression domain in leaf primordia or floral meristems to repress flower identity. These data show how the timing and spatial pattern of TFL1 expression affect overall plant architecture. This reveals that the underlying pattern of TFL1 interactors is complex and that they may be spatially more widespread than TFL1 itself, which is confined to shoots. However, the data show that while TFL1 and floral genes can both act and compete in the same meristem, it appears that the main shoot meristem is more sensitive to TFL1 rather than floral genes. This spatial analysis therefore reveals how a difference in response helps maintain the 'veg' state of the shoot meristem.