Photoperiodic and thermosensory pathways interact through CONSTANS to promote flowering at high temperature under short days

Flowering time: From physiology, through genetics to mechanism

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

A FLOWERING LOCUS T ortholog is associated with photoperiod-insensitive flowering in hemp (Cannabis sativa L.)

Hemp (Cannabis sativa L.) is an extraordinarily versatile crop, with applications ranging from medicinal compounds to seed oil and fibre products. Cannabis sativa is a short-day plant, and its flowering is highly controlled by photoperiod. However, substantial genetic variation exists for photoperiod sensitivity in C. sativa, and photoperiod-insensitive ("autoflower") cultivars are available. Using a bi-parental mapping population and bulked segregant analysis, we identified Autoflower2, a 0.5 Mbp locus significantly associated with photoperiod-insensitive flowering in hemp. Autoflower2 contains an ortholog of the central flowering time regulator FLOWERING LOCUS T (FT) from Arabidopsis thaliana which we termed CsFT1. We identified extensive sequence divergence between alleles of CsFT1 from photoperiod-sensitive and insensitive cultivars of C. sativa, including a duplication of CsFT1 and sequence differences, especially in introns. Furthermore, we observed higher expression of one of the CsFT1 copies found in the photoperiod-insensitive cultivar. Genotyping of several mapping populations and a diversity panel confirmed a correlation between CsFT1 alleles and photoperiod response, affirming that at least two independent loci involved in the photoperiodic control of flowering, Autoflower1 and Autoflower2, exist in the C. sativa gene pool. This study reveals the multiple independent origins of photoperiod insensitivity in C. sativa, supporting the likelihood of a complex domestication history in this species. By integrating the genetic relaxation of photoperiod sensitivity into novel C. sativa cultivars, expansion to higher latitudes will be permitted, thus allowing the full potential of this versatile crop to be reached.

High-throughput field phenotyping reveals that selection in breeding has affected the phenology and temperature response of wheat in the stem elongation phase

Crop growth and phenology are driven by seasonal changes in environmental variables, with temperature as one important factor. However, knowledge about genotype-specific temperature response and its influence on phenology is limited. Such information is fundamental to improve crop models and adapt selection strategies. We measured the increase in height of 352 European winter wheat varieties in 4 years to quantify phenology, and fitted an asymptotic temperature response model. The model used hourly fluctuations in temperature to parameterize the base temperature (Tmin), the temperature optimum (rmax), and the steepness (lrc) of growth responses. Our results show that higher Tmin and lrc relate to an earlier start and end of stem elongation. A higher rmax relates to an increased final height. Both final height and rmax decreased for varieties originating from the continental east of Europe towards the maritime west. A genome-wide association study (GWAS) indicated a quantitative inheritance and a large degree of independence among loci. Nevertheless, genomic prediction accuracies (GBLUPs) for Tmin and lrc were low (r≤0.32) compared with other traits (r≥0.59). As well as known, major genes related to vernalization, photoperiod, or dwarfing, the GWAS indicated additional, as yet unknown loci that dominate the temperature response.

A straightforward strategy for reducing variability in flowering time at warm ambient temperatures

Ambient temperature is one of the major environmental factors affecting flowering. As the temperature rises, most plants, including Arabidopsis, flower more rapidly. In addition, phenotypic variability in flowering time tends to increase at warm ambient temperatures. The increased variability of flowering time at warm temperatures prevents accurate flowering time measurements, particularly when evaluating the flowering time of Arabidopsis plants under short-day conditions in order to restrict the photoperiodic effect. Here, we propose a simple method for reducing the variability of flowering time at warm temperatures. Instead of growing plants at different temperatures from germination, the strategy of first vegetative growth at cool temperatures and then shifting to warm temperatures allows plants to respond more stably and robustly to warm temperatures. Consistent with flowering time measurements, plants grown under the modified growth condition exhibited higher levels of FLOWERING LOCUS T (FT) gene expression than plants grown exclusively at warm temperatures. This approach enables more precise thermo-response studies of flowering time control in Arabidopsis.

Analysis of temperature effects on the protein accumulation of the FT-FD module using newly generated Arabidopsis transgenic plants

Arabidopsis flowering is dependent on interactions between a component of the florigens FLOWERING LOCUS T (FT) and the basic leucine zipper (bZIP) transcription factor FD. These proteins form a complex that activates the genes required for flowering competence and integrates environmental cues, such as photoperiod and temperature. However, it remains largely unknown how FT and FD are regulated at the protein level. To address this, we created FT transgenic plants that express the N-terminal FLAG-tagged FT fusion protein under the control of its own promoter in ft mutant backgrounds. FT transgenic plants complemented the delayed flowering of the ft mutant and exhibited similar FT expression patterns to wild-type Col-0 plants in response to changes in photoperiod and temperature. Similarly, we generated FD transgenic plants in fd mutant backgrounds that express the N-terminal MYC-tagged FD fusion protein under the FD promoter, rescuing the late flowering phenotypes in the fd mutant. Using these transgenic plants, we investigated how temperature regulates the expression of FT and FD proteins. Temperature-dependent changes in FT and FD protein levels are primarily regulated at the transcript level, but protein-level temperature effects have also been observed to some extent. In addition, our examination of the expression patterns of FT and FD in different tissues revealed that similar to the spatial expression pattern of FT, FD mRNA was expressed in both the leaf and shoot apex, but FD protein was only detected in the apex, suggesting a regulatory mechanism that restricts FD protein expression in the leaf during the vegetative growth phase. These transgenic plants provided a valuable platform for investigating the role of the FT-FD module in flowering time regulation.

Flowering repressor CmSVP recruits the TOPLESS corepressor to control flowering in chrysanthemum

Plant flowering time is induced by environmental and endogenous signals perceived by the plant. The MCM1-AGAMOUSDEFICIENS-Serum Response Factor-box (MADS-box) protein SHORT VEGETATIVE PHASE (SVP) is a pivotal repressor that negatively regulates the floral transition during the vegetative phase; however, the transcriptional regulatory mechanism remains poorly understood. Here, we report that CmSVP, a chrysanthemum (Chrysanthemum morifolium Ramat.) homolog of SVP, can repress the expression of a key flowering gene, a chrysanthemum FLOWERING LOCUS T-like gene (CmFTL3), by binding its promoter CArG element to delay flowering in the ambient temperature pathway in chrysanthemum. Protein-protein interaction assays identified an interaction between CmSVP and CmTPL1-2, a chrysanthemum homologue of TOPLESS (TPL) that plays critical roles as transcriptional corepressor in many aspects of plant life. Genetic analyses revealed the CmSVP-CmTPL1-2 transcriptional complex is a prerequisite for CmSVP to act as a floral repressor. Furthermore, overexpression of CmSVP rescued the phenotype of the svp-31 mutant in Arabidopsis (Arabidopsis thaliana), overexpression of AtSVP or CmSVP in the Arabidopsis dominant-negative mutation tpl-1 led to ineffective late flowering, and AtSVP interacted with AtTPL, confirming the conserved function of SVP in chrysanthemum and Arabidopsis. We have validated a conserved machinery wherein SVP partially relies on TPL to inhibit flowering via a thermosensory pathway.

Genome-wide association study for temperature response and photo-thermal interaction of flowering time in soybean using a panel of cultivars with diverse maturity groups

KEY MESSAGE

A total of 101 QTNs were found to be associated with soybean flowering time responses to photo-thermal conditions; three candidate genes with non-synonymous substitutions were identified: Glyma.08G302500 (GmHY5), Glyma.08G303900 (GmPIF4c), and Glyma.16G046700 (GmVRN1). The flowering transition is a crucial component of soybean (Glycine max L. Merr.) development. The transition process is regulated by photoperiod, temperature, and their interaction. To examine the genetic architecture associated with temperature- and photo-thermal-mediated regulation of soybean flowering, we here performed a genome-wide association study using a panel of 201 soybean cultivars with maturity groups ranging from MG 000 to VIII. Each cultivar was grown in artificially controlled photoperiod and different seasons in 2017 and 2018 to assess the thermal response (TR) and the interactive photo-thermal response (IPT) of soybean flowering time. The panel contained 96,299 SNPs with minor allele frequencies > 5%; 33, 19, and 49 of these SNPs were significantly associated with only TR, only IPT, and both TR and IPT, respectively. Twenty-one SNPs were located in or near previously reported quantitative trait loci for first-flowering; 16 SNPs were located within 200 kb of the main-effect flowering genes GmFT2a, GmFT2b, GmFT3a, GmFT3b, GmFT5a, GmFT5b, GmCOL2b, GmPIF4b, and GmPIF4c, or near homologs of the known Arabidopsis thaliana flowering genes BBX19, VRN1, TFL1, FUL, AGL19, SPA1, HY5, PFT1, and EDF1. Natural non-synonymous allelic variations were identified in the candidate genes Glyma.08G302500 (GmHY5), Glyma.08G303900 (GmPIF4c), and Glyma.16G046700 (GmVRN1). Cultivars with different haplotypes showed significant variations in TR, IPT, and flowering time in multiple environments. The favorable alleles, candidate genes, and diagnostic SNP markers identified here provide valuable information for future improvement of soybean photo-thermal adaptability, enabling expansion of soybean production regions and improving plant resilience to global climate change.

Regulation of Flowering Time by Environmental Factors in Plants

The timing of floral transition is determined by both endogenous molecular pathways and external environmental conditions. Among these environmental conditions, photoperiod acts as a cue to regulate the timing of flowering in response to seasonal changes. Additionally, it has become clear that various environmental factors also control the timing of floral transition. Environmental factor acts as either a positive or negative signal to modulate the timing of flowering, thereby establishing the optimal flowering time to maximize the reproductive success of plants. This review aims to summarize the effects of environmental factors such as photoperiod, light intensity, temperature changes, vernalization, drought, and salinity on the regulation of flowering time in plants, as well as to further explain the molecular mechanisms that link environmental factors to the internal flowering time regulation pathway.

XAANTAL1 Reveals an Additional Level of Flowering Regulation in the Shoot Apical Meristem in Response to Light and Increased Temperature in Arabidopsis

Light and photoperiod are environmental signals that regulate flowering transition. In plants like Arabidopsis thaliana, this regulation relies on CONSTANS, a transcription factor that is negatively posttranslational regulated by phytochrome B during the morning, while it is stabilized by PHYA and cryptochromes 1/2 at the end of daylight hours. CO induces the expression of FT, whose protein travels from the leaves to the apical meristem, where it binds to FD to regulate some flowering genes. Although PHYB delays flowering, we show that light and PHYB positively regulate XAANTAL1 and other flowering genes in the shoot apices. Also, the genetic data indicate that XAL1 and FD participate in the same signaling pathway in flowering promotion when plants are grown under a long-day photoperiod at 22 °C. By contrast, XAL1 functions independently of FD or PIF4 to induce flowering at higher temperatures (27 °C), even under long days. Furthermore, XAL1 directly binds to FD, SOC1, LFY, and AP1 promoters. Our findings lead us to propose that light and temperature influence the floral network at the meristem level in a partially independent way of the signaling generated from the leaves.

Function of BrSOC1b gene in flowering regulation of Chinese cabbage and its protein interaction

MAIN CONCLUSION

BrSOC1b may promote early flowering of Chinese cabbage by acting on BrAGL9 a, BrAGL9 b, BrAGL2 and BrAGL8 proteins. SOC1 is a flowering signal integrator that acts as a key regulator in controlling plant flowering time. This study focuses on the cloning of the open reading frame of SOC1b (BrSOC1b, Gene ID: Bra000393) gene, and analyzes its structure and phylogenetic relationships. Additionally, various techniques such as vector construction, transgenic technology, virus-induced gene silencing technology, and protein interaction technology were employed to investigate the function of the BrSOC1b gene and its interactions with other proteins. The results indicate that BrSOC1b consists of 642 bp and encodes 213 amino acids. It contains conserved domains such as the MADS domain, K (keratin-like) domain, and SOC1 box. The phylogenetic analysis reveals that BrSOC1b shares the closest homology with BjSOC1 from Brassica juncea. Tissue localization analysis demonstrates that BrSOC1b exhibits the highest expression in the stem during the seedling stage and the highest expression in flowers during the early stage of pod formation. Sub-cellular localization analysis reveals that BrSOC1b is localized in the nucleus and plasma membrane. Furthermore, through genetic transformation of the BrSOC1b gene, it was observed that Arabidopsis thaliana plants expressing BrSOC1b flowered earlier and bolted earlier than wild-type plants. Conversely, Chinese cabbage plants with silenced BrSOC1b exhibited delayed bolting and flowering compared to the control plants. These findings indicate that BrSOC1b promotes early flowering in Chinese cabbage. Yeast two-hybrid and quantitative real-time PCR (qRT-PCR) analyses suggest that BrSOC1b may participate in the regulation of flowering by interacting with BrAGL9a, BrAGL9b, BrAGL2, and BrAGL8 proteins. Overall, this research holds significant implications for the analysis of key genes involved in regulating bolting and flowering in Chinese cabbage, as well as for enhancing germplasm innovation in Chinese cabbage breeding.

High ambient temperature impacts on flowering time in Brassica napus through both H2A.Z-dependent and independent mechanisms

Knowledge concerning the integration of genetic pathways mediating the responses to environmental cues controlling flowering initiation in crops is scarce. Here, we reveal the diversity in oilseed rape (OSR) flowering response to high ambient temperature. Using a set of different spring OSR varieties, we found a consistent flowering delay at elevated temperatures. Remarkably, one of the varieties assayed exhibited the opposite behaviour. Several FT-like paralogs are plausible candidates to be part of the florigen in OSR. We revealed that BnaFTA2 plays a major role in temperature-dependent flowering initiation. Analysis of the H2A.Z histone variant occupancy at this locus in different Brassica napus varieties produced contrasting results, suggesting the involvement of additional molecular mechanisms in BnaFTA2 repression at high ambient temperature. Moreover, BnARP6 RNAi plants showed little accumulation of H2A.Z at high temperature while maintaining temperature sensitivity and delayed flowering. Furthermore, we found that H3K4me3 present in BnaFTA2 under inductive flowering conditions is reduced at high temperature, suggesting a role for this hallmark of transcriptionally active chromatin in the OSR flowering response to warming. Our work emphasises the plasticity of flowering responses in B. napus and offers venues to optimise this process in crop species grown under suboptimal environmental conditions.

Involvement of microRNA164 in responses to heat stress in Arabidopsis

MicroRNAs (miRNAs) are considered to be integral parts of plant stress regulatory networks. Under long-term heat stress, miR164 is induced. Conversely, its targets are repressed. Transgenic overexpressors (164OE) and mutants of MIR164 (mir164) were used to study miR164's functions during heat responses. Target gene expression decreased in 164OE transgenic plants and increased in mir164a-4 and mir164b mutants. Under heat stress, the mir164 mutants presented heat-sensitive phenotypes, while 164OE transgenic plants showed better thermotolerance than wild-type (WT) plants. Overexpression of miR164 decreased heat-inhibition of hypocotyl lengths. Under heat stress, miR164 target genes modulated the expression of chlorophyll b reductase and chlorophyll catabolic genes, reducing the chlorophyll a/b ratio. More H₂O₂ accumulated in the mir164 mutants under heat stress, which may have caused oxidative damage. In addition, expression of HSPs was altered in the experimental plants compared to that of the WT. Overall, miR164 influenced target gene expression, altering development, chlorophyll a/b ratio, H₂O₂-caused damage, and HSPs expression under long-term heat stress. These phenomena, in turn, likely influence the thermotolerance of plants.

HOS15 represses flowering by promoting GIGANTEA degradation in response to low temperature in Arabidopsis

Flowering is the primary stage of the plant developmental transition and is tightly regulated by environmental factors such as light and temperature. However, the mechanisms by which temperature signals are integrated into the photoperiodic flowering pathway are still poorly understood. Here, we demonstrate that HOS15, which is known as a GI transcriptional repressor in the photoperiodic flowering pathway, controls flowering time in response to low ambient temperature. At 16°C, the hos15 mutant exhibits an early flowering phenotype, and HOS15 acts upstream of photoperiodic flowering genes (GI, CO, and FT). GI protein abundance is increased in the hos15 mutant and is insensitive to the proteasome inhibitor MG132. Furthermore, the hos15 mutant has a defect in low ambient temperature-mediated GI degradation, and HOS15 interacts with COP1, an E3 ubiquitin ligase for GI degradation. Phenotypic analyses of the hos15 cop1 double mutant revealed that repression of flowering by HOS15 is dependent on COP1 at 16°C. However, the HOS15-COP1 interaction was attenuated at 16°C, and GI protein abundance was additively increased in the hos15 cop1 double mutant, indicating that HOS15 acts independently of COP1 in GI turnover at low ambient temperature. This study proposes that HOS15 controls GI abundance through multiple modes as an E3 ubiquitin ligase and transcriptional repressor to coordinate appropriate flowering time in response to ambient environmental conditions such as temperature and day length.

De Novo Transcriptome Analysis Reveals Flowering-Related Genes That Potentially Contribute to Flowering-Time Control in the Japanese Cultivated Gentian Gentiana triflora

Japanese cultivated gentians are perennial plants that flower in early summer to late autumn in Japan, depending on the cultivar. Several flowering-related genes, including GtFT1 and GtTFL1, are known to be involved in regulating flowering time, but many such genes remain unidentified. In this study, we obtained transcriptome profiling data using the Gentiana triflora cultivar ‘Maciry’, which typically flowers in late July. We conducted deep RNA sequencing analysis using gentian plants grown under natural field conditions for three months before flowering. To investigate diurnal changes, the plants were sampled at 4 h intervals over 24 h. Using these transcriptome data, we determined the expression profiles of leaves based on homology searches against the Flowering-Interactive Database of Arabidopsis. In particular, we focused on transcription factor genes, belonging to the BBX and MADS-box families, and analyzed their developmental and diurnal variation. The expression levels of representative BBX genes were also analyzed under long- and short-day conditions using in-vitro-grown seedlings, and the expression patterns of some BBX genes differed. Clustering analysis revealed that the transcription factor genes were coexpressed with GtFT1. Overall, these expression profiles will facilitate further analysis of the molecular mechanisms underlying the control of flowering time in gentians.

Transcriptomic Analysis of the Interaction Between FLOWERING LOCUS T Induction and Photoperiodic Signaling in Response to Spaceflight

Spaceflight has an impact on the growth and development of higher plants at both the vegetative stage and reproductive stage. A great deal of information has been available on the vegetative stage in space, but relatively little is known about the influence of spaceflight on plants at the reproductive stage. In this study, we constructed transgenic Arabidopsis thaliana plants expressing the flowering control gene, FLOWERING LOCUS T (FT), together with the green fluorescent protein gene (GFP) under control of a heat shock-inducible promoter (HSP17.4), by which we induced FT expression inflight through remote controlling heat shock (HS) treatment. Inflight photography data showed that induction of FT expression in transgenic plants in space under non-inductive short-day conditions could promote flowering and reduce the length of the inflorescence stem in comparison with that of wild-type plants under the same conditions. Whole-genome microarray analysis of gene expression changes in leaves of wild-type and these transgenic plants grown under the long-day and short-day photoperiod conditions in space indicated that the function of the photoperiod-related spaceflight responsive genes is mainly involved in protein synthesis and post-translation protein modulation, notably protein phosphorylation. In addition, changes of the circadian component of gene expression in response to spaceflight under different photoperiods indicated that roles of the circadian oscillator could act as integrators of spaceflight response and photoperiodic signals in Arabidopsis plants grown in space.

Transcriptome and Metabolome Analyses Reveal the Involvement of Multiple Pathways in Flowering Intensity in Mango

Mango (Mangifera indica L.) is famous for its sweet flavor and aroma. China is one of the major mango-producing countries. Mango is known for variations in flowering intensity that impacts fruit yield and farmers' profitability. In the present study, transcriptome and metabolome analyses of three cultivars with different flowering intensities were performed to preliminarily elucidate their regulatory mechanisms. The transcriptome profiling identified 36,242 genes. The major observation was the differential expression patterns of 334 flowering-related genes among the three mango varieties. The metabolome profiling detected 1,023 metabolites that were grouped into 11 compound classes. Our results show that the interplay of the FLOWERING LOCUS T and CONSTANS together with their upstream/downstream regulators/repressors modulate flowering robustness. We found that both gibberellins and auxins are associated with the flowering intensities of studied mango varieties. Finally, we discuss the roles of sugar biosynthesis and ambient temperature pathways in mango flowering. Overall, this study presents multiple pathways that can be manipulated in mango trees regarding flowering robustness.

High Ambient Temperatures Inhibit Ghd7-Mediated Flowering Repression in Rice

The anticipation of changing seasons is crucial for reproduction in plants. Despite the broad cultivation area, the effects of ambient temperature on photoperiodic flowering are largely unknown in rice. Here, we first examined flowering time under four distinct conditions: short-day or long-day and high or low temperature, using cultivars, nearly isogenic lines, and mutants in rice. We also examined gene expression patterns of key flowering-time genes using the same lines under various conditions including temporal dynamics after light pulses. In addition to delayed flowering because of low growth rates, we found that photoperiodic flowering is clearly enhanced by both Hd1 and Ghd7 genes under low-temperature conditions in rice. We also revealed that PhyB can control Ghd7 repressor activity as a temperature sensor to inhibit Ehd1, Hd3a and RFT1 at lower temperatures, likely through a post-transcriptional regulation, despite inductive photoperiod conditions. Furthermore, we found that rapid reduction of Ghd7 messenger RNA (mRNA) under high-temperature conditions can lead to mRNA increase in a rice florigen gene, RFT1. Thus, multiple temperature-sensing mechanisms can affect photoperiodic flowering in rice. The rising of ambient temperatures in early summer likely contributes to the inhibition of Ghd7 repressor activity, resulting in the appropriate floral induction of rice in temperate climates.

Unraveling the role of MADS transcription factor complexes in apple tree dormancy

A group of MADS transcription factors (TFs) are believed to control temperature-mediated bud dormancy. These TFs, called DORMANCY-ASSOCIATED MADS-BOX (DAM), are encoded by genes similar to SHORT VEGETATIVE PHASE (SVP) from Arabidopsis. MADS proteins form transcriptional complexes whose combinatory composition defines their molecular function. However, how MADS multimeric complexes control the dormancy cycle in trees is unclear. Apple MdDAM and other dormancy-related MADS proteins form complexes with MdSVPa, which is essential for the ability of transcriptional complexes to bind to DNA. Sequential DNA-affinity purification sequencing (seq-DAP-seq) was performed to identify the genome-wide binding sites of apple MADS TF complexes. Target genes associated with the binding sites were identified by combining seq-DAP-seq data with transcriptomics datasets obtained using a glucocorticoid receptor fusion system, and RNA-seq data related to apple dormancy. We describe a gene regulatory network (GRN) formed by MdSVPa-containing complexes, which regulate the dormancy cycle in response to environmental cues and hormonal signaling pathways. Additionally, novel molecular evidence regarding the evolutionary functional segregation between DAM and SVP proteins in the Rosaceae is presented. MdSVPa sequentially forms complexes with the MADS TFs that predominate at each dormancy phase, altering its DNA-binding specificity and, therefore, the transcriptional regulation of its target genes.

Mapping and identification of genetic loci affecting earliness of bolting and flowering in lettuce

KEY MESSAGE

Photoperiod and temperature conditions elicit different genetic regulation over lettuce bolting and flowering. This study identifies environment-specific QTLs and putative genes and provides information for genetic marker assay. Bolting, defined as stem elongation, marks the plant life cycle transition from vegetative to reproductive stage. Lettuce is grown for its leaf rosettes, and premature bolting may reduce crop quality resulting in economic losses. The transition to reproductive stage is a complex process that involves many genetic and environmental factors. In this study, the effects of photoperiod and ambient temperature on bolting and flowering regulation were studied by utilizing a lettuce mapping population to identify quantitative trait loci (QTL) and by gene expression analyses of genotypes with contrasting phenotypes. A recombinant inbred line (RIL) population, derived from a cross between PI 251246 (early bolting) and cv. Salinas (late bolting), was grown in four combinations of short (8 h) and long (16 h) days and low (20 °C) and high (35 °C) temperature. QTL models revealed both genetic (G) and environmental (E) effects, and GxE interactions. A major QTL for bolting and flowering time was found on chromosome 7 (qFLT7.2), and two candidate genes were identified by fine mapping, homology, and gene expression studies. In short days and high temperature conditions, qFLT7.2 had no effect on plant development, while several small-effect loci on chromosomes 2, 3, 6, 8, and 9 were associated with bolting and flowering. Of these, the QTL on chromosome 2, qBFr2.1, co-located with the Flowering Locus T (LsFT) gene. Polymorphisms between parent genotypes in the promotor region may explain identified gene expression differences and were used to design a genetic marker which may be used to identify the late bolting trait.

Studies on the expression patterns of the circadian rhythm regulated genes in mango

Mango, an important fruit crop of the tropical and subtropical regions shows alternate bearing in most varieties causing a financial loss to the farmer. Genetic reasons for this undesirable trait have not been studied so far. In our attempts to investigate the genetic reasons for alternate bearing we have initiated studies on genes associated with the induction, repression and regulation of flowering in mango. We have previously identified and characterized FLOWERING LOCUS T (FT) genes that induce flowering and two TERMINAL FLOWER1 (TFL1) genes that repress flowering. In this communication, we have explored the association of GI-FKF1-CDF1-CO module with the regulation of flowering in mango. The role of this module in regulating flowering has been well documented in photoperiod sensitive plants. We have characterized these genes and their expressions during flowering in Ratna variety as also their diurnal fluctuations and tissue specific expressions. The data taken together suggest that GI-FKF1-CDF1-CO module may also be employed by mango in regulating its flowering. Further, we suggest that the temperature dependent flowering in mango is probably associated with the presence of temperature sensitive elements present in the promoter region of one of the GIGANTEA genes that have been shown to be closely associated with floral induction.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s12298-021-01053-8.

Transcriptome analysis of flowering regulation by sowing date in Japonica Rice (Oryza sativa L.)

Hybrid japonica cultivars, such as the Yongyou series, have shown high yield potential in the field in both the early and late growing seasons. Moreover, understanding the responses of rice flowering dates to temperature and light is critical for improving yield performance. However, few studies have analyzed flowering genes in high-yielding japonica cultivars. Based on the five sowing date experiments from 2019 to 2020, select the sensitive cultivar Yongyou 538 and the insensitive cultivar Ninggeng 4 and take their flag leaves and panicles for transcriptome analysis. The results showed that compared with sowing date 1 (6/16), after the sowing date was postponed (sowing date 5, 7/9), 4480 and 890 differentially expressed genes (DEGs) were detected in the leaves and panicles in Ninggeng 4, 9275 and 2475 DEGs were detected in the leaves and panicles in Yongyou 538, respectively. KEGG pathway analysis showed that both Ninggeng 4 and Yongyou 538 regulated rice flowering through the plant circadian rhythm and plant hormone signal transduction pathways. Gene expression analysis showed that Os01g0566050 (OsELF3-2), Os01g0182600 (OsGI), Os11g0547000 (OsFKF1), Os06g0275000 (Hd1), and Os09g0513500 (FT-1) were expressed higher and Os02g0771100 (COP1-1) was expressed lower in Yongyou 538 compared with Ninggeng 4 as the climate conditions changed, which may be the key genes that regulate the flowering process with the change of temperature and light resources in sensitive cultivar Yongyou 538 in the late season.

Exploring PIF4 's contribution to early flowering in plants under daily variable temperature and its tissue-specific flowering gene network

Molecular mechanisms of how constant temperatures affect flowering time have been largely characterized in the model plant Arabidopsis thaliana; however, the effect of natural daily variable temperature outside laboratories is only partly explored. Several flowering genes have been shown to play important roles in temperature responses, including PHYTOCHROME-INTERACTING FACTOR 4 (PIF4) and FLOWERING LOCUS C (FLC), the two genes encoding for the transcription factors (TFs) that act antagonistically to regulate flowering time by activating and repressing floral integrator FLOWERING LOCUS T (FT), respectively. In this study, we have taken a multidisciplinary approach to explore the contribution of PIF4 to the early flowering observed in the daily variable temperature (VAR) and to broaden its transcriptional network using publicly available transcriptomic data. We observed early flowering in the natural accessions Col-0, C24 and their late flowering hybrid C24xCol grown under VAR, as compared with a constant temperature (CON). The loss-of-function mutation of PIF4 exhibits later flowering in VAR in both the Col-0 parent and the C24xCol hybrid, suggesting that PIF4, at least in part, contributes to acceleration of flowering in the VAR condition. To investigate the interplay between PIF4 and its flowering regulator counterparts, FLC and FT, we performed transcriptional analyses and found that VAR increased PIF4 transcription at the end of the day when temperature peaked at 32°C, when FT transcription was also elevated. On the other hand, we observed a decrease in FLC transcription in the 4-week-old plants grown in VAR, as well as in the plants with PIF4 overexpression grown in CON. These results raise a possibility that PIF4 might also regulate FT indirectly through the repression of FLC, in addition to the well-characterized direct control of PIF4 over FT. To further expand our view on the PIF4-orientated flowering gene network in response to temperature changes, we have constructed a coexpression-transcriptional regulatory network by combining publicly available transcriptomic data and gene regulatory interactions of PIF4 and its closely related flowering genes, PIF5, FLC, and ELF3. The network model reveals conserved and tissue-specific regulatory functions, which are useful for confirming as well as predicting the functions and regulatory interactions between these key flowering genes.

Beyond the Genetic Pathways, Flowering Regulation Complexity in Arabidopsis thaliana

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

Plant responses to high temperature: a view from pre-mRNA alternative splicing

This review focused on the recent breakthroughs in plant high temperature responses from an alternative splicing angle. With the inevitable global warming, high temperature triggers plants to change their growth and developmental programs for adapting temperature increase. In the past decades, the signaling mechanisms from plant thermo-sensing to downstream transcriptional cascades have been extensively studied. Plenty of elegant review papers have summarized these breakthroughs from signal transduction to cross-talk within plant hormones and environmental cues. Precursor messenger RNA (pre-mRNA) splicing enables plants to produce a series of functional un-related proteins and thus enhances the regulation flexibility. Plants take advantage of this strategy to modulate their proteome diversity under high ambient temperature and elicit developmental plasticity. In this review, we particularly focus on pre-mRNA splicing regulation underlying plant high temperature responses, and will shed new light on the understanding of post-transcriptional regulation on plant growth and development.

A critical role of the soybean evening complex in the control of photoperiod sensitivity and adaptation

Photoperiod sensitivity is a key factor in plant adaptation and crop production. In the short-day plant soybean, adaptation to low latitude environments is provided by mutations at the J locus, which confer extended flowering phase and thereby improve yield. The identity of J as an ortholog of Arabidopsis ELF3, a component of the circadian evening complex (EC), implies that orthologs of other EC components may have similar roles. Here we show that the two soybean homeologs of LUX ARRYTHMO interact with J to form a soybean EC. Characterization of mutants reveals that these genes are highly redundant in function but together are critical for flowering under short day, where the lux1 lux2 double mutant shows extremely late flowering and a massively extended flowering phase. This phenotype exceeds that of any soybean flowering mutant reported to date, and is strongly reminiscent of the "Maryland Mammoth" tobacco mutant that featured in the seminal 1920 study of plant photoperiodism by Garner and Allard [W. W. Garner, H. A. Allard, J. Agric. Res. 18, 553-606 (1920)]. We further demonstrate that the J-LUX complex suppresses transcription of the key flowering repressor E1 and its two homologs via LUX binding sites in their promoters. These results indicate that the EC-E1 interaction has a central role in soybean photoperiod sensitivity, a phenomenon also first described by Garner and Allard. EC and E1 family genes may therefore constitute key targets for customized breeding of soybean varieties with precise flowering time adaptation, either by introgression of natural variation or generation of new mutants by gene editing.

High-Temperature Conditions Promote Soybean Flowering through the Transcriptional Reprograming of Flowering Genes in the Photoperiod Pathway

Global warming has an impact on crop growth and development. Flowering time is particularly sensitive to environmental factors such as day length and temperature. In this study, we investigated the effects of global warming on flowering using an open-top Climatron chamber, which has a higher temperature and CO2 concentration than in the field. Two different soybean cultivars, Williams 82 and IT153414, which exhibited different flowering times, were promoted flowering in the open-top Climatron chamber than in the field. We more specifically examined the expression patterns of soybean flowering genes on the molecular level under high-temperature conditions. The elevated temperature induced the expression of soybean floral activators, GmFT2a and GmFT5a as well as a set of GmCOL genes. In contrast, it suppressed floral repressors, E1 and E2 homologs. Moreover, high-temperature conditions affected the expression of these flowering genes in a day length-independent manner. Taken together, our data suggest that soybean plants properly respond and adapt to changing environments by modulating the expression of a set of flowering genes in the photoperiod pathway for the successful production of seeds and offspring.

What is going on with the hormonal control of flowering in plants?

Molecular genetic studies using Arabidopsis thaliana as a model system have overwhelmingly revealed many important molecular mechanisms underlying the control of various biological events, including floral induction in plants. The major genetic pathways of flowering have been characterized in-depth, and include the photoperiod, vernalization, autonomous and gibberellin pathways. In recent years, novel flowering pathways are increasingly being identified. These include age, thermosensory, sugar, stress and hormonal signals to control floral transition. Among them, hormonal control of flowering except the gibberellin pathway is not formally considered a major flowering pathway per se, due to relatively weak and often pleiotropic genetic effects, complex phenotypic variations, including some controversial ones. However, a number of recent studies have suggested that various stress signals may be mediated by hormonal regulation of flowering. In view of molecular diversity in plant kingdoms, this review begins with an assessment of photoperiodic flowering, not in A. thaliana, but in rice (Oryza sativa); rice is a staple crop for human consumption worldwide, and is a model system of short-day plants, cereals and breeding crops. The rice flowering pathway is then compared with that of A. thaliana. This review then aims to update our knowledge on hormonal control of flowering, and integrate it into the entire flowering gene network.

Photoperiod Control of Plant Growth: Flowering Time Genes Beyond Flowering

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

Environmental Signal-Dependent Regulation of Flowering Time in Rice

The transition from the vegetative to the reproductive stage of growth is a critical event in the lifecycle of a plant and is required for the plant’s reproductive success. Flowering time is tightly regulated by an internal time-keeping system and external light conditions, including photoperiod, light quality, and light quantity. Other environmental factors, such as drought and temperature, also participate in the regulation of flowering time. Thus, flexibility in flowering time in response to environmental factors is required for the successful adaptation of plants to the environment. In this review, we summarize our current understanding of the molecular mechanisms by which internal and environmental signals are integrated to regulate flowering time in Arabidopsis thaliana and rice (Oryza sativa).

Let it bloom: cross-talk between light and flowering signaling in Arabidopsis

The terrestrial environment is complex, with many parameters fluctuating on daily and seasonal basis. Plants, in particular, have developed complex sensory and signaling networks to extract and integrate information about their surroundings in order to maximize their fitness and mitigate some of the detrimental effects of their sessile lifestyles. Light and temperature each provide crucial insights on the surrounding environment and, in combination, allow plants to appropriately develop, grow and adapt. Cross-talk between light and temperature signaling cascades allows plants to time key developmental decisions to ensure they are 'in sync' with their environment. In this review, we discuss the major players that regulate light and temperature signaling, and the cross-talk between them, in reference to a crucial developmental decision faced by plants: to bloom or not to bloom?

PHYTOCHROME-INTERACTING FACTORS at the interface of light and temperature signalling

Plant development displays a remarkable degree of plasticity and continuously adjusts to the plant's surroundings, a process that is triggered by the perception of environmental cues such as light and temperature. Transcription factors of the PHYTOCHROME-INTERACTING FACTOR (PIF) family have long been established as key negative regulators of light responses; within the last decade, increasing evidence suggests that they are also core components of temperature signalling, and multiple mechanisms by which temperature regulates activity of these transcription factors have been discovered. It has become clear that these temperature responses cannot be considered in isolation, but that they occur in the context of, and are influenced by, other environmental signals. This review discusses recent advances in the understanding of the mechanisms through which temperature affects PIF function and how these mechanisms are influenced by the light environment.

Genetic and molecular basis of floral induction in Arabidopsis thaliana

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

An RNA thermoswitch regulates daytime growth in Arabidopsis

Temperature is a major environmental cue affecting plant growth and development. Plants often experience higher temperatures in the context of a 24 h day-night cycle, with temperatures peaking in the middle of the day. Here, we find that the transcript encoding the bHLH transcription factor PIF7 undergoes a direct increase in translation in response to warmer temperature. Diurnal expression of PIF7 transcript gates this response, allowing PIF7 protein to quickly accumulate in response to warm daytime temperature. Enhanced PIF7 protein levels directly activate the thermomorphogenesis pathway by inducing the transcription of key genes such as the auxin biosynthetic gene YUCCA8, and are necessary for thermomorphogenesis to occur under warm cycling daytime temperatures. The temperature-dependent translational enhancement of PIF7 messenger RNA is mediated by the formation of an RNA hairpin within its 5' untranslated region, which adopts an alternative conformation at higher temperature, leading to increased protein synthesis. We identified similar hairpin sequences that control translation in additional transcripts including WRKY22 and the key heat shock regulator HSFA2, suggesting that this is a conserved mechanism enabling plants to respond and adapt rapidly to high temperatures.

A Soybean Deletion Mutant That Moderates the Repression of Flowering by Cool Temperatures

Ambient growing temperature and photoperiod are major environmental stimuli that summer annual crops use to adjust their reproductive phenology so as to maximize yield. Variation in flowering time among soybean (Glycine max) cultivars results mainly from allelic diversity at loci that control photoperiod sensitivity and FLOWERING LOCUS T (FT) orthologs. However, variation in the thermal regulation of flowering and its underlying mechanisms are poorly understood. In this study, we identified a novel mutant (ef1) that confers altered thermal regulation of flowering in response to cool ambient temperatures. Mapping analysis with simple sequence repeat (SSR) markers located the mutation in the upper part of chromosome 19, where no QTL for flowering has been previously reported. Fine-mapping and re-sequencing revealed that the mutation was caused by deletion of a 214 kbp genomic region that contains 11 annotated genes, including CONSTANS-LIKE 2b (COL2b), a soybean ortholog of Arabidopsis CONSTANS. Comparison of flowering times under different photo-thermal conditions revealed that early flowering in the mutant lines was most distinct under cool ambient temperatures. The expression of two FT orthologs, FT2a and FT5a, was dramatically downregulated by cool temperature, but the magnitude of the downregulation was lower in the mutant lines. Cool temperatures upregulated COL2b expression or delayed peak expression, particularly at the fourth trifoliate-leaf stage. Intriguingly, they also upregulated E1, a soybean-specific repressor of FT orthologs. Our results suggest that the ef1 mutation is involved in thermal regulation of flowering in response to cool ambient temperature, and the lack of COL2b in the mutant likely alleviates the repression of flowering by cool temperature. The ef1 mutant can be used as a novel gene resource in breeding soybean cultivars adapted to cool climate and in research to improve our understanding of thermal regulation of flowering in soybean.

The epidermis coordinates thermoresponsive growth through the phyB-PIF4-auxin pathway

In plants, an elevation in ambient temperature induces adaptive morphological changes including elongated hypocotyls, which is predominantly regulated by a bHLH transcription factor, PIF4. Although PIF4 is expressed in all aerial tissues including the epidermis, mesophyll, and vascular bundle, its tissue-specific functions in thermomorphogenesis are not known. Here, we show that epidermis-specific expression of PIF4 induces constitutive long hypocotyls, while vasculature-specific expression of PIF4 has no effect on hypocotyl growth. RNA-Seq and qRT-PCR analyses reveal that auxin-responsive genes and growth-related genes are highly activated by epidermal, but not by vascular, PIF4. Additionally, inactivation of epidermal PIF4 or auxin signaling, and overexpression of epidermal phyB suppresses thermoresponsive growth, indicating that epidermal PIF4-auxin pathways are essential for the temperature responses. Further, we show that high temperatures increase both epidermal PIF4 transcription and the epidermal PIF4 DNA-binding ability. Taken together, our study demonstrates that the epidermis regulates thermoresponsive growth through the phyB-PIF4-auxin pathway.

The PIF4 transcription factor along with the phyB photoreceptor, regulates growth responses to elevated temperature in plants. Here the authors show that PIF4 expression in the epidermis, rather than the vasculature, stimulates auxin responses and thermoresponsive growth in Arabidopsis.

New insights into gibberellin signaling in regulating flowering in Arabidopsis

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

A PIF7-CONSTANS-Centered Molecular Regulatory Network Underlying Shade-Accelerated Flowering

To compete with their neighbors for light and escape shaded environments, sun-loving plants have developed the shade-avoidance syndrome (SAS), a set of responses including alteration of plant architecture and initiation of early flowering and seed set. Previous studies on SAS mainly focused on dissecting molecular basis of hypocotyl elongation in seedlings under shade light; however, the molecular mechanisms underlying shade-accelerated flowering in adult plants remain unknown. In this study, we found that CONSTANS (CO) and PHYTOCHROME-INTERACTING FACTOR 7 (PIF7) have an additive effect on shade-induced flowering, but that LONG HYPOCOTYL IN FAR-RED1 (HFR1) represses early flowering by binding to CO and PIF7 and preventing the binding of CO to the promoter of FLOWERING LOCUS T (FT) and the binding of PIF7 to the promoter of pri-MIR156E/F. Under shade, de-phosphorylated PIF7 and accumulated CO, balanced by HFR1, upregulate the expression of FT, TSF, SOC1, and SPLs to accelerate flowering. Moreover, we found that the function of PIF7 in flowering time is independent of phyA. Collectively, these regulatory interactions establish a crucial link between the light signal and genetic network that regulates flowering transition under shade.

PIF transcription factors link a neighbor threat cue to accelerated reproduction in Arabidopsis

Changes in light quality indicative of competition for this essential resource influence plant growth and developmental transitions; however, little is known about neighbor proximity-induced acceleration of reproduction. Phytochrome B (phyB) senses light cues from plant competitors, ultimately leading to the expression of the floral inducers FLOWERING LOCUS T (FT) and TWIN SISTER of FT (TSF). Here we show that PHYTOCHROME INTERACTING FACTORs 4, 5 and 7 (PIF4, PIF5 and PIF7) mediate neighbor proximity-induced flowering, with PIF7 playing a prominent role. These transcriptional regulators act directly downstream of phyB to promote expression of FT and TSF. Neighbor proximity enhances PIF accumulation towards the end of the day, coinciding with enhanced floral inducer expression. We present evidence supporting direct PIF-regulated TSF expression. The relevance of our findings is illustrated by the prior identification of FT, TSF and PIF4 as loci underlying flowering time regulation in natural conditions.

Large-effect flowering time mutations reveal conditionally adaptive paths through fitness landscapes in Arabidopsis thaliana

Mutations are often assumed to be largely detrimental to fitness, but they may also be beneficial, and mutations with large phenotypic effects can persist in nature. One explanation for these observations is that mutations may be beneficial in specific environments because these conditions shift trait expression toward higher fitness. This hypothesis is rarely tested due to the difficulty of replicating mutants in multiple natural environments and measuring their phenotypes. We did so by planting Arabidopsis thaliana genotypes with large-effect flowering time mutations in field sites across the species’ European climate range. We quantified the adaptive value of mutant traits, finding that certain mutations increased fitness in some environments but not in others.

Contrary to previous assumptions that most mutations are deleterious, there is increasing evidence for persistence of large-effect mutations in natural populations. A possible explanation for these observations is that mutant phenotypes and fitness may depend upon the specific environmental conditions to which a mutant is exposed. Here, we tested this hypothesis by growing large-effect flowering time mutants of Arabidopsis thaliana in multiple field sites and seasons to quantify their fitness effects in realistic natural conditions. By constructing environment-specific fitness landscapes based on flowering time and branching architecture, we observed that a subset of mutations increased fitness, but only in specific environments. These mutations increased fitness via different paths: through shifting flowering time, branching, or both. Branching was under stronger selection, but flowering time was more genetically variable, pointing to the importance of indirect selection on mutations through their pleiotropic effects on multiple phenotypes. Finally, mutations in hub genes with greater connectedness in their regulatory networks had greater effects on both phenotypes and fitness. Together, these findings indicate that large-effect mutations may persist in populations because they influence traits that are adaptive only under specific environmental conditions. Understanding their evolutionary dynamics therefore requires measuring their effects in multiple natural environments.

Regulation of stomatal opening and histone modification by photoperiod in Arabidopsis thaliana

Stomatal movements are regulated by many environmental signals, such as light, CO₂, temperature, humidity, and drought. Recently, we showed that photoperiodic flowering components have positive effects on light-induced stomatal opening in Arabidopsis thaliana. In this study, we determined that light-induced stomatal opening and increased stomatal conductance were larger in plants grown under long-day (LD) conditions than in those grown under short-day (SD) conditions. Gene expression analyses using purified guard cell protoplasts revealed that FT and SOC1 expression levels were significantly increased under LD conditions. Interestingly, the enhancement of light-induced stomatal opening and increased SOC1 expression in guard cells due to LD conditions persisted for at least 1 week after plants were transferred to SD conditions. We then investigated histone modification using chromatin immunoprecipitation–PCR, and observed increased trimethylation of lysine 4 on histone 3 (H3K4) around SOC1. We also found that LD-dependent enhancement of light-induced stomatal opening and H3K4 trimethylation in SOC1 were suppressed in the ft-2 mutant. These results indicate that photoperiod is an important environmental cue regulating stomatal opening, and that LD conditions enhance light-induced stomatal opening and epigenetic modification (H3K4 trimethylation) around SOC1, a positive regulator of stomatal opening, in an FT-dependent manner. Thus, this study provides novel insights into stomatal responses to photoperiod.

SHB1 and CCA1 interaction desensitizes light responses and enhances thermomorphogenesis

Light and temperature are two important environmental signals to plants. After dawn, photo-activated phytochromes translocate into the nucleus and interact with a family of negative basic helix-loop-helix PIF regulators. Subsequent phosphorylation and degradation of PIFs triggers a series of photomorphogenic responses. However, excess light can damage the photosynthetic apparatus and leads to photoinhibition. Plants acclimate to a balanced state of photomorphogenesis to avoid photodamage. Here, we show that upregulation of PIF4 expression by SHB1 and CCA1 under red light represents a desensitization step. After dawn, the highly expressed circadian clock protein CCA1 brings circadian signals to the regulatory region of the PIF4 signaling hub. Recruitment of SHB1 by CCA1 modulates red light-specific induction of PIF4 expression thus integrating circadian and light signals. As noon approaches and light intensity and ambient temperature tend to increase, the SHB1–CCA1 interaction sustains PIF4 expression to trigger thermomorphogenic responses to changing light and temperature conditions.

The PIF4 transcription factor promotes adaptation to elevated temperature but is degraded under red light to trigger photomorphogenesis. Here Sun et al. show that the core circadian component CCA1 recruits SHB1 to sustain PIF4 expression after dawn to balance thermomorphogenesis and light responses.

An explanatory model of temperature influence on flowering through whole-plant accumulation of FLOWERING LOCUS T in Arabidopsis thaliana

We assessed mechanistic temperature influence on flowering by incorporating temperature-responsive flowering mechanisms across developmental age into an existing model. Temperature influences the leaf production rate as well as expression of FLOWERING LOCUS T (FT), a photoperiodic flowering regulator that is expressed in leaves. The Arabidopsis Framework Model incorporated temperature influence on leaf growth but ignored the consequences of leaf growth on and direct temperature influence of FT expression. We measured FT production in differently aged leaves and modified the model, adding mechanistic temperature influence on FT transcription, and causing whole-plant FT to accumulate with leaf growth. Our simulations suggest that in long days, the developmental stage (leaf number) at which the reproductive transition occurs is influenced by day length and temperature through FT, while temperature influences the rate of leaf production and the time (in days) the transition occurs. Further, we demonstrate that FT is mainly produced in the first 10 leaves in the Columbia (Col-0) accession, and that FT accumulation alone cannot explain flowering in conditions in which flowering is delayed. Our simulations supported our hypotheses that: (i) temperature regulation of FT, accumulated with leaf growth, is a component of thermal time, and (ii) incorporating mechanistic temperature regulation of FT can improve model predictions when temperatures change over time.

Thermomorphogenesis

When exposed to warmer, nonstressful average temperatures, some plant organs grow and develop at a faster rate without affecting their final dimensions. Other plant organs show specific changes in morphology or development in a response termed thermomorphogenesis. Selected coding and noncoding RNA, chromatin features, alternative splicing variants, and signaling proteins change their abundance, localization, and/or intrinsic activity to mediate thermomorphogenesis. Temperature, light, and circadian clock cues are integrated to impinge on the level or signaling of hormones such as auxin, brassinosteroids, and gibberellins. The light receptor phytochrome B (phyB) is a temperature sensor, and the phyB-PHYTOCHROME-INTERACTING FACTOR 4 (PIF4)-auxin module is only one thread in a complex network that governs temperature sensitivity. Thermomorphogenesis offers an avenue to search for climate-smart plants to sustain crop and pasture productivity in the context of global climate change.

Arabidopsis ELF4-like proteins EFL1 and EFL3 influence flowering time

The circadian clock synchronizes internal and external stimuli to ensure numerous biological processes occur at the optimal time. EARLY FLOWERING 4 (ELF4) is a key evening-phased component of the circadian clock and essential for photoperiod-dependent flowering time regulation in Arabidopsis thaliana. There are four homologous ELF4-like (EFL1-EFL4) genes in the Arabidopsis genome but their functions are unknown. Protein sequence alignment and phylogenetic analysis showed that these four EFL proteins contained an evolutionarily conserved domain, DUF1313, of unknown function. To investigate the physical roles of these genes in Arabidopsis, we overexpressed the four homologous EFL genes in the elf4 mutant background. Under both long-day (LD) and short-day (SD) conditions, overexpression of EFL1 not only completely rescued the early flowering phenotype of the elf4 mutant, but also delayed flowering. Overexpression of EFL2, however, failed to rescue this phenotype and overexpression of EFL3 partially rescued the early flowering phenotype. The transcription levels of the key flowering time regulation genes CONSTANS (CO) and FLOWERING LOCUS T (FT) were significantly decreased in the EFL1- and EFL3-overexpressing transgenic lines in a dose-dependent manner, compared with the elf4 mutant. These results suggest that EFL1 and EFL3 are involved in flowering time regulation in Arabidopsis.

CONSTANS delays Arabidopsis flowering under short days

Long days (LD) promote flowering of Arabidopsis thaliana compared with short days (SD) by activating the photoperiodic pathway. Here we show that growth under very-SD (3 h) or darkness (on sucrose) also accelerates flowering on a biological scale, indicating that SD actively repress flowering compared with very-SD. CONSTANS (CO) repressed flowering under SD, and the early flowering of co under SD required FLOWERING LOCUS T (FT). FT was expressed at a basal level in the leaves under SD, but these levels were not enhanced in co. This indicates that the action of CO in A. thaliana is not the mirror image of the action of its homologue in rice. In the apex, CO enhanced the expression of TERMINAL FLOWER 1 (TFL1) around the time when FT expression is important to promote flowering. Under SD, the tfl1 mutation was epistatic to co and in turn ft was epistatic to tfl1. These observations are consistent with the long-standing but not demonstrated model where CO can inhibit FT induction of flowering by affecting TFL1 expression.

Translating Flowering Time From Arabidopsis thaliana to Brassicaceae and Asteraceae Crop Species

Flowering and seed set are essential for plant species to survive, hence plants need to adapt to highly variable environments to flower in the most favorable conditions. Endogenous cues such as plant age and hormones coordinate with the environmental cues like temperature and day length to determine optimal time for the transition from vegetative to reproductive growth. In a breeding context, controlling flowering time would help to speed up the production of new hybrids and produce high yield throughout the year. The flowering time genetic network is extensively studied in the plant model species Arabidopsis thaliana, however this knowledge is still limited in most crops. This article reviews evidence of conservation and divergence of flowering time regulation in A. thaliana with its related crop species in the Brassicaceae and with more distant vegetable crops within the Asteraceae family. Despite the overall conservation of most flowering time pathways in these families, many genes controlling this trait remain elusive, and the function of most Arabidopsis homologs in these crops are yet to be determined. However, the knowledge gathered so far in both model and crop species can be already exploited in vegetable crop breeding for flowering time control.

Two CONSTANS-LIKE genes jointly control flowering time in beet

Breeding vegetative crops (e.g. beets, cabbage, forage grasses) is challenged by two conflicting aims. For field production, flowering must be avoided while flowering and seed set is necessary for breeding and seed production. The biennial species sugar beet makes shoot elongation (‘bolting’) followed by flowering after a long period of cold temperatures. Field production in northern geographical regions starts in spring. A thickened storage root is formed only during vegetative growth. It is expected that winter beets, which are sown before winter would have a much higher yield potential. However, field production was not possible so far due to bolting after winter. We propose a strategy to breed winter beets exploiting haplotype variation at two major bolting time loci, B and B2. Both genes encode transcription factors controlling the expression of two orthologs of the Arabidopsis gene FLOWERING LOCUS T (FT). We detected an epistatic interaction between both genes because F₂ plants homozygous for two B/B2 mutant alleles did not bolt even after vernalization. Fluorescence complementation studies revealed that both proteins form a heterodimer in vivo. In non-bolting plants, the bolting activator BvFT2 was completely downregulated whereas the repressor BvFT1 was upregulated which suggests that both genes acquire a CONSTANS (CO) like function in beet. Like CO, B and B2 proteins house CCT and BBX domains which, in contrast to CO are split between the two beet genes. We propose an alternative regulation of FT orthologs in beet that can be exploited to breed winter beets.

Ambient Temperature-Responsive Mechanisms Coordinate Regulation of Flowering Time

In plants, environmental conditions such as temperature affect survival, growth, and fitness, particularly during key stages such as seedling growth and reproduction. To survive and thrive in changing conditions, plants have evolved adaptive responses that tightly regulate developmental processes such as hypocotyl elongation and flowering time in response to environmental temperature changes. Increases in temperature, coupled with increasing fluctuations in local climate and weather, severely affect our agricultural systems; therefore, understanding the mechanisms by which plants perceive and respond to temperature is critical for agricultural sustainability. In this review, we summarize recent findings on the molecular mechanisms of ambient temperature perception as well as possible temperature sensing components in plants. Based on recent publications, we highlight several temperature response mechanisms, including the deposition and eviction of histone variants, DNA methylation, alternative splicing, protein degradation, and protein localization. We discuss roles of each proposed temperature-sensing mechanism that affects plant development, with an emphasis on flowering time. Studies of plant ambient temperature responses are advancing rapidly, and this review provides insights for future research aimed at understanding the mechanisms of temperature perception and responses in plants.

Convergent regulation of PIFs and the E3 ligase COP1/SPA1 mediates thermosensory hypocotyl elongation by plant phytochromes

The ability of plants to sense and integrate daily and seasonal changes in light and temperature and to adjust their growth and development accordingly, is critical to withstand severe weather oscillations in a year. While molecular mechanisms controlling light responses are relatively well established, those involved in the perception and response to temperature are just beginning to be understood. Phytochromes emerged as major temperature sensors; due to warmer temperatures accelerate the dark reversal reaction to the Pr inactive state. Downstream of phytochromes, the bHLH Phytochrome Interacting Factors, and in particular PIF4, act as central signaling hubs to growth coordination in response to light and temperature cues, and to the gibberellin and brassinosteroid pathways. Here we discuss recent findings showing that phytochromes control PIFs activity not only by signaling their destruction in the light, but by modulating transcriptional repression of these factors by the circadian clock. Together with this repression, phytochromes inactivate the COP1/SPA ubiquitin ligase, which negatively regulates light signaling through degradation of a large set of nuclear photomorphogenesis-promoting factors that suppress PIFs activity.