Significance Plants know the exact time of flowering by sensing the photoperiod. Flowering time is an important agronomic trait in crops. In order to ensure that crops maintain high yields in different latitudes, cultivars need to accurately adjust the flowering time of plants according to local photoperiod and environmental conditions. In many plants, phytochromes have been found to be involved in photoperiodic flowering, but the molecular mechanisms of how they control photoperiod flowering are not fully understood. Through a series of biochemical, molecular, and genetic analyses of soybean phytochrome A, we reveal a photoperiod flowering mechanism in plants by which the phytochrome A regulates LUX and E1 activity.

Novel and multifaceted regulations of photoperiodic flowering by phytochrome A in soybean

The photoperiodic response is critical for plants to adjust their reproductive phase to the most favorable season. Wheat heads earlier under long days (LD) than under short days (SD) and this difference is mainly regulated by the PHOTOPERIOD1 (PPD1) gene. Tetraploid wheat plants carrying the Ppd-A1a allele with a large deletion in the promoter head earlier under SD than plants carrying the wildtype Ppd-A1b allele with an intact promoter. Phytochromes PHYB and PHYC are necessary for the light activation of PPD1, and mutations in either of these genes result in the downregulation of PPD1 and very late heading time. We show here that both effects are reverted when the phyB mutant is combined with loss-of-function mutations in EARLY FLOWERING 3 (ELF3), a component of the Evening Complex (EC) in the circadian clock. We also show that the wheat ELF3 protein interacts with PHYB and PHYC, is rapidly modified by light, and binds to the PPD1 promoter in planta (likely as part of the EC). Deletion of the ELF3 binding region in the Ppd-A1a promoter results in PPD1 upregulation at dawn, similar to PPD1 alleles with intact promoters in the elf3 mutant background. The upregulation of PPD1 is correlated with the upregulation of the florigen gene FLOWERING LOCUS T1 (FT1) and early heading time. Loss-of-function mutations in PPD1 result in the downregulation of FT1 and delayed heading, even when combined with the elf3 mutation. Taken together, these results indicate that ELF3 operates downstream of PHYB as a direct transcriptional repressor of PPD1, and that this repression is relaxed both by light and by the deletion of the ELF3 binding region in the Ppd-A1a promoter. In summary, the regulation of the light mediated activation of PPD1 by ELF3 is critical for the photoperiodic regulation of wheat heading time. 

/pdf/early-flowering-3-interactions-with-phytochrome-b-and-1msmmyjj.pdf

EARLY FLOWERING 3 interactions with PHYTOCHROME B and PHOTOPERIOD1 are critical for the photoperiodic regulation of wheat heading time

Correct measurement of environmental parameters is fundamental for plant fitness and survival, as well as for timing developmental transitions, including the switch from vegetative to reproductive growth. Important parameters that affect flowering time include day length (photoperiod) and temperature. Their response pathways have been best described in Arabidopsis, which currently offers a detailed conceptual framework and serves as a comparison for other species. Rice, the focus of this review, also possesses a photoperiodic flowering pathway, but 150 million years of divergent evolution in very different environments have diversified its molecular architecture. The ambient temperature perception pathway is strongly intertwined with the photoperiod pathway and essentially converges on the same genes to modify flowering time. When observing network topologies, it is evident that the rice flowering network is centered on EARLY HEADING DATE 1, a rice-specific transcriptional regulator. Here, we summarize the most important features of the rice photoperiodic flowering network, with an emphasis on its uniqueness, and discuss its connections with hormonal, temperature perception, and stress pathways. 

Environmental Control of Rice Flowering Time.

Plant basic helix-loop-helix (bHLH) transcription factors are involved in many physiological processes, and they play important roles in the abiotic stress responses. The literature related to genome sequences has increased, with genome-wide studies on the bHLH transcription factors in plants. Researchers have detailed the functionally characterized bHLH transcription factors from different aspects in the model plant Arabidopsis thaliana, such as iron homeostasis and abiotic stresses; however, other important economic crops, such as rice, have not been summarized and highlighted. The bHLH members in the same subfamily have similar functions; therefore, unraveling their regulatory mechanisms will help us to identify and understand the roles of some of the unknown bHLH transcription factors in the same subfamily. In this review, we summarize the available knowledge on functionally characterized bHLH transcription factors according to four categories: plant growth and development; metabolism synthesis; plant signaling, and abiotic stress responses. We also highlight the roles of the bHLH transcription factors in some economic crops, especially in rice, and discuss future research directions for possible genetic applications in crop breeding.

/pdf/basic-helix-loop-helix-transcription-factors-regulators-for-3nx92cum.pdf

Basic Helix-Loop-Helix Transcription Factors: Regulators for Plant Growth Development and Abiotic Stress Responses

Soybean (Glycine max) is a major source of protein and edible oil worldwide and is cultivated in a wide range of latitudes. However, it is extremely sensitive to photoperiod, which influences flowering time, maturity and yield, and severely limits soybean latitude adaptation. In this study, a genome-wide association study (GWAS) identified a novel locus in accessions harboring the E1 allele, called Time of flowering 8 (Tof8), which promotes flowering and enhances adaptation to high latitude in cultivated soybean. Gene functional analyses showed that Tof8 is an ortholog of Arabidopsis FKF1. We identified two FKF1 homologs in the soybean genome. Both FKF1 homologs are genetically dependent on E1 by binding to E1 promoter to activate E1 transcription, thus repressing FLOWERING LOCUS T 2a (FT2a) and FT5a transcription, which modulate flowering and maturity through the E1 pathway. We also demonstrate that the natural allele FKF1bH3 facilitated adaptation of soybean to high-latitude environments and was selected during domestication and improvement, leading to its rapid expansion in cultivated soybean. These findings provide novel insights into the roles of FKF1 in controlling flowering time and maturity in soybean and offer new means to fine tune adaptation to high latitudes and increase grain yield.

Natural variation of FKF1 controls flowering and adaptation during soybean domestication and improvement.

Significance Plants use photoperiod information to control flowering. Flowering in rice is accelerated by short days, while other plants, such as Arabidopsis, flower in response to long days. The molecular mechanisms controlling photoperiod-dependent flowering in rice are not fully understood. Previous experiments have demonstrated the presence of several floral repressors that confer relatively mild flowering phenotypes. Here we show that the rice evening complex of the circadian clock is essential for the activation of flowering. We find that the evening complex (EC) binds directly to the promoters of floral repressors, reducing their transcription. These findings are consistent with a key role for the EC in controlling flowering in many diverse species including soybean, barley, Brachypodium, and Arabidopsis.

The evening complex integrates photoperiod signals to control flowering in rice

Light is a key determinant for plant growth, development, and ultimately yield. Phytochromes, the red/far-red photoreceptors, play an important role in plant architecture, stress tolerance, and productivity. In the model plant Arabidopsis thaliana, it has been shown that PHYTOCHROME-INTERACTING FACTORS (PIFs; bHLH transcription factors) act as central hubs in the integration of external stimuli to regulate plant development. Recent studies have unveiled the importance of PIFs in crops. They are involved in the modulation of plant architecture and productivity through the regulation of cell division and elongation in response to different environmental cues. These studies show that different PIFs have overlapping but also distinct functions in the regulation of plant growth. Therefore, understanding the molecular mechanisms by which PIFs regulate plant development is crucial to improve crop productivity under both optimal and adverse environmental conditions. In this review, we discuss the current knowledge of PIFs acting as integrators of light and other signals in different crops, with particular focus on the role of PIFs in responding to different environmental conditions and how this can be used to improve crop productivity.

Phytochrome-Interacting Factors: a promising tool to improve crop productivity.

Angiosperms are the most dominant land plant flora and have colonised most of the terrestrial habitats, thriving in different environmental conditions, among which light and temperature play a crucial role. In the eudicot Arabidopsis thaliana, light and temperature are integrated into a phytochrome B (phyB)-dependent signalling network that regulates development. However, whether this signal integration controls the development in other angiosperm lineages and if phyB is a conserved hub of this integratory network in angiosperms is unclear. We used a combination of phylogenetic, phenotypic, and transcriptomic analyses to understand the phyB-dependent light and temperature integratory network in the monocot Oryza sativa and infer its conservation in angiosperms. Here, we show that light and temperature co-regulate rice growth through a phyB-dependent regulatory network that shares conserved features between O. sativa and A. thaliana. Despite the conservation of the components of this regulatory network, the transcriptional regulation between the components has changed qualitatively since monocots and eudicots diverged (~192-145 MYA). The evolutionary flexibility of this integratory network might underlie the successful adaptation of plants to diverse ecological niches. Furthermore, our findings provide promising candidate genes whose activity and expression can be fine-tuned to improve plant growth and productivity in a warming planet.

Light and temperature signals are integrated through a phyB-dependent gene regulatory network in rice.

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The evening complex integrates photoperiod signals to control flowering in rice

Phytochrome-Interacting Factors: a promising tool to improve crop productivity.

Light and temperature signals are integrated through a phyB-dependent gene regulatory network in rice.