Downregulation of PHYTOCHROME-INTERACTING FACTOR 4 Influences Plant Development and Fruit Production

SlSPA3 regulates the nuclear abundance of SlUVR8 in tomato

Tomato (Solanum lycopersicum L.) is an important model plant species in photomorphogenesis research. Ultraviolet B (UV-B) induces the dissociation of homodimers of the photoreceptor UV RESISTANCE LOCUS8 (UVR8) into monomers, which translocate into the nucleus. Nuclear accumulation of UVR8 is a prerequisite for its signaling function. Previous studies have reported that SUPPRESSOR OF PHYTOCHROME A-105 (SPA) family members may regulate UV-B signaling in Arabidopsis (Arabidopsis thaliana); however, the underlying mechanism is unknown. Here, we show that the tomato genome encodes four SPA (SlSPA) orthologs. Genome-edited Slspa3 mutants exhibited enhanced photomorphogenic responses in white light, suggesting that SlSPA3 inhibits general photomorphogenesis. By contrast, UVR8-mediated gene expression in response to UV-B was compromised in Slspa3 mutants, suggesting that SlSPA3 promotes UV-B signaling. UV-B-induced nuclear accumulation of UVR8, which is essential for UV-B signaling, was reduced in the Slspa3 mutants. Moreover, UV-B-induced nuclear accumulation of UVR8 was also reduced in the Arabidopsis spa1 spa2 spa3 and spa1 spa2 spa4 triple mutants, indicating a conserved mechanism in these two species. Notably, spa1 spa2 spa4 exhibited normal UV-B-induced interaction between UVR8 and the plant morphogenesis repressor CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1). This suggests that the well-established mechanisms of UVR8 nuclear retention remained unaffected in spa1 spa2 spa4. Thus, our work uncovered a potentially unrecognized mechanism by which SPA proteins regulate UV-B signaling through the promotion of UVR8 nuclear abundance in land plants.

SlCPK27 cross-links SlHY5 and SlPIF4 in brassinosteroid-dependent photo- and thermo-morphogenesis in tomato

ELONGATED HYPOCOTOYL5 (HY5) and PHYTOCHROME INTERACTING FACTORs (PIFs) are two types of important light-related regulators of plant growth, however, their interplay remains elusive. Here, we report that the activated tomato (Solanum lycopersicum) HY5 (SlHY5) triggers the transcription of a Calcium-dependent Protein Kinase SlCPK27. SlCPK27 interacts with and phosphorylates SlPIF4 at Ser-252 and Ser-308 phosphosites to promote its degradation. SlPIF4 promotes hypocotyl elongation mainly by activating the transcription of SlDWF, a key gene in brassinosteroid (BR) biosynthesis. Such a SlHY5-SlCPK27-SlPIF4-BR cascade not only plays a crucial role in photomorphogenesis but also regulates thermomorphogenesis. Our results uncover a previously unidentified mechanism that integrates Ca2+ signaling with the light signaling pathways to regulate plant growth by modulating BR biosynthesis in response to changes in ambient light and temperature.

Genome-wide investigation of the PIF gene family in alfalfa (Medicago sativa L.) expression profiles during development and stress

BACKGROUND

Phytochrome-interacting factors (PIFs) plays an important role in plants as hubs for intracellular signaling regulation. The PIF gene family has been identified and characterized in many plants, but alfalfa (Medicago sativa L.), an important perennial high-quality legume forage, has not been reported on the PIF gene family.

RESULTS

In this study, we presented the identification and characterization of five MsPIF genes in alfalfa (Medicago sativa L.). Phylogenetic analysis indicated that PIFs from alfalfa and other four plant species could be divided into three groups supported by similar motif analysis. The collinearity analysis of the MsPIF gene family showed the presence of two gene pairs, and the collinearity analysis with AtPIFs showed three gene pairs, indicating that the evolutionary process of this family is relatively conservative. Analysis of cis-acting elements in promoter regions of MsPIF genes indicated that various elements were related to light, abiotic stress, and plant hormone responsiveness. Gene expression analyses demonstrated that MsPIFs were primarily expressed in the leaves and were induced by various abiotic stresses.

CONCLUSION

This study conducted genome-wide identification, evolution, synteny analysis, and expression analysis of the PIFs in alfalfa. Our study lays a foundation for the study of the biological functions of the PIF gene family and provides a useful reference for improving abiotic stress resistance in alfalfa.

Near-infrared light and PIF4 promote plant antiviral defense by enhancing RNA interference

The molecular mechanism underlying phototherapy and light treatment, which utilize various wavelength spectra of light, including near-infrared (NIR), to cure human and plant diseases, is obscure. Here we revealed that NIR light confers antiviral immunity by positively regulating PHYTOCHROME-INTERACTING FACTOR 4 (PIF4)-activated RNA interference (RNAi) in plants. PIF4, a central transcription factor involved in light signaling, accumulates to high levels under NIR light in plants. PIF4 directly induces the transcription of two essential components of RNAi, RNA-DEPENDENT RNA POLYMERASE 6 (RDR6) and ARGONAUTE 1 (AGO1), which play important roles in resistance to both DNA and RNA viruses. Moreover, the pathogenic determinant βC1 protein, which is evolutionarily conserved and encoded by betasatellites, interacts with PIF4 and inhibits its positive regulation of RNAi by disrupting PIF4 dimerization. These findings shed light on the molecular mechanism of PIF4-mediated plant defense and provide a new perspective for the exploration of NIR antiviral treatment.

Recent Advances in Studying the Regulation of Fruit Ripening in Tomato Using Genetic Engineering Approaches

Tomato (Solanum lycopersicum L.) is one of the most commercially essential vegetable crops cultivated worldwide. In addition to the nutritional value, tomato is an excellent model for studying climacteric fruits' ripening processes. Despite this, the available natural pool of genes that allows expanding phenotypic diversity is limited, and the difficulties of crossing using classical selection methods when stacking traits increase proportionally with each additional feature. Modern methods of the genetic engineering of tomatoes have extensive potential applications, such as enhancing the expression of existing gene(s), integrating artificial and heterologous gene(s), pointing changes in target gene sequences while keeping allelic combinations characteristic of successful commercial varieties, and many others. However, it is necessary to understand the fundamental principles of the gene molecular regulation involved in tomato fruit ripening for its successful use in creating new varieties. Although the candidate genes mediate ripening have been identified, a complete picture of their relationship has yet to be formed. This review summarizes the latest (2017-2023) achievements related to studying the ripening processes of tomato fruits. This work attempts to systematize the results of various research articles and display the interaction pattern of genes regulating the process of tomato fruit ripening.

Genome-wide identification and comprehensive analysis of the phytochrome-interacting factor (PIF) gene family in wheat

Phytochrome-interacting factors (PIFs) are essential transcription factors for plant growth, development, and stress responses. Although PIF genes have been extensively studied in many plant species, they have not been thoroughly investigated in wheat. Here, we identified 18 PIF genes in cultivated hexaploid wheat (Triticum aestivum L). Phylogenetic analysis, exon-intron structures, and motif compositions revealed the presence of four distinct groups of TaPIFs. Genome-wide collinearity analysis of PIF genes revealed the evolutionary history of PIFs in wheat, Oryza sativa, and Brachypodium distachyon. Cis-regulatory element analysis suggested that TaPIF genes indicated participated in plant development and stress responses. Subcellular localization assays indicated that TaPIF2-1B and TaPIF4-5B were transcriptionally active. Both were found to be localized to the nucleus. Gene expression analyses demonstrated that TaPIFs were primarily expressed in the leaves and were induced by various biotic and abiotic stresses and phytohormone treatments. This study provides new insights into PIF-mediated stress responses and lays a strong foundation for future investigation of PIF genes in wheat.

Carotenoids and Tocopherol Profiling in Fleshy Fruits

Carotenoids and tocopherols are among the most powerful lipophilic antioxidants accumulated in fruit and vegetable crops. This chapter describes a method for the separation and quantification of carotenoids/chlorophylls and tocopherols based on microextraction followed by reverse- and normal-phase HPLC, respectively. Using this method, high-throughput, accurate analysis of these compounds can be performed in leaf and fruit samples.

Two adjacent NAC transcription factors regulate fruit maturity date and flavor in peach

Although maturity date (MD) is an essential factor affecting fresh fruit marketing and has a pleiotropic effect on fruit taste qualities, the underlying mechanisms remain largely unclear. In this study, we functionally characterized two adjacent NAM-ATAF1/2-CUC2 (NAC) transcription factors (TFs), PpNAC1 and PpNAC5, both of which were associated with fruit MD in peach. PpNAC1 and PpNAC5 were found capable of activating transcription of genes associated with cell elongation, cell wall degradation and ethylene biosynthesis, suggesting their regulatory roles in fruit enlargement and ripening. Furthermore, PpNAC1 and PpNAC5 had pleiotropic effects on fruit taste due to their ability to activate transcription of genes for sugar accumulation and organic acid degradation. Interestingly, both PpNAC1 and PpNAC5 orthologues were found in fruit-producing angiosperms and adjacently arranged in all 91 tested dicots but absent in fruitless gymnosperms, suggesting their important roles in fruit development. Our results provide insight into the regulatory roles of NAC TFs in MD and fruit taste.

Overexpression of GmPIF4b affects morpho-physiological traits to reduce heat-induced grain loss in soybean

Heat waves associated with climate change seriously threaten crop productivity. Crop seed yield depends on the success of reproduction. However, reproductive development is most vulnerable to heat stress conditions. Perception of heat and its conversion into cellular signals is a complex process. The basic helix loop helix (bHLH) transcription factor, Phytochrome Interacting Factor 4 (PIF4), plays a significant role in this process. However, studies on PIF4- mediated impacts on crop grain yield at a higher temperature are lacking. We investigated the overexpression of GmPIF4b in soybean to alleviate heat-induced damage and yield using a transgenic approach. Our results showed that under high-temperature conditions (38°C/28°C), overexpressing soybeans plants had higher chlorophyll a and b, and lower proline accumulation compared to WT. Further, overexpression of GmPIF4b improved pollen viability under heat stress and reduced heat-induced structural abnormalities in the male and female reproductive organs. Consequently, the transgenic plants produced higher pods and seeds per plant at high temperatures. Quantitative RT-PCR analysis showed that the overexpressing GmPIF4b soybeans had higher transcripts of heat shock factor, GmHSF-34, and heat-shock protein, GmHSP90A2. Collectively, our results suggest that GmPIF4b regulates multiple morpho-physiological traits for better yield under warmer climatic conditions.

Exogenous application of nanocarrier-mediated double-stranded RNA manipulates physiological traits and defence response against bacterial diseases

Stability and delivery are major challenges associated with exogenous double-stranded RNA (dsRNA) application into plants. We report the encapsulation and delivery of dsRNA in cationic poly-aspartic acid-derived polymer (CPP6) into plant cells. CPP6 stabilizes the dsRNAs during long exposure at varied temperatures and pH, and protects against RNase A degradation. CPP6 helps dsRNA uptake through roots or foliar spray and facilitates systemic movement to induce endogenous gene silencing. The fluorescence of Arabidopsis GFP-overexpressing transgenic plants was significantly reduced after infiltration with gfp-dsRNA-CPP6 by silencing of the transgene compared to plants treated only with gfp-dsRNA. The plant endogenous genes flowering locus T (FT) and phytochrome interacting factor 4 (PIF4) were downregulated by a foliar spray of ft-dsRNA-CPP6 and pif4-dsRNA-CPP6 in Arabidopsis, with delayed flowering and enhanced biomass. The rice PDS gene targeted by pds-dsRNA-CPP6 through root uptake was effectively silenced and plants showed a dwarf and albino phenotype. The NaCl-induced OsbZIP23 was targeted through root uptake of bzip23-dsRNA-CPP6 and showed reduced transcripts and seedling growth compared to treatment with naked dsRNA. The negative regulators of plant defence SDIR1 and SWEET14 were targeted through foliar spray to provide durable resistance against bacterial leaf blight disease caused by Xanthomonas oryzae pv. oryzae (Xoo). Overall, the study demonstrates that transient silencing of plant endogenous genes using polymer-encapsulated dsRNA provides prolonged and durable resistance against Xoo, which could be a promising tool for crop protection and for sustaining productivity.

Novel transcriptome networks are associated with adaptation of capsicum fruit development to a light-blocking glasshouse film

Light-blocking films (LBFs) can contribute to significant energy savings for protected cropping via altering light transmitting, such as UVA, photosynthetically active radiation, blue and red spectra affecting photosynthesis, and capsicum yield. Here, we investigated the effects of LBF on orange color capsicum (O06614, Capsicum annuum L.) fruit transcriptome at 35 (mature green) and 65 (mature ripe) days after pollination (DAP) relative to untreated control in a high-technology glasshouse. The results of targeted metabolites showed that LBF significantly promotes the percentage of lutein but decreased the percentage of zeaxanthin and neoxanthin only at 35 DAP. At 35 DAP, fruits were less impacted by LBF treatment (versus control) with a total of 1,192 differentially expressed genes (DEGs) compared with that at 65 DAP with 2,654 DEGs. Response to stress and response to light stimulus in biological process of Gene Ontology were found in 65-DAP fruits under LBF vs. control, and clustering analysis revealed a predominant role of light receptors and phytohormone signaling transduction as well as starch and sucrose metabolism in LBF adaptation. The light-signaling DEGs, UV light receptor UVR8, transcription factors phytochrome-interacting factor 4 (PIF4), and an E3 ubiquitin ligase (COP1) were significantly downregulated at 65 DAP. Moreover, key DEGs in starch and sucrose metabolism (SUS, SUC, and INV), carotenoid synthesis (PSY2 and BCH1), ascorbic acid biosynthesis (VTC2, AAO, and GME), abscisic acid (ABA) signaling (NCED3, ABA2, AO4, and PYL2/4), and phenylpropanoid biosynthesis (PAL and DFR) are important for the adaptation of 65-DAP fruits to LBF. Our results provide new candidate genes for improving quality traits of low-light adaptation of capsicum in protected cropping.

Understanding the mechanism of red light-induced melatonin biosynthesis facilitates the engineering of melatonin-enriched tomatoes

Melatonin is a functionally conserved broad-spectrum physiological regulator found in most biological organisms in nature. Enrichment of tomato fruit with melatonin not only enhances its agronomic traits but also provides extra health benefits. In this study, we elucidate the full melatonin biosynthesis pathway in tomato fruit by identifying biosynthesis-related genes that encode caffeic acid O-methyltransferase 2 (SlCOMT2) and N-acetyl-5-hydroxytryptamine-methyltransferases 5/7 (SlASMT5/7). We further reveal that red light supplementation significantly enhances the melatonin content in tomato fruit. This induction relies on the "serotonin-N-acetylserotonin-melatonin" biosynthesis route via the SlphyB2-SlPIF4-SlCOMT2 module. Based on the regulatory mechanism, we design a gene-editing strategy to target the binding motif of SlPIF4 in the promoter of SlCOMT2, which significantly enhances the production of melatonin in tomato fruit. Our study provides a good example of how the understanding of plant metabolic pathways responding to environmental factors can guide the engineering of health-promoting foods.

Photobiotechnology for abiotic stress resilient crops: Recent advances and prospects

Massive crop failures worldwide are caused by abiotic stress. In plants, adverse environmental conditions cause extensive damage to the overall physiology and agronomic yield at various levels. Phytochromes are photosensory phosphoproteins that absorb red (R)/far red (FR) light and play critical roles in different physiological and biochemical responses to light. Considering the role of phytochrome in essential plant developmental processes, genetically manipulating its expression offers a promising approach to crop improvement. Through modulated phytochrome-mediated signalling pathways, plants can become more resistant to environmental stresses by increasing photosynthetic efficiency, antioxidant activity, and expression of genes associated with stress resistance. Plant growth and development in adverse environments can be improved by understanding the roles of phytochromes in stress tolerance characteristics. A comprehensive overview of recent findings regarding the role of phytochromes in modulating abiotic stress by discussing biochemical and molecular aspects of these mechanisms of photoreceptors is offered in this review.

Functions of Phytochrome-Interacting Factors (PIFs) in the regulation of plant growth and development: A comprehensive review

Transcription factors play important roles in governing plant responses upon changes in their ambient conditions. Any fluctuation in the supply of critical requirements for plants, such as optimum light, temperature, and water leads to the reprogramming of gene-signaling pathways. At the same time, plants also evaluate and shift their metabolism according to the various stages of development. Phytochrome-Interacting Factors are one of the most important classes of transcription factors that regulate both developmental and external stimuli-based growth of plants. This review focuses on the identification of PIFs in various organisms, regulation of PIFs by various proteins, functions of PIFs of Arabidopsis in diverse developmental pathways such as seed germination, photomorphogenesis, flowering, senescence, seed and fruit development, and external stimuli-induced plant responses such as shade avoidance response, thermomorphogenesis, and various abiotic stress responses. Recent advances related to the functional characterization of PIFs of crops such as rice, maize, and tomato have also been incorporated in this review, to ascertain the potential of PIFs as key regulators to enhance the agronomic traits of these crops. Thus, an attempt has been made to provide a holistic view of the function of PIFs in various processes in plants.

Identification and characterization of cotton PHYTOCHROME-INTERACTING FACTORs in temperature-dependent flowering

PHYTOCHROME INTERACTING FACTORs (PIFs) assimilate with light and temperature signs to control plant growth and development. However, little is known about PIFs in crop plants such as cotton. Here, we identified 68 PIF proteins and their coding genes from an allotetraploid and three diploid ancestors. Cotton PIFs contain typical APA and APB motifs by means of which they bind to phytochrome phyA and phyB, respectively, and have a bHLH domain and a nuclear localization sequence necessary for bHLH-type transcription factors. Bioinformatics analysis showed that the promoter of each PIF gene contains multiple cis-acting elements and that the evolution of cotton genomes likely underwent loss, recombination, and tandem replication. Further observations indicated that the sensitivity of cotton PIF expression to low or high temperature was significantly different, of which allotetraploid Gossypium hirsutum PIF4a (GhPIF4a) was induced by high temperature. GhPIF4a promotes flowering in cotton and Arabidopsis and binds to the promoter of GhFT (FLOWERING LOCUS T) increasing with temperature rise. In conclusion, our work identifies the evolutionary and structural characteristics and functions of PIF family members in cotton.

Genome-Wide Characterization of the PIFs Family in Sweet Potato and Functional Identification of IbPIF3.1 under Drought and Fusarium Wilt Stresses

Phytochrome-interacting factors (PIFs) are essential for plant growth, development, and defense responses. However, research on the PIFs in sweet potato has been insufficient to date. In this study, we identified PIF genes in the cultivated hexaploid sweet potato (Ipomoea batatas) and its two wild relatives, Ipomoea triloba, and Ipomoea trifida. Phylogenetic analysis revealed that IbPIFs could be divided into four groups, showing the closest relationship with tomato and potato. Subsequently, the PIFs protein properties, chromosome location, gene structure, and protein interaction network were systematically analyzed. RNA-Seq and qRT-PCR analyses showed that IbPIFs were mainly expressed in stem, as well as had different gene expression patterns in response to various stresses. Among them, the expression of IbPIF3.1 was strongly induced by salt, drought, H₂O₂, cold, heat, Fusarium oxysporum f. sp. batatas (Fob), and stem nematodes, indicating that IbPIF3.1 might play an important role in response to abiotic and biotic stresses in sweet potato. Further research revealed that overexpression of IbPIF3.1 significantly enhanced drought and Fusarium wilt tolerance in transgenic tobacco plants. This study provides new insights for understanding PIF-mediated stress responses and lays a foundation for future investigation of sweet potato PIFs.

Salt-tolerant alternative crops as sources of quality food to mitigate the negative impact of salinity on agricultural production

An increase of abiotic stress tolerance and nutritive value of foods is currently a priority because of climate change and rising world population. Among abiotic stresses, salt stress is one of the main problems in agriculture. Mounting urbanization and industrialization, and increasing global food demand, are pressing farmers to make use of marginal lands affected by salinity and low-quality saline water. In that situation, one of the most promising approaches is searching for new sources of genetic variation like salt-tolerant alternative crops or underexploited crops. They are generally less efficient than cultivated crops in optimal conditions due to lower yield but represent an alternative in stressful growth conditions. In this review, we summarize the advances achieved in research on underexploited species differing in their genetic nature. First, we highlight advances in research on salt tolerance of traditional varieties of tomato or landraces; varieties selected and developed by smallholder farmers for adaptation to their local environments showing specific attractive fruit quality traits. We remark advances attained in screening a collection of tomato traditional varieties gathered in Spanish Southeast, a very productive region which environment is extremely stressing. Second, we explore the opportunities of exploiting the natural variation of halophytes, in particular quinoa and amaranth. The adaptation of both species in stressful growth conditions is becoming an increasingly important issue, especially for their cultivation in arid and semiarid areas prone to be affected by salinity. Here we present a project developed in Spanish Southeast, where quinoa and amaranth varieties are being adapted for their culture under abiotic stress targeting high quality grain.

SlBBX28 positively regulates plant growth and flower number in an auxin-mediated manner in tomato

SlBBX28 is a positive regulator of auxin metabolism and signaling, affecting plant growth and flower number in tomato B-box domain-containing proteins (BBXs) comprise a family of transcription factors that regulate several processes, such as photomorphogenesis, flowering, and stress responses. For this reason, attention is being directed toward the functional characterization of these proteins, although knowledge in species other than Arabidopsis thaliana remains scarce. Particularly in the tomato, Solanum lycopersicum, only three out of 31 SlBBX proteins have been functionally characterized to date. To deepen the understanding of the role of these proteins in tomato plant development and yield, SlBBX28, a light-responsive gene, was constitutively silenced, resulting in plants with smaller leaves and fewer flowers per inflorescence. Moreover, SlBBX28 knockdown reduced hypocotyl elongation in darkness-grown tomato. Analyses of auxin content and responsiveness revealed that SlBBX28 promotes auxin-mediated responses. Altogether, the data revealed that SlBBX28 promotes auxin production and signaling, ultimately leading to proper hypocotyl elongation, leaf expansion, and inflorescence development, which are crucial traits determining tomato yield.

Molecular basis of nitrogen starvation-induced leaf senescence

Nitrogen (N), a macronutrient, is often a limiting factor in plant growth, development, and productivity. To adapt to N-deficient environments, plants have developed elaborate N starvation responses. Under N-deficient conditions, older leaves exhibit yellowing, owing to the degradation of proteins and chlorophyll pigments in chloroplasts and subsequent N remobilization from older leaves to younger leaves and developing organs to sustain plant growth and productivity. In recent years, numerous studies have been conducted on N starvation-induced leaf senescence as one of the representative plant responses to N deficiency, revealing that leaf senescence induced by N deficiency is highly complex and intricately regulated at different levels, including transcriptional, post-transcriptional, post-translational and metabolic levels, by multiple genes and proteins. This review summarizes the current knowledge of the molecular mechanisms associated with N starvation-induced leaf senescence.

PIFs- and COP1-HY5-mediated temperature signaling in higher plants

Plants have to cope with the surrounding changing environmental stimuli to optimize their physiological and developmental response throughout their entire life cycle. Light and temperature are two critical environmental cues that fluctuate greatly during day-night cycles and seasonal changes. These two external signals coordinately control the plant growth and development. Distinct spectrum of light signals are perceived by a group of wavelength-specific photoreceptors in plants. PIFs and COP1-HY5 are two predominant signaling hubs that control the expression of a large number of light-responsive genes and subsequent light-mediated development in plants. In parallel, plants also transmit low or warm temperature signals to these two regulatory modules that precisely modulate the responsiveness of low or warm temperatures. The core component of circadian clock ELF3 integrates signals from light and warm temperatures to regulate physiological and developmental processes in plants. In this review, we summarize and discuss recent advances and progresses on PIFs-, COP1-HY5- and ELF3-mediated light, low or warm temperature signaling, and highlight emerging insights regarding the interactions between light and low or warm temperature signal transduction pathways in the control of plant growth.

PHYTOCHROME-INTERACTING FACTORS: a promising tool to improve crop productivity

Light is a key determinant for plant growth, development, and ultimately yield. Phytochromes, red/far-red photoreceptors, play an important role in plant architecture, stress tolerance, and productivity. In the model plant Arabidopsis, 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 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.

Pivotal roles of ELONGATED HYPOCOTYL5 in regulation of plant development and fruit metabolism in tomato

The transcription factor ELONGATED HYPOCOTYL5 (HY5) plays critical roles in plant photomorphogenesis. Previous studies on HY5 have mainly focused on the seedling stage in Arabidopsis (Arabidopsis thaliana), and its functions in other plant species have not been well characterized, particularly at adult stages of development. In this report, we investigated the functions of tomato (Solanum lycopersicum) HY5 (SlHY5) from seedlings to adult plants with a focus on fruits. Genome-edited slhy5 mutants exhibited typical compromised photomorphogenesis in response to various light conditions. The slhy5 mutants showed reduced primary root length and secondary root number, which is associated with altered auxin signaling. SlHY5 promoted chlorophyll biosynthesis from seedling to adult stages. Notably, the promotive role of SlHY5 on chlorophyll accumulation was more pronounced on the illuminated side of green fruits than on their shaded side. Consistent with this light-dependent effect, we determined that SlHY5 protein is stabilized by light. Transcriptome and metabolome analyses in fruits revealed that SlHY5 has major functions in the regulation of metabolism, including the biosynthesis of phenylpropanoids and steroidal glycoalkaloids. These data demonstrate that SlHY5 performs both shared and distinct functions in relation to its Arabidopsis counterpart. The manipulation of SlHY5 represents a powerful tool to influence the two vital agricultural traits of seedling fitness and fruit quality in tomato.

Red light-transmittance bagging promotes carotenoid accumulation of grapefruit during ripening

Light, a crucial environmental signal, is involved in the regulation of secondary metabolites. To understand the mechanism by which light influences carotenoid metabolism, grapefruits were bagged with four types of light-transmitting bags that altered the transmission of solar light. We show that light-transmitting bagging induced changes in carotenoid metabolism during fruit ripening. Compared with natural light, red light (RL)-transmittance treatment significantly increases the total carotenoid content by 62%. Based on weighted gene co-expression network analysis (WGCNA), ‘blue’ and ‘turquoise’ modules are remarkably associated with carotenoid metabolism under different light treatment (p < 0.05). Transcriptome analysis identifies transcription factors (TFs) bHLH128, NAC2-like/21/72, MYB-like, AGL11/AGL61, ERF023/062, WRKY20, SBPlike-7/13 as being involved in the regulation of carotenoid metabolism in response to RL. Under RL treatment, these TFs regulate the accumulation of carotenoids by directly modulating the expression of carotenogenic genes, including GGPPS2, PDS, Z-ISO, ZDS2/7, CRTISO3, CYP97A, CHYB, ZEP2, CCD1-2. Based on these results, a network of the regulation of carotenoid metabolism by light in citrus fruits is preliminarily proposed. These results show that RL treatments have great potential to improve coloration and nutritional quality of citrus fruits.

Grapefruits ripened in red light-transmitting bags have 62% more carotenoid content than those ripened in natural light, leading to better coloration and higher nutritional quality.

Phytochrome interacting factor MdPIF7 modulates anthocyanin biosynthesis and hypocotyl growth in apple

Light affects many physiological and developmental processes of plants by regulating the expression and activity of light-responsive proteins. Among them, phytochrome interacting factors (PIFs) play pivotal roles in the regulation of anthocyanin accumulation and hypocotyl growth. However, the molecular mechanism is not well understood, especially in woody plants, such as apple (Malus × domestica). In this study, we identified a light-responsive PIF protein, MdPIF7, in apple and investigated the molecular mechanism of its regulation of anthocyanin biosynthesis and hypocotyl growth. We found that overexpression of MdPIF7 decreased anthocyanin accumulation in transgenic apple materials and promoted hypocotyl elongation in ectopically expressed Arabidopsis (Arabidopsis thaliana). Further investigation showed that MdPIF7 functioned by interacting with B-box 23 (MdBBX23), a positive regulator of anthocyanin biosynthesis in apple and hypocotyl growth inhibition in ectopically expressed Arabidopsis, and attenuating the transcriptional activation of MdBBX23 on LONG HYPOCOTYL 5 (MdHY5). In addition, MdPIF7 interacted with basic region leucine zipper 44 (MdbZIP44) and ethylene response factor 38 (MdERF38), two positive regulators of anthocyanin biosynthesis, and it negatively regulated MdbZIP44- and MdERF38-promoted anthocyanin accumulation by interfering with the interaction between MdbZIP44/MdERF38 and MdMYB1. Taken together, our results reveal that MdPIF7 regulates anthocyanin biosynthesis in apple and hypocotyl growth in ectopically expressed Arabidopsis through MdPIF7-MdBBX23-MdHY5 and MdPIF7-MdbZIP44/MdERF38-MdMYB1 modules. Our findings enrich the functional studies of PIF proteins and provide insights into the molecular mechanism of PIF-mediated anthocyanin biosynthesis and hypocotyl growth.

Soybean GmMYB133 Inhibits Hypocotyl Elongation and Confers Salt Tolerance in Arabidopsis

REVEILLE (RVE) genes generally act as core circadian oscillators to regulate multiple developmental events and stress responses in plants. It is of importance to document their roles in crops for utilizing them to improve agronomic traits. Soybean is one of the most important crops worldwide. However, the knowledge regarding the functional roles of RVEs is extremely limited in soybean. In this study, the soybean gene GmMYB133 was shown to be homologous to the RVE8 clade genes of Arabidopsis. GmMYB133 displayed a non-rhythmical but salt-inducible expression pattern. Like AtRVE8, overexpression of GmMYB133 in Arabidopsis led to developmental defects such as short hypocotyl and late flowering. Seven light-responsive or auxin-associated genes including AtPIF4 were transcriptionally depressed by GmMYB133, suggesting that GmMYB133 might negatively regulate plant growth. Noticeably, the overexpression of GmMYB133 in Arabidopsis promoted seed germination and plant growth under salt stress, and the contents of chlorophylls and malondialdehyde (MDA) were also enhanced and decreased, respectively. Consistently, the expressions of four positive regulators responsive to salt tolerance were remarkably elevated by GmMYB133 overexpression, indicating that GmMYB133 might confer salt stress tolerance. Further observation showed that GmMYB133 overexpression perturbed the clock rhythm of AtPRR5, and yeast one-hybrid assay indicated that GmMYB133 could bind to the AtPRR5 promoter. Moreover, the retrieved ChIP-Seq data showed that AtPRR5 could directly target five clients including AtPIF4. Thus, a regulatory module GmMYB133-PRR5-PIF4 was proposed to regulate plant growth and salt stress tolerance. These findings laid a foundation to further address the functional roles of GmMYB133 and its regulatory mechanisms in soybean.

PIF4 negatively modulates cold tolerance in tomato anthers via temperature-dependent regulation of tapetal cell death

Extreme temperature conditions seriously impair male reproductive development in plants; however, the molecular mechanisms underlying the response of anthers to extreme temperatures remain poorly described. The transcription factor phytochrome-interacting factor4 (PIF4) acts as a hub that integrates multiple signaling pathways to regulate thermosensory growth and architectural adaptation in plants. Here, we report that SlPIF4 in tomato (Solanum lycopersicum) plays a pivotal role in regulating cold tolerance in anthers. CRISPR (clustered regularly interspaced short palindromic repeats)-associated nuclease Cas9-generated SlPIF4 knockout mutants showed enhanced cold tolerance in pollen due to reduced temperature sensitivity of the tapetum, while overexpressing SlPIF4 conferred pollen abortion by delaying tapetal programmed cell death (PCD). SlPIF4 directly interacts with SlDYT1, a direct upstream regulator of SlTDF1, both of which (SlDYT1 and SlTDF1) play important roles in regulating tapetum development and tapetal PCD. Moderately low temperature (MLT) promotes the transcriptional activation of SlTDF1 by the SlPIF4-SlDYT1 complex, resulting in pollen abortion, while knocking out SlPIF4 blocked the MLT-induced activation of SlTDF1. Furthermore, SlPIF4 directly binds to the canonical E-box sequence in the SlDYT1 promoter. Collectively, these findings suggest that SlPIF4 negatively regulates cold tolerance in anthers by directly interacting with the tapetal regulatory module in a temperature-dependent manner. Our results shed light on the molecular mechanisms underlying the adaptation of anthers to low temperatures.

A transcriptomic, metabolomic and cellular approach to the physiological adaptation of tomato fruit to high temperature

High temperatures can negatively influence plant growth and development. Besides yield, the effects of heat stress on fruit quality traits remain poorly characterised. In tomato, insights into how fruits regulate cellular metabolism in response to heat stress could contribute to the development of heat-tolerant varieties, without detrimental effects on quality. In the present study, the changes occurring in wild type tomato fruits after exposure to transient heat stress have been elucidated at the transcriptome, cellular and metabolite level. An impact on fruit quality was evident as nutritional attributes changed in response to heat stress. Fruit carotenogenesis was affected, predominantly at the stage of phytoene formation, although altered desaturation/isomerisation arose during the transient exposure to high temperatures. Plastidial isoprenoid compounds showed subtle alterations in their distribution within chromoplast sub-compartments. Metabolite profiling suggests limited effects on primary/intermediary metabolism but lipid remodelling was evident. The heat-induced molecular signatures included the accumulation of sucrose and triacylglycerols, and a decrease in the degree of membrane lipid unsaturation, which influenced the volatile profile. Collectively, these data provide valuable insights into the underlying biochemical and molecular adaptation of fruit to heat stress and will impact on our ability to develop future climate resilient tomato varieties.

Light-Mediated Regulation of Leaf Senescence

Light is the primary regulator of various biological processes during the plant life cycle. Although plants utilize photosynthetically active radiation to generate chemical energy, they possess several photoreceptors that perceive light of specific wavelengths and then induce wavelength-specific responses. Light is also one of the key determinants of the initiation of leaf senescence, the last stage of leaf development. As the leaf photosynthetic activity decreases during the senescence phase, chloroplasts generate a variety of light-mediated retrograde signals to alter the expression of nuclear genes. On the other hand, phytochrome B (phyB)-mediated red-light signaling inhibits the initiation of leaf senescence by repressing the phytochrome interacting factor (PIF)-mediated transcriptional regulatory network involved in leaf senescence. In recent years, significant progress has been made in the field of leaf senescence to elucidate the role of light in the regulation of nuclear gene expression at the molecular level during the senescence phase. This review presents a summary of the current knowledge of the molecular mechanisms underlying light-mediated regulation of leaf senescence.

The conserved brassinosteroid-related transcription factor BIM1a negatively regulates fruit growth in tomato

Brassinosteroids (BRs) are steroid hormones that play key roles in plant development and defense. Our goal is to harness the extensive knowledge of the Arabidopsis BR signaling network to improve productivity in crop species. This first requires identifying components of the conserved network and their function in the target species. Here, we investigated the function of SlBIM1a, the closest tomato homolog of AtBIM1, which is highly expressed in fruit. SlBIM1a-overexpressing lines displayed severe plant and fruit dwarfism, and histological characterization of different transgenic lines revealed that SlBIM1a expression negatively correlated with fruit pericarp cell size, resulting in fruit size modifications. These growth phenotypes were in contrast to those found in Arabidopsis, and this was confirmed by the reciprocal ectopic expression of SlBIM1a/b in Arabidopsis and of AtBIM1 in tomato. These results determined that BIM1 function depends more on the recipient species than on its primary sequence. Yeast two-hybrid interaction studies and transcriptomic analyses of SlBIM1a-overexpressing fruit further suggested that SlBIM1a acts through its interaction with SlBZH1 to govern the transcriptional regulation of growth-related BR target genes. Together, these results suggest that SlBIM1a is a negative regulator of pericarp cell expansion, possibly at the crossroads with auxin and light signaling.

Far-red radiation stimulates dry mass partitioning to fruits by increasing fruit sink strength in tomato

Far-red (FR) light promotes fruit growth by increasing dry mass partitioning to fruits, but the mechanism behind this is unknown. We hypothesise that it is due to an increased fruit sink strength as FR radiation enhances sugar transportation and metabolism. Tomato plants were grown with or without 50-80 μmol m^-2  s^-1 of FR radiation added to a common background 150-170 μmol m^-2  s^-1 red + blue light-emitting diode lighting. Potential fruit growth, achieved by pruning each truss to one remaining fruit, was measured to quantify fruit sink strength. Model simulation was conducted to test whether the measured fruit sink strength quantitatively explained the FR effect on dry mass partitioning. Starch, sucrose, fructose and glucose content were measured. Expression levels of key genes involved in sugar transportation and metabolism were determined. FR radiation increased fruit sink strength by 38%, which, in model simulation, led to an increased dry mass partitioned to fruits that quantitatively agreed very well with measured partitioning. FR radiation increased fruit sugar concentration and upregulated the expression of genes associated with both sugar transportation and metabolism. This is the first study to demonstrate that FR radiation stimulates dry mass partitioning to fruits mainly by increasing fruit sink strength via simultaneous upregulation of sugar transportation and metabolism.

Light and ripening-regulated BBX protein-encoding genes in Solanum lycopersicum

Light controls several aspects of plant development through a complex signalling cascade. Several B-box domain containing proteins (BBX) were identified as regulators of Arabidopsis thaliana seedling photomorphogenesis. However, the knowledge about the role of this protein family in other physiological processes and species remains scarce. To fill this gap, here BBX protein encoding genes in tomato genome were characterised. The robust phylogeny obtained revealed how the domain diversity in this protein family evolved in Viridiplantae and allowed the precise identification of 31 tomato SlBBX proteins. The mRNA profiling in different organs revealed that SlBBX genes are regulated by light and their transcripts accumulation is directly affected by the chloroplast maturation status in both vegetative and fruit tissues. As tomato fruits develops, three SlBBXs were found to be upregulated in the early stages, controlled by the proper chloroplast differentiation and by the PHYTOCHROME (PHY)-dependent light perception. Upon ripening, other three SlBBXs were transcriptionally induced by RIPENING INHIBITOR master transcriptional factor, as well as by PHY-mediated signalling and proper plastid biogenesis. Altogether, the results obtained revealed a conserved role of SlBBX gene family in the light signalling cascade and identified putative members affecting tomato fruit development and ripening.

The regulatory pathways of distinct flowering characteristics in Chinese jujube

Flowering is the most important event in higher plants. Compared to most fruit tree species, Chinese jujube (Ziziphus jujuba Mill.), the most important member of the large, diverse Rhamnaceae family and a leading dry fruit-producing species, has unique characteristics that include a short juvenile phase and extremely fast flower bud differentiation. However, the distinct mechanism of flowering regulation in Chinese jujube is still unclear. The morphological and cytological development period of jujube flowering was first investigated, and the crucial developmental stages were defined. Flower bud differentiation in Chinese jujube took only approximately 11-13 days, which is a distinct characteristic of perennial fruit trees. Afterward, 44 genes related to six flowering pathways were identified in the jujube genome and were found to be randomly distributed among 11 of the 12 chromosomes. Tissue-specific and spatiotemporal expression patterns showed that all these genes were expressed in the flowers. Overall, photoperiod-related genes were highly expressed during flower bud differentiation. These genes were also positively responsive to photoperiod regulation and phase change processes, indicating that photoperiod- related genes play crucial roles in jujube flower bud differentiation. Under protected cultivation, ZjPIF4, a temperature-related gene, was expressed in the early stages of flowering and responded to increasing temperatures. Moreover, STRING analysis and yeast two-hybrid screening indicated that photoperiod-related (ZjCO) and temperature-related (ZjPIF4) proteins could interact with ZjFT, the key protein involved in the determination of flowering time, indicating crosstalk between photoperiod-related pathways and ambient temperature-related pathways in jujube. This study is the first report to comprehensively analyze the flowering pathways in Chinese jujube and revealed that photoperiod-related and ambient temperature-related pathways are the main mechanisms regulating the distinct flowering process and that members of the ZjPHY family (ZjPIF4, ZjFT, and ZjCO5) are the key factors involved in the regulatory network. These results will increase our understanding of the molecular and genetic mechanisms of flowering in Chinese jujube and provide meaningful clues for the flowering regulation of other fruit tree species.

Phytochrome-Dependent Temperature Perception Modulates Isoprenoid Metabolism

Changes in environmental temperature influence many aspects of plant metabolism; however, the underlying regulatory mechanisms remain poorly understood. In addition to their role in light perception, phytochromes (PHYs) have been recently recognized as temperature sensors affecting plant growth. In particular, in Arabidopsis (Arabidopsis thaliana), high temperature reversibly inactivates PHYB, reducing photomorphogenesis-dependent responses. Here, we show the role of phytochrome-dependent temperature perception in modulating the accumulation of isoprenoid-derived compounds in tomato (Solanum lycopersicum) leaves and fruits. The growth of tomato plants under contrasting temperature regimes revealed that high temperatures resulted in coordinated up-regulation of chlorophyll catabolic genes, impairment of chloroplast biogenesis, and reduction of carotenoid synthesis in leaves in a PHYB1B2-dependent manner. Furthermore, by assessing a triple phyAB1B2 mutant and fruit-specific PHYA- or PHYB2-silenced plants, we demonstrated that biosynthesis of the major tomato fruit carotenoid, lycopene, is sensitive to fruit-localized PHY-dependent temperature perception. The collected data provide compelling evidence concerning the impact of PHY-mediated temperature perception on plastid metabolism in both leaves and fruit, specifically on the accumulation of isoprenoid-derived compounds.