Light signaling and the phytohormonal regulation of shoot growth

The TCP transcription factor TAC8 positively regulates the tiller angle in rice (Oryza sativa L.)

The tiller angle, one of the critical factors that determine the rice plant type, is closely related to rice yield. An appropriate rice tiller angle can improve rice photosynthetic efficiency and increase yields. In this study, we identified a transcription factor, TILLRE ANGLE CONTROL 8 (TAC8), that is highly expressed in the rice tiller base and positively regulates the tiller angle by regulating cell length and endogenous auxin content; TAC8 encodes a TEOSINTE BRANCHED1/CYCLOIDEA/PCF transcriptional activator that is highly expressed in the nucleus. RNA-seq revealed that TAC8 is involved mainly in the photoperiod and abiotic stress response in rice. Yeast two-hybrid assays verified that TAC8 interacts with CHLOROPHYLL A/B-BINDING PROTEIN 1, which responds to photoperiod, and haplotype analysis revealed that a 34-bp deletion at position 1516 in the promoter region and a 9-bp deletion at position 153 in the coding region can result in impaired function or loss of function of TAC8. This study provides a new genetic resource for designing ideal plant types with appropriate rice tiller angle.

Impact of Seasonal Atmospheric Factors and Photoperiod on Floral Biology, Plant-Pollinator Interactions, and Plant Reproduction on Turnera ulmifolia L. (Passifloraceae)

Reproductive traits and plant-pollinator interactions largely depend on seasonal weather conditions, which are species-specific. Turnera ulmifolia is an ornamental plant distributed worldwide. There is little information about plant species' reproductive ecology and environmental factors' impact on it. Here, we aimed to examine the effects of seasonal atmospheric factors (e.g., temperature, light, relative humidity, rainfall) and photoperiod on flowering, interactions with flower visitors, and the reproductive success of Turnera ulmifolia in West Bengal, India. Flowering intensity peaked in hot summers and dropped in cold winters, correlating positively with temperature and humidity. Flower opening and closing occurred earlier on hot days, while flower longevity increased in winter, showing a negative correlation with temperature and humidity. Pollen and ovule production were lower in cold weather, positively linked to temperature and humidity. The self-compatible plant was moderately dependent on pollinators and had no pollination deficit in open conditions. Visitor abundance, richness, and diversity varied season-wise, with higher values during spring-summer. Based on pollinating agents, the plant showed multiple pollination modes (e.g., melittophily, myophily, myrmecophily, and psychophily). Effective pollinators were Amegilla zonata, Borbo cinnara, Halictus acrocephalus, Nomia (Curvinomia) strigata, and Tetragonula iridipennis. The fruit set (%) did not differ significantly season-wise, but the seed set remained higher in the hot days of summer than in cold winter. Therefore, it can be concluded that atmospheric factors and photoperiod significantly impact floral traits, plant-pollinator interactions, and plant reproduction.

Heterogeneity in Mechanical Properties of Plant Cell Walls

The acquisition and utilization of cell walls have fundamentally shaped the plant lifestyle. While the walls provide mechanical strength and enable plants to grow and occupy a three-dimensional space, successful sessile life also requires the walls to undergo dynamic modifications to accommodate size and shape changes accurately. Plant cell walls exhibit substantial mechanical heterogeneity due to the diverse polysaccharide composition and different development stages. Here, we review recent research advances, both methodological and experimental, that shed new light on the architecture of cell walls, with a focus on the mechanical heterogeneity of plant cell walls. Facilitated by advanced techniques and tools, especially atomic force microscopy (AFM), research efforts over the last decade have contributed to impressive progress in our understanding of how mechanical properties are associated with cell growth. In particular, the pivotal importance of pectin, the most complex wall polysaccharide, in wall mechanics is rapidly emerging. Pectin is regarded as an important determinant for establishing anisotropic growth patterns of elongating cells. Altogether, the diversity of plant cell walls can lead to heterogeneity in the mechanical properties, which will help to reveal how mechanical factors regulate plant cell growth and organ morphogenesis.

Non-Invasive Assessment, Classification, and Prediction of Biophysical Parameters Using Reflectance Hyperspectroscopy

Hyperspectral technology offers significant potential for non-invasive monitoring and prediction of morphological parameters in plants. In this study, UV-VIS-NIR-SWIR reflectance hyperspectral data were collected from Nicotiana tabacum L. plants using a spectroradiometer. These plants were grown under different light and gibberellic acid (GA₃) concentrations. Through spectroscopy and multivariate analyses, key growth parameters, such as height, leaf area, energy yield, and biomass, were effectively evaluated based on the interaction of light with leaf structures. The shortwave infrared (SWIR) bands, specifically SWIR1 and SWIR2, showed the strongest correlations with these growth parameters. When classifying tobacco plants grown under different GA₃ concentrations in greenhouses, artificial intelligence (AI) and machine learning (ML) algorithms were employed, achieving an average accuracy of over 99.1% using neural network (NN) and gradient boosting (GB) algorithms. Among the 34 tested vegetation indices, the photochemical reflectance index (PRI) demonstrated the strongest correlations with all evaluated plant phenotypes. Partial least squares regression (PLSR) models effectively predicted morphological attributes, with R²_CV values ranging from 0.81 to 0.87 and RPD_P values exceeding 2.09 for all parameters. Based on Pearson's coefficient XYZ interpolations and HVI algorithms, the NIR-SWIR band combination proved the most effective for predicting height and leaf area, while VIS-NIR was optimal for optimal energy yield, and VIS-VIS was best for predicting biomass. To further corroborate these findings, the SWIR bands for certain morphological characteristic wavelengths selected with s-PLS were most significant for SWIR1 and SWIR2, while i-PLS showed a more uniform distribution in VIS-NIR-SWIR bands. Therefore, SWIR hyperspectral bands provide valuable insights into developing alternative bands for remote sensing measurements to estimate plant morphological parameters. These findings underscore the potential of remote sensing technology for rapid, accurate, and non-invasive monitoring within stationary high-throughput phenotyping systems in greenhouses. These insights align with advancements in digital and precision technology, indicating a promising future for research and innovation in this field.

Physiological response of anthocyanin synthesis to different light intensities in blueberry

Fruit color is an important economic character of blueberry, determined by the amount of anthocyanin content. Anthocyanin synthesis within the blueberry fruits is significantly affected by light. To reveal the physiological response mechanism of anthocyanin synthesis in blueberry fruits in different light intensities, four light intensities (100% (CK), 75%, 50% and 25%) were set for the 'O'Neal' southern highbush blueberry as the experimental material in our study. The relationship between endogenous hormones content, associated enzyme activities, and variations with the anthocyanin content in blueberry fruits under various light intensities during the white fruit stage (S1), purple fruit stage (S2), and blue fruit stage (S3) were studied. The results showed that adequate light could significantly promote anthocyanin synthesis in blueberry fruits (P < 0.05). Blueberry fruits had an anthocyanin content that was 1.76~24.13 times higher under 100% light intensity than it was under non-full light intensity. Different light intensities significantly affected the content of endogenous hormones and the activity of associated enzymes in anthocyanin synthesis pathway (P < 0.05). Among them, the JA (jasmonic acid) content and PAL (phenylalanine ammonia lyase) activity of fruits under 100% light intensity were 2.49%~41.83% and 2.47%~48.48% higher than those under other light intensity, respectively. And a significant correlation was found between the variations in anthocyanin content in fruits and the content or activities of JA, ABA (abscisic acid), ETH (ethylene), GA3 (gibberellin 3), IAA (indoleacetic acid), PAL, CHI (chalcone isomerase), DFR (dihydroflavonol reductase) and UFGT (UDP-glucose: flavonoid 3-glucosyltransferase) (P < 0.05). It indicated that 100% light intensity significantly promoted anthocyanin synthesis in blueberry fruits by affecting endogenous hormones content and associated enzyme activities in the anthocyanin synthesis pathway. This study will lay a foundation for further research on the molecular mechanism of light intensity regulating anthocyanin synthesis in blueberry.

A Novel LED Light Radiation Approach Enhances Growth in Green and Albino Tea Varieties

Light, as an energy source, has been proven to strongly affect photosynthesis and, thus, can regulate the yield and quality of tea leaves (Camellia sinensis L.). However, few comprehensive studies have investigated the synergistic effects of light wavelengths on tea growth and development in green and albino varieties. Thus, the objective of this study was to investigate different ratios of red, blue and yellow light and their effects on tea plants' growth and quality. In this study, Zhongcha108 (green variety) and Zhongbai4 (albino variety) were exposed to lights of different wavelengths for a photoperiod of 5 months under the following seven treatments: white light simulated from the solar spectrum, which served as the control, and L1 (red 75%, blue 15% and yellow 10%), L2 (red 60%, blue 30% and yellow 10%), L3 (red 45%, far-red light 15%, blue 30% and yellow 10%), L4 (red 55%, blue 25% and yellow 20%), L5 (red 45%, blue 45% and yellow 10%) and L6 (red 30%, blue 60% and yellow 10%), respectively. We examined how different ratios of red light, blue light and yellow light affected tea growth by investigating the photosynthesis response curve, chlorophyll content, leaf structure, growth parameters and quality. Our results showed that far-red light interacted with red, blue and yellow light (L3 treatments) and significantly promoted leaf photosynthesis by 48.51% in the green variety, Zhongcha108, compared with the control treatments, and the length of the new shoots, number of new leaves, internode length, new leaf area, new shoots biomass and leaf thickness increased by 70.43%, 32.64%, 25.97%, 15.61%, 76.39% and 13.30%, respectively. Additionally, the polyphenol in the green variety, Zhongcha108, was significantly increased by 15.6% compared to that of the plants subjected to the control treatment. In addition, for the albino variety Zhongbai4, the highest ratio of red light (L1 treatment) remarkably enhanced leaf photosynthesis by 50.48% compared with the plants under the control treatment, resulting in the greatest new shoot length, number of new leaves, internode length, new leaf area, new shoot biomass, leaf thickness and polyphenol in the albino variety, Zhongbai4, compared to those of the control treatments, which increased by 50.48%, 26.11%, 69.29%, 31.61%, 42.86% and 10.09%, respectively. Our study provided these new light modes to serve as a new agricultural method for the production of green and albino varieties.

Adaptive photosynthetic strategies of the invasive plant Sphagneticola trilobata and its hybrid to a low-light environment

In stressful environments, invasive plants acclimate more efficiently than native plants and hybridization mainly contributes to this process. We examined changes in the morphological characteristics, photosynthetic characteristics, and antioxidant capacity of Sphagneticola trilobata and its hybrids in a low-light environment to explore their invasiveness, with Sphagneticola calendulacea serving as the control. The morphological plasticity of S. trilobata was not dominant, the maximal photochemical efficiency of PSII, actual quantum yield of PSII, and electron transport rate of PSII increased and nonphotochemical quenching decreased, while S. calendulacea and the hybrid produced opposite results. S. trilobata showed fewer spots stained for reactive oxygen species in tissues, with an increase in superoxide dismutase activity. Although S. trilobata is a heliophilous plant, we found that the shade tolerance of S. trilobata and the hybrid were stronger than that of S. calendulacea, which may be one important mechanism of invasion.

Exposure to low levels of photocatalytic TiO2 nanoparticles enhances seed germination and seedling growth of amaranth and cruciferous vegetables

Titanium dioxide (TiO₂) is one of the most common compounds on Earth, and it is used in natural forms or engineered bulks or nanoparticles (NPs) with increasing rates. However, the effect of TiO₂ NPs on plants remains controversial. Previous studies demonstrated that TiO₂ NPs are toxic to plants, because the photocatalytic property of TiO₂ produces biohazardous reactive oxygen species. In contrast, another line of evidence suggested that TiO₂ NPs are beneficial to plant growth. To verify this argument, in this study, we used seed germination of amaranth and cruciferous vegetables as a model system. Intriguingly, our data suggested that the controversy was due to the dosage effect. The photocatalytic activity of TiO₂ NPs positively affected seed germination and growth through gibberellins in a plant-tolerable range (0.1 and 0.2 mg/cm²), whereas overdosing (1 mg/cm²) induced tissue damage. Given that plants are the foundations of the ecosystem; these findings are useful for agricultural application, sustainable development and maintenance of healthy environments.

Integrated metabolomic and transcriptomic analyses reveal different metabolite biosynthesis profiles of Juglans mandshurica in shade

Light is not only a very important source of energy for the normal growth and development of plants, but also a regulator of many development and metabolic processes. The mechanism of plant growth and development under low light conditions is an important scientific question. With the promulgation of the law to stop natural forest cutting, understory regeneration is an important method for artificial forest afforestation. Here, the growth and physiological indexes of Juglans mandshurica, an important hardwood species in Northeast China, were measured under different shade treatments. In addition, transcriptome and metabolome were compared to analyze the molecular mechanism of shade tolerance in J. mandshurica. The results showed that the seedling height of the shade treatment group was significantly higher than that of the control group, and the 50% light (L50) treatment was the highest. Compared with the control group, the contents of gibberellin, abscisic acid, brassinolide, chlorophyll a, and chlorophyll b in all shade treatments were significantly higher. However, the net photosynthetic rate and water use efficiency decreased with increasing shade. Furthermore, the transcriptome identified thousands of differentially expressed genes in three samples. Using enrichment analysis, we found that most of the differentially expressed genes were enriched in photosynthesis, plant hormone signal transduction and chlorophyll synthesis pathways, and the expression levels of many genes encoding transcription factors were also changed. In addition, analysis of differentially accumulated metabolites showed that a total of 470 differential metabolites were identified, and flavonoids were the major differential metabolites of J. mandshurica under light stress. These results improved our understanding of the molecular mechanism and metabolite accumulation under light stress in J. mandshurica.

Growth Quality and Development of Olive Plants Cultured In-Vitro under Different Illumination Regimes

Light-emitting diodes (LEDs) are useful for the in-vitro micropropagation of plants, but little information is available on woody species. This work compares the effects of light quality and intensity on the growth and development of micropropagated olive plants from two different subspecies. Illumination was provided with fluorescent and LED lamps covering different red/blue ratios (90/10, 80/20, 70/30, 60/40) or red/blue/white combinations, as well as different light intensities (30, 34, 40, 52, 56, 84, 98 and 137 µmol m⁻² s⁻¹ of photosynthetic photon fluxes, PPF). Olive plants exhibited high sensitivity to light quality and intensity. Higher red/blue ratios or lower light intensities stimulated plant growth and biomass mainly as a consequence of a higher internodal elongation rate, not affecting either the total number of nodes or shoots. In comparison to fluorescent illumination, LED lighting improved leaf area and biomass, which additionally was positively correlated with light intensity. Stomatal frequency was positively, and pigments content negatively, correlated with light intensity, while no clear correlation was observed with light quality. In comparison with fluorescent lamps, LED illumination (particularly the 70/30 red/blue ratio with 34 µmol m⁻² s⁻¹ PPF intensity) allowed optimal manipulation and improved the quality of in-vitro micropropagated olive plants.

Dynamic nutrient removal potential of a novel submerged macrophyte Rotala rotundifolia, and its growth and physiological response to reduced light available

Rotala rotundifolia is a novel submerged macrophyte able to survive across the winter under temperature as low as 4 °C. Dynamic nutrient removal potential of R. rotundifolia was estimated using the Eco-tank system simulating natural eutrophic waters. The growth and physiological response of R. rotundifolia by cutting and division propagation to light (100%, 60%, and 20% natural light) were investigated. The results showed that R. rotundifolia was superior in removing N and P from eutrophic waters. As influent concentrations of NH₄⁺-N and total phosphorus (TP) were 4.81-5.87 and 0.61-0.78 mg L^-1, effluent concentrations of NH₄⁺-N, total nitrogen (TN), and TP were separately 0.06-1.10, 0.40-1.59, and 0.05-0.17 mg L^-1, with removal efficiencies of 93.6%, 84.6%, and 82.5% at a flow rate of 200 L d^-1. The growth and morphology of the plant under two propagation patterns were influenced by light and the responses were quite different. The biomass of the plant by cutting was higher at low light conditions, and the plant allocated more biomass on above ground. However, there was no significant difference in the height. By division, the plant preferred to high light. The biomass and height were significantly higher at 100% natural light. The peroxidase (POD), superoxide dismutase (SOD) and root activities of plant by cutting showed a trend of decrease and followed by an increase with light reduction, while by division, they increased with reduced light available. Variations of chlorophyll and soluble protein of the plant by cutting and division were contrary to the changes of POD activity. These results suggest that R. rotundifolia can be used to effectively remove nitrogen and phosphorus in eutrophic waters, and high light promotes the growth of the plant by division, while suitable shade is needed for the plant by cutting.

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.

Regulation of Early Plant Development by Red and Blue Light: A Comparative Analysis Between Arabidopsis thaliana and Solanum lycopersicum

In vertical farming, plants are grown in multi-layered growth chambers supplied with energy-efficient LEDs that produce less heat and can thus be placed in close proximity to the plants. The spectral quality control allowed by LED lighting potentially enables steering plant development toward desired phenotypes. However, this requires detailed knowledge on how light quality affects different developmental processes per plant species or even cultivar, and how well information from model plants translates to horticultural crops. Here we have grown the model dicot Arabidopsis thaliana (Arabidopsis) and the crop plant Solanum lycopersicum (tomato) under white or monochromatic red or blue LED conditions. In addition, seedlings were grown in vitro in either light-grown roots (LGR) or dark-grown roots (DGR) LED conditions. Our results present an overview of phenotypic traits that are sensitive to red or blue light, which may be used as a basis for application by tomato nurseries. Our comparative analysis showed that young tomato plants were remarkably indifferent to the LED conditions, with red and blue light effects on primary growth, but not on organ formation or flowering. In contrast, Arabidopsis appeared to be highly sensitive to light quality, as dramatic differences in shoot and root elongation, organ formation, and developmental phase transitions were observed between red, blue, and white LED conditions. Our results highlight once more that growth responses to environmental conditions can differ significantly between model and crop species. Understanding the molecular basis for this difference will be important for designing lighting systems tailored for specific crops.

Hydrogen-rich water promotes elongation of hypocotyls and roots in plants through mediating the level of endogenous gibberellin and auxin

The aim of this study was to investigate effects of the hydrogen-rich water (HRW) on the vegetable growth, and explore the possibility of applying HRW for protected cultivation of vegetables. Results showed that compared with control, HRW treatment significantly promoted fresh weight, hypocotyl length and root length of mung bean seedlings. The strongest stimulation was observed for 480 μM H2 (60% of saturated HRW concentration) treatment. This concentration was used in the following experiments. The enhanced cell elongation was correlated with the changes in the level of endogenous phytohormones. In the dark-grown hypocotyls and roots of mung bean seedlings, HRW significantly increased the content of IAA and GA3. Addition of GA3 enhanced the hypocotyl elongation only. uniconazole, an inhibitor of GA3 biosynthesis, inhibited HRW-induced hypocotyl elongation, but did not affect root elongation. Exogenous application of IAA promoted HRW effects on elongation of both the hypocotyl and the root, while the IAA biosynthesis inhibitor TIBA negated the above affects. The general nature of HRW-induced growth-promoting effects was further confirmed in experiments involving cucumber and radish seedlings. Taken together, HRW treatment promoted growth of seedlings, by stimulating elongation of hypocotyl and root cells, via HRW-induced increase in GA and IAA content in the hypocotyl and the root respectively.

Transcriptome and metabolite analyses provide insights into zigzag-shaped stem formation in tea plants (Camellia sinensis)

BACKGROUND

Shoot orientation is important for plant architecture formation, and zigzag-shaped shoots are a special trait found in many plants. Zigzag-shaped shoots have been selected and thoroughly studied in Arabidopsis; however, the regulatory mechanism underlying zigzag-shaped shoot development in other plants, especially woody plants, is largely unknown.

RESULTS

In this study, tea plants with zigzag-shaped shoots, namely, Qiqu (QQ) and Lianyuanqiqu (LYQQ), were investigated and compared with the erect-shoot tea plant Meizhan (MZ) in an attempt to reveal the regulation of zigzag-shaped shoot formation. Tissue section observation showed that the cell arrangement and shape of zigzag-shaped stems were aberrant compared with those of normal shoots. Moreover, a total of 2175 differentially expressed genes (DEGs) were identified from the zigzag-shaped shoots of the tea plants QQ and LYQQ compared to the shoots of MZ using transcriptome sequencing, and the DEGs involved in the "Plant-pathogen interaction", "Phenylpropanoid biosynthesis", "Flavonoid biosynthesis" and "Linoleic acid metabolism" pathways were significantly enriched. Additionally, the DEGs associated with cell expansion, vesicular trafficking, phytohormones, and transcription factors were identified and analysed. Metabolomic analysis showed that 13 metabolites overlapped and were significantly changed in the shoots of QQ and LYQQ compared to MZ.

CONCLUSIONS

Our results suggest that zigzag-shaped shoot formation might be associated with the gravitropism response and polar auxin transport in tea plants. This study provides a valuable foundation for further understanding the regulation of plant architecture formation and for the cultivation and application of horticultural plants in the future.

Root-expressed phytochromes B1 and B2, but not PhyA and Cry2, regulate shoot growth in nature

Although photoreceptors are expressed throughout all plant organs, most studies have focused on their function in aerial parts with laboratory-grown plants. Photoreceptor function in naturally dark-grown roots of plants in their native habitats is lacking. We characterized patterns of photoreceptor expression in field- and glasshouse-grown Nicotiana attenuata plants, silenced the expression of PhyB1/B2/A/Cry2 whose root transcripts levels were greater/equal to those of shoots, and by micrografting combined empty vector transformed shoots onto photoreceptor-silenced roots, creating chimeric plants with "blind" roots but "sighted" shoots. Micrografting procedure was robust in both field and glasshouse, as demonstrated by transcript accumulation patterns, and a spatially-explicit lignin visual reporter chimeric line. Field- and glasshouse-grown plants with PhyB1B2, but not PhyA or Cry2, -blind roots, were delayed in stalk elongation compared with control plants, robustly for two field seasons. Wild-type plants with roots directly exposed to FR phenocopied the growth of irPhyB1B2-blind root grafts. Additionally, root-expressed PhyB1B2 was required to activate the positive photomorphogenic regulator, HY5, in response to aboveground light. We conclude that roots of plants growing deep into the soil in nature sense aboveground light, and possibly soil temperature, via PhyB1B2 to control key traits, such as stalk elongation.

The interplay between cytokinins and light during senescence in detached Arabidopsis leaves

Light and cytokinins are known to be the key players in the regulation of plant senescence. In detached leaves, the retarding effect of light on senescence is well described; however, it is not clear to what extent is this effect connected with changes in endogenous cytokinin levels. We have performed a detailed analysis of changes in endogenous content of 29 cytokinin forms in detached leaves of Arabidopsis thaliana (wild-type and 3 cytokinin receptor double mutants). Leaves were kept under different light conditions, and changes in cytokinin content were correlated with changes in chlorophyll content, efficiency of photosystem II photochemistry, and lipid peroxidation. In leaves kept in darkness, we have observed decreased content of the most abundant cytokinin free bases and ribosides, but the content of cis-zeatin increased, which indicates the role of this cytokinin in the maintenance of basal leaf viability. Our findings underscore the importance of light conditions on the content of specific cytokinins, especially N⁶ -(Δ² -isopentenyl)adenine. On the basis of our results, we present a scheme summarizing the contribution of the main active forms of cytokinins, cytokinin receptors, and light to senescence regulation. We conclude that light can compensate the disrupted cytokinin signalling in detached leaves.

Efficiency of biogas slurry and Burkholderia phytofirmans PsJN to improve growth, physiology, and antioxidant activity of Brassica napus L. in chromium-contaminated soil

Contamination of soil is a major problem globally with colligated danger for ecosystem and human health. Chromium (Cr) is a toxic heavy metal and caused harmful effect on growth and development of plants. Phytostabilization reduced the mobility of heavy metals with addition of amendments which can significantly decrease metal solubility in soil. Phytostabilization can be achieved by application of biogas slurry (BGS) and endophytic bacteria as amendments in the contaminated soils. The present study revealed that the Burkholderia phytofirmans PsJN and BGS improved the growth, physiology, and antioxidant activity and reduced Cr uptake under a pot experiment spiked with Cr (20 mg kg^-1 soil). The experiment was designed under completely randomized design, four treatments with three replications in normal and Cr-contaminated soil. The inoculation of endophytic bacteria improved the growth and physiology of Brassica. This study showed that the inoculation of endophytic bacteria stabilized the Cr levels in soil and minimized the uptake by the plant shoots and roots in BGS-amended soil. Similarly, activity of antioxidants such as catalase (CAT), reduced glutathione (GSH), glutathione peroxidase (GSH-Px), and glutathione s-transferase (GST) was decreased to normal with combined treatment of BGS and endophytic bacteria in Cr-stressed soil. Overall, the best results were analyzed by combined treatment of BGS and endophytic bacteria to improve growth, physiology, and antioxidant activity of Brassica and immobilize Cr in soil. Moreover, results emphasized the need to use BGS alone or in combination with endophytic bacteria to optimize crop performance, stabilize Cr concentration, and improve environmental efficiency.

Increased Gibberellins and Light Levels Promotes Cell Wall Thickness and Enhance Lignin Deposition in Xylem Fibers

Light intensity and hormones (gibberellins; GAs) alter plant growth and development. A fine regulation triggered by light and GAs induces changes in stem cell walls (CW). Cross-talk between light-stimulated and GAs-induced processes as well as the phenolic compounds metabolism leads to modifications in lignin formation and deposition on cell walls. How these factors (light and GAs) promote changes in lignin content and composition. In addition, structural changes were evaluated in the stem anatomy of tobacco plants. GA₃ was sprayed onto the leaves and paclobutrazol (PAC), a GA biosynthesis inhibitor, via soil, at different irradiance levels. Fluorescence microscopy techniques were applied to detect lignin, and electron microscopy (SEM and TEM) was used to obtain details on cell wall structure. Furthermore, determination of total lignin and monomer contents were analyzed. Both light and GAs induces increased lignin content and CW thickening as well as greater number of fiber-like cells but not tracheary elements. The assays demonstrate that light exerts a role in lignification under GA₃ supplementation. In addition, the existence of an exclusive response mechanism to light was detected, that GAs are not able to replace.

Comparative Transcriptome Analysis Reveal Candidate Genes Potentially Involved in Regulation of Primocane Apex Rooting in Raspberry (Rubus spp.)

Raspberries (Rubus spp.) exhibit a unique rooting process that is initiated from the stem apex of primocane, conferring an unusual asexual mode of reproduction to this plant. However, the full complement of genes involved in this process has not been identified. To this end, the present study analyzed the transcriptomes of the Rubus primocane and floricane stem apex at three developmental stages by Digital Gene Expression profiling to identify genes that regulate rooting. Sequencing and de novo assembly yielded 26.82 Gb of nucleotides and 59,173 unigenes; 498, 7,346, 4,110, 7,900, 9,397, and 4,776 differently expressed genes were identified in paired comparisons of SAF1 (floricane at developmental stage 1) vs. SAP1 (primocane at developmental stage 1), SAF2 vs. SAP2, SAF3 vs. SAP3, SAP1 vs. SAP2, SAP1 vs. SAP3, and SAP2 vs. SAP3, respectively. SAP1 maintains an extension growth pattern; SAP2 then exhibits growth arrest and vertical (downward) gravitropic deflection; and finally, short roots begin to form on the apex of SAP3. The Kyoto Encyclopedia of Genes and Genomes enrichment analysis of SAP1 vs. SAP2 revealed 12 pathways that were activated in response to shoot growth arrest and root differentiation, including circadian rhythm-plant (ko04712) and plant hormone signal transduction (ko04075). Our results indicate that genes related to circadian rhythm, ethylene and auxin signaling, shoot growth, and root development are potentially involved in the regulation of primocane apex rooting in Rubus. These findings provide a basis for elucidating the molecular mechanisms of primocane apex rooting in this economically valuable crop.

FAR-RED INSENSITIVE 219/JAR1 Contributes to Shade Avoidance Responses of Arabidopsis Seedlings by Modulating Key Shade Signaling Components

To receive an ample amount of light, plants use elongation growth in response to vegetation shade. The combined interaction of light and hormones, including jasmonic acid (JA) signaling controls this elongation. However, the detailed molecular mechanisms underlying the response are still emerging. FAR-RED INSENSITIVE 219/JASMONATE RESISTANCE 1 (FIN219/JAR1), a cytoplasmic localized JA-conjugating enzyme, integrates far-red light and JA signaling. Here, we report that FIN219/JAR1 negatively regulates shade-induced hypocotyl elongation and gene expression in Arabidopsis seedlings in response to shade. In turn, simulated shade reduces FIN219 protein accumulation. Analysis of phyA 211 fin219-2 double mutants indicated that FIN219 and phyA are synergistic in regulating shade-induced hypocotyl elongation and gene expression. Moreover, FIN219 differentially affected the expression of the shade-signaling bHLH factors PIF5 and PAR1, thereby increasing the expression of the auxin-response genes IAA29 and SAUR68 on exposure to shade. Furthermore, the protein level of CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1) was affected in both fin219 mutants and overexpression lines as compared with the wild type under shade. Intriguingly, ectopic expression of FIN219 inhibited the nuclear accumulation of COP1 in response to shade. Further co-immunoprecipitation studies revealed that FIN219 interacted with COP1 and phyA under shade. Therefore, FIN219/JAR1 may play a vital role in modulating the Arabidopsis response to simulated shade via multiple layers of molecular mechanisms.

Morphology and Hydraulic Architecture of Vitis vinifera L. cv. Syrah and Torrontés Riojano Plants Are Unaffected by Variations in Red to Far-Red Ratio

Plants have evolved an array of specific photoreceptors to acclimate to the light environment. By sensing light signals, photoreceptors modulate plant morphology, carbon- and water-physiology, crop yield and quality of harvestable organs, among other responses. Many cultural practices and crop management decisions alter light quantity and quality perceived by plants cultivated in the field. Under full sunlight, phytochromes perceive high red to far red ratios (R:FR; 1.1), whereas overhead or lateral low R:FR (below 1.1) are sensed in the presence of plant shade or neighboring plants, respectively. Grapevine is one of the most important fruit crops in the world. To date, studies on grapevine response to light focused on different Photosynthetic Active Radiation (PAR) levels; however, limited data exist about its response to light quality. In this study we aimed to investigate morphological, biochemical, and hydraulic responses of Vitis vinifera to variations in R:FR. Therefore, we irradiated Syrah and Torrontés Riojano plants, grown in a glasshouse, with lateral FR light (low lateral R:FR treatment), while others, that were kept as controls, were not irradiated (ambient lateral R:FR treatment). In response to the low lateral R:FR treatment, grapevine plants did not display any of the SAS morphological markers (i.e. stem length, petiole length and angle, number of lateral shoots) in any of the cultivars assessed, despite an increase in gibberelins and auxin concentrations in leaf tissues. Low lateral R:FR did not affect dry matter partitioning, water-related traits (stomata density and index, wood anatomy), or water-related physiology (plant conductance, transpiration rate, stem hydraulic conductivity, stomatal conductance). None of the Vitis vinifera varieties assessed displayed the classical morphological and hydraulic responses associated to SAS induced by phytochromes. We discuss these results in the context of natural grapevine environment and agronomical relevance.

Photosynthetic acclimation, vernalization, crop productivity and 'the grand design of photosynthesis'

Daniel Arnon first proposed the notion of a 'grand design of photosynthesis' in 1982 to illustrate the central role of photosynthesis as the primary energy transformer for all life on Earth. However, we suggest that this concept can be extended to the broad impact of photosynthesis not only in global energy transformation but also in the regulation of plant growth, development, survival and crop productivity through chloroplast redox signalling. We compare and contrast the role of chloroplast redox imbalance, measured as excitation pressure, in governing acclimation to abiotic stress and phenotypic plasticity. Although all photoautrophs sense excessive excitation energy through changes in excitation pressure, the response to this chloroplast redox signal is species dependent. Due to a limited capacity to adjust metabolic sinks, cyanobacteria and green algae induce photoprotective mechanisms which dissipate excess excitation energy at a cost of decreased photosynthetic performance. In contrast, terrestrial, cold tolerant plants such as wheat enhance metabolic sink capacity which leads to enhanced photosynthetic performance and biomass accumulation with minimal dependence on photoprotection. We suggest that the family of nuclear C-repeat binding transcription factors (CBFs) associated with the frost resistance locus, FR2, contiguous with the vernalization locus,VRN1, and mapped to chromosome 5A of wheat, may be critical components that link leaf chloroplast redox regulation to enhanced photosynthetic performance, the accumulation of growth-active gibberellins and the dwarf phenotype during cold acclimation prior to the vegetative to reproductive transition controlled by vernalization in winter cereals. Further genetic, molecular and biochemical research to confirm these links and to elucidate the molecular mechanism by which chloroplast redox modulation of CBF expression leads to enhanced photosynthetic performance is required. Because of the superior abiotic stress tolerance of cold tolerant winter wheat and seed yields that historically exceed those of spring wheat by 30-40%, we discuss the potential to exploit winter cereals for the maintenance or perhaps even the enhancement of cereal productivity under future climate change scenarios that will be required to feed a growing human population.

Mapping transcription factor interactome networks using HaloTag protein arrays

Protein microarrays enable investigation of diverse biochemical properties for thousands of proteins in a single experiment, an unparalleled capacity. Using a high-density system called HaloTag nucleic acid programmable protein array (HaloTag-NAPPA), we created high-density protein arrays comprising 12,000 Arabidopsis ORFs. We used these arrays to query protein-protein interactions for a set of 38 transcription factors and transcriptional regulators (TFs) that function in diverse plant hormone regulatory pathways. The resulting transcription factor interactome network, TF-NAPPA, contains thousands of novel interactions. Validation in a benchmarked in vitro pull-down assay revealed that a random subset of TF-NAPPA validated at the same rate of 64% as a positive reference set of literature-curated interactions. Moreover, using a bimolecular fluorescence complementation (BiFC) assay, we confirmed in planta several interactions of biological interest and determined the interaction localizations for seven pairs. The application of HaloTag-NAPPA technology to plant hormone signaling pathways allowed the identification of many novel transcription factor-protein interactions and led to the development of a proteome-wide plant hormone TF interactome network.

LEAFDATA: a literature-curated database for Arabidopsis leaf development

BACKGROUND

In the post-genomic era, biological databases provide an easy access to a wide variety of scientific data. The vast quantity of literature calls for curated databases where existing knowledge is carefully organized in order to aid novel discoveries. Leaves, the main photosynthetic organs are not only vital for plant growth but also essential for maintaining the global ecosystem by producing oxygen and food. Therefore, studying and understanding leaf formation and growth are key objectives in biology. Arabidopsis thaliana to this date remains the prime experimental model organism in plant science.

DESCRIPTION

LEAFDATA was created as an easily accessible and searchable web tool to assemble a relevant collection of Arabidopsis leaf literature. LEAFDATA currently contains 13,553 categorized statements from 380 processed publications. LEAFDATA can be searched for genes of interest using Arabidopsis Genome Initiative identifiers, for selected papers by means of PubMed IDs, authors and specific keywords. The results page contains details of the original publications, text fragments from the curated literature grouped according to information types and direct links to PubMed pages of the original papers.

CONCLUSIONS

The LEAFDATA database offers access to searchable entries curated from a large number of scientific publications. Due to the unprecedented details of annotations and the fact that LEAFDATA already provides records about approximately 1600 individual loci, this database is useful for the entire plant research community.

Evaluating the use of plant hormones and biostimulators in forage pastures to enhance shoot dry biomass production by perennial ryegrass (Lolium perenne L.)

Fertilisation of established perennial ryegrass forage pastures with nitrogen (N)-based fertilisers is currently the most common practice used on farms to increase pasture forage biomass yield. However, over-fertilisation can lead to undesired environmental impacts, including nitrate leaching into waterways and increased gaseous emissions of ammonia and nitrous oxide to the atmosphere. Additionally, there is growing interest from pastoral farmers to adopt methods for increasing pasture dry matter yield which use 'natural', environmentally safe plant growth stimulators, together with N-based fertilisers. Such plant growth stimulators include plant hormones and plant growth promotive microorganisms such as bacteria and fungi ('biostimulators', which may produce plant growth-inducing hormones), as well as extracts of seaweed (marine algae). This review presents examples and discusses current uses of plant hormones and biostimulators, applied alone or together with N-based fertilisers, to enhance shoot dry matter yield of forage pasture species, with an emphasis on perennial ryegrass.

Stress-related hormones and glycinebetaine interplay in protection of photosynthesis under abiotic stress conditions

Plants subjected to abiotic stresses such as extreme high and low temperatures, drought or salinity, often exhibit decreased vegetative growth and reduced reproductive capabilities. This is often associated with decreased photosynthesis via an increase in photoinhibition, and accompanied by rapid changes in endogenous levels of stress-related hormones such as abscisic acid (ABA), salicylic acid (SA) and ethylene. However, certain plant species and/or genotypes exhibit greater tolerance to abiotic stress because they are capable of accumulating endogenous levels of the zwitterionic osmolyte-glycinebetaine (GB). The accumulation of GB via natural production, exogenous application or genetic engineering, enhances plant osmoregulation and thus increases abiotic stress tolerance. The final steps of GB biosynthesis occur in chloroplasts where GB has been shown to play a key role in increasing the protection of soluble stromal and lumenal enzymes, lipids and proteins, of the photosynthetic apparatus. In addition, we suggest that the stress-induced GB biosynthesis pathway may well serve as an additional or alternative biochemical sink, one which consumes excess photosynthesis-generated electrons, thus protecting photosynthetic apparatus from overreduction. Glycinebetaine biosynthesis in chloroplasts is up-regulated by increases in endogenous ABA or SA levels. In this review, we propose and discuss a model describing the close interaction and synergistic physiological effects of GB and ABA in the process of cold acclimation of higher plants.

Overexpression of gibberellin 20-oxidase1 from Pinus densiflora results in enhanced wood formation with gelatinous fiber development in a transgenic hybrid poplar

Gibberellins (GAs) are important regulators of plant shoot biomass growth, and GA 20-oxidase (GA20ox) is one of the major regulatory enzymes in the GA biosynthetic pathway. Previously, we showed that the expression levels of a putative GA20ox1 (i.e., PdGA20ox1) in stem tissue of 3-month-old seedlings of 12 families of Pinus densiflora were positively correlated with stem diameter growth across those same families growing in an even-aged 32-year-old pine forest (Park EJ, Lee WY, Kurepin LV, Zhang R, Janzen L, Pharis RP (2015) Plant hormone-assisted early family selection in Pinus densiflora via a retrospective approach. Tree Physiol 35:86-94). To further investigate the molecular function of this gene in the stem wood growth of forest trees, we produced transgenic poplar lines expressing PdGA20ox1 under the control of the 35S promoter (designated as 35S::PdGA20ox1). By age 3 months, most of the 35S::PdGA20ox1 poplar trees were showing an exceptional enhancement of stem wood growth, i.e., up to fourfold increases in stem dry weight, compared with the nontransformed control poplar plants. Significant increases in endogenous GA1, its immediate precursor (GA20) and its catabolite (GA8) in elongating internode tissue accompanied the increased stem growth in the transgenic lines. Additionally, the development of gelatinous fibers occurred in vertically grown stems of the 35S::PdGA20ox1 poplars. An analysis of the cell wall monosaccharide composition of the 35S::PdGA20ox1 poplars showed significant increases in xylose and glucose contents, indicating a qualitative increase in secondary wall depositions. Microarray analyses led us to find a total of 276 probe sets that were upregulated (using threefold as a threshold) in the stem tissues of 35S::PdGA20ox1 poplars relative to the controls. 'Cell organization or biogenesis'- and 'cell wall'-related genes were overrepresented, including many of genes that are involved in cell wall modification. Several transcriptional regulators, which positively regulate cell elongation through GA signaling, were also upregulated. In contrast, genes involved in defense signaling were appreciably downregulated in the 35S::PdGA20ox1 stem tissues, suggesting a growth versus defense trade-off. Taken together, our results suggest that PdGA20ox1 functions to promote stem growth and wood formation in poplar, probably by activating GA signaling while coincidentally depressing defense signaling.

Phenotypic plasticity of sun and shade ecotypes of Stellaria longipes in response to light quality signaling, gibberellins and auxin

Stellaria longipes plant communities (ecotypes) occur in several environmentally distinct habitats along the eastern slopes of southern Alberta's Rocky Mountains. One ecotype occurs in a prairie habitat at ∼1000 m elevation where Stellaria plants grow in an environment in which the light is filtered by taller neighbouring vegetation, i.e. sunlight with a low red to far-red (R/FR) ratio. This ecotype exhibits a high degree of phenotypic plasticity by increasing stem elongation in response to the low R/FR ratio light signal. Another Stellaria ecotype occurs nearby at ∼2400 m elevation in a much cooler alpine habitat, one where plants rarely experience low R/FR ratio shade light. Stem elongation of plants is largely regulated by gibberellins (GAs) and auxin, indole-3-acetic acid (IAA). Shoots of the prairie ecotype plants show increased IAA levels under low R/FR ratio light and they also increase their stem growth in response to applied IAA. The alpine ecotype plants show neither response. Plants from both ecotypes produce high levels of growth-active GA1 under low R/FR ratio light, though they differ appreciably in their catabolism of GA1. The alpine ecotype plants exhibit very high levels of GA8, the inactive product of GA1 metabolism, under both normal and low R/FR ratio light. Alpine origin plants may de-activate GA1 by conversion to GA8 via a constitutively high level of expression of the GA2ox gene, thereby maintaining their dwarf phenotype and exhibiting a reduced phenotypic plasticity in terms of shoot elongation. In contrast, prairie plants exhibit a high degree of phenotypic plasticity, using low R/FR ratio light-mediated changes in GA and IAA concentrations to increase shoot elongation, thereby accessing direct sunlight to optimize photosynthesis. There thus appear to be complex adaptation strategies for the two ecotypes, ones which involve modifications in the homeostasis of endogenous hormones.