Pitfalls and potential of high-throughput plant phenotyping platforms

Automated high-throughput plant phenotyping (HTPP) enables non-invasive, fast and standardized evaluations of a large number of plants for size, development, and certain physiological variables. Many research groups recognize the potential of HTPP and have made significant investments in HTPP infrastructure, or are considering doing so. To make optimal use of limited resources, it is important to plan and use these facilities prudently and to interpret the results carefully. Here we present a number of points that users should consider before purchasing, building or utilizing such equipment. They relate to (1) the financial and time investment for acquisition, operation, and maintenance, (2) the constraints associated with such machines in terms of flexibility and growth conditions, (3) the pros and cons of frequent non-destructive measurements, (4) the level of information provided by proxy traits, and (5) the utilization of calibration curves. Using data from an Arabidopsis experiment, we demonstrate how diurnal changes in leaf angle can impact plant size estimates from top-view cameras, causing deviations of more than 20% over the day. Growth analysis data from another rosette species showed that there was a curvilinear relationship between total and projected leaf area. Neglecting this curvilinearity resulted in linear calibration curves that, although having a high r2 (> 0.92), also exhibited large relative errors. Another important consideration we discussed is the frequency at which calibration curves need to be generated and whether different treatments, seasons, or genotypes require distinct calibration curves. In conclusion, HTPP systems have become a valuable addition to the toolbox of plant biologists, provided that these systems are tailored to the research questions of interest, and users are aware of both the possible pitfalls and potential involved.

Tomato leaves under stress: a comparison of stress response to mild abiotic stress between a cultivated and a wild tomato species

Tomato is one of the most produced crop plants on earth and growing in the fields and greenhouses all over the world. Breeding with known traits of wild species can enhance stress tolerance of cultivated crops. In this study, we investigated responses of the transcriptome as well as primary and secondary metabolites in leaves of a cultivated and a wild tomato to several abiotic stresses such as nitrogen deficiency, chilling or warmer temperatures, elevated light intensities and combinations thereof. The wild species responded different to varied temperature conditions compared to the cultivated tomato. Nitrogen deficiency caused the strongest responses and induced in particular the secondary metabolism in both species but to much higher extent in the cultivated tomato. Our study supports the potential of a targeted induction of valuable secondary metabolites in green residues of horticultural production, that will otherwise only be composted after fruit harvest. In particular, the cultivated tomato showed a strong induction in the group of mono caffeoylquinic acids in response to nitrogen deficiency. In addition, the observed differences in stress responses between cultivated and wild tomato can lead to new breeding targets for better stress tolerance.

Impact of Moderate Cold and Salt Stress on the Accumulation of Antioxidant Flavonoids in the Leaves of Two Capsicum Cultivars

The horticultural production of bell peppers generates large quantities of residual biomass. Abiotic stress stimulates the production of protective flavonoids, so the deliberate application of stress to the plants after fruit harvest could provide a strategy to valorize horticultural residuals by increasing flavonoid concentrations, facilitating their industrial extraction. Here we exposed two Capsicum cultivars, a chilli and a bell pepper, to cold and salt stress and combinations thereof to determine their valorization potential. Noninvasive image-based phenotyping and multiparametric fluorescence measurements indicated that all stress treatments inhibited plant growth and reduced the leaf chlorophyll fluorescence index, with the chilli cultivar showing greater sensitivity. The fluorescence-based FLAV index allowed the noninvasive assessment of foliar luteolin glycosides. High-performance liquid chromatography-mass spectrometry (HPLC-MS) analysis showed that moderate cold increased the levels of two foliar antioxidant luteolin glycosides in both cultivars, with bell pepper containing the highest amounts (induced to maximum 5.5 mg g^-1 DW cynaroside and 37.0 mg g^-1 DW graveobioside A) after combined stress treatment. These data confirm the potential of abiotic stress for the valorization of residual leaf biomass to enhance the industrial extraction of antioxidant and bioactive flavonoids.

Tomato's Green Gold: Bioeconomy Potential of Residual Tomato Leaf Biomass as a Novel Source for the Secondary Metabolite Rutin

At the end of the annual horticultural production cycle of greenhouse-grown crops, large quantities of residual biomass are discarded. Here, we propose a new value chain to utilize horticultural leaf biomass for the extraction of secondary metabolites. To increase the secondary metabolite content of leaves, greenhouse-grown crop plants were exposed to low-cost abiotic stress treatments after the last fruit harvest. As proof of concept, we evaluated the production of the flavonoid rutin in tomato plants subjected to nitrogen deficiency. In an interdisciplinary approach, we observed the steady accumulation of rutin in young plants under nitrogen deficiency, tested the applicability of nitrogen deficiency in a commercial-like greenhouse, developed a high efficiency extraction for rutin, and evaluated the acceptance of the proposed value chain by its key actors economically. On the basis of the positive interdisciplinary evaluation, we identified opportunities and challenges for the successful establishment of horticultural leaf biomass as a novel source for secondary metabolites.

Regulation of growth by the trehalose pathway: relationship to temperature and sucrose

Carbon signaling can override carbon supply in the regulation of growth. At least some of this regulation is imparted by the sugar signal trehalose 6-phosphate (T6P) through the protein kinase, SnRK1. This signaling pathway regulates biosynthetic processes involved in growth under optimal growing conditions. Recently, using a seedling system we showed that under sub-optimal conditions, such as cold, carbon signaling by T6P/ SnRK1 enables recovery of growth following relief of the stress. The T6P/ SnRK1 mechanism thus could be selected as a means of improving low temperature tolerance. High-throughput automated Fv/Fm measurements provide a potential means to screen for T6P/ SnRK1, and here we confirm through measurements of Fv/Fm in rosettes that T6P promotes low temperature tolerance and recovery during cold to warm transfer. Further, to better understand the coordination between sugars, trehalose pathway, and temperature-dependent growth, we examine the interrelationship between sugars, trehalose phosphate synthase (TPS), and trehalose phosphate phosphatase (TPP) gene expression and T6P content in seedlings. Sucrose, particularly when fed exogenously, correlated well with TPS1 and TPPB gene expression, suggesting that these enzymes are involved in maintaining carbon flux through the pathway in relation to sucrose supply. However, when sucrose accumulated to higher levels under low temperature and low N, TPS1 and TPPB expression were less directly related to sucrose; other factors may also contribute to regulation of TPS1 and TPPB expression under these conditions. TPPA expression was not related to sucrose content and all genes were not well correlated with endogenous glucose. Our work has implications for understanding acclimation to sink-limited growth conditions such as low temperature and for screening cold-tolerant genotypes with altered T6P/ SnRK1 signaling.

Aberrant temporal growth pattern and morphology of root and shoot caused by a defective circadian clock in Arabidopsis thaliana

Circadian clocks synchronized with the environment allow plants to anticipate recurring daily changes and give a fitness advantage. Here, we mapped the dynamic growth phenotype of leaves and roots in two lines of Arabidopsis thaliana with a disrupted circadian clock: the CCA1 over-expressing line (CCA1ox) and the prr9 prr7 prr5 (prr975) mutant. We demonstrate leaf growth defects due to a disrupted circadian clock over a 24 h time scale. Both lines showed enhanced leaf growth compared with the wild-type during the diurnal period, suggesting increased partitioning of photosynthates for leaf growth. Nocturnal leaf growth was reduced and growth inhibition occurred by dawn, which may be explained by ineffective starch degradation in the leaves of the mutants. However, this growth inhibition was not caused by starch exhaustion. Overall, these results are consistent with the notion that the defective clock affects carbon and energy allocation, thereby reducing growth capacity during the night. Furthermore, rosette morphology and size as well as root architecture were strikingly altered by the defective clock control. Separate analysis of the primary root and lateral roots revealed strong suppression of lateral root formation in both CCA1ox and prr975, accompanied by unusual changes in lateral root growth direction under light-dark cycles and increased lateral extension of the root system. We conclude that growth of the whole plant is severely affected by improper clock regulation in A. thaliana, resulting not only in altered timing and capacity for growth but also aberrant development of shoot and root architecture.

Aberrant temporal growth pattern and morphology of root and shoot caused by a defective circadian clock in Arabidopsis thaliana

Circadian clocks synchronized with the environment allow plants to anticipate recurring daily changes and give a fitness advantage. Here, we mapped the dynamic growth phenotype of leaves and roots in two lines of Arabidopsis thaliana with a disrupted circadian clock: the CCA1 over-expressing line (CCA1ox) and the prr9 prr7 prr5 (prr975) mutant. We demonstrate leaf growth defects due to a disrupted circadian clock over a 24 h time scale. Both lines showed enhanced leaf growth compared with the wild-type during the diurnal period, suggesting increased partitioning of photosynthates for leaf growth. Nocturnal leaf growth was reduced and growth inhibition occurred by dawn, which may be explained by ineffective starch degradation in the leaves of the mutants. However, this growth inhibition was not caused by starch exhaustion. Overall, these results are consistent with the notion that the defective clock affects carbon and energy allocation, thereby reducing growth capacity during the night. Furthermore, rosette morphology and size as well as root architecture were strikingly altered by the defective clock control. Separate analysis of the primary root and lateral roots revealed strong suppression of lateral root formation in both CCA1ox and prr975, accompanied by unusual changes in lateral root growth direction under light-dark cycles and increased lateral extension of the root system. We conclude that growth of the whole plant is severely affected by improper clock regulation in A. thaliana, resulting not only in altered timing and capacity for growth but also aberrant development of shoot and root architecture.

Effect of blue light on endogenous isopentenyladenine and endoreduplication during photomorphogenesis and de-etiolation of tomato (Solanum lycopersicum L.) seedlings

Light is one of the most important factor influencing plant growth and development all through their life cycle. One of the well-known light-regulated processes is de-etiolation, i.e. the switch from skotomorphogenesis to photomorphogenesis. The hormones cytokinins (CKs) play an important role during the establishment of photomorphogenesis as exogenous CKs induced photomorphogenesis of dark-grown seedlings. Most of the studies are conducted on the plant model Arabidopsis, but no or few information are available for important crop species, such as tomato (Solanum lycopersicum L.). In our study, we analyzed for the first time the endogenous CKs content in tomato hypocotyls during skotomorphogenesis, photomorphogenesis and de-etiolation. For this purpose, two tomato genotypes were used: cv. Rutgers (wild-type; WT) and its corresponding mutant (7B-1) affected in its responses to blue light (BL). Using physiological and molecular approaches, we identified that the skotomorphogenesis is characterized by an endoreduplication-mediated cell expansion, which is inhibited upon BL exposure as seen by the accumulation of trancripts encoding CycD3, key regulators of the cell cycle. Our study showed for the first time that iP (isopentenyladenine) is the CK accumulated in the tomato hypocotyl upon BL exposure, suggesting its specific role in photomorphogenesis. This result was supported by physiological experiments and gene expression data. We propose a common model to explain the role and the relationship between CKs, namely iP, and endoreduplication during de-etiolation and photomorphogenesis.

Diel patterns of leaf and root growth: endogenous rhythmicity or environmental response?

Plants are sessile organisms forced to adjust to their surrounding environment. In a single plant the photoautotrophic shoot is exposed to pronounced environmental variations recurring in a day-night 24 h (diel) cycle, whereas the heterotrophic root grows in a temporally less fluctuating environment. The contrasting habitats of shoots and roots are reflected in different diel growth patterns and their responsiveness to environmental stimuli. Differences between diel leaf growth patterns of mono- and dicotyledonous plants correspond to their different organization and placement of growth zones. In monocots, heterotrophic growth zones are organized linearly and protected from the environment by sheaths of older leaves. In contrast, photosynthetically active growth zones of dicot leaves are exposed directly to the environment and show characteristic, species-specific diel growth patterns. It is hypothesized that the different exposure to environmental constraints and simultaneously the sink/source status of the growing organs may have induced distinct endogenous control of diel growth patterns in roots and leaves of monocot and dicot plants. Confronted by strong temporal fluctuations in environment, the circadian clock may facilitate robust intrinsic control of leaf growth in dicot plants.

Growth arrest by trehalose-6-phosphate: an astonishing case of primary metabolite control over growth by way of the SnRK1 signaling pathway

The strong regulation of plant carbon allocation and growth by trehalose metabolism is important for our understanding of the mechanisms that determine growth and yield, with obvious applications in crop improvement. To gain further insight on the growth arrest by trehalose feeding, we first established that starch-deficient seedlings of the plastidic phosphoglucomutase1 mutant were similarly affected as the wild type on trehalose. Starch accumulation in the source cotyledons, therefore, did not cause starvation and consequent growth arrest in the growing zones. We then screened the FOX collection of Arabidopsis (Arabidopsis thaliana) expressing full-length cDNAs for seedling resistance to 100 mm trehalose. Three independent transgenic lines were identified with dominant segregation of the trehalose resistance trait that overexpress the bZIP11 (for basic region/leucine zipper motif) transcription factor. The resistance of these lines to trehalose could not be explained simply through enhanced trehalase activity or through inhibition of bZIP11 translation. Instead, trehalose-6-phosphate (T6P) accumulation was much increased in bZIP11-overexpressing lines, suggesting that these lines may be insensitive to the effects of T6P. T6P is known to inhibit the central stress-integrating kinase SnRK1 (KIN10) activity. We confirmed that this holds true in extracts from seedlings grown on trehalose, then showed that two independent transgenic lines overexpressing KIN10 were insensitive to trehalose. Moreover, the expression of marker genes known to be jointly controlled by SnRK1 activity and bZIP11 was consistent with low SnRK1 or bZIP11 activity in seedlings on trehalose. These results reveal an astonishing case of primary metabolite control over growth by way of the SnRK1 signaling pathway involving T6P, SnRK1, and bZIP11.

Diel time-courses of leaf growth in monocot and dicot species: endogenous rhythms and temperature effects

Diel (24 h) leaf growth patterns were differently affected by temperature variations and the circadian clock in several plant species. In the monocotyledon Zea mays, leaf elongation rate closely followed changes in temperature. In the dicotyledons Nicotiana tabacum, Ricinus communis, and Flaveria bidentis, the effect of temperature regimes was less obvious and leaf growth exhibited a clear circadian oscillation. These differences were related neither to primary metabolism nor to altered carbohydrate availability for growth. The effect of endogenous rhythms on leaf growth was analysed under continuous light in Arabidopsis thaliana, Ricinus communis, Zea mays, and Oryza sativa. No rhythmic growth was observed under continuous light in the two monocotyledons, while growth rhythmicity persisted in the two dicotyledons. Based on model simulations it is concluded that diel leaf growth patterns in mono- and dicotyledons result from the additive effects of both circadian-clock-controlled processes and responses to environmental changes such as temperature and evaporative demand. Apparently very distinct diel leaf growth behaviour of monocotyledons and dicotyledons can thus be explained by the different degrees to which diel temperature variations affect leaf growth in the two groups of species which, in turn, depends on the extent of the leaf growth control by internal clocks.

Sucrose control of translation mediated by an upstream open reading frame-encoded peptide

Regulation of gene expression through translational control is common in many organisms. The Arabidopsis (Arabidopsis thaliana) transcription factor bZIP11 is translational repressed in response to sucrose (Suc), resulting in Suc-regulated changes in amino acid metabolism. The 5' leader of the bZIP11 mRNA harbors several upstream open reading frames (uORFs), of which the second uORF is well conserved among bZIP11 homologous genes. The uORF2 element encodes a Suc control peptide (SC-peptide) of 28 residues that is sufficient for imposing Suc-induced repression of translation (SIRT) on a heterologous mRNA. Detailed analysis of the SC-peptide suggests that it functions as an attenuator peptide. Results suggest that the SC-peptide inhibits bZIP11 translation in response to high Suc levels by stalling the ribosome on the mRNA. The conserved noncanonical AUG contexts of bZIP11 uORFs allow inefficient translational initiation of the uORF, resulting in translation initiation of the scanning ribosome at the AUG codon of the bZIP11 main ORF. The results presented show that Suc-dependent signaling mediates differential translation of mRNAs containing SC-peptides encoding uORFs.

Diel growth cycle of isolated leaf discs analyzed with a novel, high-throughput three-dimensional imaging method is identical to that of intact leaves

Dicot leaves grow with pronounced diel (24-h) cycles that are controlled by a complex network of factors. It is an open question to what extent leaf growth dynamics are controlled by long-range or by local signals. To address this question, we established a stereoscopic imaging system, GROWSCREEN 3D, which quantifies surface growth of isolated leaf discs floating on nutrient solution in wells of microtiter plates. A total of 458 leaf discs of tobacco (Nicotiana tabacum) were cut at different developmental stages, incubated, and analyzed for their relative growth rates. The camera system was automatically displaced across the array of leaf discs; visualization and camera displacement took about 12 s for each leaf disc, resulting in a time interval of 1.5 h for consecutive size analyses. Leaf discs showed a comparable diel leaf growth cycle as intact leaves but weaker peak growth activity. Hence, it can be concluded that the timing of leaf growth is regulated by local rather than by systemic control processes. This conclusion was supported by results from leaf discs of Arabidopsis (Arabidopsis thaliana) Landsberg erecta wild-type plants and starch-free1 mutants. At night, utilization of transitory starch leads to increased growth of Landsberg erecta wild-type discs compared with starch-free1 discs. Moreover, the decrease of leaf disc growth when exposed to different concentrations of glyphosate showed an immediate dose-dependent response. Our results demonstrate that a dynamic leaf disc growth analysis as we present it here is a promising approach to uncover the effects of internal and external cues on dicot leaf development.