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Salinity is one of the most significant environmental stresses for sustainable crop production in major arable lands of the globe. Thus, we conducted experiments with 27 tomato genotypes to screen for salinity tolerance at seedling stage, which were treated with non-salinized (S1) control (18.2 mM NaCl) and salinized (S2) (200 mM NaCl) irrigation water. In all genotypes, the elevated salinity treatment contributed to a major depression in morphological and physiological characteristics, however, a smaller decrease was found in certain tolerant genotypes. Principal component analyses (PCA) and clustering with percentage reduction in growth parameters and different salt tolerance indices classified the tomato accessions into five key clusters. In particular, the tolerant genotypes were assembled into one cluster. The growth and tolerance indices PCA also showed the order of salt-tolerance of the studied genotypes, where Saniora was the most tolerant genotype and P.Guyu was the most susceptible genotype. To investigate the possible biochemical basis for salt stress tolerance, we further characterized six tomato genotypes with varying levels of salinity tolerance. A higher increase in proline content, and antioxidants activities were observed for the salt-tolerant genotypes in comparison to the susceptible genotypes. Salt-tolerant genotypes identified in this work herald a promising source in the tomato improvement program or for grafting as scions with improved salinity tolerance in tomato.

Quinoa is a crop originating in the Andes but grown more widely and with the genetic potential for significant further expansion. Due to the phenotypic plasticity of quinoa, varieties need to be assessed across years and multiple locations. To improve comparability among field trials across the globe and to facilitate collaborations, components of the trials need to be kept consistent, including the type and methods of data collected. Here, an internationally open-access framework for phenotyping a wide range of quinoa features is proposed to facilitate the systematic agronomic, physiological and genetic characterization of quinoa for crop adaptation and improvement. Mature plant phenotyping is a central aspect of this paper, including detailed descriptions and the provision of phenotyping cards to facilitate consistency in data collection. High-throughput methods for multi-temporal phenotyping based on remote sensing technologies are described. Tools for higher-throughput post-harvest phenotyping of seeds are presented. A guideline for approaching quinoa field trials including the collection of environmental data and designing layouts with statistical robustness is suggested. To move towards developing resources for quinoa in line with major cereal crops, a database was created. The Quinoa Germinate Platform will serve as a central repository of data for quinoa researchers globally. EEA Famaillá Fil: Stanschewski, Clara S. King Abdullah University of Science and Technology. Center for Desert Agriculture, Biological and Environmental Sciences and Engineering Division; Arabia Saudita Fil: Rey, Elodie. King Abdullah University of Science and Technology. Center for Desert Agriculture, Biological and Environmental Sciences and Engineering Division; Arabia Saudita Fil: Fiene, Gabriele. King Abdullah University of Science and Technology. Center for Desert Agriculture, Biological and Environmental Sciences and Engineering Division; Arabia Saudita Fil: Craine, Evan B. Washington State University. Department of Crop and Soil Sciences; Estados Unidos Fil: Wellman, Gordon. King Abdullah University of Science and Technology. Center for Desert Agriculture, Biological and Environmental Sciences and Engineering Division; Arabia Saudita Fil: Melino, Vanessa J. King Abdullah University of Science and Technology. Center for Desert Agriculture, Biological and Environmental Sciences and Engineering Division; Arabia Saudita Fil: Patiranage, Dilan S.R. King Abdullah University of Science and Technology. Center for Desert Agriculture, Biological and Environmental Sciences and Engineering Division; Arabia Saudita Fil: Patiranage, Dilan S.R. Christian-Albrechts-University of Kiel. Plant Breeding Institute; Alemania Fil: Johansen, Kasper. King Abdullah University of Science and Technology. Water Desalination and Reuse Center; Arabia Saudita Fil: Schmöckel, Sandra M. University of Hohenheim. Institute of Crop Science. Department Physiology of Yield Stability; Alemania Fil: Erazzu, Luis Ernesto. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Famaillá; Argentina. Fil: Tester, Mark. King Abdullah University of Science and Technology. Center for Desert Agriculture, Biological and Environmental Sciences and Engineering Division; Arabia Saudita

Biomass and yield are key variables for assessing the production and performance of agricultural systems. Modeling and predicting the biomass and yield of individual plants at the farm scale represents a major challenge in precision agriculture, particularly when salinity and other abiotic stresses may play a role. Here, we evaluate a diversity panel of the wild tomato species (Solanum pimpinellifolium) through both field and unmanned aerial vehicle (UAV)-based phenotyping of 600 control and 600 salt-treated plants. The study objective was to predict fresh shoot mass, tomato fruit numbers, and yield mass at harvest based on a range of variables derived from the UAV imagery. UAV-based red–green–blue (RGB) imageries collected 1, 2, 4, 6, 7, and 8 weeks before harvest were also used to determine if prediction accuracies varied between control and salt-treated plants. Multispectral UAV-based imagery was also collected 1 and 2 weeks prior to harvest to further explore predictive insights. In order to estimate the end of season biomass and yield, a random forest machine learning approach was implemented using UAV-imagery-derived predictors as input variables. Shape features derived from the UAV, such as plant area, border length, width, and length, were found to have the highest importance in the predictions, followed by vegetation indices and the entropy texture measure. The multispectral UAV imagery collected 2 weeks prior to harvest produced the highest explained variances for fresh shoot mass (87.95%), fruit numbers (63.88%), and yield mass per plant (66.51%). The RGB UAV imagery produced very similar results to those of the multispectral UAV dataset, with the explained variance reducing as a function of increasing time to harvest. The results showed that predicting the yield of salt-stressed plants produced higher accuracies when the models excluded control plants, whereas predicting the yield of control plants was not affected by the inclusion of salt-stressed plants within the models. This research demonstrates that it is possible to predict the average biomass and yield up to 8 weeks prior to harvest within 4.23% of field-based measurements and up to 4 weeks prior to harvest at the individual plant level. Results from this work may be useful in providing guidance for yield forecasting of healthy and salt-stressed tomato plants, which in turn may inform growing practices, logistical planning, and sales operations.

Biomass and yield are important variables used for assessing agricultural production. However, these variables are difficult to estimate for individual plants at the farm scale and may be affected by abiotic stressors such as salinity. In this study, the wild tomato species, Solanum pimpinellifolium, was evaluated through field and UAV-based assessment of 600 control and 600 salt-treated plants. The aim of this research was to determine, if UAV-based imagery, collected one, two, four, six, seven and eight weeks before harvest could predict fresh shoot mass, tomato fruit numbers, and yield mass at harvest and if predictions varied for control and salt-treated plants. A Random Forest approach was used to model biomass and yield. The results showed that shape features such as plant area, border length, width and length had the highest importance in the random forest models. A week prior to harvest, the explained variance of fresh shoot mass, number of fruits and yield mass were 86.60%, 59.46% and 61.09%, respectively. The explained variance was reduced as a function of time to harvest. Separate models may be required for predicting yield of salt-stressed plants, whereas the prediction of yield for control plants was less affected if the model included salt-stressed plants. This research demonstrates that it is possible to predict biomass and yield of tomato plants up to four weeks prior to harvest, and potentially earlier in the absence of severe weather events.

With salt stress presenting a major threat to global food production, attention has turned to the identification and breeding of crop cultivars with improved salt tolerance. For instance, some accessions of wild species with higher salt tolerance than commercial varieties are being investigated for their potential to expand food production into marginal areas or to use brackish waters for irrigation. However, assessment of individual plant responses to salt stress in field trials is time-consuming, limiting, for example, longitudinal assessment of large numbers of plants. Developments in Unmanned Aerial Vehicle (UAV) sensing technologies provide a means for extensive, repeated and consistent phenotyping and have significant advantages over standard approaches. In this study, 199 accessions of the wild tomato species, Solanum pimpinellifolium, were evaluated through a field assessment of 600 control and 600 salt-treated plants. UAV imagery was used to: (1) delineate tomato plants from a time-series of eight RGB and two multi-spectral datasets, using an automated object-based image analysis approach; (2) assess four traits, i.e., plant area, growth rates, condition and Plant Projective Cover (PPC) over the growing season; and (3) use the mapped traits to identify the best-performing accessions in terms of yield and salt tolerance. For the first five campaigns, >99% of all tomato plants were automatically detected. The omission rate increased to 2–5% for the last three campaigns because of the presence of dead and senescent plants. Salt-treated plants exhibited a significantly smaller plant area (average control and salt-treated plant areas of 0.55 and 0.29 m2, respectively), maximum growth rate (daily maximum growth rate of control and salt-treated plant of 0.034 and 0.013 m2, respectively) and PPC (5–16% difference) relative to control plants. Using mapped plant condition, area, growth rate and PPC, we show that it was possible to identify eight out of the top 10 highest yielding accessions and that only five accessions produced high yield under both treatments. Apart from showcasing multi-temporal UAV-based phenotyping capabilities for the assessment of plant performance, this research has implications for agronomic studies of plant salt tolerance and for optimizing agricultural production under saline conditions.

Stomatal development is tightly regulated through internal and external factors that are integrated by a complex signalling network. Light represents an external factor that strongly promotes stomata formation. Here, we show that auxin-resistant aux/iaa mutants, e.g. axr3-1, exhibit a de-repression of stomata differentiation in dark-grown seedlings. The higher stomatal index in dark-grown axr3-1 mutants when compared with the wild type is due to increased cell division in the stomatal lineage. Excessive stomata in dark-grown seedlings were also observed in mutants defective in auxin biosynthesis or auxin perception and in seedlings treated with the polar auxin transport inhibitor NPA. Consistent with these findings, exogenous auxin repressed stomata formation in light-grown seedlings. Taken together, these results indicate that auxin is a negative regulator of stomatal development in dark-grown seedlings. Epistasis analysis revealed that axr3-1 acts genetically upstream of the bHLH transcription factors SPCH, MUTE and FAMA, as well as the YDA MAP kinase cascade, but in parallel with the repressor of photomorphogenesis COP1 and the receptor-like protein TMM. The effect of exogenous auxin required the ER family of leucine-rich repeat receptor-like kinases, suggesting that auxin acts at least in part through the ER family. Expression of axr3-1 in the stomatal lineage was insufficient to alter the stomatal index, implying that cell-cell communication is necessary to mediate the effect of auxin. In summary, our results show that auxin signalling contributes to the suppression of stomatal differentiation observed in dark-grown seedlings.

Plants sense vegetative shade as a reduction in the ratio of red light to far-red light (R:FR). Arabidopsis (Arabidopsis thaliana) responds to a reduced R:FR with increased elongation of the hypocotyl and the leaf petioles as well as with an acceleration of flowering time. The repressor of light signaling, CONSTITUTIVELY PHOTOMORPHOGENIC1 (COP1), has been shown previously to be essential for the shade-avoidance response in seedlings. Here, we have investigated the roles of COP1 and the COP1-interacting SUPPRESSOR OF PHYA-105 (SPA) proteins in seedling and adult facets of the shade-avoidance response. We show that COP1 and the four SPA genes are essential for hypocotyl and leaf petiole elongation in response to low R:FR, in a fashion that involves the COP1/SPA ubiquitination target LONG HYPOCOTYL IN FR LIGHT1 but not ELONGATED HYPOCOTYL5. In contrast, the acceleration of flowering in response to a low R:FR was normal in cop1 and spa mutants, thus demonstrating that the COP1/SPA complex is only required for elongation responses to vegetative shade and not for shade-induced early flowering. We further show that spa mutant seedlings fail to exhibit an increase in the transcript levels of the auxin biosynthesis genes YUCCA2 (YUC2), YUC8, and YUC9 in response to low R:FR, suggesting that an increase in auxin biosynthesis in vegetative shade requires SPA function. Consistent with this finding, expression of the auxin-response marker gene DR5::GUS did not increase in spa mutant seedlings exposed to low R:FR. We propose that COP1/SPA activity, via LONG HYPOCOTYL IN FR LIGHT1, is required for shade-induced modulation of the auxin biosynthesis pathway and thereby enhances cell elongation in low R:FR.

Summary The COP1/SPA complex acts as an E3 ubiquitin ligase to repress photomorphogenesis by targeting activators of the light response for degradation. Genetic analysis has shown that the four members of the SPA gene family (SPA1–SPA4) have overlapping but distinct functions. In particular, SPA1 and SPA2 differ in that SPA1 encodes a potent repressor in light- and dark-grown seedlings, but SPA2 fully loses its function when seedlings are exposed to light, indicating that SPA2 function is hyper-inactivated by light. Here, we have used chimeric SPA1/SPA2 constructs to show that the distinct functions of SPA1 and SPA2 genes in light-grown seedlings are due to the SPA protein sequences and independent of the SPA promoter sequences. Biochemical analysis of SPA1 and SPA2 protein levels shows that light exposure leads to rapid proteasomal degradation of SPA2, and, more weakly, of SPA1, but not of COP1. This suggests that light inactivates the COP1/SPA complex partly by reducing SPA protein levels. Although SPA2 was more strongly degraded than SPA1, this was not the sole reason for the lack of SPA2 function in the light. We found that the SPA2 protein is inherently incapable of repressing photomorphogenesis in light-grown seedlings. The data therefore indicate that light inactivates the function of SPA2 through a post-translational mechanism that eliminates the activity of the remaining SPA2 protein in the cell.

The Arabidopsis thalianachlorophyll a/b binding protein underexpressed (cue1) mutant, which has been isolated in a screen for chlorophyll a/b binding protein (CAB) underexpressors, exhibits a reticulate leaf phenotype combined with delayed chloroplast development and aberrant shape of the palisade parenchyma cells. The affected gene in cue1 is a phosphoenolpyruvate (PEP)/phosphate translocator (PPT) of the plastid inner envelope membrane. The proposed function of the PPT in C3-plants is the import of PEP into the stroma as one of the substrates for the shikimate pathway, from which aromatic amino acids and a variety of secondary plant products derive. The mutant phenotype could be: (i) complemented by constitutive overexpression of a heterologous PPT from cauliflower; and (ii) rescued by overexpression of a C4-type pyruvate,orthophosphate dikinase (PPDK). The latter approach indicates that PEP deficiency within plastids triggers developmental constraints in cue1. The impact of the mutation on aspects of primary and secondary metabolism was assessed in cue1 as well as in the individual transformant lines. The majority of the data obtained in this and an accompanying paper suggest that the mutant phenotype is not simply caused by a general restriction of the shikimate pathway because of a defect in a PPT.

Plants adjust their growth and development in response to the ambient light environment. These light responses involve systemic signals that coordinate differentiation of different tissues and organs. Here, we have investigated the function of the key repressor of photomorphogenesis SPA1 in different tissues of the plant by expressing GUS-SPA1 under the control of tissue-specific promoters in a spa mutant background. We show that SPA1 expression in the phloem vasculature is sufficient to rescue the spa1 mutant phenotype in dark-grown spa mutant seedlings. Expression of SPA1 in mesophyll, epidermis or root tissues of the seedling, by contrast, has no or only slight effects. In the leaf, SPA1 expression in both the phloem and the mesophyll is required for full complementation of the defect in leaf expansion. SPA1 in phloem and mesophyll tissues affected division and expansion of cells in the epidermal layer, indicating that SPA1 induces non-cell-autonomous responses also in the leaf. Photoperiodic flowering is exclusively controlled by SPA1 expression in the phloem, which is consistent with previous results showing that the direct substrate of the COP1/SPA complex, CONSTANS, also acts in the phloem. Taken together, our results highlight the importance of phloem vascular tissue in coordinating growth and development. Because the SPA1 protein itself is incapable of moving from cell to cell, we suggest that SPA1 regulates the activity of downstream component(s) of light signaling that subsequently act in a non-cell-autonomous manner. SPA1 action in the phloem may also result in mechanical stimuli that affect cell elongation and cell division in other tissues.

The COP1/SPA complex acts as an E3 ubiquitin ligase to repress photomorphogenesis by targeting activators of the light response for degradation. Genetic analysis has shown that the four members of the SPA gene family (SPA1-SPA4) have overlapping but distinct functions. In particular, SPA1 and SPA2 differ in that SPA1 encodes a potent repressor in light- and dark-grown seedlings, but SPA2 fully loses its function when seedlings are exposed to light, indicating that SPA2 function is hyper-inactivated by light. Here, we have used chimeric SPA1/SPA2 constructs to show that the distinct functions of SPA1 and SPA2 genes in light-grown seedlings are due to the SPA protein sequences and independent of the SPA promoter sequences. Biochemical analysis of SPA1 and SPA2 protein levels shows that light exposure leads to rapid proteasomal degradation of SPA2, and, more weakly, of SPA1, but not of COP1. This suggests that light inactivates the COP1/SPA complex partly by reducing SPA protein levels. Although SPA2 was more strongly degraded than SPA1, this was not the sole reason for the lack of SPA2 function in the light. We found that the SPA2 protein is inherently incapable of repressing photomorphogenesis in light-grown seedlings. The data therefore indicate that light inactivates the function of SPA2 through a post-translational mechanism that eliminates the activity of the remaining SPA2 protein in the cell.

Enhancing nitrogen use efficiency (NUE) of wheat is a major focus for wheat breeding programs. NUE may be improved by identifying genotypes that are competitive for nitrogen (N) uptake in early vegetative stages of growth and are able to invest that N in grain. Breeders tend to select high yielding genotypes under conditions of medium to high N supply, but it is not known whether this influences the selection of root plasticity traits or whether, over time, breeders have selected genotypes with higher N uptake efficiency. To address this, genotypes were selected from CIMMYT (1966–1985) and Australian (1999–2007) breeding programs. Genotypes from both programs responded to low N supply by expanding their root surface area through increased total root number and/or length of lateral roots. Australian genotypes were N responsive (accumulated more N under high N than under low N) whereas CIMMYT genotypes were not very N responsive. This could not be explained by differences in N uptake capacity as shown by 15N flux analysis of two representative genotypes with contrasting N accumulation. Expression analysis of nitrate transporter genes revealed that the high-affinity transport system accounted for the majority of root nitrate uptake in wheat seedlings under both low and high N conditions. Refereed/Peer-reviewed

Amino acids and amino acid analogs have been used in numerous genetic screens to isolate mutants deficient in amino acid biosynthetic pathways or in the regulation of amino acid metabolism. Several of these mutants exhibit relaxed feedback control of branched amino acid biosynthetic pathways and are thus resistant to accumulation of pathway end products. For example, feedback-regulated enzymes of the shikimate pathway are anthranilate synthase on the branch leading to Trp and chorismate mutase on the branch leading to Phe and Tyr. A feedback-insensitive mutant of anthranilate synthase α, trp5-1, is resistant to toxic Trp analogs. Mutants resistant to Phe have not previously been reported, and this article describes the isolation of the recessive Arabidopsis Phe insensitive growth mutant pig1-1 by a forward genetic screen. pig1-1 was not only tolerant to Phe, Tyr, and Trp, but also to other, not biosynthetically related amino acids. Amino acid contents in pig1-1 were significantly elevated with respect to wild-type controls but, in contrast to the wild type, dramatically decreased when plants were supplemented with 2 mm Phe. Protein contents were similar in the mutant and the wild type at all tested conditions. Phe catabolism was similar to the wild type in pig1-1 roots but was significantly increased in pig1-1 shoots. Phenylalanine uptake into the root, its root-to-shoot translocation, and Phe and phenylpropanoid contents were unaltered in pig1-1, indicating that pig1-1 is not affected in amino acid translocation or the shikimate pathway. Instead, the response of pig1-1 toward amino acid feeding indicates that amino acid metabolism is generally deregulated in pig1-1.