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Proximal sensing has been used extensively for decades to assess crop nitrogen (N) status using either a hand-held chlorophyll meter or vegetation indices such as the normalized difference vegetation index (NDVI) for various crops. However, little has been done on quinoa (Chenopodium quinoa Willd.). In this study, we investigated how the SPAD chlorophyll meter values and NDVI could be used as indicators for N status and how they can be linked to quinoa performance in terms of photosynthesis and yield. The objectives of this study were to: 1) evaluate SPAD values and NDVI as indicators of N status, 2) assess their relevance over the crop cycle, and 3) investigate their link to the performance in terms of net CO2 assimilation and grain yield at harvest. A pot experiment based on varying nitrogen and phosphorus (P) input conditions was conducted in the glasshouse at Cranfield University, UK. The results showed that both SPAD and NDVI correlated similarly with the leaf N content (%) (R2=0.76, R2=0.82, p

The revolution in digital phenotyping combined with the new layers of omics and envirotyping tools offers great promise to improve selection and accelerate genetic gains for crop improvement. This chapter examines the latest methods involving digital phenotyping tools to predict complex traits in cereals crops. The chapter has two parts. In the first part, entitled “Digital phenotyping as a tool to support breeding programs”, the secondary phenotypes measured by high-throughput plant phenotyping that are potentially useful for breeding are reviewed. In the second part, “Implementing complex G2P models in breeding programs”, the integration of data from digital phenotyping into genotype to phenotype (G2P) models to improve the prediction of complex traits using genomic information is discussed. The current status of statistical models to incorporate secondary traits in univariate and multivariate models, as well as how to better handle longitudinal (for example light interception, biomass accumulation, canopy height) traits, is reviewed.

Efficient use of nitrogen (N) by plants and particularly crops, is of global importance. In agriculture, high crop yields and protein content depend upon extensive N-inputs, however fertilizer N is costly to the farmer, and overuse can be damaging to the environment. A critical component of optimised usage is efficient capture by crop root systems. This chapter focusses on principal mechanisms of uptake and factors influencing efficiency. Genetic variation in root architecture and in an array of transporters known to be involved in nitrogen capture is detailed. The impacts of abiotic stress factors such as soil structure are described. Finally prospects and opportunities for crop improvement are discussed.

Crop nutrient and especially nitrogen use efficiency (NUE) is both an economically and an environmentally highly desirable trait. It has been estimated that only a third of nitrogen inputs to cereal crop worldwide are recovered in grain for consumption, resulting in a huge waste of resource with major negative impacts on the environment. Most measures of NUE in wheat and other cereals are based on field assessments of crop yields at given N inputs, performance responses to added N fertilizer, or by quantifying N fertilizer recovery rates. However, NUE is a complex trait comprising two key major components, N uptake and N utilization efficiency, both also complex traits in themselves, each involving many physiological processes and biochemical pathways. A deeper understanding of the processes involved in NUE has been a target of the UK Wheat Genetic Improvement Network project (http://www.wgin.org.uk/). This has enabled the breakdown of characteristics contributing to NUE and an assessment of the variation present in those characteristics, predominantly in modern cultivars; a total of 13 years of data have been obtained to date. Significant but limited variation suggests a requirement for broader germplasm screening such as older varieties, landraces, and wild relatives.

Deprivation of mineral nutrients causes significant retardation of plant growth. This retardation is associated with nutrient-specific and general stress-induced transcriptional responses. In this study, we adjusted the external supply of iron, potassium and sulfur to cause the same retardation of shoot growth. Nevertheless, limitation by individual nutrients resulted in specific morphological adaptations and distinct shifts within the root metabolite fingerprint. The metabolic shifts affected key metabolites of primary metabolism and the stress-related phytohormones, jasmonic, salicylic and abscisic acid. These phytohormone signatures contributed to specific nutrient deficiency-induced transcriptional regulation. Limitation by the micronutrient iron caused the strongest regulation and affected 18% of the root transcriptome. Only 130 genes were regulated by all nutrients. Specific co-regulation between the iron and sulfur metabolic routes upon iron or sulfur deficiency was observed. Interestingly, iron deficiency caused regulation of a different set of genes of the sulfur assimilation pathway compared with sulfur deficiency itself, which demonstrates the presence of specific signal-transduction systems for the cross-regulation of the pathways. Combined iron and sulfur starvation experiments demonstrated that a requirement for a specific nutrient can overrule this cross-regulation. The comparative metabolomics and transcriptomics approach used dissected general stress from nutrient-specific regulation in roots of Arabidopsis.

Optimum use of mineral nutrients (fertilisers) by crops is essential for sustainable agricultural production. With increasing world demands for food and energy, this is set to become an ever-increasing priority. Fertilisers are costly to produce and apply, both financially and environmentally. There is an absolute requirement to maximise efficiency using both agronomic and plant breeding approaches. Nutrient use efficiency may be defined as yield per unit fertiliser input or in terms of recovery of fertiliser applied. Improving yield alone may be at the expense of mineral nutrient content and hence quality, therefore yield improvements must be matched by appropriate increases in nutrient uptake. Multiple complex processes contribute to the overall nutrient use efficiency trait, and all are multigenic and developmentally and environmentally modulated. Key breeding traits for improvement includes root characteristics to enhance acquisition, canopy functioning for yield generation, and sink tissue attributes for final yield and quality aspects. Multidisciplinary approaches involving traditional breeding and biotechnology will contribute to future improvements. Key Concepts: Optimum use of mineral fertilisers by crops is essential for sustainable agriculture. Some fertilisers are nonrenewal resources. Nutrient use efficiency may be defined as yield per unit fertiliser input or in terms of recovery of fertiliser applied. Nutrient use efficiency comprises two main traits, uptake efficiency and utilisation efficiency. Agronomic practice is an important part of nutrient use efficiency. Crop improvement may be targeted at roots, canopy or harvested material. Root systems and transporters are required for capture of nutrients to produce an effective canopy. An effective canopy will result in high yield. Efficient captures and partitioning of nutrients contributes to quality components of crops. Huge unexploited natural germplasm diversity for nutrient use efficiency exists for most crops. Keywords: nutrient use efficiency; fertiliser; nitrogen; phosphorus; agriculture; crop breeding; transporters; roots; canopy; grain

A major challenge for biologists is to understand the underlying mechanisms which enable a plant to adapt to its environment and perform optimally in as broad a range of conditions as possible. A complete understanding is only obtained by the integration of many disciplines of research from ecology to the molecular biology of individual genes.

This proceedings volume contains the invited and a selection of the contributed papers of the 8th International Workshop on Sulfur Metabolism in Higher Plants, which was held at Department of Forest and Ecosystem Science, University of Melbourne, Water Street, Creswick, Victoria 3363, Australia, from November 22-27, 2010. The content of the volume shows that the understanding of sulfur metabolism in plants and the interaction of the environment are rapidly progressing. This volume covers various aspects of the regulation of sulfate uptake and assimilation in plants, from a cellular to a whole plant level, and additionally emphasizes interactions with other minerals. Moreover the significance of sulfur metabolism in biotic and abiotic stress responses, in food security and quality, and in relation to interactions with global change factors is discussed in detail.

Rice (Oryza sativa) takes up arsenite mainly through the silicic acid transport pathway. Understanding the uptake and sequestration of arsenic (As) into the rice plant is important for developing strategies to reduce As concentration in rice grain. In this study, the cellular and subcellular distributions of As and silicon (Si) in rice roots were investigated using high-pressure freezing, high-resolution secondary ion mass spectrometry, and transmission electron microscopy. Rice plants, both the lsi2 mutant lacking the Si/arsenite efflux transporter Lsi2 and its wild-type cultivar, with or without an iron plaque, were treated with arsenate or arsenite. The formation of iron plaque on the root surface resulted in strong accumulation of As and phosphorous on the epidermis. The lsi2 mutant showed stronger As accumulation in the endodermal vacuoles, where the Lsi2 transporter is located in the plasma membranes, than the wild-type line. As also accumulated in the vacuoles of some xylem parenchyma cells and in some pericycle cells, particularly in the wild-type mature root zone. Vacuolar accumulation of As is associated with sulfur, suggesting that As may be stored as arsenite-phytochelatin complexes. Si was localized in the cell walls of the endodermal cells with little apparent effect of the Lsi2 mutation on its distribution. This study reveals the vacuolar sequestration of As in rice roots and contrasting patterns of As and Si subcellular localization, despite both being transported across the plasma membranes by the same transporters.

Organically bound sulfur makes up about 90% of the total sulfur in soils, with sulfonates often the dominant fraction. Actinobacteria affiliated to the genus Rhodococcus were able to desulfonate arylsulfonates in wheat rhizospheres from the Broadbalk long-term field wheat experiment, which includes plots treated with inorganic fertilizer with and without sulfate, with farmyard manure, and unfertilized plots. Direct isolation of desulfonating rhizobacteria yielded Rhodococcus strains which grew well with a range of sulfonates, and contained the asfAB genes, known to be involved in sulfonate desulfurization by bacteria. Expression of asfA in vitro increased > 100-fold during growth of the Rhodococcus isolates with toluenesulfonate as sulfur source, compared with growth with sulfate. By contrast, the closely related Rhodococcus erythropolis and Rhodococcus opacus type strains had no desulfonating activity and did not contain asfA homologues. The overall actinobacterial community structure in wheat rhizospheres was influenced by the sulfur fertilization regime, as shown by specific denaturing gradient gel electrophoresis of PCR amplified 16S rRNA gene fragments, and asfAB clone library analysis identified nine different asfAB genotypes closely affiliated to the Rhodococcus isolates. However, asfAB-based multiplex restriction fragment length polymorphism (RFLP)/terminal-RFLP analysis of wheat rhizosphere communities revealed only slight differences between the fertilization regimes, suggesting that the desulfonating Rhodococcus community does not specifically respond to changes in sulfate supply.

Characterization of the relationship between sulfur and iron in both Strategy I and Strategy II plants, has proven that low sulfur availability often limits plant capability to cope with iron shortage. Here it was investigated whether the adaptation to iron deficiency in tomato (Solanum lycopersicum L.) plants was associated with an increased root sulfate uptake and translocation capacity, and modified dynamics of total sulfur and thiols accumulation between roots and shoots. Most of the tomato sulfate transporter genes belonging to Groups 1, 2, and 4 were significantly upregulated in iron-deficient roots, as it commonly occurs under S-deficient conditions. The upregulation of the two high affinity sulfate transporter genes, SlST1.1 and SlST1.2, by iron deprivation clearly suggests an increased root capability to take up sulfate. Furthermore, the upregulation of the two low affinity sulfate transporter genes SlST2.1 and SlST4.1 in iron-deficient roots, accompanied by a substantial accumulation of total sulfur and thiols in shoots of iron-starved plants, likely supports an increased root-to-shoot translocation of sulfate. Results suggest that tomato plants exposed to iron-deficiency are able to change sulfur metabolic balance mimicking sulfur starvation responses to meet the increased demand for methionine and its derivatives, allowing them to cope with this stress.

Sulfonates are a key component of the sulfur present in agricultural soils. Their mobilization as part of the soil sulfur cycle is mediated by rhizobacteria, and involves the oxidoreductase AsfA. In this study, the effect of fertilization regime on rhizosphere bacterial asfA distribution was examined at the Broadbalk long-term wheat experiment, Rothamsted, UK, which was established in 1843, and has included a sulfur-free treatment since 2001. Direct isolation of desulfonating rhizobacteria from the wheat rhizospheres led to the identification of several Variovorax and Polaromonas strains, all of which contained the asfA gene. Rhizosphere DNA was isolated from wheat rhizospheres in plots fertilized with inorganic fertilizer with and without sulfur, with farmyard manure or from unfertilized plots. Genetic profiling of 16S rRNA gene fragments [denaturing gradient gel electrophoresis (DGGE)] from the wheat rhizospheres revealed that the level of inorganic sulfate in the inorganic fertilizer was correlated with changes in the general bacterial community structure and the betaproteobacterial community structure in particular. Community analysis at the functional gene level (asfA) showed that 40% of clones in asfAB clone libraries were affiliated to the genus Variovorax. Analysis of asfAB-based terminal restriction fragment length polymorphism (T-RFLP) fingerprints showed considerable differences between sulfate-free treatments and those where sulfate was applied. The results suggest the occurrence of desulfonating bacterial communities that are specific to the fertilization regime chosen and that arylsulfonates play an important role in rhizobacterial sulfur nutrition.

Progress in improving crop growth is an absolute goal despite the influence multifactorial components have on crop yield and quality. An Avalon × Cadenza doubled-haploid wheat mapping population was used to study the leaf metabolome of field grown wheat at weekly intervals during the time in which the canopy contributes to grain filling, i.e.,from anthesis to 5 weeks post-anthesis. Wheat was grown under four different nitrogen supplies reaching from residual soil N to a luxury over-fertilization (0, 100, 200, and 350 kg N ha−1). Four lines from a segregating doubled haploid population derived of a cross of the wheat elite cvs. Avalon and Cadenza were chosen as they showed pairwise differences in either N utilization efficiency (NUtE) or senescence timing. 108 annotated metabolites of primary metabolism and ions were determined. The analysis did not provide genotype specific markers because of a remarkable stability of the metabolome between lines. We speculate that the reason for failing to identify genotypic markers might be due to insufficient genetic diversity of the wheat parents and/or the known tendency of plants to keep metabolome homeostasis even under adverse conditions through multiple adaptations and rescue mechanism. The data, however, provided a consistent catalogue of metabolites and their respective responses to environmental and developmental factors and may bode well for future systems biology approaches, and support plant breeding and crop improvement.

Early key research milestones for sulfate transport in plants include the first description of kinetics of sulfate uptake into plant roots (Leggett and Epstein, Plant Physiol 31:222–226, 1956), nutritionally regulated sulfate uptake into plants (Clarkson et al., J Exp Bot 34:1463–1483, 1983), and the first gene for a plant sulfate transporter (Smith et al., Proc Natl Acad Sci U S A 92:9373–9377, 1995a). Since then a well-described gene family encoding putative sulfate transporters has been characterized in multiple species, initially most notably in Arabidopsis but subsequently for a number of other models or important crops (examples: Brassica, wheat, rice, poplar and Medicago, see Buchner et al., Genome 47:526–534, 2004a; Buchner et al., Plant Physiol 136:3396–3408, 2004b; Buchner et al., Mol Plant 3:374–389, 2010; Kumar et al., Plant Signal Behav 10:e990843, 2015; Durr et al., Plant Mol Biol 72:499–517, 2010; Gao et al., Planta 239:79–96, 2014). Regulation of expression has been well documented and this regulation is both a useful marker of sulfur-nutritional status and a model for the elucidation of control pathways. The complexity of the gene family in relation to functional, regulatory and spatial distribution indicates an apparent whole plant management system for sulfur, coordinated with growth and demand and interacting with nutrient availability. In addition to sulfate, there is direct involvement of this transporter family in the uptake and accumulation of both selenate and molybdate, with clear consequences for nutritional quality. Is the story now complete almost 60 years since the first transport description and 20 years since the first sulfate transporter gene isolation, and a plethora of research projects and publications? Do we know how sulfur is acquired and appropriately distributed within the plant? Do we know the critical signals that control these processes? Are we even sure that these processes are coordinated? This review documents research progress and assesses to what extent the key questions have been addressed.

This proceedings volume contains a selection of invited and contributed papers of the 10th International Workshop on Sulfur Metabolism in Plants, which was hosted by Ewald Schung and Silvana Haneklausand was held in Goslar, Germany September 1-4, 2015. The focus of this workshop was on the fundamental, environmental and agricultural aspects of sulfur in plants, and presents an overview of the progress in the research developments in this field in the 28 years since the first of these workshops. The volume covers various aspects of the regulation of the uptake and assimilation of sulfate in plants from a molecular to a whole plant level with an emphasis on the significance of sulfur metabolism in plant responses to stress and in food security.

Manganese (Mn) is an essential plant nutrient, though at elevated levels in plant tissues it may become toxic. The physiological basis for phytotoxicity is largely unclear. Exposure of Brassica rapa to elevated levels of Mn2+ in the nutrient solution resulted in decreased biomass production at ≥ 20 µM and chlorosis. The Mn content in the shoot increased with the Mn2+ concentration in the nutrient solution and became toxic when it exceeded a 4-fold concentration of the control. In contrast to observations with Cu and Zn, elevated and toxic Mn2+ levels did not affect the water-soluble non-protein thiols in both root and shoot and the expression the sulfate transporters, Sultr1;1 and Sultr1;2, in the root.

Sulfur remains an important issue on the agenda for crop plant nutrition. In addition to avoidance of sulfur deficiency, which will impact on yield and quality, there are requirements for adequate fertilization of crops for resistance to biotic and abiotic stresses. Equally importantly, there are clear consequences for efficient nitrogen utilization and there are interactions with micronutrient acquisition (selenium and molybdenum). Substantial advances have been made at the cellular level, dissecting the signal transduction pathways linking cellular nutritional status with expression of sulfur regulated genes and pathways. However cellular processes need to be placed in the context of whole plant regulation of sulfur uptake and assimilation, which encompasses developmental, spatial and environmental factors, and which facilitates optimum growth and fecundity (and yield in the case of crops) with available sulfur supply. During development, adequate sulfur must be acquired for optimum growth, ideally with any excess being sequestered into re-mobilizable temporary stores. As the plant develops, efficient utilization of sulfur will require organ to organ transfer, and additionally degradation pathways, metabolic inter-conversions and multiple trans-membrane and vascular tissue mediated transport steps for both inorganic and organic sulfur compounds. For crops, efficient transfer of sulfur to harvested sink tissues and its incorporation into protein are important agronomic traits. Insufficient sulfur to meet the demand for growth results in a number of plant responses, targeted at optimising uptake and use of available sulfur. Notable early and specific responses are the up-regulation of transporters and key steps of the assimilatory pathways in sulfur-deficient tissues, and the allocation of resources to stimulate growth of root tissues compared to the shoots. These responses involving root proliferation and transporter functionality are adaptations to improve pedospheric sulfur acquisition. A long standing question has concerned the existence and nature of inter-organ signals of nutrient status. It is possible that local sulfur availability, coupled with intrinsic cell specific programmed function, is sufficient to mediate local gene and pathway expression, influence organ responses and effect whole plant sulfur management without inter organ signals. Developmental cues will influence organ specific pathways, most clearly demonstrated in processes of leaf senescence and associated nutrient remobilization. Conversely, the recognition of possibly mobile phloem located miRNAs may be indicative of long distance regulatory mechanisms. Similarly, root proliferation will almost certainly have a hormonal basis.

Sulphate leaching losses may reduce the long-term possibility of maintaining the S supply of crops in low input farming systems. In order to maintain a sufficient S supply in the future when further reductions in the atmospheric deposition are expected, it is important to reduce leaching losses of sulphate. As leaching primarily occurs during autumn and winter, a plant cover in this period must be expected to affect the quantity of S leached. It has been demonstrated that a catch crop succeeding the main crop can absorb nitrate from the root zone during autumn and winter and thereby reduce nitrate leaching (Thorup-Kristensen and Nielsen 1998). Similar beneficial effects of catch crops on sulphate leaching may be expected. The ability of catch crops (Italian ryegrass [Lolium multiflorum Lam], winter rape [Brassica napus L.] and fodder radish [Raphanus sativus L.]) to reduce soil sulphate concentrations in autumn and make it available to a succeeding crop was investigated in a field experiment on sandy loam soil, as described by Eriksen and Thorup-Kristensen (2002). All catch crops reduced soil sulphate concentrations in the autumn compared to bare soil (Fig. 1). Especially the cruciferous catch crops had the ability to deplete efficiently soil sulphate levels and thus, reduce the sulphate leaching potential. The S uptake in aboveground catch crop was 8, 22 and 36 kg S ha-1 for ryegrass, winter rape and fodder radish, respectively. In the following spring, sulphate levels of the autumn bare soil were low in the top 0.5 m and a peak of sulphate was found at 0.75-1 m depth (Fig. 1). In contrast, where a fodder radish catch crop had been grown, high sulphate levels were present in the top 0.5 m but only small amounts of sulphate were found at 0.5-1.5 m depth. The release of S to barley (Hordeum vulgare L.) were investigated in pot experiments (setup described by Eriksen et al. 1995) after incorporation of the catch crops Cichorium intybus L., Medicago lupulina L., Anthyllis vulneraria L., Trifolium repens L., Pastinaca sativa L., Sanguisorba minor, Lupinus polyphyllos L., Lolium perenne L. and Raphanus sativus L. The S mineralisation rates were highest for cruciferous crops and lowest for legumes and differences were partly explained by the C/S-ratio (r2=0,49) that varied from 48 to 265 (Fig. 2). In the field, Eriksen and Askegaard (2000) found that sulphate leaching from an organic dairy crop rotation, on sandy soil was 20 kg S ha-1 as average of 4 years or equivalent to 60 % of the total input. Sulphate leaching was very variable and ranged from 4 to 45 kg S ha-1 for the same crop in different years. The catch crops showed a great potential for reducing sulphate leaching. Especially cruciferous crops, having a high S-demand and vigorous root growth efficiently depleted the soil sulphate pool. In a crop rotation, including both low-S-demanding cereals and high-S-demanding main crops a suitable catch crop strategy may prevent excess sulphate from leaching in years with low-S-demanding crops and instead transfer S to the following high-S-demanding crop. This is most important in low input systems, e.g., organic farming, but also of relevance to other farming systems.