On-Farm Experimentation to transform global agriculture.

Restructuring farmer-researcher relationships and addressing complexity and uncertainty through joint exploration are at the heart of On-Farm Experimentation (OFE). OFE describes new approaches to agricultural research and innovation that are embedded in real-world farm management, and reflects new demands for decentralized and inclusive research that bridges sources of knowledge and fosters open innovation. Here we propose that OFE research could help to transform agriculture globally. We highlight the role of digitalization, which motivates and enables OFE by dramatically increasing scales and complexity when investigating agricultural challenges.

FGF signaling is required for chemokinesis and ventral migration of trunk neural crest cells.

BACKGROUND: Neural crest cells (NCCs) delaminate from the neural tube (NT) and migrate ventrally to generate the trunk peripheral nervous system (PNS). Although several signaling pathways have been identified that steer NCCs once they are on their ventral trajectory, no molecules have been identified that are required for the initial migration between the NT and the dorsal root ganglion. Given the critical role of fibroblast growth factor (FGF) signaling in embryogenesis, we investigated its function in this initial migration. RESULTS: FGFR1 signaling is required for the migration of newly delaminated NCCs onto the ventral pathway. Live imaging of migrating NCCs revealed that inhibition of FGFR1 signaling caused the dorsally stalled NCCs to lose their dorsal/ventral oriented polarity and instead adopt a rounded morphology while dynamically extending filopodia. FGF8, an FGFR1 ligand, increased motility of NCCs away from the NT by acting chemokinetically. Finally, we provide evidence that inhibition of FGFR1-mediated chemokinesis is partially rescued by increasing Akt signaling, inhibiting RhoA, and activation of N-cadherin signaling. CONCLUSION: These data support a model in which NCCs are stimulated chemokinetically by FGF:FGFR1 signaling, and that this activation positions and orients NCCs on their ventral migratory route-a process that is essential for patterning the trunk PNS.

Distal spinal nerve development and divergence of avian groups.

The avian transition from long to short, distally fused tails during the Mesozoic ushered in the Pygostylian group, which includes modern birds. The avian tail embodies a bipartite anatomy, with the proximal separate caudal vertebrae region, and the distal pygostyle, formed by vertebral fusion. This study investigates developmental features of the two tail domains in different bird groups, and analyzes them in reference to evolutionary origins. We first defined the early developmental boundary between the two tail halves in the chicken, then followed major developmental structures from early embryo to post-hatching stages. Differences between regions were observed in sclerotome anterior/posterior polarity and peripheral nervous system development, and these were consistent in other neognathous birds. However, in the paleognathous emu, the neognathous pattern was not observed, such that spinal nerve development extends through the pygostyle region. Disparities between the neognaths and paleognaths studied were also reflected in the morphology of their pygostyles. The ancestral long-tailed spinal nerve configuration was hypothesized from brown anole and alligator, which unexpectedly more resembles the neognathous birds. This study shows that tail anatomy is not universal in avians, and suggests several possible scenarios regarding bird evolution, including an independent paleognathous long-tailed ancestor.

A Roadmap for Lowering Crop Nitrogen Requirement.

Increasing nitrogen fertilizer applications have sustained a growing world population in the 20th century. However, to avoid any further associated environmental damage, new sustainable agronomic practices together with new cultivars must be developed. To date the concept of nitrogen use efficiency (NUE) has been useful in quantifying the processes of nitrogen uptake and utilization, but we propose a shift in focus to consider nitrogen responsiveness as a more appropriate trait to select varieties with lower nitrogen requirements. We provide a roadmap to integrate the regulation of nitrogen uptake and assimilation into varietal selection and crop breeding programs. The overall goal is to reduce nitrogen inputs by farmers growing crops in contrasting cropping systems around the world, while sustaining yields and reducing greenhouse gas (GHG) emissions.

The voltage sensing phosphatase (VSP) localizes to the apical membrane of kidney tubule epithelial cells.

Voltage-sensing phosphatases (VSPs) are transmembrane proteins that couple changes in membrane potential to hydrolysis of inositol signaling lipids. VSPs catalyze the dephosphorylation of phosphatidylinositol phosphates (PIPs) that regulate diverse aspects of cell membrane physiology including cell division, growth and migration. VSPs are highly conserved among chordates, and their RNA transcripts have been detected in the adult and embryonic stages of frogs, fish, chickens, mice and humans. However, the subcellular localization and biological function of VSP remains unknown. Using reverse transcriptase-PCR (RT-PCR), we show that both Xenopus laevis VSPs (Xl-VSP1 and Xl-VSP2) mRNAs are expressed in early embryos, suggesting that both Xl-VSPs are involved in early tadpole development. To understand which embryonic tissues express Xl-VSP mRNA, we used in situ hybridization (ISH) and found Xl-VSP mRNA in both the brain and kidney of NF stage 32-36 embryos. By Western blot analysis with a VSP antibody, we show increasing levels of Xl-VSP protein in the developing embryo, and by immunohistochemistry (IHC), we demonstrate that Xl-VSP protein is specifically localized to the apical membrane of both embryonic and adult kidney tubules. We further characterized the catalytic activity of both Xl-VSP homologs and found that while Xl-VSP1 catalyzes 3- and 5-phosphate removal, Xl-VSP2 is a less efficient 3-phosphatase with different substrate specificity. Our results suggest that Xl-VSP1 and Xl-VSP2 serve different functional roles and that VSPs are an integral component of voltage-dependent PIP signaling pathways during vertebrate kidney tubule development and function.

Gross N transformation rates and related N2O emissions in Chinese and UK agricultural soils.

The properties of agricultural soils in various regions of the world are variable and can have a significant but poorly understood impact on soil nitrogen (N) transformations and nitrous oxide (N2O) emissions. For this reason, we undertook a study of gross N transformations and related N2O emissions in contrasting agricultural soils from China and the UK. Seven Chinese and three UK agricultural soils were collected for study using a 15N tracing approach. The soil pH ranged from 5.4 to 8.7, with three acidic soils collected from Jinjing, Lishu and Boghall; one neutral soil collected from Changshu, and the other six alkaline soils collected from Quzhou, Zhangye, Changwu, Jinzhong, Boxworth and Stetchworth. Our results showed that the main N transformation processes were oxidation of ammonium (NH4+) to nitrate (NO3-) (ONH4), and mineralization of organic N to NH4+. The gross autotrophic nitrification rates calculated in the three acidic soils were between 0.25 and 4.15 mg N kg-1 d-1, which were significantly lower (p < 0.05) than those in the remaining neutral and alkaline soils ranging from 6.94 to 14.43 mg N kg-1 d-1. Generally, soil pH was positively correlated (p < 0.001) with gross autotrophic nitrification rate and cumulative N2O emissions, indicating that soil pH was an important factor regulating autotrophic nitrification and N2O emissions. There was also a significant positive correlation between the gross autotrophic nitrification rate and cumulative N2O emissions, highlighting the importance of this process for producing N2O emissions in these agricultural soils under aerobic conditions. Gross NH4+ immobilization rates were very low in most soils except for the Jinjing soil with the lowest pH. In conclusion, the gross autotrophic nitrification rates and related N2O emissions were controlled by soil pH irrespectively of the soil's origin in these agricultural soils.

The Order and Place of Neuronal Differentiation Establish the Topography of Sensory Projections and the Entry Points within the Hindbrain.

Establishing topographical maps of the external world is an important but still poorly understood feature of the vertebrate sensory system. To study the selective innervation of hindbrain regions by sensory afferents in the zebrafish embryo, we mapped the fine-grained topographical representation of sensory projections at the central level by specific photoconversion of sensory neurons. Sensory ganglia located anteriorly project more medially than do ganglia located posteriorly, and this relates to the order of sensory ganglion differentiation. By single-plane illumination microscopy (SPIM) in vivo imaging, we show that (1) the sequence of arrival of cranial ganglion inputs predicts the topography of central projections, and (2) delaminated neuroblasts differentiate in close contact with the neural tube, and they never loose contact with the neural ectoderm. Afferent entrance points are established by plasma membrane interactions between primary differentiated peripheral sensory neurons and neural tube border cells with the cooperation of neural crest cells. These first contacts remain during ensuing morphological growth to establish pioneer axons. Neural crest cells and repulsive slit1/robo2 signals then guide axons from later-differentiating neurons toward the neural tube. Thus, this study proposes a new model by which the topographical representation of cranial sensory ganglia is established by entrance order, with the entry points determined by cell contact between the sensory ganglion cell bodies and the hindbrain.

Root length densities of UK wheat and oilseed rape crops with implications for water capture and yield.

Root length density (RLD) was measured to 1 m depth for 17 commercial crops of winter wheat (Triticum aestivum) and 40 crops of winter oilseed rape [Brassica napus; oilseed rape (OSR)] grown in the UK between 2004 and 2013. Taking the critical RLD (cRLD) for water capture as 1cm cm(-3), RLDs appeared inadequate for full water capture on average below a depth of 0.32 m for winter wheat and below 0.45 m for OSR. These depths compare unfavourably (for wheat) with average depths of 'full capture' of 0.86 m and 0.48 m, respectively, determined for three wheat crops and one OSR crop studied in the 1970s and 1980s, and treated as references here. A simple model of water uptake and yield indicated that these shortfalls in wheat and OSR rooting compared with the reference data might be associated with shortfalls of up to 3.5 t ha(-1) and 1.2 t ha(-1), respectively, in grain yields under water-limited conditions, as increasingly occur through climate change. Coupled with decreased summer rainfall, poor rooting of modern arable crops could explain much of the yield stagnation that has been observed on UK farms since the 1990s. Methods of monitoring and improving rooting under commercial conditions are reviewed and discussed.

Feed the crop not the soil: rethinking phosphorus management in the food chain.

Society relies heavily on inorganic phosphorus (P) compounds throughout its food chain. This dependency is not only very inefficient and increasingly costly but is depleting finite global reserves of rock phosphate. It has also left a legacy of P accumulation in soils, sediments and wastes that is leaking into our surface waters and contributing to widespread eutrophication. We argue for a new, more precise but more challenging paradigm in P fertilizer management that seeks to develop more sustainable food chains that maintain P availability to crops and livestock but with reduced amounts of imported mineral P and improved soil function. This new strategy requires greater public awareness of the environmental consequences of dietary choice, better understanding of soil-plant-animal P dynamics, increased recovery of both used P and unutilized legacy soil P, and new innovative technologies to improve fertilizer P recovery. In combination, they are expected to deliver significant economic, environmental, and resource-protection gains, and contribute to future global P stewardship.

Stability, across environments, of grain and alcohol yield, in soft wheat varieties grown for grain distilling or bioethanol production.

BACKGROUND: Soft-milling wheat has potential use for both grain whisky distilling and bioethanol production. Varietal comparisons over wide-ranging environments would permit assessment of both grain and alcohol yield potential and also permit the stability across environments, for these parameters, to be compared. RESULTS: For 12 varieties, analysis of variance showed highly significant effects of variety, site, season and fertiliser application on grain and alcohol yield. There were also significant interactions between these factors and, consequently, varieties varied in stability across environments as well as in mean values for the parameters assessed. Alcohol production per hectare was affected more strongly by variation in grain yield than alcohol yield, but increasing grain protein content reduced alcohol yield and, therefore, utility for grain distilling. CONCLUSION: To maximise energy production, the best varieties for bioethanol would combine high and stable grain yield with slower reduction of alcohol yield as grain protein increases. For grain distilling, where the energy balance is less important, high alcohol yield will remain the key factor. Data derived using near infrared spectroscopy can be valuable in assessing stability of quality traits across environments.

From dinosaurs to birds: a tail of evolution.

A particularly critical event in avian evolution was the transition from long- to short-tailed birds. Primitive bird tails underwent significant alteration, most notably reduction of the number of caudal vertebrae and fusion of the distal caudal vertebrae into an ossified pygostyle. These changes, among others, occurred over a very short evolutionary interval, which brings into focus the underlying mechanisms behind those changes. Despite the wealth of studies delving into avian evolution, virtually nothing is understood about the genetic and developmental events responsible for the emergence of short, fused tails. In this review, we summarize the current understanding of the signaling pathways and morphological events that contribute to tail extension and termination and examine how mutations affecting the genes that control these pathways might influence the evolution of the avian tail. To generate a list of candidate genes that may have been modulated in the transition to short-tailed birds, we analyzed a comprehensive set of mouse mutants. Interestingly, a prevalent pleiotropic effect of mutations that cause fused caudal vertebral bodies (as in the pygostyles of birds) is tail truncation. We identified 23 mutations in this class, and these were primarily restricted to genes involved in axial extension. At least half of the mutations that cause short, fused tails lie in the Notch/Wnt pathway of somite boundary formation or differentiation, leading to changes in somite number or size. Several of the mutations also cause additional bone fusions in the trunk skeleton, reminiscent of those observed in primitive and modern birds. All of our findings were correlated to the fossil record. An open question is whether the relatively sudden appearance of short-tailed birds in the fossil record could be accounted for, at least in part, by the pleiotropic effects generated by a relatively small number of mutational events.

Raising yield potential of wheat. III. Optimizing partitioning to grain while maintaining lodging resistance.

A substantial increase in grain yield potential is required, along with better use of water and fertilizer, to ensure food security and environmental protection in future decades. For improvements in photosynthetic capacity to result in additional wheat yield, extra assimilates must be partitioned to developing spikes and grains and/or potential grain weight increased to accommodate the extra assimilates. At the same time, improvement in dry matter partitioning to spikes should ensure that it does not increase stem or root lodging. It is therefore crucial that improvements in structural and reproductive aspects of growth accompany increases in photosynthesis to enhance the net agronomic benefits of genetic modifications. In this article, six complementary approaches are proposed, namely: (i) optimizing developmental pattern to maximize spike fertility and grain number, (ii) optimizing spike growth to maximize grain number and dry matter harvest index, (iii) improving spike fertility through desensitizing floret abortion to environmental cues, (iv) improving potential grain size and grain filling, and (v) improving lodging resistance. Since many of the traits tackled in these approaches interact strongly, an integrative modelling approach is also proposed, to (vi) identify any trade-offs between key traits, hence to define target ideotypes in quantitative terms. The potential for genetic dissection of key traits via quantitative trait loci analysis is discussed for the efficient deployment of existing variation in breeding programmes. These proposals should maximize returns in food production from investments in increased crop biomass by increasing spike fertility, grain number per unit area and harvest index whilst optimizing the trade-offs with potential grain weight and lodging resistance.

Analysing nitrogen responses of cereals to prioritize routes to the improvement of nitrogen use efficiency.

The efficient use of fertilizer nitrogen (N) is crucial to sustainable human nutrition. All crops receive significant amounts of additional N in temperate environments, through fixation or fertilizer use. This paper reviews progress towards the efficient use of fertilizer N by winter wheat (Triticum aesitivum L.) and spring barley (Hordeum vulgare L.) in the UK, acknowledging that on-farm this is governed by economics. Recent multi-site N response experiments on old and modern varieties show that yield improvements since the 1980s have been accompanied by increases in economic optimum N amounts for wheat but not for spring barley. On-farm N use efficiency (NUE) has increased for barley because increased yields with optimum N were associated with compensatory decreases in grain N concentration, whereas on-farm NUE has not increased for wheat because grain N concentration has not changed and improvements in N capture were insufficient to make up for the increased yield. Genetic effects on NUE are shown to differ markedly depending on whether they are determined at a single N rate, as in variety trials, or with optimum N amounts. It is suggested that, in order to elicit faster improvement in NUE on farms, breeding and variety testing should be conducted at some sites with more than one level of applied N, and that grain N%, N harvest index, and perhaps canopy N ratio (kg N ha(-1) green area) should be measured more widely. It is also suggested that, instead of using empirical functions, N responses might be analysed more effectively using functions based on explanations of yield determination for which the parameters have some physiological meaning.

Chicken protocadherin-1 functions to localize neural crest cells to the dorsal root ganglia during PNS formation.

In vertebrate embryos, neural crest cells emerge from the dorsal neural tube and migrate along well defined pathways to form a wide diversity of tissues, including the majority of the peripheral nervous system (PNS). Members of the cadherin family of cell adhesion molecules play key roles during the initiation of migration, mediating the delamination of cells from the neural tube. However, a role for cadherins in the sorting and re-aggregation of the neural crest to form the PNS has not been established. We report the requirement for a protocadherin, chicken protocadherin-1 (Pcdh1), in neural crest cell sorting during the formation of the dorsal root ganglia (DRG). In embryos, cPcdh1 is highly expressed in the developing DRG, where it co-localizes with the undifferentiated and mitotically active cells along the perimeter. Pcdh1 can promote cell adhesion in vivo and disrupting Pcdh1 function in embryos results in fewer neural crest cells localizing to the DRG, with a concomitant increase in cells that migrate to the sympathetic ganglia. Furthermore, those cells that still localize to the DRG, when Pcdh1 is inhibited, are no longer found at the perimeter, but are instead dispersed throughout the DRG and are now more likely to differentiate along the sensory neuron pathway. These results demonstrate that Pcdh1-mediated cell adhesion plays an important role as neural crest cells coalesce to form the DRG, where it serves to sort cells to the mitotically active perimeter.

NF-protocadherin and TAF1 regulate retinal axon initiation and elongation in vivo.

NF-protocadherin (NFPC)-mediated cell-cell adhesion plays a critical role in vertebrate neural tube formation. NFPC is also expressed during the period of axon tract formation, but little is known about its function in axonogenesis. Here we have tested the role of NFPC and its cytosolic cofactor template-activating factor 1 (TAF1) in the emergence of the Xenopus retinotectal projection. NFPC is expressed in the developing retina and optic pathway and is abundant in growing retinal axons. Inhibition of NFPC function in developing retinal ganglion cells (RGCs) severely reduces axon initiation and elongation and suppresses dendrite genesis. Furthermore, an identical phenotype occurs when TAF1 function is blocked. These data provide evidence that NFPC regulates axon initiation and elongation and indicate a conserved role for TAF1, a transcriptional regulator, as a downstream cytosolic effector of NFPC in RGCs.

Eph/ephrins and N-cadherin coordinate to control the pattern of sympathetic ganglia.

Previous studies have suggested that the segmental pattern of neural-crest-derived sympathetic ganglia arises as a direct result of signals that restrict neural crest cell migratory streams through rostral somite halves. We recently showed that the spatiotemporal pattern of chick sympathetic ganglia formation is a two-phase process. Neural crest cells migrate laterally to the dorsal aorta, then surprisingly spread out in the longitudinal direction, before sorting into discrete ganglia. Here, we investigate the function of two families of molecules that are thought to regulate cell sorting and aggregation. By blocking Eph/ephrins or N-cadherin function, we measure changes in neural crest cell migratory behaviors that lead to alterations in sympathetic ganglia formation using a recently developed sagittal slice explant culture and 3D confocal time-lapse imaging. Our results demonstrate that local inhibitory interactions within inter-ganglionic regions, mediated by Eph/ephrins, and adhesive cell-cell contacts at ganglia sites, mediated by N-cadherin, coordinate to sculpt discrete sympathetic ganglia.

A requirement for NF-protocadherin and TAF1/Set in cell adhesion and neural tube formation.

Neurulation in vertebrates is an intricate process requiring extensive alterations in cell contacts and cellular morphologies as the cells in the neural ectoderm shape and form the neural folds and neural tube. Despite these complex interactions, little is known concerning the molecules that mediate cell adhesion within the embryonic neural plate and neural folds. Here, we demonstrate the requirement for NF-protocadherin (NFPC) and its cytosolic partner TAF1/Set for proper neurulation in Xenopus. Both NFPC and TAF1 function in cell-cell adhesion in the neural ectoderm, and disruptions in either NFPC or TAF1 result in a failure of the neural tube to close. This neural tube defect can be attributed to a lack of proper organization of the cells in the dorsal neural folds, manifested by a loss in the columnar epithelial morphology and apical localization of F-actin. However, the epidermal ectoderm is still able to migrate and cover the open neural tube, indicating that the fusions of the neural tube and epidermis are separate events. These studies demonstrate that NFPC and TAF1 function to maintain proper cell-cell interactions within the neural folds and suggest that NFPC and TAF1 participate in novel adhesive mechanisms that contribute to the final events of vertebrate neurulation.

The cytoplasmic domain of Xenopus NF-protocadherin interacts with TAF1/set.

Protocadherins are members of the cadherin superfamily of cell adhesion molecules proposed to play important roles in early development, but whose mechanisms of action are largely unknown. We examined the function of NF-protocadherin (NFPC), a novel cell adhesion molecule essential for the histogenesis of the embryonic ectoderm in Xenopus, and demonstrate that the cellular protein TAF1, previously identified as a histone-associated protein, binds the NFPC cytoplasmic domain. NFPC and TAF1 coprecipitate from embryo extracts when ectopically expressed, and TAF1 can rescue the ectodermal disruptions caused by a dominant-negative NFPC construct lacking the extracellular domain. Furthermore, disruptions in either NFPC or TAF1 expression, using NFPC- or TAF1-specific antisense morpholinos, result in essentially identical ectodermal defects. These results indicate a role for TAF1 in the differentiation of the embryonic ectoderm, as a cytosolic cofactor of NFPC.

Modelling cereal root systems for water and nitrogen capture: towards an economic optimum.

A quantitative model of wheat root systems is developed that links the size and distribution of the root system to the capture of water and nitrogen (which are assumed to be evenly distributed with depth) during grain filling, and allows estimates of the economic consequences of this capture to be assessed. A particular feature of the model is its use of summarizing concepts, and reliance on only the minimum number of parameters (each with a clear biological meaning). The model is then used to provide an economic sensitivity analysis of possible target characteristics for manipulating root systems. These characteristics were: root distribution with depth, proportional dry matter partitioning to roots, resource capture coefficients, shoot dry weight at anthesis, specific root weight and water use efficiency. From the current estimates of parameters it is concluded that a larger investment by the crop in fine roots at depth in the soil, and less proliferation of roots in surface layers, would improve yields by accessing extra resources. The economic return on investment in roots for water capture was twice that of the same amount invested for nitrogen capture.