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Abstract Date palm (Phoenix dactylifera L.) is able to grow and complete its life cycle while being rooted in highly saline soils. Which of the many well‐known salt‐tolerance strategies are combined to fine‐tune this remarkable resilience is unknown. The precise location, whether in the shoot or the root, where these strategies are employed remains uncertain, leaving us unaware of how the various known salt‐tolerance mechanisms are integrated to fine‐tune this remarkable resilience. To address this shortcoming, we exposed date palm to a salt stress dose equivalent to seawater for up to 4 weeks and applied integrative multi‐omics analyses followed by targeted metabolomics, hormone, and ion analyses. Integration of proteomic into transcriptomic data allowed a view beyond simple correlation, revealing a remarkably high degree of convergence between gene expression and protein abundance. This sheds a clear light on the acclimatization mechanisms employed, which depend on reprogramming of protein biosynthesis. For growth in highly saline habitats, date palm effectively combines various salt‐tolerance mechanisms found in both halophytes and glycophytes: “avoidance” by efficient sodium and chloride exclusion at the roots, and “acclimation” by osmotic adjustment, reactive oxygen species scavenging in leaves, and remodeling of the ribosome‐associated proteome in salt‐exposed root cells. Combined efficiently as in P. dactylifera L., these sets of mechanisms seem to explain the palm's excellent salt stress tolerance.

Abstract Background Due to climate change and reduced use of fertilizers combined stress scenarios are becoming increasingly frequent in crop production. In a field experiment we tested the effect of combined water and phosphorus limitation on the growth performance and plant traits of eight tetraploid and two diploid potato varieties as well as on root-associated microbiome diversity and functional potential. Microbiome and metagenome analysis targeted the diversity and potential functions of prokaryotes, fungi, plasmids, and bacteriophages and was linked to plant traits like tuber yield or timing of canopy closure. Results The different potato genotypes responded differently to the combined stress and hosted distinct microbiota in the rhizosphere and the root endosphere. Proximity to the root, stress and potato genotype had significant effects on bacteria, whereas fungi were only mildly affected. To address the involvement of microbial functions, we investigated well and poorly performing potato genotypes (Stirling and Desirée, respectively) under stress conditions and executed a metagenome analysis of rhizosphere microbiomes subjected to stress and no stress conditions. Functions like ROS detoxification, aromatic amino acid and terpene metabolism were enriched and in synchrony with the metabolism of stressed plants. In Desirée, Pseudonocardiales had the genetic potential to take up assimilates produced in the fast-growing canopy and to reduce plant stress-sensing by degrading ethylene, but overall yield losses were high. In Stirling, Xanthomonadales had the genetic potential to reduce oxidative stress and to produce biofilms, potentially around roots. Biofilm formation could be involved in drought resilience and nutrient accessibility of Stirling and explain the recorded low yield losses. In the rhizosphere exposed to combined stress, the relative abundance of plasmids was reduced, and the diversity of phages was enriched. Moreover, mobile elements like plasmids and phages were affected by combined stresses in a genotype-specific manner. Conclusion Our study gives new insights into the interconnectedness of root-associated microbiota and plant stress responses in the field. Functional genes in the metagenome, phylogenetic composition and mobile elements play a role in potato stress adaption. In a poor and a well performing potato genotype grown under stress conditions, distinct functional genes pinpoint to a distinct stress sensing, water availability and compounds in the rhizospheres.

Abstract Large quantities of fertilizers, mainly nitrogen (N), phosphorus (P), and potassium (K), are used in China's crop production; however, whether N, P, and K still limit yield under the current high input remains unknown. In addition, it is not clear whether magnesium (Mg) potentially limits crop production. To address these issues, a national survey of the soil nutrient status and farmers' fertilization practices was conducted in China to determine the soil N, P, K, and Mg status and current fertilization practices. In addition, various experiments, including optimized NPK (OPTNPK) and Mg fertilizer combined with OPTNPK (OPTNPK + Mg) in comparison with farmers' practices (FFP), were performed across China to identify the potential for reducing NPK application and the need for Mg application in crop production. The survey data from 2699 questionnaires indicated that (1) all soil samples were not deficient in NPK, but 73.0% were limited by Mg. (2) The average N, P (in P2O5), K (in K2O), and Mg (in MgO) balances were 422.6, 334.1, 326.3, and −22.6 kg ha−1, respectively. Only 15.7% of all farmers applied Mg fertilizer. (3) NPK fertilization can be reduced by an average of 28.8% without reducing the crop yield and quality. (4) For most crops, the application of Mg fertilizer increased the crop yield by 5.5–40.6% and improved the quality. However, different crops under different conditions had different responses to Mg fertilization. These results indicate that reduced NPK inputs and increased Mg inputs are equally important for the healthy development and sustainability of China's agriculture.

Abstract Phosphorus (P) and zinc (Zn) uptake and its physiological use in plants are interconnected and are tightly controlled. However, there is still conflicting information about the interactions of these two nutrients, thus a better understanding of nutritional homeostasis is needed. The objective of this work was to evaluate responses of photosynthesis parameters, P-Zn nutritional homeostasis and antioxidant metabolism to variation in the P × Zn supply of cotton (Gossypium hirsutum L.). Plants were grown in pots and watered with nutrient solution containing combinations of P and Zn supply. An excess of either P or Zn limited plant growth, reduced photosynthesis-related parameters, and antioxidant scavenging enzymes. Phosphorus uptake favoured photochemical dissipation of energy decreasing oxidative stress, notably on Zn-well-nourished plants. On the other hand, excessive P uptake reduces Zn-shoot concentration and decreasing carbonic anhydrase activity. Adequate Zn supply facilitated adaptation responses to P deficiency, upregulating acid phosphatase activity, whereas Zn and P excess were alleviated by increasing P and Zn supply, respectively. Collectively, the results showed that inter ionic effects of P and Zn uptake affected light use and CO2 assimilation rate on photosynthesis, activation of antioxidant metabolism, acid phosphatase and carbonic anhydrase activities, and plant growth-related responses to different extents.

Abstract Background Agriculture is facing an unprecedented challenge in having to reduce its environmental footprint whilst ensuring food security to an ever-growing global population. Towards this end, several strategies have been investigated and implemented to help maintain or improve crop yield under reduced water and/or nutrient provision for key commercial commodities such as tomatoes. Despite the high commercial, nutritional, and food-cultural value, there is no synthesis of evidence regarding yield maintenance of tomato (as a model crop) under resource-deficit. This systematic map therefore provides an overview of the evidence that exists on the effectiveness of techniques and management approaches aimed at improving the productivity of field-grown tomatoes under conditions of water-, nitrogen- (N) and/or phosphorus (P)-deficit. Methods Following the published map protocol, systematic searches of peer reviewed- and grey-literature were conducted using research publication databases, and specialist websites. A total of 14,377 unique articles were identified as potentially relevant to our research question, of which 927 were screened at the full-text level. Of that subset, 291 articles met all the pre-defined eligibility criteria. Basic information and meta-data on the interventions reported were recorded for these articles and a systematic map was compiled with the extracted data. Results The articles included in the systematic map database were used to identify several significant points including: (1) from the year 2000, the number of articles investigating strategies to improve field-grown tomato yield under conditions of water and/or nutrient deficit follows an upward trend; (2) large evidence bases (> 50%) originated from the United States, India, and Italy; (3) most studies addressed water alone as a resource (49%), with only 18% of studies focussing on N and 4% on P alone. Only 4% of records assessed all three resources simultaneously; (4) most evidence (77%) aims to improve resource use-efficiency via either irrigation, fertilisation, or crop and soil management strategies; and (5) different geographical regions appear to focus on different groups of interventions. Conclusions This systematic map identifies a range of interventions that have been successfully implemented in fields to improve the yield of commercial tomatoes under conditions of water, N and/or P deficit. However, only half of the relevant literature reported evidence on more than one intervention, which highlights the need for more integrated approaches to assess multiple interventions to adapt to deficits of key-resources simultaneously. In addition, the use of ‘techno-chemical’, ‘breeding and genetic’ and ‘computational’ interventions are only reported in a small number of records (

Abstract Background Phosphorus (P) deficiency limits crop production worldwide. Crops differ in their ability to acquire and utilise the P available. The aim of this study was to determine root traits (root exudates, root system architecture (RSA), tissue-specific allocation of P, and gene expression in roots) that (a) play a role in P-use efficiency and (b) contribute to large shoot zinc (Zn) concentration in Brassica oleracea. Results Two B. oleracea accessions (var. sabellica C6, a kale, and var. italica F103, a broccoli) were grown in a hydroponic system or in a high-throughput-root phenotyping (HTRP) system where they received Low P (0.025 mM) or High P (0.25 mM) supply for 2 weeks. In hydroponics, root and shoot P and Zn concentrations were measured, root exudates were profiled using both Fourier-Transform-Infrared spectroscopy and gas-chromatography-mass spectrometry and previously published RNAseq data from roots was re-examined. In HTRP experiments, RSA (main and lateral root number and lateral root length) was assessed and the tissue-specific distribution of P was determined using micro-particle-induced-X-ray emission. The C6 accession had greater root and shoot biomass than the F103 accession, but the latter had a larger shoot P concentration than the C6 accession, regardless of the P supply in the hydroponic system. The F103 accession had a larger shoot Zn concentration than the C6 accession in the High P treatment. Although the F103 accession had a larger number of lateral roots, which were also longer than in the C6 accession, the C6 accession released a larger quantity and number of polar compounds than the F103 accession. A larger number of P-responsive genes were found in the Low P treatment in roots of the F103 accession than in roots of the C6 accession. Expression of genes linked with “phosphate starvation” was up-regulated, while those linked with iron homeostasis were down-regulated in the Low P treatment. Conclusions The results illustrate large within-species variability in root acclimatory responses to P supply in the composition of root exudates, RSA and gene expression, but not in P distribution in root cross sections, enabling P sufficiency in the two B. oleracea accessions studied.

Abstract Background There is an urgent need to ensure that food production is maintained in response to either a reduction in use or lack of availability of natural resources. To this end, several strategies have been investigated to determine which agronomic approaches may improve crop yields under conditions of reduced water and/or nutrients provision, with special attention upon nitrogen (N) and phosphorus (P). New technologies and practices have been developed for key commercial crops, such as tomatoes. However, few of these are widely adopted in the field and evidence of their value in this production setting is limited. Methods This protocol sets out a systematic map methodology that aims to provide a coherent synthesis of the available evidence among the literature on the techniques and management approaches that may ensure the productivity of field-grown tomatoes under conditions of water-, N- and/or P-deficits, either as single or combined stresses. To conduct the literature search, a search strategy was produced to define the scope of the systematic map and to allow reproducibility of the approach. A list of published and unpublished sources of literature were selected and a preliminary trial identified best-fit-for-purpose search-terms and -strings. A literature screening process was set with consistency checks amongst reviewers at the title, abstract and full text screening stages. A series of eligibility criteria were defined to ensure objectivity and consistency in the selection of studies that are best suited to address the research question of the systematic map. In addition, a coding strategy was designed to set the means for meta-data extraction out from the literature for review. A drafted structured questionnaire will serve as the base for collating the meta-data to produce a database where variables will be queried for the evidence synthesis. This work is expected to inform stakeholders, researchers and policy makers regarding the extent and nature of the existing evidence base, and so serve as a basis by-which specific approaches may be highlighted as potential focal-areas in future.

Plant root angle determines the vertical and horizontal distribution of roots in the soil layer, which further influences the acquisition of phosphorus (P) in topsoil. Large genetic variability for the lateral root angle (root angle) was observed in a linkage mapping population (BnaTNDH population) and an association panel of Brassica napus whether at a low P (LP) or at an optimal P (OP). At LP, the average root angle of both populations became smaller. Nine quantitative trait loci (QTLs) at LP and three QTLs at OP for the root angle and five QTLs for the relative root angle (RRA) were identified by the linkage mapping analysis in the BnaTNDH population. Genome-wide association studies (GWASs) revealed 11 single-nucleotide polymorphisms (SNPs) significantly associated with the root angle at LP (LPRA). The interval of a QTL for LPRA on A06 (qLPRA-A06c) overlapped with the confidence region of the leading SNP (Bn-A06-p14439400) significantly associated with LPRA. In addition, a QTL cluster on chromosome C01 associated with the root angle and the primary root length (PRL) in the “pouch and wick” high-throughput phenotyping (HTP) system, the root P concentration in the agar system, and the seed yield in the field was identified in the BnaTNDH population at LP. A total of 87 genes on A06 and 192 genes on C01 were identified within the confidence interval, and 14 genes related to auxin asymmetric redistribution and root developmental process were predicted to be candidate genes. The identification and functional analyses of these genes affecting LPRA are of benefit to the cultivar selection with optimal root system architecture (RSA) under P deficiency in Brassica napus.

Stoichiometry of leaf macronutrients can provide insight into the tradeoffs between leaf structural and metabolic investments. Structural carbon (C) in cell walls is contained in lignin and polysaccharides (cellulose, hemicellulose, and pectins). Much of leaf calcium (Ca) and a fraction of magnesium (Mg) were further bounded with cell wall pectins. The macronutrients phosphorus (P), potassium (K), and nitrogen (N) are primarily involved in cell metabolic functions. There is limited information on the functional interrelations among leaf C and macronutrients, and the functional dimensions characterizing the leaf structural and metabolic tradeoffs are not widely appreciated. We investigated the relationships between leaf C and macronutrient (N, P, K, Ca, Mg) concentrations in two widespread broad-leaved deciduous woody species Quercus wutaishanica (90 individuals) and Betula platyphylla (47 individuals), and further tested the generality of the observed relationships in 222 woody eudicots from 15 forest ecosystems. In a subsample of 20 broad-leaved species, we also analyzed the relationships among C, Ca, lignin, and pectin concentrations in leaf cell walls. We found a significant leaf C–Ca tradeoff operating within and across species and across ecosystems. This basic relationship was explained by variations in the share of cell wall lignin and pectin investments at the cell scale. The C–Ca tradeoffs were mainly driven by soil pH and mean annual temperature and precipitation, suggesting that leaves were more economically built with less C and more Ca as soil pH increased and at lower temperature and lower precipitation. However, we did not detect consistent patterns among C–N, and C–Mg at different levels of biological organization, suggesting substantial plasticity in N and Mg distribution among cell organelles and cell protoplast and cell wall. We observed two major axes of macronutrient differentiation: the cell-wall structural axis consisting of protein-free C and Ca and the protoplasm metabolic axis consisting of P and K, underscoring the decoupling of structural and metabolic elements inherently linked with cell wall from protoplasm investment strategies. We conclude that the tradeoffs between leaf C and Ca highlight how carbon is allocated to leaf structural function and suggest that this might indicate biogeochemical niche differentiation of species.

Abstract Background There are numerous systems and techniques to measure the growth of plant roots. However, phenotyping large numbers of plant roots for breeding and genetic analyses remains challenging. One major difficulty is to achieve high throughput and resolution at a reasonable cost per plant sample. Here we describe a cost-effective root phenotyping pipeline, on which we perform time and accuracy benchmarking to identify bottlenecks in such pipelines and strategies for their acceleration. Results Our root phenotyping pipeline was assembled with custom software and low cost material and equipment. Results show that sample preparation and handling of samples during screening are the most time consuming task in root phenotyping. Algorithms can be used to speed up the extraction of root traits from image data, but when applied to large numbers of images, there is a trade-off between time of processing the data and errors contained in the database. Conclusions Scaling-up root phenotyping to large numbers of genotypes will require not only automation of sample preparation and sample handling, but also efficient algorithms for error detection for more reliable replacement of manual interventions.

Abstract Selection breeding has played a key role in the improvement of seed yield and quality in oilseed rape (Brassica napus L.). We genotyped Tapidor (European), Ningyou7 (Chinese) and their progenitors with the Brassica 60 K Illumina Infinium SNP array and mapped a total of 29,347 SNP markers onto the reference genome of Darmor-bzh. Identity by descent (IBD) refers to a haplotype segment of a chromosome inherited from a shared common ancestor. IBDs identified on the C subgenome were larger than those on the A subgenome within both the Tapidor and Ningyou7 pedigrees. IBD number and length were greater in the Ningyou7 pedigree than in the Tapidor pedigree. Seventy nine QTLs for flowering time, seed quality and root morphology traits were identified in the IBDs of Tapidor and Ningyou7. Many more candidate genes had been selected within the Ningyou7 pedigree than within the Tapidor pedigree. These results highlight differences in the transfer of favorable gene clusters controlling key traits during selection breeding in Europe and China.

Shoot zinc (Zn) concentration in Brassica oleracea is affected by soil Zn and phosphorus (P) supply. Most problematic is the negative impact of P fertilizers on Zn concentrations in crops, which makes balancing yield and mineral quality challenging. To evaluate early molecular mechanisms involved in the accumulation of large shoot Zn concentrations regardless of the P supply, two B. oleracea accessions differing in root architecture and root exudates were grown hydroponically for two weeks with different combinations of P and Zn supply. Ionome profiling and deep RNA sequencing of roots revealed interactions of P and Zn in planta, without apparent phenotypic effects. In addition, increasing P supply did not reduce tissue Zn concentration. Substantial changes in gene expression in response to different P and/or Zn supplies in roots of both accessions ensured nutritionally sufficient P and Zn uptake. Numerous genes were differentially expressed after changing Zn or P supply and most of them were unique to only one accession, highlighting their different strategies in achieving nutrient sufficiency. Thus, different gene networks responded to the changing P and Zn supply in the two accessions. Additionally, enrichment analysis of gene ontology classes revealed that genes involved in lipid metabolism, response to starvation, and anion transport mechanisms were most responsive to differences in P and Zn supply in both accessions. The results agreed with previously studies demonstrating alterations in P and Zn transport and phospholipid metabolism in response to reduced P and Zn supply. It is anticipated that improved knowledge of genes responsive to P or Zn supply will help illuminate the roles in uptake and accumulation of P and Zn and might identify candidate genes for breeding high-yield-high-Zn brassicas.

Date palm (Phoenix dactylifera) can accumulate as much as 1% silicon (Si), but not much is known about the mechanisms inherent to this process. Here, we investigated in detail the uptake, accumulation and distribution of Si in date palms, and the phylogeny of Si transporter genes in plants. We characterized the PdNIP2 transporter following heterologous expression in Xenopus oocytes and used qPCR to determine the relative expression of Si transporter genes. Silicon accumulation and distribution was investigated by light microscopy, scanning electron microscopy coupled with X-ray microanalysis and Raman microspectroscopy. We proved that PdNIP2-1 codes for a functional Si-permeable protein and demonstrated that PdNIP2 transporter genes were constitutively expressed in date palm. Silicon aggregates/phytoliths were found in specific stegmata cells present in roots, stems and leaves and their surfaces were composed of pure silica. Stegmata were organized on the outer surface of the sclerenchyma bundles or associated with the sclerenchyma of the vascular bundles. Phylogenetic analysis clustered NIP2 transporters of the Arecaceae in a sister position to those of the Poaceae. It is suggested, that Si uptake in date palm is mediated by a constitutively expressed Si influx transporter and accumulated as Si aggregates in stegmata cells abundant in the outer surface of the sclerenchyma bundles (fibers).

Zinc (Zn) is an essential micronutrient for plants and animals, and Zn deficiency is a widespread problem for agricultural production. Although many studies have been performed on biofortification of staple crops with Zn, few studies have focused on forages. Here, the molecular mechanisms of Zn transport in alfalfa (Medicago sativa L.) were investigated following foliar Zn applications. Zinc uptake and redistribution between shoot and root were determined following application of six Zn doses to leaves. Twelve putative genes encoding proteins involved in Zn transport (MsZIP1-7, MsZIF1, MsMTP1, MsYSL1, MsHMA4, and MsNAS1) were identified and changes in their expression following Zn application were quantified using newly designed RT-qPCR assays. These assays are the first designed specifically for alfalfa and resulted in being more efficient than the ones already available for Medicago truncatula (i.e., MtZIP1-7 and MtMTP1). Shoot and root Zn concentration was increased following foliar Zn applications ≥ 0.1 mg plant−1. Increased expression of MsZIP2, MsHMA4, and MsNAS1 in shoots, and of MsZIP2 and MsHMA4 in roots was observed with the largest Zn dose (10 mg Zn plant−1). By contrast, MsZIP3 was downregulated in shoots at Zn doses ≥ 0.1 mg plant−1. Three functional gene modules, involved in Zn uptake by cells, vacuolar Zn sequestration, and Zn redistribution within the plant, were identified. These results will inform genetic engineering strategies aimed at increasing the efficiency of crop Zn biofortification.

Large nitrogen, phosphorus and potassium fertilizer inputs are used in many crop systems. Identifying genetic loci controlling nutrient accumulation may be useful in crop breeding strategies to increase fertilizer use efficiency and reduce financial and environmental costs. Here, variation in leaf nitrate concentration across a diversity population of 383 genotypes of Brassica napus was characterized. Genetic loci controlling variation in leaf nitrate, phosphorus and potassium concentration were then identified through Associative Transcriptomics using single nucleotide polymorphism (SNP) markers and gene expression markers (GEMs). Leaf nitrate concentration varied over 8-fold across the diversity population. A total of 455 SNP markers were associated with leaf nitrate concentration after false-discovery-rate (FDR) correction. In linkage disequilibrium of highly associated markers are a number of known nitrate transporters and sensors, including a gene thought to mediate expression of the major nitrate transporter NRT1.1. Several genes influencing root and root-hair development co-localize with chromosomal regions associated with leaf P concentration. Orthologs of three ABC-transporters involved in suberin synthesis in roots also co-localize with association peaks for both leaf nitrate and phosphorus. Allelic variation at nearby, highly associated SNPs confers large variation in leaf nitrate and phosphorus concentration. A total of five GEMs associated with leaf K concentration after FDR correction including a GEM that corresponds to an auxin-response family protein. Candidate loci, genes and favorable alleles identified here may prove useful in marker-assisted selection strategies to improve fertilizer use efficiency in B. napus.

Calcium (Ca) and magnesium (Mg) are essential plant nutrients and vital for human and animal nutrition. Biofortification of crops has previously been suggested to alleviate widespread human Ca and Mg deficiencies. In this study, new candidate genes influencing the leaf accumulation of Ca and Mg were identified in young Brassica napus plants using associative transcriptomics of ionomics datasets. A total of 247 and 166 SNP markers were associated with leaf Ca and Mg concentration, respectively, after false discovery rate correction and removal of SNPs with low second allele frequency. Gene expression markers at similar positions were also associated with leaf Ca and Mg concentration, including loci on chromosomes A10 and C2, within which lie previously identified transporter genes ACA8 and MGT7. Further candidate genes were selected from seven loci and the mineral composition of whole Arabidopsis thaliana shoots were characterized from lines mutated in orthologous genes. Four and two mutant lines had reduced shoot Ca and Mg concentration, respectively, compared to wild type plants. Three of these mutations were found to have tissue specific effects; notably reduced silique Ca in all three such mutant lines. This knowledge could be applied in targeted breeding, with the possibility of increasing Ca and Mg in plant tissue for improving human and livestock nutrition.

Vitamin and mineral deficiencies are prevalent in human populations throughout the world. Vitamin A deficiency affects hundreds of millions of pre-school age children in low income countries. Fruits of pepper (Capsicum annuum L.) can be a major dietary source of precursors to Vitamin A biosynthesis, such as β-carotene. Recently, pepper breeding programs have introduced the orange-fruited (of) trait of the mutant variety Oranzheva kapiya, which is associated with high fruit β-carotene concentrations, to the mutant variety Albena. In this manuscript, concentrations of β-carotene and mineral elements (magnesium, phosphorus, sulphur, potassium, zinc, calcium, manganese, iron and copper) were compared in fruit from P31, a red-fruited genotype derived from the variety Albena, and M38, a genotype developed by transferring the orange-fruited mutation (of) into Albena. It was observed that fruit from M38 plants had greater β-carotene concentration at both commercial and botanical maturity (4.9 and 52.7 mg / kg fresh weight, respectively) than fruit from P31 plants (2.3 and 30.1 mg / kg fresh weight, respectively). The mutation producing high β-carotene concentrations in pepper fruits had no detrimental effect on the concentrations of mineral elements required for human nutrition.

Many humans lack sufficient zinc (Zn) in their diet for their wellbeing and increasing Zn concentrations in edible produce (biofortification) can mitigate this. Recent efforts have focused on biofortifying staple crops. However, greater Zn concentrations can be achieved in leafy vegetables than in fruits, seeds, or tubers. Brassicas, such as cabbage and broccoli, are widely consumed and might provide an additional means to increase dietary Zn intake. Zinc concentrations in brassicas are limited primarily by Zn phytotoxicity. To assess the limits of Zn biofortification of brassicas, the Zn concentration in a peat:sand (v/v 75:25) medium was manipulated to examine the relationship between shoot Zn concentration and shoot dry weight (DW) and thereby determine the critical shoot Zn concentrations, defined as the shoot Zn concentration at which yield is reduced below 90%. The critical shoot Zn concentration was regarded as the commercial limit to Zn biofortification. Experiments were undertaken over six successive years. A linear relationship between Zn fertiliser application and shoot Zn concentration was observed at low application rates. Critical shoot Zn concentrations ranged from 0.074 to 1.201 mg Zn g−1 DW among cabbage genotypes studied in 2014, and between 0.117 and 1.666 mg Zn g−1 DW among broccoli genotypes studied in 2015–2017. It is concluded that if 5% of the dietary Zn intake of a population is currently delivered through brassicas, then the biofortification of brassicas from 0.057 to > 0.100 mg Zn g−1 DW through the application of Zn fertilisers could increase dietary Zn intake substantially.

Excessive N fertilization results in low N-use efficiency (NUE) without any yield benefits and can have profound, long-term environmental consequences including soil acidification, N leaching and increased production of greenhouse gases. Improving NUE in crop production has been a longstanding, worldwide challenge. A crucial strategy to improve NUE is to enhance N uptake by roots. Taking maize as a model crop, we have compared root dry weight (RDW), root/shoot biomass ratio (R/S), and NUE of maize grown in the field in China and in western countries using data from 106 studies published since 1959. Detailed analysis revealed that the differences in the RDW and R/S of maize at silking in China and the western countries were not derived from variations in climate, geography, and stress factors. Instead, NUE was positively correlated with R/S and RDW; R/S and NUE of maize varieties grown in western countries were significantly greater than those grown in China. We then testified this conclusion by conducting field trials with representative maize hybrids in China (ZD958 and XY335) and the US (P32D79). We found that US P32D79 had a better root architecture for increased N uptake and removed more mineral N than Chinese cultivars from the 0-60 cm soil profile. Reported data and our field results demonstrate that a large and deep root, with an appropriate architecture and higher stress tolerance (higher plant density, drought and N deficiency), underlies high NUE in maize production. We recommend breeding for these traits to reduce the N-fertilizer use and thus N-leaching in maize production and paying more attention to increase tolerance to stresses in China.

Larger, and deeper, root systems of new maize varieties, compared to older varieties, are thought to have enabled improved acquisition of soil resources and, consequently, greater grain yields. To compare the spatial distributions of the root systems of new and old maize varieties and their relationships with spatial variations in soil concentrations of available nitrogen (N), phosphorus (P) and potassium (K), two years of field experiments were performed using six Chinese maize varieties released in different eras. Vertical distributions of roots, and available N, P and K in the 0-60 cm soil profile were determined in excavated soil monoliths at silking and maturity. The results demonstrated that new maize varieties had larger root dry weight, higher grain yield and greater nutrient accumulation than older varieties. All varieties had similar total root length and vertical root distribution at silking, but newer varieties maintained greater total root length and had more roots in the 30-60 cm soil layers at maturity. The spatial variation of soil mineral N (Nmin) in each soil horizon was larger than that of Olsen-P and ammonium-acetate-extractable K, and was inversely correlated with root length density (RLD), especially in the 0-20 cm soil layer. It was concluded that greater acquisition of mineral nutrients and higher yields of newer varieties were associated with greater total root length at maturity. The negative relationship between RLD and soil Nmin at harvest for all varieties suggests the importance of the spatial distribution of the root system for N uptake by maize.

Currently, the UK has a high self-sufficiency rate in barley production. This paper assessed the effects of projected climate and land use changes on feed barley production and, consequently, on meat supply in the UK from the 2030s to the 2050s. Total barley production under projected land use and climate changes ranged from 4.6 million tons in the 2030s to 9.0 million tons in the 2050s. From these, the projected feed barley supply ranged from approximately 2.3 to 4.6 million tons from the 2030s to the 2050s, respectively. The results indicate that while UK spring barley production will thrive under, and benefit from climate change, total land area allocated to barley production will ultimately determine self-sufficiency. Without expansion in the area of land and/or further significant increases in yields, the UK may face large deficits in domestic feed barley production and, for that matter, meat supply in the future. Hence, agricultural and food security policy needs to consider, principally, the effect of agricultural land use change on key crops, such as barley. Even though the UK can import feed barley or meat to address the deficits observed in this study, the question that needs to be addressed is where all that import will come from.

One definition of food security is having sufficient, safe, and nutritious food to meet dietary needs. This paper highlights the role of plant mineral nutrition in food production, delivering of essential mineral elements to the human diet, and preventing harmful mineral elements entering the food chain. To maximise crop production, the gap between actual and potential yield must be addressed. This gap is 15–95% of potential yield, depending on the crop and agricultural system. Current research in plant mineral nutrition aims to develop appropriate agronomy and improved genotypes, for both infertile and productive soils, that allow inorganic and organic fertilisers to be utilised more efficiently. Mineral malnutrition affects two-thirds of the world's population. It can be addressed by the application of fertilisers, soil amelioration, and the development of genotypes that accumulate greater concentrations of mineral elements lacking in human diets in their edible tissues. Excessive concentrations of harmful mineral elements also compromise crop production and human health. To reduce the entry of these elements into the food chain, strict quality requirements for fertilisers might be enforced, agronomic strategies employed to reduce their phytoavailability, and crop genotypes developed that do not accumulate high concentrations of these elements in edible tissues.

Zinc (Zn) and cadmium (Cd) hyperaccumulation may have evolved twice in the Brassicaceae, in Arabidopsis halleri and in the Noccaea genus. Tandem gene duplication and deregulated expression of the Zn transporter, HMA4, has previously been linked to Zn/Cd hyperaccumulation in A. halleri. Here, we tested the hypothesis that tandem duplication and deregulation of HMA4 expression also occurs in Noccaea.A Noccaea caerulescens genomic library was generated, containing 36,864 fosmid pCC1FOS™ clones with insert sizes ∼20-40 kbp, and screened with a PCR-generated HMA4 genomic probe. Gene copy number within the genome was estimated through DNA fingerprinting and pooled fosmid pyrosequencing. Gene copy numbers within individual clones was determined by PCR analyses with novel locus specific primers. Entire fosmids were then sequenced individually and reads equivalent to 20-fold coverage were assembled to generate complete whole contigs.Four tandem HMA4 repeats were identified in a contiguous sequence of 101,480 bp based on sequence overlap identities. These were flanked by regions syntenous with up and downstream regions of AtHMA4 in Arabidopsis thaliana. Promoter-reporter β-glucuronidase (GUS) fusion analysis of a NcHMA4 in A. thaliana revealed deregulated expression in roots and shoots, analogous to AhHMA4 promoters, but distinct from AtHMA4 expression which localised to the root vascular tissue.This remarkable consistency in tandem duplication and deregulated expression of metal transport genes between N. caerulescens and A. halleri, which last shared a common ancestor >40 mya, provides intriguing evidence that parallel evolutionary pathways may underlie Zn/Cd hyperaccumulation in Brassicaceae.

BACKGROUND: There are compelling economic and environmental reasons to reduce our reliance on inorganic phosphate (Pi) fertilisers. Better management of Pi fertiliser applications is one option to improve the efficiency of Pi fertiliser use, whilst maintaining crop yields. Application rates of Pi fertilisers are traditionally determined from analyses of soil or plant tissues. Alternatively, diagnostic genes with altered expression under Pi limiting conditions that suggest a physiological requirement for Pi fertilisation, could be used to manage Pifertiliser applications, and might be more precise than indirect measurements of soil or tissue samples. RESULTS: We grew potato (Solanum tuberosum L.) plants hydroponically, under glasshouse conditions, to control their nutrient status accurately. Samples of total leaf RNA taken periodically after Pi was removed from the nutrient solution were labelled and hybridised to potato oligonucleotide arrays. A total of 1,659 genes were significantly differentially expressed following Pi withdrawal. These included genes that encode proteins involved in lipid, protein, and carbohydrate metabolism, characteristic of Pi deficient leaves and included potential novel roles for genes encoding patatin like proteins in potatoes. The array data were analysed using a support vector machine algorithm to identify groups of genes that could predict the Pi status of the crop. These groups of diagnostic genes were tested using field grown potatoes that had either been fertilised or unfertilised. A group of 200 genes could correctly predict the Pi status of field grown potatoes. CONCLUSIONS: This paper provides a proof-of-concept demonstration for using microarrays and class prediction tools to predict the Pi status of a field grown potato crop. There is potential to develop this technology for other biotic and abiotic stresses in field grown crops. Ultimately, a better understanding of crop stresses may improve our management of the crop, improving the sustainability of agriculture.

Affymetrix GeneChip® arrays are used widely to study transcriptional changes in response to developmental and environmental stimuli. GeneChip® arrays comprise multiple 25-mer oligonucleotide probes per gene and retain certain advantages over direct sequencing. For plants, there are several public GeneChip® arrays whose probes are localised primarily in 3' exons. Plant whole-transcript (WT) GeneChip® arrays are not yet publicly available, although WT resolution is needed to study complex crop genomes such as Brassica, which are typified by segmental duplications containing paralogous genes and/or allopolyploidy. Available sequence data were sampled from the Brassica A and C genomes, and 142,997 gene models identified. The assembled gene models were then used to establish a comprehensive public WT exon array for transcriptomics studies. The Affymetrix GeneChip® Brassica Exon 1.0 ST Array is a 5 µM feature size array, containing 2.4 million 25-base oligonucleotide probes representing 135,201 gene models, with 15 probes per gene distributed among exons. Discrimination of the gene models was based on an E-value cut-off of 1E(-5), with ≤98% sequence identity. The 135 k Brassica Exon Array was validated by quantifying transcriptome differences between leaf and root tissue from a reference Brassica rapa line (R-o-18), and categorisation by Gene Ontologies (GO) based on gene orthology with Arabidopsis thaliana. Technical validation involved comparison of the exon array with a 60-mer array platform using the same starting RNA samples. The 135 k Brassica Exon Array is a robust platform. All data relating to the array design and probe identities are available in the public domain and are curated within the BrassEnsembl genome viewer at http://www.brassica.info/BrassEnsembl/index.html.