A comprehensive analysis of root morphological changes and nitrogen allocation in maize in response to low nitrogen stress

Seedling root system adaptation to water availability during maize domestication and global expansion

The maize root system has been reshaped by indirect selection during global adaptation to new agricultural environments. In this study, we characterized the root systems of more than 9,000 global maize accessions and its wild relatives, defining the geographical signature and genomic basis of variation in seminal root number. We demonstrate that seminal root number has increased during maize domestication followed by a decrease in response to limited water availability in locally adapted varieties. By combining environmental and phenotypic association analyses with linkage mapping, we identified genes linking environmental variation and seminal root number. Functional characterization of the transcription factor ZmHb77 and in silico root modeling provides evidence that reshaping root system architecture by reducing the number of seminal roots and promoting lateral root density is beneficial for the resilience of maize seedlings to drought.

Preliminary study on the diagnosis of NK stress based on the puncture mechanical characteristics of cucumber stem

To investigate the relationship between stem puncture mechanical characteristics and NK stress diagnosis, the microstructure, surface morphology, cellulose and lignin content, puncture mechanical characteristics, and epidermal cell morphology of cucumber stems were measured herein. The results indicated that the middle stem, which had a diameter of approximately 7000 μm, was more suitable for puncturing due to its lower amount of epidermal hair, and its gradual regularity in shape. Further, the cucumber stems were protected from puncture damage due to their ability to rapidly heal within 25 h.. The epidermal penetration of the cucumber stems increased with the increase in cellulose and lignin, though cellulose played a more decisive role. The epidermal break distance increased with an increase in N application and decreased with an increase in K+ application, but the change in intercellular space caused by K+ supply was the most critical factor affecting the epidermal break distance. In addition, a decrease in K+ concentration led to a decrease in epidermal brittleness, whereas the factors affecting epidermal toughness were more complex. Finally, we found that although the detection of epidermal brittleness and toughness on nutrient stress was poor under certain treatment, the puncture mechanical characteristics of the stem still had a significant indicative effect on N application rate. Therefore, elucidating of the relationship between the puncture mechanical characteristics of the stems and crop nutritional stress is not only beneficial for promoting stem stress physiology research but also for designing on-site nutritional testing equipment in the future.

Integrated physiological, biochemical, and transcriptomics analyses reveal the underlying mechanisms of high nitrogen use efficiency of black sesame

Cultivating high nitrogen use efficient varieties is a sustainable solution to mitigating adverse effects on the environment caused by excessive nitrogen fertilizer application. However, in sesame, although immoderate nitrogen fertilizers are used to promote yield, the molecular basis of high nitrogen use efficiency (NUE) is largely unknown. Hence, this study aimed to identify high NUE black sesame variety and dissect the underlying physiological and molecular mechanisms. To achieve this, seventeen seedling traits of 30 black sesame varieties were evaluated under low nitrogen (LN) and high nitrogen (HN) conditions. Dry matter accumulation, root parameters, shoot nitrogen accumulation, and chlorophyll content are important factors for evaluating the NUE of sesame genotypes. The variety 17-156 was identified as the most efficient for N utilization. Comparative physiological and transcriptomics analyses revealed that 17-156 possesses a sophisticated nitrogen metabolizing machinery to uptake and assimilate higher quantities of inorganic nitrogen into amino acids and proteins, and simultaneously improving carbon metabolism and growth. Specifically, the total nitrogen and soluble protein contents significantly increased with the increase in nitrogen concentrations. Many important genes, including nitrate transporters (NPFs), amino acid metabolism-related (GS, GOGAT, GDH, etc.), phytohormone-related, and transcription factors, were significantly up-regulated in 17-156 under HN condition. In addition, 38 potential candidate genes were identified for future studies toward improving sesame's NUE. These findings offer valuable resources for deciphering the regulatory network of nitrogen metabolism and developing sesame cultivars with improved NUE.

Physiological and Transcriptomic Analysis Provides Insights into Low Nitrogen Stress in Foxtail Millet (Setaria italica L.)

Foxtail millet (Setaria italica (L.) P. Beauv) is an important food and forage crop that is well adapted to nutrient-poor soils. However, our understanding of how different LN-tolerant foxtail millet varieties adapt to long-term low nitrogen (LN) stress at the physiological and molecular levels remains limited. In this study, two foxtail millet varieties with contrasting LN tolerance properties were investigated through analyses of physiological parameters and transcriptomics. The physiological results indicate that JG20 (high tolerance to LN) exhibited superior biomass accumulation both in its shoots and roots, and higher nitrogen content, soluble sugar concentration, soluble protein concentration, zeatin concentration in shoot, and lower soluble sugar and soluble protein concentration in its roots compared to JG22 (sensitive to LN) under LN, this indicated that the LN-tolerant foxtail millet variety can allocate more functional substance to its shoots to sustain aboveground growth and maintain high root activity by utilizing low soluble sugar and protein under LN conditions. In the transcriptomics analysis, JG20 exhibited a greater number of differentially expressed genes (DEGs) compared to JG22 in both its shoots and roots in response to LN stress. These LN-responsive genes were enriched in glycolysis metabolism, photosynthesis, hormone metabolism, and nitrogen metabolism. Furthermore, in the shoots, the glutamine synthetase gene SiGS5, chlorophyll apoprotein of photosystem II gene SiPsbQ, ATP synthase subunit gene Sib, zeatin synthesis genes SiAHP1, and aldose 1-epimerase gene SiAEP, and, in the roots, the high-affinity nitrate transporter genes SiNRT2.3, SiNRT2.4, glutamate synthase gene SiGOGAT2, fructose-bisphosphate aldolase gene SiFBA5, were important genes involved in the LN tolerance of the foxtail millet variety. Hence, our study implies that the identified genes and metabolic pathways contribute valuable insights into the mechanisms underlying LN tolerance in foxtail millet.

Varietal responses of root characteristics to low nitrogen application explain the differing nitrogen uptake and grain yield in two rice varieties

Rice root characteristics are tightly associated with high-efficient nitrogen uptake. To understand the relationship of root plastic responses with nitrogen uptake when reducing nitrogen application for green rice production, a hydroponic experiment and a soil pot experiment were conducted under high (HN) and low (LN) nitrogen applications, using two rice (Oryza sativa L.) varieties, NK57 and YD6, three nitrogen absorption traits (total nitrogen accumulation, net NH4 + influx on root surface, nitrogen uptake via apoplasmic pathway) and root characteristics were investigated. In comparison with HN, LN significantly reduced nitrogen absorption and grain yield in both varieties. Concomitantly, there was a decrease in total root length, root surface area, root number, root volume, and root cortical area under LN, while single root length, root aerenchyma area, and root lignin content increased. The expression of OsAMT1;1 and OsAMT1;2 down-regulated in both varieties. The findings revealed that YD6 had smaller reduction degree for the three nitrogen absorption traits and grain yield, accompanied by smaller reduction degree in total root length, root surface area, root cortical area, and expression of the two genes under LN. These root characteristics were significantly and positively correlated with the three nitrogen absorption traits and grain yield, especially under LN. These results indicate that a large root system, lower reduction degree in several root characters, and high expression of OsAMT genes in YD6 explains its high nitrogen accumulation and grain yield under reduced nitrogen application. The study may provide rationale for developing varieties with low nitrogen fertilizer requirements for enabling green rice production.

An Integrated Analysis of Metabolome, Transcriptome, and Physiology Revealed the Molecular and Physiological Response of Citrus sinensis Roots to Prolonged Nitrogen Deficiency

Citrus sinensis seedlings were supplied with a nutrient solution containing 15 (control) or 0 (nitrogen (N) deficiency) mM N for 10 weeks. Extensive metabolic and gene reprogramming occurred in 0 mM N-treated roots (RN0) to cope with N deficiency, including: (a) enhancing the ability to keep phosphate homeostasis by elevating the abundances of metabolites containing phosphorus and the compartmentation of phosphate in plastids, and/or downregulating low-phosphate-inducible genes; (b) improving the ability to keep N homeostasis by lowering the levels of metabolites containing N but not phosphorus, upregulating N compound degradation, the root/shoot ratio, and the expression of genes involved in N uptake, and resulting in transitions from N-rich alkaloids to carbon (C)-rich phenylpropanoids and phenolic compounds (excluding indole alkaloids) and from N-rich amino acids to C-rich carbohydrates and organic acids; (c) upregulating the ability to maintain energy homeostasis by increasing energy production (tricarboxylic acid cycle, glycolysis/gluconeogenesis, oxidative phosphorylation, and ATP biosynthetic process) and decreasing energy utilization for amino acid and protein biosynthesis and new root building; (d) elevating the transmembrane transport of metabolites, thus enhancing the remobilization and recycling of useful compounds; and (e) activating protein processing in the endoplasmic reticulum. RN0 had a higher ability to detoxify reactive oxygen species and aldehydes, thus protecting RN0 against oxidative injury and delaying root senescence.

A temporal analysis and response to nitrate availability of 3D root system architecture in diverse pennycress (Thlaspi arvense L.) accessions

Introduction

Roots have a central role in plant resource capture and are the interface between the plant and the soil that affect multiple ecosystem processes. Field pennycress (Thlaspi arvense L.) is a diploid annual cover crop species that has potential utility for reducing soil erosion and nutrient losses; and has rich seeds (30-35% oil) amenable to biofuel production and as a protein animal feed. The objective of this research was to (1) precisely characterize root system architecture and development, (2) understand plastic responses of pennycress roots to nitrate nutrition, (3) and determine genotypic variance available in root development and nitrate plasticity.

Methods

Using a root imaging and analysis pipeline, the 4D architecture of the pennycress root system was characterized under four nitrate regimes, ranging from zero to high nitrate concentrations. These measurements were taken at four time points (days 5, 9, 13, and 17 after sowing).

Results

Significant nitrate condition response and genotype interactions were identified for many root traits, with the greatest impact observed on lateral root traits. In trace nitrate conditions, a greater lateral root count, length, density, and a steeper lateral root angle was observed compared to high nitrate conditions. Additionally, genotype-by-nitrate condition interaction was observed for root width, width:depth ratio, mean lateral root length, and lateral root density.

Discussion

These findings illustrate root trait variance among pennycress accessions. These traits could serve as targets for breeding programs aimed at developing improved cover crops that are responsive to nitrate, leading to enhanced productivity, resilience, and ecosystem service.

Comparative transcriptome and genome analysis unravels the response of Tatary buckwheat root to nitrogen deficiency

Tartary buckwheat (Fagopyrum tataricum Garetn.), a dicotyledonous herbaceous crop, has good adaptation to low nitrogen (LN) condition. The plasticity of roots drives the adaption of Tartary buckwheat under LN, but the detailed mechanism behind the response of TB roots to LN remains unclear. In this study, the molecular mechanism of two Tartary buckwheat genotypes' roots with contrasting sensitivity in response to LN was investigated by integrating physiological, transcriptome and whole-genome re-sequencing analysis. LN improved primary and lateral root growth of LN-sensitive genotype, whereas the roots of LN-insensitive genotype showed no response to LN. 2, 661 LN-responsive differentially expressed genes (DEGs) were identified by transcriptome analysis. Of these genes, 17 N transport and assimilation-related and 29 hormone biosynthesis and signaling genes showed response to LN, and they may play important role in Tartary buckwheat root development under LN. The flavonoid biosynthetic genes' expression was improved by LN, and their transcriptional regulations mediated by MYB and bHLH were analyzed. 78 transcription factors, 124 small secreted peptides and 38 receptor-like protein kinases encoding genes involved in LN response. 438 genes were differentially expressed between LN-sensitive and LN-insensitive genotypes by comparing their transcriptome, including 176 LN-responsive DEGs. Furthermore, nine key LN-responsive genes with sequence variation were identified, including FtNRT2.4, FtNPF2.6 and FtMYB1R1. This paper provided useful information on the response and adaptation of Tartary buckwheat root to LN, and the candidate genes for breeding Tartary buckwheat with high N use efficiency were identified.

Auxin efflux carrier ZmPIN1a modulates auxin reallocation involved in nitrate-mediated root formation

BACKGROUND

Auxin plays a crucial role in nitrate (NO₃^-)-mediated root architecture, and it is still unclear that if NO₃^- supply modulates auxin reallocation for regulating root formation in maize (Zea mays L.). This study was conducted to investigate the role of auxin efflux carrier ZmPIN1a in the root formation in response to NO₃^- supply.

RESULTS

Low NO₃^- (LN) promoted primary root (PR) elongation, while repressed the development of lateral root primordia (LRP) and total root length. LN modulated auxin levels and polar transport and regulated the expression of auxin-responsive and -signaling genes in roots. Moreover, LN up-regulated the expression level of ZmPIN1a, and overexpression of ZmPIN1a enhanced IAA efflux and accumulation in PR tip, while repressed IAA accumulation in LRP initiation zone, which consequently induced LN-mediated PR elongation and LR inhibition. The inhibition rate of PR length, LRP density and number of ZmPIN1a-OE plants was higher than that of wild-type plants after auxin transport inhibitor NPA treatment under NN and LN conditions, and the degree of inhibition of root growth in ZmPIN1a-OE plants was more obvious under LN condition.

CONCLUSION

These findings suggest that ZmPIN1a was involved in modulating auxin levels and transport to alter NO₃^--mediated root formation in maize.

Maize Breeding for Low Nitrogen Inputs in Agriculture: Mechanisms Underlying the Tolerance to the Abiotic Stress

Nitrogen (N) is essential for sustaining life on Earth and plays a vital role in plant growth and thus agricultural production. The excessive use of N fertilizers not only harms the economy, but also the environment. In the context of the environmental impacts caused by agriculture, global maize improvement programs aim to develop cultivars with high N-use efficiency (NUE) to reduce the use of N fertilizers. Since N is highly mobile in plants, NUE is related to numerous little-known morphophysiological and molecular mechanisms. In this review paper we present an overview of the morpho-physiological adaptations of shoot and root, molecular mechanisms involved in plant response to low nitrogen environment, and the genetic effects involved in the control of key traits for NUE. Some studies show that the efficiency of cultivars growing under low N is related to deep root architecture, more lateral roots (LR), and sparser branching of LR, resulting in lower metabolic costs. The NUE cultivars also exhibit more efficient photosynthesis, which affects plant growth under suboptimal nitrogen conditions. In this sense, obtaining superior genotypes for NUE can be achieved with the exploitation of heterosis, as non-additive effects are more important in the expression of traits associated with NUE.

Genome-wide dissection of changes in maize root system architecture during modern breeding

Appropriate root system architecture (RSA) can improve maize yields in densely planted fields, but little is known about its genetic basis in maize. Here we performed root phenotyping of 14,301 field-grown plants from an association mapping panel to study the genetic architecture of maize RSA. A genome-wide association study identified 81 high-confidence RSA-associated candidate genes and revealed that 28 (24.3%) of known root-related genes were selected during maize domestication and improvement. We found that modern maize breeding has selected for a steeply angled root system. Favourable alleles related to steep root system angle have continuously accumulated over the course of modern breeding, and our data pinpoint the root-related genes that have been selected in different breeding eras. We confirm that two auxin-related genes, ZmRSA3.1 and ZmRSA3.2, contribute to the regulation of root angle and depth in maize. Our genome-wide identification of RSA-associated genes provides new strategies and genetic resources for breeding maize suitable for high-density planting.

Plant nitrogen availability and crosstalk with phytohormones signallings and their biotechnology breeding application in crops

Nitrogen (N), one of the most important nutrients, limits plant growth and crop yields in sustainable agriculture system, in which phytohormones are known to play essential roles in N availability. Hence, it is not surprising that massive studies about the crosstalk between N and phytohormones have been constantly emerging. In this review, with the intellectual landscape of N and phytohormones crosstalk provided by the bibliometric analysis, we trace the research story of best-known crosstalk between N and various phytohormones over the last 20 years. Then, we discuss how N regulates various phytohormones biosynthesis and transport in plants. In reverse, we also summarize how phytohormones signallings modulate root system architecture (RSA) in response to N availability. Besides, we expand to outline how phytohormones signallings regulate uptake, transport, and assimilation of N in plants. Further, we conclude advanced biotechnology strategies, explain their application, and provide potential phytohormones-regulated N use efficiency (NUE) targets in crops. Collectively, this review provides not only a better understanding on the recent progress of crosstalk between N and phytohormones, but also targeted strategies for improvement of NUE to increase crop yields in future biotechnology breeding of crops.

Variation in morpho-physiological and metabolic responses to low nitrogen stress across the sorghum association panel

BACKGROUND

Access to biologically available nitrogen is a key constraint on plant growth in both natural and agricultural settings. Variation in tolerance to nitrogen deficit stress and productivity in nitrogen limited conditions exists both within and between plant species. However, our understanding of changes in different phenotypes under long term low nitrogen stress and their impact on important agronomic traits, such as yield, is still limited.

RESULTS

Here we quantified variation in the metabolic, physiological, and morphological responses of a sorghum association panel assembled to represent global genetic diversity to long term, nitrogen deficit stress and the relationship of these responses to grain yield under both conditions. Grain yield exhibits substantial genotype by environment interaction while many other morphological and physiological traits exhibited consistent responses to nitrogen stress across the population. Large scale nontargeted metabolic profiling for a subset of lines in both conditions identified a range of metabolic responses to long term nitrogen deficit stress. Several metabolites were associated with yield under high and low nitrogen conditions.

CONCLUSION

Our results highlight that grain yield in sorghum, unlike many morpho-physiological traits, exhibits substantial variability of genotype specific responses to long term low severity nitrogen deficit stress. Metabolic response to long term nitrogen stress shown higher proportion of variability explained by genotype specific responses than did morpho-pysiological traits and several metabolites were correlated with yield. This suggest, that it might be possible to build predictive models using metabolite abundance to estimate which sorghum genotypes will exhibit greater or lesser decreases in yield in response to nitrogen deficit, however further research needs to be done to evaluate such model.

Lateral root elongation enhances nitrogen-use efficiency in maize genotypes at the seedling stage

BACKGROUND

Maize plants show great variation in root morphological response to nitrogen (N) deficit, and such alterations often determine N-use efficiency (NUE) plants. This study assessed genotypic variation in root morphology and NUE in selected 20 maize genotypes with contrasting root system size grown in a semi-hydroponic phenotyping system for 38 days under control (4 mmol L^-1 NO₃ ^- ) and low N (LN) (40 μmol L^-1 ) for 38 days after transplanting.

RESULTS

Maize genotypes exhibited different responses to LN stress in each of the 28 measured shoot and root traits. The 20 genotypes were assigned into one of the three groups: N-efficient (eight genotypes), medium (four genotypes), and N-inefficient (eight genotypes), based on shoot dry weight ratio (the ratio of shoot dry weight at LN and control) ± one standard error. In response to LN stress, the N-inefficient genotypes had significant reduction in biomass production by ~58% in shoots and ~64% in roots, while the N-efficient genotypes maintained their biomass. Under LN supply N-efficient genotypes showed a plasticity response that would result in both sparse lateral branching and increased root elongation as a whole or at each growth strata, and N efficiency positively correlated with lateral or axial root elongation and root elongation at different depths.

CONCLUTSION

The total lateral root length was the main contributor to the improved N foraging and utilization in maize under LN conditions, followed by axial root length. Total lateral root length can be considered in breeding programs for producing maize cultivars with high NUE at the early seedling stage. © 2022 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

LjAMT2;2 Promotes Ammonium Nitrogen Transport during Arbuscular Mycorrhizal Fungi Symbiosis in Lotus japonicus

Arbuscular mycorrhizal fungi (AMF) are important symbiotic microorganisms in soil that engage in symbiotic relationships with legumes, resulting in mycorrhizal symbiosis. Establishment of strong symbiotic relationships between AMF and legumes promotes the absorption of nitrogen by plants. Ammonium nitrogen can be directly utilised by plants following ammonium transport, but there are few reports on ammonium transporters (AMTs) promoting ammonium nitrogen transport during AM symbiosis. Lotus japonicus is a typical legume model plant that hosts AMF. In this study, we analysed the characteristics of the Lotus japonicus ammonium transporter LjAMT2;2, and found that it is a typical ammonium transporter with mycorrhizal-induced and ammonium nitrogen transport-related cis-acting elements in its promoter region. LjAMT2;2 facilitated ammonium transfer in yeast mutant supplement experiments. In the presence of different nitrogen concentrations, the LjAMT2;2 gene was significantly upregulated following inoculation with AMF, and induced by low nitrogen. Overexpression of LjAMT2;2 increased the absorption of ammonium nitrogen, resulting in doubling of nitrogen content in leaves and roots, thus alleviating nitrogen stress and promoting plant growth.

Foxtail millet [Setaria italica (L.) Beauv.] over-accumulates ammonium under low nitrogen supply

Nitrogen (N) deficiency is a primary limiting factor for crop production worldwide. Previously, we reported root system architectural modifications of hydroponically cultured foxtail millet [Setaria italica (L.) Beauv.] to facilitate N translocation under N limitation. Here, we investigated foxtail millet for its shoot adaptation to low N in terms of internal N regulation under hydroponic culture. The results of this study revealed that the shoot N and nitrate (NO₃^-) concentrations significantly declined as compared to control (CK); however, the shoot over-accumulated ammonium (NH₄⁺) under low N (LN). N shortage resulted in down-regulation of expressions of SiPetA, SiccsA, SipsbA, SirpoB, SipsaA, SiatpA, Sirps16, and SiPEPC which, undermined chloroplast functioning and CO₂ assimilation for the provision of carbon skeleton. Carbon deficiency and lower activities of GS decelerated ammonia assimilation and led to over-accumulation of NH₄⁺ in the LN-shoot, as indicated by lower concentrations of total amino acids. Thus, enhanced GOGAT activity was to assimilate NH₄⁺ while, those of catalase (CAT), superoxide dismutase (SOD) and peroxidase (POD) were to scavenge reactive oxygen species (ROS) of NH₄⁺ toxicity framework. The weakened chloroplast factory eventually minimized photosynthesis and reduced dry mass of the LN shoot. Such regulation of N by the shoot, perhaps, resurrected physiological functions which maintained internal mineral status under nitrogen limitation in foxtail millet.

Adaptive responses of carbon and nitrogen metabolisms to nitrogen-deficiency in Citrus sinensis seedlings

BACKGROUND

In China, nitrogen (N)-deficiency often occurs in Citrus orchards, which is one of the main causes of yield loss and fruit quality decline. Little information is known about the adaptive responses of Citrus carbon (C) and N metabolisms to N-deficiency. Seedlings of 'Xuegan' (Citrus sinensis (L.) Osbeck) were supplied with nutrient solution at an N concentration of 0 (N-deficiency), 5, 10, 15 or 20 mM for 10 weeks. Thereafter, we examined the effects of N supply on the levels of C and N in roots, stems and leaves, and the levels of organic acids, nonstructural carbohydrates, NH₄⁺-N, NO₃^--N, total soluble proteins, free amino acids (FAAs) and derivatives (FAADs), and the activities of key enzymes related to N assimilation and organic acid metabolism in roots and leaves.

RESULTS

N-deficiency elevated sucrose export from leaves to roots, C and N distributions in roots and C/N ratio in roots, stems and leaves, thus enhancing root dry weight/shoot dry weight ratio and N use efficiency. N-deficient leaves displayed decreased accumulation of starch and total nonstructural carbohydrates (TNC) and increased sucrose/starch ratio as well as a partitioning trend of assimilated C toward to sucrose, but N-deficient roots displayed elevated accumulation of starch and TNC and reduced sucrose/starch ratio as well as a partitioning trend of assimilated C toward to starch. N-deficiency reduced the concentrations of most FAADs and the ratios of total FAADs (TFAADs)/N in leaves and roots. N-deficiency reduced the demand for C skeleton precursors for amino acid biosynthesis, thus lowering TFAADs/C ratio in leaves and roots. N-deficiency increased (decreased) the relative amounts of C-rich (N-rich) FAADs, thus increasing the molar ratio of C/N in TFAADs in leaves and roots.

CONCLUSIONS

Our findings corroborated our hypothesis that C and N metabolisms displayed adaptive responses to N-deficiency in C. sinensis seedlings, and that some differences existed between roots and leaves in N-deficiency-induced alterations of and C and N metabolisms.

Differential Responses of Wheat (Triticum aestivum L.) and Cotton (Gossypium hirsutum L.) to Nitrogen Deficiency in the Root Morpho-Physiological Characteristics and Potential MicroRNA-Mediated Mechanisms

Understanding the mechanism of crop response to nitrogen (N) deficiency is very important for developing sustainable agriculture. In addition, it is unclear if the microRNA-mediated mechanism related to root growth complies with a common mechanism in monocots and dicots under N deficiency. Therefore, the root morpho-physiological characteristics and microRNA-mediated mechanisms were studied under N deficiency in wheat (Triticum aestivum L.) and cotton (Gossypium hirsutum L.). For both crops, shoot dry weight, plant dry weight and total leaf area as well as some physiological traits, i.e., the oxygen consuming rate in leaf and root, the performance index based on light energy absorption were significantly decreased after 8 days of N deficiency. Although N deficiency did not significantly impact the root biomass, an obvious change on the root morphological traits was observed in both wheat and cotton. After 8 days of treatment with N deficiency, the total root length, root surface area, root volume of both crops showed an opposite trend with significantly decreasing in wheat but significantly increasing in cotton, while the lateral root density was significantly increased in wheat but significantly decreased in cotton. At the same time, the seminal root length in wheat and the primary root length in cotton were increased after 8 days of N deficiency treatment. Additionally, the two crops had different root regulatory mechanisms of microRNAs (miRNAs) to N deficiency. In wheat, the expressions of miR167, miR319, miR390, miR827, miR847, and miR165/166 were induced by N treatment; these miRNAs inhibited the total root growth but promoted the seminal roots growth and lateral root formation to tolerate N deficiency. In cotton, the expressions of miR156, miR167, miR171, miR172, miR390, miR396 were induced and the expressions of miR162 and miR393 were inhibited; which contributed to increasing in the total root length and primary root growth and to decreasing in the lateral root formation to adapt the N deficiency. In conclusion, N deficiency significantly affected the morpho-physiological characteristics of roots that were regulated by miRNAs, but the miRNA-mediated mechanisms were different in wheat and cotton.

Comparative Transcriptome Analysis Reveals Common and Developmental Stage-Specific Genes That Respond to Low Nitrogen in Maize Leaves

A growing leaf can be divided into three sections: division zone, elongation zone, and maturation zone. In previous studies, low nitrogen (LN) inhibited maize growth and development, especially leaf growth; however, the gene expression in response to LN in different regions in leaf were not clear. Here, using hydroponics and a transcriptome approach, we systematically analyzed the molecular responses of those zones and differentially expressed genes (DEG) in response to LN supply. Developmental stage-specific genes (SGs) were highly stage-specific and involved in distinct biological processes. SGs from division (SGs–DZ) and elongation zones (SGs–EZ) were more related to developmentally dependent processes, whereas SGs of the maturation zone (SGs–MZ) were more related to metabolic processes. The common genes (CGs) were overrepresented in carbon and N metabolism, suggesting that rebalancing carbon and N metabolism in maize leaves under LN condition was independent of developmental stage. Coexpression modules (CMs) were also constructed in our experiment and a total of eight CMs were detected. Most of SGs–DZ and SGs–EZ were classified into a set termed CM turquoise, which was mainly enriched in ribosome and DNA replication, whereas several genes from SGs–MZ and CGs were clustered into CM blue, which mainly focused on photosynthesis and carbon metabolism. Finally, a comprehensive coexpression network was extracted from CM blue, and several maize CONSTANS-LIKE(ZmCOL) genes seemed to participate in regulating photosynthesis in maize leaves under LN condition in a developmental stage-specific manner. With this study, we uncovered the LN-responsive CGs and SGs that are important for promoting plant growth and development under insufficient nitrogen supply.

Phenotypic Acclimation of Maize Plants Grown under S Deprivation and Implications to Sulfur and Iron Allocation Dynamics

The aim of this work was to study maize root phenotype under sulfur deficiency stress towards revealing potential correlations between the altered phenotypic traits and the corresponding dry mass, sulfur, and iron allocation within plants at the whole-plant level. The dynamics of root morphological and anatomical traits were monitored. These traits were then correlated with plant foliage traits along with dry mass and sulfur and iron allocation dynamics in the shoot versus root. Plants grown under sulfate deprivation did not seem to invest in new root axes. Crown roots presented anatomical differences in all parameters studied; e.g., more and larger xylem vessels in order to maximize water and nutrient transport in the xylem sap. In the root system of S-deficient plants, a reduced concentration of sulfur was observed, whilst organic sulfur predominated over sulfates. A reduction in total iron concentration was monitored, and differences in its subcellular localization were observed. As expected, S-deprivation negatively affected the total sulfur concentration in the aerial plant part, as well as greatly impacted iron allocation in the foliage. Phenotypic adaptation to sulfur deprivation in maize presented alterations mainly in the root anatomy; towards competent handling of the initial sulfur and the induced iron deficiencies.

Effects of exogenous L-Glutamine as a sole nitrogen source on physiological characteristics and nitrogen use efficiency of poplar

L-Glutamine (Gln) is a proteinogenic amino acid, N transporter and NH₃ carrier, engaging in diversified pathways for synthesizing many important molecules. However, the effects of exogenous Gln on plant growth and development remain largely unknown. In this study, different concentrations of Gln were supplemented in the poplar hybrid 'Nanlin895' culture medium as a sole N source. Their effects on poplar growth, photosynthesis, N metabolism-related enzymes and metabolites were elucidated. Strikingly, 0.5 mM Gln-fed poplars showed no considerable growth compromise compared to the inorganic N control (CK-N), even though their N supply level was only half that of the CK-N control. What's more, their NUE was enhanced. In addition, 0.5 mM Gln treatment significantly increased the contents of amino acids in coordination with soluble sugars in the roots, while marginal effects in the leaves were observed compared to CK-N. By contrast, applying a high level of Gln (>0.5 mM) resulted in larger accumulation of amino acids and starch, but lower level of soluble sugars, particularly in the roots, followed by adverse effects on poplar biomass, photosynthesis, enzyme activities and NUE; consequently, poplar growth was inhibited. Collectively, these findings allow us to deduce that poplar plants are competent to take up and utilize Gln as a sole N source. When applied at an appropriate level, Gln could promote a dynamic equilibrium of N and C, conferring sound growth performance and additional benefit for the environment as indicated by higher NUE, lower N input and higher biocompatible nature than the inorganic N.

Genotypic diversity and plasticity of root system architecture to nitrogen availability in oilseed rape

In the emerging new agricultural context, a drastic reduction in fertilizer usage is required. A promising way to maintain high crop yields while reducing fertilizer inputs is to breed new varieties with optimized root system architecture (RSA), designed to reach soil resources more efficiently. This relies on identifying key traits that underlie genotypic variability and plasticity of RSA in response to nutrient availability. The aim of our study was to characterize the RSA plasticity in response to nitrogen limitation of a set of contrasted oilseed rape genotypes, by using the ArchiSimple model parameters as screening traits. Eight accessions of Brassica napus were grown in long tubes in the greenhouse, under two contrasting levels of nitrogen availability. After plant excavation, roots were scanned at high resolution. Six RSA traits relative to root diameter, elongation rate and branching were measured, as well as nine growth and biomass allocation traits. The plasticity of each trait to nitrogen availability was estimated. Nitrogen-limited plants were characterized by a strong reduction in total biomass and leaf area. Even if the architecture traits were shown to be less plastic than allocation traits, significant nitrogen and genotype effects were highlighted on each RSA trait, except the root minimal diameter. Thus, the RSA of nitrogen-limited plants was primarily characterised by a reduced lateral root density, a smaller primary root diameter, associated with a stronger root dominance. Among the RSA traits measured, the inter-branch distance showed the highest plasticity with a level of 70%, in the same range as the most plastic allocation traits. This work suggests that lateral root density plays the key role in the adaptation of the root system to nitrogen availability and highlights inter-branch distance as a major target trait for breeding new varieties, better adapted to low input systems.

Selection of nitrogen responsive root architectural traits in spinach using machine learning and genetic correlations

The efficient acquisition and transport of nutrients by plants largely depend on the root architecture. Due to the absence of complex microbial network interactions and soil heterogeneity in a restricted soilless medium, the architecture of roots is a function of genetics defined by the soilless matrix and exogenously supplied nutrients such as nitrogen (N). The knowledge of root trait combinations that offer the optimal nitrogen use efficiency (NUE) is far from being conclusive. The objective of this study was to define the root trait(s) that best predicts and correlates with vegetative biomass under differed N treatments. We used eight image-derived root architectural traits of 202 diverse spinach lines grown in two N concentrations (high N, HN, and low N, LN) in randomized complete blocks design. Supervised random forest (RF) machine learning augmented by ranger hyperparameter grid search was used to predict the variable importance of the root traits. We also determined the broad-sense heritability (H) and genetic (r_g) and phenotypic (r_p) correlations between root traits and the vegetative biomass (shoot weight, SWt). Each root trait was assigned a predicted importance rank based on the trait’s contribution to the cumulative reduction in the mean square error (MSE) in the RF tree regression models for SWt. The root traits were further prioritized for potential selection based on the r_g and SWt correlated response (CR). The predicted importance of the eight root traits showed that the number of root tips (Tips) and root length (RLength) under HN and crossings (Xsings) and root average diameter (RAvdiam) under LN were the most relevant. SWt had a highly antagonistic r_g (− 0.83) to RAvdiam, but a high predicted indirect selection efficiency (− 112.8%) with RAvdiam under LN; RAvdiam showed no significant rg or rp to SWt under HN. In limited N availability, we suggest that selecting against larger RAvdiam as a secondary trait might improve biomass and, hence, NUE with no apparent yield penalty under HN.

Nitrate dose-responsive transcriptome analysis identifies transcription factors and small secreted peptides involved in nitrogen response in Tartary buckwheat

Tartary buckwheat (Fagopyrum tataricum Gaertn.) is an economically important pseudocereal crop, which can adapt well to extreme environments, including low nitrogen (LN) stress. However, little is known regarding the associated molecular mechanisms. In this study, the molecular mechanism of Tartary buckwheat roots in response to different doses of nitrate was investigated by combining physiological changes with transcriptional regulatory network. LN improved elongation and branching of lateral roots, indicating that the plasticity of lateral roots drives the adaption of Tartary buckwheat under LN condition. The roots of the seedlings that were cultivated under four N conditions were selected for RNA-Seq analysis. In total 1686 nitrate dose-responsive genes were identified. Of these genes, 16 genes encoding N transporters showed response to N availability, and they may play important roles in N transport and root system architecture in Tartary buckwheat roots. 108 transcription factors (TFs) showed dose-response to N availability, and they may regulate N response and root growth under varied N conditions by modulating the expression of N transporters. A NIN-like protein, FtNLP7, was identified and it may contribute to the transcriptional regulation of N transporters. Furthermore, 81 N-responsive genes were identified as the small secreted peptides (SSPs). 48 N-responsive SSPs were annotated as hypothetical proteins and they may be the species-specific proteins of Tartary buckwheat. This paper provides useful information for further investigation of the mechanisms underlying the adaptation of Tartary buckwheat under N-deficient condition.

Nodal root diameter and node number in maize (Zea mays L.) interact to influence plant growth under nitrogen stress

Under nitrogen limitation, plants increase resource allocation to root growth relative to shoot growth. The utility of various root architectural and anatomical phenotypes for nitrogen acquisition are not well understood. Nodal root number and root cross-sectional area were evaluated in maize in field and greenhouse environments. Nodal root number and root cross-sectional area were inversely correlated under both high and low nitrogen conditions. Attenuated emergence of root nodes, as opposed to differences in the number of axial roots per node, was associated with substantially reduced root number. Greater root cross-sectional area was associated with a greater stele area and number of cortical cell files. Genotypes that produced few, thick nodal roots rather than many, thin nodal roots had deeper rooting and better shoot growth in low nitrogen environments. Fewer nodal roots offset the respiratory and nitrogen costs of thicker diameter roots, since total nodal root respiration and nitrogen content was similar for genotypes with many, thin and few, thick nodal roots. We propose that few, thick nodal roots may enable greater capture of deep soil nitrogen and improve plant performance under nitrogen stress. Synergistic interactions between an architectural and anatomical trait may be an important strategy for nitrogen acquisition. Understanding trait interactions among different root nodes has important implications in for improving crop nutrient uptake and stress tolerance.

Low nitrogen induces root elongation via auxin-induced acid growth and auxin-regulated target of rapamycin (TOR) pathway in maize

Under low nitrogen (N) supply, an important adaption of the maize root system is to promote the root elongation so as to increase N uptake from a larger soil space. The underlying physiological mechanism is largely unknown. In the present study, two maize inbred lines (Ye478 and Wu312) were used to study the possible involvement of the auxin and target of rapamycin (TOR) pathway in low-N-induced root elongation. Compared to Wu312, primary root elongation of Ye478 was more sensitive to low nitrate supply. Correspondingly, more auxin was accumulated in the root tip, and more protons were secreted, increasing the acidity of the apoplast space. On the other hand, low-N-induced root elongation was greatly reduced when shoot-to-root auxin transport was inhibited by applying N-1-naphthylphthalamic acid (NPA) at the plant base or by pruning the top leaf where auxin is mostly synthesized. Furthermore, exogenous application of TOR inhibitor also eliminated the response of root elongation under low N. The content of TOR kinase and the expression of TOR pathway-related genes were significantly changed when shoot-to-root auxin transport was reduced by NPA treatment. Taken together, it is concluded that low-N stress increases shoot-to-root auxin transport which enhances root elongation via auxin-dependent acid growth and the auxin-regulated TOR pathway in maize.

Signaling pathways underlying nitrogen-dependent changes in root system architecture: from model to crop species

Among all essential mineral elements, nitrogen (N) is required in the largest amounts and thus is often a limiting factor for plant growth. N is taken up by plant roots in the form of water-soluble nitrate, ammonium, and, depending on abundance, low-molecular weight organic N. In soils, the availability and composition of these N forms can vary over space and time, which exposes roots to various local N signals that regulate root system architecture in combination with systemic signals reflecting the N nutritional status of the shoot. Uncovering the molecular mechanisms underlying N-dependent signaling provides great potential to optimize root system architecture for the sake of higher N uptake efficiency in crop breeding. In this review, we summarize prominent signaling mechanisms and their underlying molecular players that derive from external N forms or the internal N nutritional status and modulate root development including root hair formation and gravitropism. We also compare the current state of knowledge of these pathways between Arabidopsis and graminaceous plant species.

Seminal and Nodal Roots of Barley Differ in Anatomy, Proteome and Nitrate Uptake Capacity

The root system of barley plants is composed of embryogenic, seminal roots as well as lateral and nodal roots that are formed postembryonically from seminal roots and from the basal part of shoots, respectively. Due to their distinct developmental origin, seminal and nodal roots may differ in function during plant development; however, a clear comparison between these two root types has not yet been undertaken. In this study, anatomical, proteomic and physiological traits were compared between seminal and nodal roots of similar developmental stages. Nodal roots have larger diameter, larger metaxylem area and a larger number of metaxylem vessels than seminal roots. Proteome profiling uncovered a set of root-type-specific proteins, including proteins related to the cell wall and cytoskeleton organization, which could potentially be implicated with differential metaxylem development. We also found that nodal roots have higher levels of auxin, which is known to trigger metaxylem development. At millimolar nitrate supply, nodal roots had approximately 2-fold higher nitrate uptake and root-to-shoot translocation capacities than seminal roots, whereas no differences were found at micromolar nitrate supply. Since these marked differences were not reflected by the transcript levels of low-affinity nitrate transporter genes, we hypothesize that the larger metaxylem volume of nodal roots enhances predominantly the low-affinity uptake and translocation capacities of nutrients that are transported with the bulk flow of water, like nitrate.

Photosynthetic performance and photosynthesis-related gene expression coordinated in a shade-tolerant species Panax notoginseng under nitrogen regimes

BACKGROUND

Nitrogen (N) is an essential component of photosynthetic apparatus. However, the mechanism that photosynthetic capacity is suppressed by N is not completely understood. Photosynthetic capacity and photosynthesis-related genes were comparatively analyzed in a shade-tolerant species Panax notoginseng grown under the levels of low N (LN), moderate N (MN) and high N (HN).

RESULTS

Photosynthetic assimilation was significantly suppressed in the LN- and HN-grown plants. Compared with the MN-grown plants, the HN-grown plants showed thicker anatomic structure and larger chloroplast accompanied with decreased ratio of mesophyll conductance (gm) to Rubisco content (gm/Rubisco) and lower Rubisco activity. Meanwhile, LN-grown plants displayed smaller chloroplast and accordingly lower internal conductance (gi). LN- and HN-grown individuals allocated less N to light-harvesting system (NL) and carboxylation system (NC), respectively. N surplus negatively affected the expression of genes in Car biosynthesis (GGPS, DXR, PSY, IPI and DXS). The LN individuals outperformed others with respect to non-photochemical quenching. The expression of genes (FBA, PGK, RAF2, GAPC, CAB, PsbA and PsbH) encoding enzymes of Calvin cycle and structural protein of light reaction were obviously repressed in the LN individuals, accompanying with a reduction in Rubisco content and activity. Correspondingly, the expression of genes encoding RAF2, RPI4, CAB and PetE were repressed in the HN-grown plants.

CONCLUSIONS

LN-induced depression of photosynthetic capacity might be caused by the deceleration on Calvin cycle and light reaction of photosynthesis, and HN-induced depression of ones might derive from an increase in the form of inactivated Rubisco.

The physiological mechanism underlying root elongation in response to nitrogen deficiency in crop plants

In response to low nitrogen stress, multiple hormones together with nitric oxide signaling pathways work synergistically and antagonistically in crop root elongation. Changing root morphology allows plants to adapt to soil nutrient availability. Nitrogen is the most important essential nutrient for plant growth. An important adaptive strategy for crops responding to nitrogen deficiency is root elongation, thereby accessing increased soil space and nitrogen resources. Multiple signaling pathways are involved in this regulatory network, working together to fine-tune root elongation in response to soil nitrogen availability. Based on existing research, we propose a model to explain how different signaling pathways interact to regulate root elongation in response to low nitrogen stress. In response to a low shoot nitrogen status signal, auxin transport from the shoot to the root increases. High auxin levels in the root tip stimulate the production of nitric oxide, which promotes the synthesis of strigolactones to accelerate cell division. In this process, cytokinin, ethylene, and abscisic acid play an antagonistic role, while brassinosteroids and auxin play a synergistic role in regulating root elongation. Further study is required to identify the QTLs, genes, and favorable alleles which control the root elongation response to low nitrogen stress in crops.

Genotypic variation and nitrogen stress effects on root anatomy in maize are node specific

Root phenotypes that improve nitrogen acquisition are avenues for crop improvement. Root anatomy affects resource capture, metabolic cost, hydraulic conductance, anchorage, and soil penetration. Cereal root phenotyping has centered on primary, seminal, and early nodal roots, yet critical nitrogen uptake occurs when the nodal root system is well developed. This study examined root anatomy across nodes in field-grown maize (Zea mays L.) hybrid and inbred lines under high and low nitrogen regimes. Genotypes with high nitrogen use efficiency (NUE) had larger root diameter and less cortical aerenchyma across nodes under stress than genotypes with lower NUE. Anatomical phenes displayed slightly hyperallometric relationships to shoot biomass. Anatomical plasticity varied across genotypes; most genotypes decreased root diameter under stress when averaged across nodes. Cortex, stele, total metaxylem vessel areas, and cortical cell file and metaxylem vessel numbers scaled strongly with root diameter across nodes. Within nodes, metaxylem vessel size and cortical cell size were correlated, and root anatomical phenotypes in the first and second nodes were not representative of subsequent nodes. Node, genotype, and nitrogen treatment affect root anatomy. Understanding nodal variation in root phenes will enable the development of plants that are adapted to low nitrogen conditions.

Growth and Distribution of Maize Roots in Response to Nitrogen Accumulation in Soil Profiles after Long-Term Fertilization Management on a Calcareous Soil

The replacement of inorganic fertilizer nitrogen by manure is highlighted to have great potential to maintain crop yield while delivering multiple functions, including the improvement of soil quality. However, information on the dynamics of root distributions in response to chemical fertilizers and manure along the soil profile is still lacking. The aim of this study was to investigate the temporal-spatial root distributions of summer maize (Zea mays L.) from 2013 to 2015 under four treatments (unfertilized control (CK), inorganic fertilizer (NPK), manure + 70% NPK (NPKM), and NPKM + straw (NPKMS)). Root efficiency for shoot N accumulation was increased by 89% in the NPKM treatment compared with the NPK treatment at V12 (the emergence of the twelfth leaf) of 2014. Root growth at 40–60 cm was consistently stimulated after manure and/or straw additions, especially at V12 and R3 (the milk stage) across three years. Root length density (RLD) in the diameter <0.2 mm at 0–20 cm was significantly positively correlated with soil water content and negatively with soil mineral N contents in 2015. The RLD in the diameter >0.4 mm at 20–60 cm, and RLD <0.2 mm, was positively correlated with shoot N uptake in 2015. The root length density was insensitive in response to fertilization treatments, but the variations in RLD along the soil profile in response to fertilization implies that there is a great potential to manipulate N supply levels and rooting depths to increase nutrient use efficiency. The importance of incorporating a manure application together with straw to increase soil fertility in the North China Plain (NCP) needs further studies.

Photosynthetic characteristics and metabolic analyses of two soybean genotypes revealed adaptive strategies to low-nitrogen stress

Nitrogen is an essential macronutrient for plants and the common limiting factor for crop productivity worldwide. An effective approach to combat N deficiency and overuse is to understand the mechanism of low-nitrogen tolerance in plants and develop low-nitrogen-tolerant crop cultivars. Wild soybean has a high tolerance to poor environmental conditions, but, until now, no study has illustrated the mechanism of low-nitrogen tolerance at a metabolomic level. In this study, the photosynthetic characteristics and metabolomics of wild and cultivated soybean seedlings were analyzed, and the mechanism of wild soybean's low-nitrogen tolerance was explained using a sand culture experiment. Wild soybean was less affected by low-nitrogen stress than cultivated soybean as assessed by plant growth parameters and photosynthesis. The root length of wild soybean increased, and a high root-shoot ratio was maintained under low-nitrogen stress. Carotenoids accumulated, which contributed to its higher low-nitrogen tolerance. A total of 48 and 60 differentially accumulated metabolites were identified in leaves and roots, respectively, between the low-nitrogen stress and control groups. The ability of wild soybean to tolerate low nitrogen also resulted from its capability to enhance the TCA cycle, synthesize key amino acids, accumulate metabolites, such as soluble sugars and organic acids, and synthesize favorable secondary metabolites under low-nitrogen stress. The current results reveal the mechanism underlying wild soybean's high low-nitrogen tolerance and provide the methodology and theoretical basis for utilizing wild soybean, improving cultivated soybean, and studying the low-nitrogen tolerance of other plants.

A newly formed hexaploid wheat exhibits immediate higher tolerance to nitrogen-deficiency than its parental lines

BACKGROUND

It is known that hexaploid common wheat (Triticum aestivum L.) has stronger adaptability to many stressful environments than its tetraploid wheat progenitor. However, the physiological basis and evolutionary course to acquire these enhanced adaptabilities by common wheat remain understudied. Here, we aimed to investigate whether and by what means tolerance to low-nitrogen manifested by common wheat may emerge immediately following allohexaploidization.

RESULTS

We compared traits related to nitrogen (N) metabolism in a synthetic allohexaploid wheat (neo-6×, BBAADD) mimicking natural common wheat, together with its tetraploid (BBAA, 4×) and diploid (DD, 2×) parents. We found that, under low nitrogen condition, neo-6× maintained largely normal photosynthesis, higher shoot N accumulation, and better N assimilation than its 4× and 2× parents. We showed that multiple mechanisms underlie the enhanced tolerance to N-deficiency in neo-6×. At morphological level, neo-6× has higher root/shoot ratio of biomass than its parents, which might be an adaptive growth strategy as more roots feed less shoots with N, thereby enabling higher N accumulation in the shoots. At electrophysiological level, H⁺ efflux in neo-6× is higher than in its 4× parent. A stronger H⁺ efflux may enable a higher N uptake capacity of neo-6×. At gene expression level, neo-6× displayed markedly higher expression levels of critical genes involved in N uptake than both of its 4× and 2× parents.

CONCLUSIONS

This study documents that allohexaploid wheat can attain immediate higher tolerance to N-deficiency compared with both of its 4× and 2× parents, and which was accomplished via multiple mechanisms.

Uptake and metabolism of ammonium and nitrate in response to drought stress in Malus prunifolia

Using a hydroponics culture system, we monitored morphological, physiological, and molecular changes in Malus prunifolia seedlings when drought conditions induced by 5% polyethylene glycol (PEG) were combined with a low or normal supply of N (0.05 mM or 1 mM NH₄NO₃, respectively). Under either nutrient level, drought stress negatively inhibited seedling performance, as manifested by reduced photosynthesis and biomass production, decreased accumulations of total N, and inhibited root growth. Concentrations of NO₃^- and NH₄⁺ and the activities of enzymes involved in N metabolism (nitrate reductase, glutamine synthetase, and glutamate synthase) were also significantly decreased under drought stress. The net influx of NO₃^- at the surface of the fine roots declined while that of NH₄⁺ rose markedly, suggesting that the latter may play a more important role in improving drought tolerance in M. prunifolia. Consistently, two ammonium transporters (AMT1;2 and AMT4;2) were notably up-regulated in response to drought stress, whereas most genes related to nitrate uptake, reduction, and N metabolism were down-regulated. At the normal N level, PEG-treated plants showed higher values for biomass production, root growth, and N uptake/reduction when compared with plants exposed to the lower N supply. These results suggest that the negative effect of drought stress on M. prunifolia may be alleviated when more nitrogen is available.

Foxtail Millet [Setaria italica (L.) Beauv.] Grown under Low Nitrogen Shows a Smaller Root System, Enhanced Biomass Accumulation, and Nitrate Transporter Expression

Foxtail millet (FM) [Setaria italica (L.) Beauv.] is a grain and forage crop well adapted to nutrient-poor soils. To date little is known how FM adapts to low nitrogen (LN) at the morphological, physiological, and molecular levels. Using the FM variety Yugu1, we found that LN led to lower chlorophyll contents and N concentrations, and higher root/shoot and C/N ratios and N utilization efficiencies under hydroponic culture. Importantly, enhanced biomass accumulation in the root under LN was in contrast to a smaller root system, as indicated by significant decreases in total root length; crown root number and length; and lateral root number, length, and density. Enhanced carbon allocation toward the root was rather for significant increases in average diameter of the LN root, potentially favorable for wider xylem vessels or other anatomical alterations facilitating nutrient transport. Lower levels of IAA and CKs were consistent with a smaller root system and higher levels of GA may promote root thickening under LN. Further, up-regulation of SiNRT1.1, SiNRT2.1, and SiNAR2.1 expression and nitrate influx in the root and that of SiNRT1.11 and SiNRT1.12 expression in the shoot probably favored nitrate uptake and remobilization as a whole. Lastly, more soluble proteins accumulated in the N-deficient root likely as a result of increases of N utilization efficiencies. Such "excessive" protein-N was possibly available for shoot delivery. Thus, FM may preferentially transport carbon toward the root facilitating root thickening/nutrient transport and allocate N toward the shoot maximizing photosynthesis/carbon fixation as a primary adaptive strategy to N limitation.

A RNA-Seq Analysis of the Response of Photosynthetic System to Low Nitrogen Supply in Maize Leaf

Nitrogen is a major limiting factor for crop productivity. The relationship between photosynthesis and nitrogen nutrition has been widely studied. However, the molecular response of leaf photosynthesis to low nitrogen supply in crops is less clear. In this study, RNA sequencing technology (RNA-Seq) was used to investigate the gene expressions related to photosynthesis in maize in response to low nitrogen supply. It was found that low nitrogen supply down-regulated the expression of genes involved in photosystem I (PSI) and photosystem II (PSII). Thus, low nitrogen supply down-regulated the expression of genes related to the antenna system, reduced light absorption, light transport, and electron transport. Correspondingly, the parameters related to chlorophyll fluorescence were very sensitive to nitrogen deficiency. Under low nitrogen supply, leaf chlorophyll content, actual quantum yield of PSII photochemistry, photochemical quenching, and electron transport rate, were reduced. However, the thermal diffusion and chlorophyll fluorescence were increased. RNA-Seq was used to analyze the genes involved in the response of leaf photosynthesis to low nitrogen supply in maize. These results highlight the possibility of utilizing chlorophyll fluorescence parameters, and the related genes, as indicators for plant nitrogen nutrition. This could lead to the development of new tools to make precise nitrogen fertilizer recommendations and select nitrogen-efficient genotypes.

Reduced crown root number improves water acquisition under water deficit stress in maize (Zea mays L.)

In this study we test the hypothesis that maize genotypes with reduced crown root number (CN) will have greater root depth and improved water acquisition from drying soil. Maize recombinant inbred lines with contrasting CN were evaluated under water stress in greenhouse mesocosms and field rainout shelters. CN varied from 25 to 62 among genotypes. Under water stress in the mesocosms, genotypes with low CN had 31% fewer crown roots, 30% deeper rooting, 56% greater stomatal conductance, 45% greater leaf CO2 assimilation, 61% net canopy CO2 assimilation, and 55% greater shoot biomass than genotypes with high CN at 35 days after planting. Under water stress in the field, genotypes with low CN had 21% fewer crown roots, 41% deeper rooting, 48% lighter stem water oxygen isotope enrichment (δ(18)O) signature signifying deeper water capture, 13% greater leaf relative water content, 33% greater shoot biomass at anthesis, and 57% greater yield than genotypes with high CN. These results support the hypothesis that low CN improves drought tolerance by increasing rooting depth and water acquisition from the subsoil.

Impact of treated wastewater on growth, respiration and hydraulic conductivity of citrus root systems in light and heavy soils

Roots interact with soil properties and irrigation water quality leading to changes in root growth, structure and function. We studied these interactions in an orchard and in lysimeters with clay and sandy loam soils. Minirhizotron imaging and manual sampling showed that root growth was three times lower in the clay relative to sandy loam soil. Treated wastewater (TWW) led to a large reduction in root growth with clay (45-55%) but not with sandy loam soil (<20%). Treated wastewater increased salt uptake, membrane leakage and proline content, and decreased root viability, carbohydrate content and osmotic potentials in the fine roots, especially in clay. These results provide evidence that TWW challenges and damages the root system. The phenology and physiology of root orders were studied in lysimeters. Soil type influenced diameter, specific root area, tissue density and cortex area similarly in all root orders, while TWW influenced these only in clay soil. Respiration rates were similar in both soils, and root hydraulic conductivity was severely reduced in clay soil. Treated wastewater increased respiration rate and reduced hydraulic conductivity of all root orders in clay but only of the lower root orders in sandy loam soil. Loss of hydraulic conductivity increased with root order in clay and clay irrigated with TWW. Respiration and hydraulic properties of all root orders were significantly affected by sodium-amended TWW in sandy loam soil. These changes in root order morphology, anatomy, physiology and hydraulic properties indicate rapid and major modifications of root systems in response to differences in soil type and water quality.

Comparative RNA-Seq Analysis Reveals That Regulatory Network of Maize Root Development Controls the Expression of Genes in Response to N Stress

Nitrogen (N) is an essential nutrient for plants, and it directly affects grain yield and protein content in cereal crops. Plant root systems are not only critical for anchorage in the soil, but also for N acquisition. Therefore, genes controlling root development might also affect N uptake by plants. In this study, the responses of nitrogen on root architecture of mutant rtcs and wild-type of maize were investigated by morphological and physiological analysis. Subsequently, we performed a comparative RNA-Seq analysis to compare gene expression profiles between mutant rtcs roots and wild-type roots under different N conditions. We identified 786 co-modulated differentially expressed genes (DEGs) related to root development. These genes participated in various metabolic processes. A co-expression cluster analysis and a cis-regulatory motifs analysis revealed the importance of the AP2-EREBP transcription factor family in the rtcs-dependent regulatory network. Some genotype-specific DEGs contained at least one LBD motif in their promoter region. Further analyses of the differences in gene transcript levels between rtcs and wild-type under different N conditions revealed 403 co-modulated DEGs with distinct functions. A comparative analysis revealed that the regulatory network controlling root development also controlled gene expression in response to N-deficiency. Several AP2-EREBP family members involved in multiple hormone signaling pathways were among the DEGs. These transcription factors might play important roles in the rtcs-dependent regulatory network related to root development and the N-deficiency response. Genes encoding the nitrate transporters NRT2-1, NAR2.1, NAR2.2, and NAR2.3 showed much higher transcript levels in rtcs than in wild-type under normal-N conditions. This result indicated that the LBD gene family mainly functions as transcriptional repressors, as noted in other studies. In summary, using a comparative RNA-Seq-based approach, we identified DEGs related to root development that also participated in the N-deficiency response in maize. These findings will increase our understanding of the molecular regulatory networks controlling root development and N-stress responses.

Use of genotype-environment interactions to elucidate the pattern of maize root plasticity to nitrogen deficiency

Maize (Zea mays L.) root morphology exhibits a high degree of phenotypic plasticity to nitrogen (N) deficiency, but the underlying genetic architecture remains to be investigated. Using an advanced BC4 F3 population, we investigated the root growth plasticity under two contrasted N levels and identified the quantitative trait loci (QTLs) with QTL-environment (Q × E) interaction effects. Principal components analysis (PCA) on changes of root traits to N deficiency (ΔLN-HN) showed that root length and biomass contributed for 45.8% in the same magnitude and direction on the first PC, while root traits scattered highly on PC2 and PC3. Hierarchical cluster analysis on traits for ΔLN-HN further assigned the BC4 F3 lines into six groups, in which the special phenotypic responses to N deficiency was presented. These results revealed the complicated root plasticity of maize in response to N deficiency that can be caused by genotype-environment (G × E) interactions. Furthermore, QTL mapping using a multi-environment analysis identified 35 QTLs for root traits. Nine of these QTLs exhibited significant Q × E interaction effects. Taken together, our findings contribute to understanding the phenotypic and genotypic pattern of root plasticity to N deficiency, which will be useful for developing maize tolerance cultivars to N deficiency.

Root-type-specific plasticity in response to localized high nitrate supply in maize (Zea mays)

BACKGROUND AND AIMS

Shoot-borne roots contribute to most of the nutrient uptake throughout the life cycle of maize (Zea mays). Compared with numerous studies with embryonic roots, detailed information on the phenotypic plasticity of shoot-borne roots in response to a heterogeneous nitrogen supply is scarce. The present study therefore provides a comprehensive profile of fine-scale plastic responses of distinct root types to localized high nitrate supply.

METHODS

Seedlings of the maize inbred line B73 were grown in split-root systems. The anatomy and morphological plasticity of the primary root and the roots initiated from the 2nd, 5th and 7th shoot nodes, and their lateral roots, were studied in response to local high nitrate supply to one side of the root system.

KEY RESULTS

In contrast to the insensitivity of axial roots, local high nitrate supply increased the length of 1st-order lateral roots on the primary root and the three whorls of shoot-borne roots at different growth stages, and increased the density of 1st-order lateral roots on the 7th shoot-borne root after silking. The length and density of 2nd-order lateral roots on the three whorls of shoot-borne roots displayed a more flexible response to local high nitrate than 1st-order lateral roots. Root diameter and number, and total area and diameter of metaxylem vessels increased from the primary root to early and then later developed shoot-borne roots, which showed a positive relationship with shoot growth and N accumulation.

CONCLUSIONS

Maize axial roots and lateral roots responded differently to local high nitrate, and this was related to their function. The extent of morphological plasticity of lateral roots in response to local high nitrate depended on the initiation time of the shoot-borne roots on which the lateral roots developed. Morphological plasticity was higher on 2nd-order than on 1st-order lateral roots. The results suggest that higher order lateral root branching might be a potential target for genetic improvement in future maize breeding.

Intensive field phenotyping of maize (Zea mays L.) root crowns identifies phenes and phene integration associated with plant growth and nitrogen acquisition

Root architecture is an important regulator of nitrogen (N) acquisition. Existing methods to phenotype the root architecture of cereal crops are generally limited to seedlings or to the outer roots of mature root crowns. The functional integration of root phenes is poorly understood. In this study, intensive phenotyping of mature root crowns of maize was conducted to discover phenes and phene modules related to N acquisition. Twelve maize genotypes were grown under replete and deficient N regimes in the field in South Africa and eight in the USA. An image was captured for every whorl of nodal roots in each crown. Custom software was used to measure root phenes including nodal occupancy, angle, diameter, distance to branching, lateral branching, and lateral length. Variation existed for all root phenes within maize root crowns. Size-related phenes such as diameter and number were substantially influenced by nodal position, while angle, lateral density, and distance to branching were not. Greater distance to branching, the length from the shoot to the emergence of laterals, is proposed to be a novel phene state that minimizes placing roots in already explored soil. Root phenes from both older and younger whorls of nodal roots contributed to variation in shoot mass and N uptake. The additive integration of root phenes accounted for 70% of the variation observed in shoot mass in low N soil. These results demonstrate the utility of intensive phenotyping of mature root systems, as well as the importance of phene integration in soil resource acquisition.