Maize (Zea mays L.) nodal roots are characterized by their ability to maintain elongation under water deficit conditions that inhibit the growth of other organs. Physiological and molecular mechanisms underlying this response were investigated using a divided-container root growth system to impose uniform and steady water deficit (WD) conditions around the nodal roots of maize cv. FR697. Kinematic growth analysis demonstrated that continued nodal root elongation under water deficit involves maintenance of both growth zone length and rates of cell production from the meristem. Nodal roots that maintain growth during WD exhibit increased rates of net solute deposition throughout the growth zone that enable osmotic adjustment and continued tissue expansion. These abilities differ from the maize primary root, which exhibits impairment of both cell expansion and cell production when grown under similar water deficit conditions. Integration of transcriptomic and metabolomic profiling revealed molecular signatures of nodal root growth maintenance, including central transcriptional responses and metabolic pathways related to osmolyte accumulation, hormone signaling, and ROS homeostasis. Several metabolic responses differed from previous characterization of the primary root, including taurine accumulation and proline synthesis via the saccharopine pathway. Further, our analysis showed that metabolic acclimation rather than transcriptional control dominated the water deficit response of the nodal root growth zone. The study highlights novel insights into the interplay of morphogenic and metabolic responses that regulate the remarkable ability of nodal roots to maintain elongation under water deficit conditions.

Drought and heat stress significantly limit crop growth and productivity. Their simultaneous occurrence, as often observed in summer crops, leads to larger yield losses. Sorghum is well adapted to dry and hot conditions. Despite the progress that has been made in determining proteomic responses to water deficit or heat stress in crops, such information remains limited for crops subjected to combined water deficit and heat stress. This study presents quantitative proteomics analyses of leaf and root tissues of two contrasting sorghum genotypes grown under normal conditions, water deficit stress, heat stress, and water deficit combined with heat stress. We identified differentially expressed proteins between the two genotypes under these different treatments. GO and KEGG annotation revealed biological processes and molecular pathways associated with sorghum responses to these treatments. Interpretation as well as integration of these proteomics data with other ‘omics’ signatures may highlight key mechanisms involved in sorghum adaptations to these stresses.

Limited water availability is a major environmental factor constraining plant development and crop yields. One of the prominent adaptations of plants to water deficits is the maintenance of root growth that enables sustained access to soil water. Despite early recognition of the adaptive significance of root growth maintenance under water deficits, progress in understanding has been hampered by the inherent complexity of root systems and their interactions with the soil environment. We highlight selected milestones in the understanding of root growth responses to water deficits, with emphasis on founding studies that have shaped current knowledge and set the stage for further investigation. We revisit the concept of integrated biophysical and metabolic regulation of plant growth and use this framework to review central growth-regulatory processes occurring within root growth zones under water stress at subcellular to organ scales. Key topics include the primary processes of modifications of cell wall-yielding properties and osmotic adjustment, as well as regulatory roles of abscisic acid and its interactions with other hormones. We include consideration of long-recognized responses for which detailed mechanistic understanding has been elusive until recently, for example hydrotropism, and identify gaps in knowledge, ongoing challenges, and opportunities for future research.

Under water stress, the primary root elongation zones of cotton and maize exhibit both conserved and divergent metabolic responses, including variations in sulfur and antioxidant metabolism. To explore the relative importance of metabolic and genetic controls of these responses for each species, and the extent to which responses are mediated by similar gene expression networks within the framework of ortholog groups, comparative transcriptomics analyses were conducted under conditions of equivalent tissue water stress. Ortholog analysis revealed that 86% of the transcriptome response to water stress was phylogenetically unrelated between cotton and maize. Elevated transcript abundances for genes involved in abscisic acid (ABA) biosynthesis and signaling, as well as key enzymes that enable osmotic adjustment, were conserved between the species. In contrast, antioxidant responses, at least with regard to glutathione metabolism and anti-oxidative enzymes, did not exhibit such a transcript abundance adaptive signature. In particular, previously characterized differential responses of the glutathione and sulfur metabolic pathways between cotton and maize were not evident in the transcriptomic responses. The findings indicate that the antioxidant response in both species results from a metabolic acclimation to water stress, and thus represents an example of water stress-related metabolic plasticity.

Certain cultivars of maize show increased tolerance to water deficit conditions by maintenance of root growth. To better understand the molecular mechanisms related to this adaptation, nodal root growth zone samples were collected from the reference inbred line B73 and inbred line FR697, which exhibits a relatively greater ability to maintain root elongation under water deficits. Plants were grown under various water stress levels in both field and controlled environment settings. FR697-specific RNA-Seq datasets were generated and used for a de novo transcriptome assembly to characterize any genotype-specific genetic features. The assembly was aided by an Iso-Seq library of transcripts generated from various FR697 plant tissue samples. The Necklace pipeline was used to combine a Trinity de novo assembly along with a reference guided assembly and the Viridiplantae proteome to generate an annotated consensus “SuperTranscriptome” assembly of 47,915 transcripts with a N50 of 3152 bp in length. The results were compared by Blastn to maize reference genes, a Benchmarking Universal Single-Copy Orthologs (BUSCO) genome completeness report and compared with three maize reference genomes. The resultant ‘SuperTranscriptome’ was demonstrated to be of high-quality and will serve as an important reference for analysis of the maize nodal root transcriptomic response to environmental perturbations.

The amino acid phenylalanine is a precursor to phenolic acids that constitute the lignin biosynthetic pathway. Although there is evidence of a role of some phenolic acids in plant responses to pathogens and salinity, characterization of the involvement of phenolic acids in plant responses to drought is limited. Drought reduces water content in plant tissue and can lead to decreased cell viability and increased cell death. We thus subjected maize seedlings to water deficit and evaluated relative water content and cell viability together with p-coumaric acid, caffeic acid and ferulic acid contents in the leaves. Furthermore, we measured the enzymatic activity of cinnamate 4-hydroxylase (EC 1.14.13.11) and p-coumarate 3-hydroxylase (EC 1.14.17.2) and associated these with the expression of genes encoding cinnamate 4-hydroxylase and p-coumarate-3 hydroxylase in response to water deficit. Water deficit reduced relative water content and cell viability in maize leaves. This corresponded with decreased p-coumaric acid but increased caffeic and ferulic acid content in the leaves. Changes in the phenolic acid content of the maize leaves were associated with increased enzymatic activities of cinnamate 4-hydroxylase and p-coumarate hydroxylase. The increased enzymatic activity of p-coumarate 3-hydroxylase was associated with increased expression of a gene encoding p-coumarate 3-hydroxylase. We thus conclude that metabolic pathways involving phenolic acids may contribute to the regulation of drought responses in maize, and we propose that further work to elucidate this regulation may contribute to the development of new maize varieties with improved drought tolerance. This can be achieved by marker-assisted selection to select maize lines with high levels of expression of genes encoding cinnamate 4-hydroxylase and/or p-coumarate 3-hydroxylase for use in breeding programs aimed and improving drought tolerance, or by overexpression of these genes via genetic engineering to confer drought tolerance.

Advances in next-generation sequencing and other high-throughput technologies have facilitated multiomics research, such as genomics, epigenomics, transcriptomics, proteomics, metabolomics, and phenomics. The resultant emerging multiomics data have brought new challenges as well as opportunities, as seen in the plant and agriculture science domains. We reviewed several bioinformatic and computational methods, models, and platforms, and we have highlighted some of our in-house developed efforts aimed at multiomics data analysis, integration, and management issues faced by the research community. A case study using multiomics datasets generated from our studies of maize nodal root growth under water deficit stress demonstrates the power of these datasets and some other publicly available tools. This analysis also sheds light on the landscape of such applied bioinformatic tools currently available for plant and crop science studies and introduces emerging trends and how they may affect the future.

Plant roots exhibit plasticity in their branching patterns to forage efficiently for heterogeneously distributed resources, such as soil water. The xerobranching response represses lateral root formation when roots lose contact with water. Here, we show that xerobranching is regulated by radial movement of the phloem-derived hormone abscisic acid, which disrupts intercellular communication between inner and outer cell layers through plasmodesmata. Closure of these intercellular pores disrupts the inward movement of the hormone signal auxin, blocking lateral root branching. Once root tips regain contact with moisture, the abscisic acid response rapidly attenuates. Our study reveals how roots adapt their branching pattern to heterogeneous soil water conditions by linking changes in hydraulic flux with dynamic hormone redistribution.

The divergence of metabolic responses to water stress in the elongation zone of cotton and maize primary roots was investigated by establishing water-deficit conditions that generated steady root elongation at equivalent tissue water potentials. In water-stressed cotton roots, cell elongation was maintained in the apical 3 mm but was progressively inhibited with further displacement from the apex. These responses are similar to previous findings in maize, providing the foundation for comparisons of metabolic responses in regions of growth maintenance and inhibition between the species. Metabolomics analyses showed region-specific and species-specific changes in metabolite abundance in response to water stress, revealing both conserved responses including osmolyte accumulation, and key differences in antioxidative and sulfur metabolism. Quantitative assessment showed contrasting glutathione responses in the root elongation zone between the species, with glutathione levels declining in cotton as stress duration progressed, whereas in maize, glutathione levels remained elevated. Despite the lesser glutathione response in cotton, hydrogen peroxide levels were low in water-stressed cotton compared with maize roots and were associated with higher catalase, ascorbate peroxidase, and superoxide dismutase activities in cotton. The results indicate alternative metabolic strategies underlying the responses of primary root growth to water stress between cotton and maize.

HIV integrase (IN) inserts viral DNA into the host genome and is the target of the strand transfer inhibitors (STIs), a class of small molecules currently in clinical use. Another potent class of antivirals is the allosteric inhibitors of integrase, or ALLINIs. ALLINIs promote IN aggregation by stabilizing an interaction between the catalytic core domain (CCD) and carboxy -terminal domain (CTD) that undermines viral particle formation in late replication. Ongoing challenges with inhibitor potency, toxicity, and viral resistance motivate research to understand their mechanism. Here, we report a 2.93 Å X-ray crystal structure of the minimal ternary complex between CCD, CTD, and the ALLINI BI-224436. This structure reveals an asymmetric ternary complex with a prominent network of π-mediated interactions that suggest specific avenues for future ALLINI development and optimization.

Soil compaction represents a major agronomic challenge, inhibiting root elongation and impacting crop yields. Roots use ethylene to sense soil compaction as the restricted air space causes this gaseous signal to accumulate around root tips. Ethylene inhibits root elongation and promotes radial expansion in compacted soil, but its mechanistic basis remains unclear. Here, we report that ethylene promotes abscisic acid (ABA) biosynthesis and cortical cell radial expansion. Rice mutants of ABA biosynthetic genes had attenuated cortical cell radial expansion in compacted soil, leading to better penetration. Soil compaction-induced ethylene also up-regulates the auxin biosynthesis gene OsYUC8. Mutants lacking OsYUC8 are better able to penetrate compacted soil. The auxin influx transporter OsAUX1 is also required to mobilize auxin from the root tip to the elongation zone during a root compaction response. Moreover, osaux1 mutants penetrate compacted soil better than the wild-type roots and do not exhibit cortical cell radial expansion. We conclude that ethylene uses auxin and ABA as downstream signals to modify rice root cell elongation and radial expansion, causing root tips to swell and reducing their ability to penetrate compacted soil.

Nutrient uptake is critical for crop growth and determined by root foraging in soil. Growth and branching of roots lead to effective root placement to acquire nutrients, but relatively less is known about absorption of nutrients at the root surface from the soil solution. This knowledge gap could be alleviated by understanding sources of genetic variation for short-term nutrient uptake on a root length basis. A new modular platform for high-throughput phenotyping of multiple ion uptake kinetics was designed to determine nutrient uptake rates in Zea mays . Using this system, uptake rates were characterized for the crop macronutrients nitrate, ammonium, potassium, phosphate and sulfate among the Nested Association Mapping (NAM) population founder lines. The data revealed that substantial genetic variation exists for multiple ion uptake rates in maize. Interestingly, specific nutrient uptake rates (nutrient uptake rate per length of root) were found to be both heritable and distinct from total uptake and plant size. The specific uptake rates of each nutrient were positively correlated with one another and with specific root respiration (root respiration rate per length of root), indicating that uptake is governed by shared mechanisms. We selected maize lines with high and low specific uptake rates and performed an RNA-seq analysis, which identified key regulatory components involved in nutrient uptake. The high-throughput multiple ion uptake kinetics pipeline will help further our understanding of nutrient uptake, parameterize holistic plant models, and identify breeding targets for crops with more efficient nutrient acquisition. Significance Statement Nutrient uptake is among the most limiting factors for plant growth and yet has not been used as a selection criterion in breeding. This is partly due to the lack of high-throughput phenotyping methods for measuring nutrient uptake. Here we describe a novel high-throughput phenotyping pipeline for quantification of multiple ion uptake rates. Using this new phenotyping system, our results demonstrate that specific ion uptake performance by maize plants is positively correlated among the macronutrients nitrogen, phosphorus, potassium and sulfur, and that substantial variation exists within a genetically diverse population. The findings reveal components of regulatory pathways possibly related with enhanced uptake, and confirm that nutrient uptake itself is a potential target for breeding of nutrient-efficient crops.

Nutrient uptake is critical for crop growth and is determined by root foraging in soil. Growth and branching of roots lead to effective root placement to acquire nutrients, but relatively little is known about absorption of nutrients at the root surface from the soil solution. This knowledge gap could be alleviated by understanding sources of genetic variation for short-term nutrient uptake on a root length basis. A modular platform called RhizoFlux was developed for high- throughput phenotyping of multiple ion-uptake rates in maize (Zea mays L.). Using this system, uptake rates were characterized for the crop macronutrients nitrate, ammonium, potassium, phosphate, and sulfate among the Nested Association Mapping (NAM) population founder lines. The data revealed substantial genetic variation for multiple ion- uptake rates in maize. Interestingly, specific nutrient uptake rates (nutrient uptake rate per length of root) were found to be both heritable and distinct from total uptake and plant size. The specific uptake rates of each nutrient were positively correlated with one another and with specific root respiration (root respiration rate per length of root), indicating that up- take is governed by shared mechanisms. We selected maize lines with high and low specific uptake rates and performed an RNA-seq analysis, which identified key regulatory components involved in nutrient uptake. The high-throughput multiple ion-uptake kinetics pipeline will help further our understanding of nutrient uptake, parameterize holistic plant models, and identify breeding targets for crops with more efficient nutrient acquisition.

Maize lateral roots exhibit determinate growth, whereby the meristem is genetically programmed to stop producing new cells. To explore whether lateral root determinacy is modified under water deficits, we studied two maize genotypes (B73 and FR697) with divergent responses of lateral root growth to mild water stress using an experimental system that provided near-stable water potential environments throughout lateral root development. First-order laterals of the primary root system of FR697 exhibited delayed determinacy when grown at a water potential of -0.28 MPa, resulting in longer and wider roots than in well-watered (WW) controls. In B73, in contrast, neither the length nor width of lateral roots was affected by water deficit. In water-stressed FR697, root elongation continued at or above the maximum rate in WW roots for 3 days longer, and was still 45% of maximum when WW roots approached their determinate length. Maintenance of root elongation was associated with sustained rates of cell production. In addition, kinematic analyses showed that reductions in tissue expansion rates with aging were delayed in the longitudinal, radial and tangential planes throughout the root growth zone. Thus, this study reveals large genotypic differences in the interaction of water stress with developmental determinacy of maize lateral roots.

Reactive oxygen species (ROS) can act as signaling molecules involved in the acclimation of plants to various abiotic and biotic stresses. However, it is not clear how the generalized increases in ROS and downstream signaling events that occur in response to stressful conditions are coordinated to modify plant growth and development. Previous studies of maize (Zea mays L.) primary root growth under water deficit stress showed that cell elongation is maintained in the apical region of the growth zone but progressively inhibited further from the apex, and that the rate of cell production is also decreased. It was observed that apoplastic ROS, particularly hydrogen peroxide (H2O2), increased specifically in the apical region of the growth zone under water stress, resulting at least partly from increased oxalate oxidase activity in this region. To assess the function of the increase in apoplastic H2O2 in root growth regulation, transgenic maize lines constitutively expressing a wheat oxalate oxidase were utilized in combination with kinematic growth analysis to examine effects of increased apoplastic H2O2 on the spatial pattern of cell elongation and on cell production in well-watered and water-stressed roots. Effects of H2O2 removal (via scavenger pretreatment) specifically from the apical region of the growth zone were also assessed. The results show that apoplastic H2O2 positively modulates cell production and root elongation under well-watered conditions, whereas the normal increase in apoplastic H2O2 in water-stressed roots is causally related to down-regulation of cell production and root growth inhibition. The effects on cell production were accompanied by changes in spatial profiles of cell elongation and in the length of the growth zone. However, effects on overall cell elongation, as reflected in final cell lengths, were minor. These results reveal a fundamental role of apoplastic H2O2 in regulating cell production and root elongation in both well-watered and water-stressed conditions.

In the published version of this editorial paper, the sentence in the first paragraph should be corrected as shown below.

Maize is one of the major food crops grown in the continental US, and as such, major interest is directed towards understanding its adaptability to drought stress. Certain cultivars of maize have shown increased resistance to water shortages, by continuing to maintain root growth even when under severe water stress. To better understand the molecular mechanisms which lead to such adaptation, we analyzed multiomics datasets generated from the growth zone of nodal roots from FR697, an inbred line that shows a superior capacity for root growth maintenance under drought stress. We used a research pipeline consisting of a discriminatory multiomics data integration approach, which uses a combination of sparse Generalized Canonical Correlation Analysis (sGCCA) and generalized Partial Least Square (PLS) analysis instead of traditional “filter funnel” approaches, to incorporate all datasets into one holistic global network and form clusters spanning all omics levels. We then linked significant elements from these clusters to various observations associated with drought stress in the root tip samples, reinforced by their roles in biological pathways.

Additional file 7: Table S7. List of miRNA-regulated gene transcripts detected in the primary root growth zone by degradome sequencing, and EdgeR-calculated fold-change value. The predicted miRNA-target transcript interactions that are conserved in other species are listed in red. The fold-change value of significantly differentially regulated transcripts (FDR

• Sustainable agriculture is complex and includes multiple interdependent goals. • Sound science and innovation are the keys to sustainable agriculture, and are already delivering results. • Greater investment is needed in the basics of agronomy, biotechnology, and plant breeding to ensure that farmers and consumers everywhere benefit from science and technology. • Farmers must receive support for implementing sustainability measures, especially in light of the downward trend of commodity prices.

Background MicroRNA-mediated gene regulatory networks play a significant role in plant growth and development and environmental stress responses. Results We identified 79 microRNAs (miRNAs) and multiple miRNA variants (isomiRs) belonging to 26 miRNA families in the primary root growth zone of maize seedlings grown at one of three water potentials: well-watered (− 0.02 MPa), mild water deficit stress (− 0.3 MPa), and severe water deficit stress (− 1.6 MPa). The abundances of 3 miRNAs (mild stress) and 34 miRNAs representing 17 families (severe stress) were significantly different in water-deficit stressed relative to well-watered controls (FDR < 0.05 and validated by stem loop RT-qPCR). Degradome sequencing revealed 213 miRNA-regulated transcripts and trancriptome profiling revealed that the abundance of 77 (miRNA-regulated) were regulated by water-defecit stress. miR399e,i,j-3p was strongly regulated by water-defcit stress implicating the possibility of nutrient deficiency during stress. Conclusions We have identified a number of maize miRNAs that respond to specific water deficits applied to the primary root growth zone. We have also identified transcripts that are targets for miRNA regulation in the root growth zone under water-deficit stress. The miR399e,i,j-3p that is known to regulate phosphate uptake in response to nutrient deficiencies responds to water-deficit stress, however, at the seedling stage the seed provides adequate nutrients for root growth thus miR399e,i,j-3p may play a separate role in water-deficit responses. A water-deficit regulated maize transcript, similar to known miR399 target mimics, was identified and we hypothesized that it is another regulatory player, moderating the role of miR399e,i,j-3p, in primary root growth zone water deficit responses.