Crop root system plasticity for improved yields in saline soils

Crop yields must increase to meet the demands of a growing world population. Soil salinization is increasing due to the impacts of climate change, reducing the area of arable land for crop production. Plant root systems are plastic, and their architecture can be modulated to (1) acquire nutrients and water for growth, and (2) respond to hostile soil environments. Saline soils inhibit primary root growth and alter root system architecture (RSA) of crop plants. In this review, we explore how crop root systems respond and adapt to salinity, focusing predominately on the staple cereal crops wheat, maize, rice, and barley, that all play a major role in global food security. Cereal crops are classified as glycophytes (salt-sensitive) however salt-tolerance can differ both between species and within a species. In the past, due to the inherent difficulties associated with visualising and measuring root traits, crop breeding strategies have tended to focus on optimising shoot traits. High-resolution phenotyping techniques now make it possible to visualise and measure root traits in soil systems. A steep, deep and cheap root ideotype has been proposed for water and nitrogen capture. Changes in RSA can be an adaptive strategy to avoid saline soils whilst optimising nutrient and water acquisition. In this review we propose a new model for designing crops with a salt-tolerant root ideotype. The proposed root ideotype would exhibit root plasticity to adapt to saline soils, root anatomical changes to conserve energy and restrict sodium (Na⁺) uptake, and transport mechanisms to reduce the amount of Na⁺ transported to leaves. In the future, combining high-resolution root phenotyping with advances in crop genetics will allow us to uncover root traits in complex crop species such as wheat, that can be incorporated into crop breeding programs for yield stability in saline soils.

Integrative Multi-omics Analyses of Barley Rootzones under Salinity Stress Reveal Two Distinctive Salt Tolerance Mechanisms

The mechanisms underlying rootzone-localized responses to salinity during early stages of barley development remain elusive. In this study, we performed the analyses of multi-root-omes (transcriptomes, metabolomes, and lipidomes) of a domesticated barley cultivar (Clipper) and a landrace (Sahara) that maintain and restrict seedling root growth under salt stress, respectively. Novel generalized linear models were designed to determine differentially expressed genes (DEGs) and abundant metabolites (DAMs) specific to salt treatments, genotypes, or rootzones (meristematic Z1, elongation Z2, and maturation Z3). Based on pathway over-representation of the DEGs and DAMs, phenylpropanoid biosynthesis is the most statistically enriched biological pathway among all salinity responses observed. Together with histological evidence, an intense salt-induced lignin impregnation was found only at stelic cell wall of Clipper Z2, compared with a unique elevation of suberin deposition across Sahara Z2. This suggests two differential salt-induced modulations of apoplastic flow between the genotypes. Based on the global correlation network of the DEGs and DAMs, callose deposition that potentially adjusted symplastic flow in roots was almost independent of salinity in rootzones of Clipper, and was markedly decreased in Sahara. Taken together, we propose two distinctive salt tolerance mechanisms in Clipper (growth-sustaining) and Sahara (salt-shielding), providing important clues for improving crop plasticity to cope with deteriorating global soil salinization.

A laser ablation technique maps differences in elemental composition in roots of two barley cultivars subjected to salinity stress

In saline soils, high levels of sodium (Na⁺ ) and chloride (Cl^- ) ions reduce root growth by inhibiting cell division and elongation, thereby impacting on crop yield. Soil salinity can lead to Na⁺ toxicity of plant cells, influencing the uptake and retention of other important ions [i.e. potassium (K⁺ )] required for growth. However, measuring and quantifying soluble ions in their native, cellular environment is inherently difficult. Technologies that allow in situ profiling of plant tissues are fundamental for our understanding of abiotic stress responses and the development of tolerant crops. Here, we employ laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS) to quantify Na, K and other elements [calcium (Ca), magnesium (Mg), sulphur (S), phosphorus (P), iron (Fe)] at high spatial resolution in the root growth zone of two genotypes of barley (Hordeum vulgare) that differ in salt-tolerance, cv. Clipper (tolerant) and Sahara (sensitive). The data show that Na⁺ was excluded from the meristem and cell division zone, indicating that Na⁺ toxicity is not directly reducing cell division in the salt-sensitive genotype, Sahara. Interestingly, in both genotypes, K⁺ was strongly correlated with Na⁺ concentration, in response to salt stress. In addition, we also show important genetic differences and salt-specific changes in elemental composition in the root growth zone. These results show that LA-ICP-MS can be used for fine mapping of soluble ions (i.e. Na⁺ and K⁺ ) in plant tissues, providing insight into the link between Na⁺ toxicity and root growth responses to salt stress.

Dynamics in plant roots and shoots minimize stress, save energy and maintain water and nutrient uptake

Plants are inherently dynamic. Dynamics minimize stress while enabling plants to flexibly acquire resources. Three examples are presented for plants tolerating saline soil: transport of sodium chloride (NaCl), water and macronutrients is nonuniform along a branched root; water and NaCl redistribute between shoot and soil at night-time; and ATP for salt exclusion is much lower in thinner branch roots than main roots, quantified using a biophysical model and geometry from anatomy. Noninvasive phenotyping and precision agriculture technologies can be used together to harness plant dynamics, but analytical methods are needed. A plant advancing in time through a soil and atmosphere space is proposed as a framework for dynamic data and their relationship to crop improvement.

Energy costs of salt tolerance in crop plants

Agriculture is expanding into regions that are affected by salinity. This review considers the energetic costs of salinity tolerance in crop plants and provides a framework for a quantitative assessment of costs. Different sources of energy, and modifications of root system architecture that would maximize water vs ion uptake are addressed. Energy requirements for transport of salt (NaCl) to leaf vacuoles for osmotic adjustment could be small if there are no substantial leaks back across plasma membrane and tonoplast in root and leaf. The coupling ratio of the H⁺ -ATPase also is a critical component. One proposed leak, that of Na⁺ influx across the plasma membrane through certain aquaporin channels, might be coupled to water flow, thus conserving energy. For the tonoplast, control of two types of cation channels is required for energy efficiency. Transporters controlling the Na⁺ and Cl^- concentrations in mitochondria and chloroplasts are largely unknown and could be a major energy cost. The complexity of the system will require a sophisticated modelling approach to identify critical transporters, apoplastic barriers and root structures. This modelling approach will inform experimentation and allow a quantitative assessment of the energy costs of NaCl tolerance to guide breeding and engineering of molecular components.

A Comparison of Petiole Hydraulics and Aquaporin Expression in an Anisohydric and Isohydric Cultivar of Grapevine in Response to Water-Stress Induced Cavitation

We report physiological, anatomical and molecular differences in two economically important grapevine (Vitis vinifera L.) cultivars cv. Grenache (near-isohydric) and Chardonnay (anisohydric) in their response to water-stress induced cavitation. The aim of the study was to compare organ vulnerability (petiole and stem) to cavitation by measuring ultrasonic acoustic emissions (UAE) and percent loss of conductance of potted grapevines subject to the onset of water-stress. Leaf (ψL) and stem water potential (ψS), stomatal conductance (gs), transpiration (E), petiole hydraulics (KPet), and xylem diameter were also measured. Chardonnay displayed hydraulic segmentation based on UAE, with cavitation occurring at a less negative ψL in the petiole than in the stem. Vulnerability segmentation was not observed in Grenache, with both petioles and stems equally vulnerable to cavitation. Leaf water potential that induced 50% of maximum UAE was significantly different between petioles and stems in Chardonnay (ψ50Petiole = -1.14 and ψ50Stem = -2.24 MPa) but not in Grenache (ψ50Petiole = -0.73 and ψ50Stem = -0.78 MPa). Grenache stems appeared more susceptible to water-stress induced cavitation than Chardonnay stems. Grenache displayed (on average) a higher KPet likely due to the presence of larger xylem vessels. A close relationship between petiole hydraulic properties and vine water status was observed in Chardonnay but not in Grenache. Transcriptional analysis of aquaporins in the petioles and leaves (VvPIP1;1, VvPIP2;1, VvPIP2;2 VvPIP2;3, VvTIP1;1, and VvTIP2;1) showed differential regulation diurnally and in response to water-stress. VvPIP2;1 showed strong diurnal regulation in the petioles and leaves of both cultivars with expression highest predawn. Expression of VvPIP2;1 and VvPIP2;2 responded to ψL and ψS in both cultivars indicating the expression of these two genes are closely linked to vine water status. Expression of several aquaporin genes correlated with gas exchange measurements, however, these genes differed between cultivars. In summary, the data shows two contrasting responses in petiole hydraulics and aquaporin expression between the near-isohydric cultivar, Grenache and anisohydric cultivar, Chardonnay.

Root spatial metabolite profiling of two genotypes of barley (Hordeum vulgare L.) reveals differences in response to short-term salt stress

Barley (Hordeum vulgare L.) is the most salt-tolerant cereal crop and has excellent genetic and genomic resources. It is therefore a good model to study salt-tolerance mechanisms in cereals. We aimed to determine metabolic differences between a cultivated barley, Clipper (tolerant), and a North African landrace, Sahara (susceptible), previously shown to have contrasting root growth phenotypes in response to the early phase of salinity stress. GC-MS was used to determine spatial changes in primary metabolites in barley roots in response to salt stress, by profiling three different regions of the root: root cap/cell division zone (R1), elongation zone (R2), and maturation zone (R3). We identified 76 known metabolites, including 29 amino acids and amines, 20 organic acids and fatty acids, and 19 sugars and sugar phosphates. The maintenance of cell division and root elongation in Clipper in response to short-term salt stress was associated with the synthesis and accumulation of amino acids (i.e. proline), sugars (maltose, sucrose, xylose), and organic acids (gluconate, shikimate), indicating a potential role for these metabolic pathways in salt tolerance and the maintenance of root elongation. The processes involved in root growth adaptation and the underlying coordination of metabolic pathways appear to be controlled in a region-specific manner. This study highlights the importance of utilizing spatial profiling and will provide us with a better understanding of abiotic stress response(s) in plants at the tissue and cellular level.

Advances in functional genomics for investigating salinity stress tolerance mechanisms in cereals

Abiotic stresses such as low water availability and high salinity are major causes of cereal crop yield losses and significantly impact on sustainability. Wheat and barley are two of the most important cereal crops (after maize and rice) and are grown in increasingly hostile environments with soil salinity and drought both expected to increase this century, reducing the availability of arable land. Barley and wheat are classified as glycophytes (salt-sensitive), yet they are more salt-tolerant than other cereal crops such as rice and so are good models for studying salt tolerance in cereals. The exploitation of genetic variation of phenotypic traits through plant breeding could significantly improve growth of cereals in salinity-affected regions, thus leading to improved crop yields. Genetic variation in phenotypic traits for abiotic stress tolerance have been identified in land races and wild germplasm but the molecular basis of these differences is often difficult to determine due to the complex genetic nature of these species. High-throughput functional genomics technologies, such as transcriptomics, metabolomics, proteomics, and ionomics are powerful tools for investigating the molecular responses of plants to abiotic stress. The advancement of these technologies has allowed for the identification and quantification of transcript/metabolites in specific cell types and/or tissues. Using these new technologies on plants will provide a powerful tool to uncovering genetic traits in more complex species such as wheat and barley and provide novel insights into the molecular mechanisms of salinity stress tolerance.

Genetic variation in the root growth response of barley genotypes to salinity stress

We aimed to identify genetic variation in root growth in the cereal crop barley (Hordeum vulgare L.) in response to the early phase of salinity stress. Seminal root elongation was examined at various concentrations of salinity in seedlings of eight barley genotypes consisting of a landrace, wild barley and cultivars. Salinity inhibited seminal root elongation in all genotypes, with considerable variation observed between genotypes. Relative root elongation rates were 60-90% and 30-70% of the control rates at 100 and 150mM NaCl, respectively. The screen identified the wild barley genotype CPI71284-48 as the most tolerant, maintaining root elongation and biomass in response to salinity. Root elongation was most significantly inhibited in the landrace Sahara. Root and shoot Na+ concentrations increased and K+ concentrations decreased in all genotypes in response to salinity. However, the root and shoot ion concentrations did not correlate with root elongation rates, suggesting that the Na+ and K+ concentrations were not directly influencing root growth, at least during the early phase of salt stress. The identification of genetic diversity in root growth responses to salt stress in barley provides important information for future genetic, physiological and biochemical characterisation of mechanisms of salinity tolerance.

Membrane topology of the cyanobacterial bicarbonate transporter, SbtA, and identification of potential regulatory loops

The transporter SbtA is a high affinity Na+-dependent HCO3- uptake system present in a majority of cyanobacterial clades. It functions in conjunction with CO2 uptake systems and other HCO3- uptake systems to allow cyanobacteria to accumulate high levels of HCO3- used to support efficient photosynthetic CO2 fixation via the CO2 concentrating mechanism in these species. The phoA/lacZ fusion reporter method was used to determine the membrane topology of the cyanobacterial bicarbonate transporter, SbtA (predicted size of ∼39.7 kD), cloned from the freshwater strain, Synechocystis PCC6803. The structure conforms to a model featuring 10 transmembrane helices (TMHs), with a distinct 5+5 duplicated structure. Both the N- and C-terminus are outside the cell and the second half of the protein is inverted relative to the first. The first putative helix appears to lack sufficient topogenic signals for its correct orientation in the membrane and instead relies on the presence of later helices. The cytoplasmic loop between helices 5 and 6 is a likely location for regulatory mechanisms that could govern activation of the transporter, and the cytoplasmic loop between helices 9 and 10 also contains some conserved putative regulatory residues.

Identification and functional characterisation of aquaporins in the grapevine, Vitis vinifera

Plant aquaporins belong to a large superfamily of conserved proteins called the major intrinsic proteins (MIPs). There is limited information about the diversity of MIPs in grapevine, and their water transport capacity. The aim of the present study was to identify MIPs from grapevine and functionally characterise water transport of a subset of MIPs. Candidate genes were identified, by screening a Vitis vinifera L. (cv. Cabernet Sauvignon) cDNA library with gene specific probes, for aquaporin cDNAs encoding members of the plasma membrane intrinsic protein (PIP) and tonoplast intrinsic protein (TIP) subfamilies. The screen resulted in the identification of 11 full-length and two partial length aquaporin cDNAs. VvTIP2;1 isoforms had different 3' UTRs, immediately upstream of the poly(A) tail, suggesting the presence of multiple cleavage sites for polyadenylation. Using published genome sequences of grapevine, we conducted a phylogenetic analysis of the MIPs with previously characterised MIPs from Arabidopsis. We identified 23 full-length MIP genes from the V. vinifera genome sequence of a near homozygous line (PN40024) that cluster into the four main subfamilies (and subgroups within) identified in other species. However, based on the identification of PIP2 genes in Cabernet Sauvignon that were not present in the PN40024 genome, there are likely to be more than 23 MIP genes in other heterozygous grapevine cultivars. Water transport capacity was determined for several PIPs and TIPs, by expression in Xenopus oocytes. Only VvPIP2 and VvTIP proteins function as water channels with the exception of VvPIP2;5. VvPIP2;5 differs from the water conducting VvPIP2;1 by the substitution of two highly conserved amino acids in Loop B (G97S, G100W), which was shown by homology modelling to likely form a hydrophobic block of the water pore.

The role of plasma membrane intrinsic protein aquaporins in water transport through roots: diurnal and drought stress responses reveal different strategies between isohydric and anisohydric cultivars of grapevine

We report physiological and anatomical characteristics of water transport across roots grown in soil of two cultivars of grapevine (Vitis vinifera) differing in response to water stress (Grenache, isohydric; Chardonnay, anisohydric). Both cultivars have similar root hydraulic conductances (Lo; normalized to root dry weight) that change diurnally. There is a positive correlation between Lo and transpiration. Under water stress, both cultivars have reduced minimum daily Lo (predawn) attributed to the development of apoplastic barriers. Water-stressed and well-watered Chardonnay had the same diurnal change in amplitude of Lo, while water-stressed Grenache showed a reduction in daily amplitude compared with well-watered plants. Hydraulic conductivity of root cortex cells (Lpcell) doubles in Chardonnay but remains unchanged in Grenache. Of the two most highly expressed plasma membrane intrinsic protein (PIP) aquaporins in roots (VvPIP1;1 and VvPIP2;2), only VvPIP2;2 functions as a water channel in Xenopus laevis oocytes. VvPIP1;1 interacts with VvPIP2;2 to induce 3-fold higher water permeability. These two aquaporins are colocated in the root from in situ hybridization and immunolocalization of VvPIP1 and VvPIP2 subfamily members. They occur in root tip, exodermis, root cortex (detected up to 30 mm), and stele. VvPIP2;2 mRNA does not change diurnally or with water stress, in contrast to VvPIP1;1, in which expression reflects the differences in Lo and Lpcell between cultivars in their responses to water stress and rewatering. VvPIP1;1 may regulate water transport across roots such that transpirational demand is matched by root water transport capacity. This occurs on a diurnal basis and in response to water stress that corresponds to the difference in drought tolerance between the cultivars.

Interactions between charged amino acid residues within transmembrane helices in the sulfate transporter SHST1

The aim of this study was to identify charged amino acid residues important for activity of the sulfate transporter SHST1. We mutated 10 charged amino acids in or near proposed transmembrane helices and expressed the resulting mutants in a sulfate transport-deficient yeast strain. Mutations affecting four residues resulted in a complete loss of sulfate transport; these residues were D107 and D122 in helix 1 and R354 and E366 in helix 8. All other mutants showed some reduction in transport activity. The E366Q mutant was unusual in that expression of the mutant protein was toxic to yeast cells. The R354Q mutant showed reduced trafficking to the plasma membrane, indicating that the protein was misfolded. However, transporter function (to a low level) and wild-type trafficking could be recovered by combining the R354Q mutation with either the E175Q or E270Q mutations. This suggested that R354 interacts with both E175 and E270. The triple mutant E175Q/E270Q/R354Q retained only marginal sulfate transport activity but was trafficked at wild-type levels, suggesting that a charge network between these three residues may be involved in the transport pathway, rather than in folding. D107 was also found to be essential for the ion transport pathway and may form a charge pair with R154, both of which are highly conserved. The information obtained on interactions between charged residues provides the first evidence for the possible spatial arrangement of transmembrane helices within any member of this transporter family. This information is used to develop a model for SHST1 tertiary structure.

Structure and function of a model member of the SulP transporter family

SHST1 is a sulfate transporter that belongs to a large and diverse family of anion transporters. Little is known about the structure and function of any member of the family. Site-directed mutagenesis of SHST1 is being used to understand the function of particular amino acids. We have mutated highly conserved amino acid residues and the results suggest that the first two helices play an important role in the transport pathway. Furthermore, mutation of equivalent residues to those altered in human genetic diseases produces deleterious effects in SHST1. These results suggest that there are similarities in the molecular mechanism of transport throughout the family and the information obtained with SHST1 may be applicable to the entire family.

Proline residues in two tightly coupled helices of the sulphate transporter, SHST1, are important for sulphate transport

The sulphate transporter SHST1, from Stylosanthes hamata, features three tightly coupled transmembrane helices which include proline residues that are conserved in most related transporters. We used site-directed mutagenesis and expression of the mutant transporters in yeast to test whether these proline residues are important for function. Four proline residues were replaced by both alanine and leucine. Only one of these proline residues, Pro-144, was essential for sulphate transport. However, mutation of either Pro-133 or Pro-160 resulted in a severe decrease in sulphate transport activity; this was due more to a decrease in transport activity than to a decrease in the amount of mutant SHST1 in the plasma membrane. These results suggest that all three proline residues are important for transport, and that the conformation of the three tightly coupled helices may play a critical role in sulphate transport. We also show that SHST1 undergoes a post-translational modification that is required for trafficking to the plasma membrane.

Homologous mutations in two diverse sulphate transporters have similar effects

Mutations in the human sulphate transporter gene, DTDST, have been implicated in several diseases. Analysis of affected patients has linked disease symptoms to faulty sulphate transporter activity. We have reproduced two of these mutations in SHST1, a homologous member of the family isolated from the tropical legume, Stylosanthes hamata. Both mutations significantly reduce sulphate transport activity of SHST1. These results indicate that conserved residues between distinct members of the family may share essential roles in structure or function. The results also suggest that putative helix 9 may be important for stability and/or trafficking of SHST1 to the plasma membrane.