Root plasticity under abiotic stress

1Climate change alters rainfall patterns and temperature, forcing ecological and agricultural systems to shift, transform or collapse. These changes in the environment, coupled with intensive agriculture, lead to soil degradation. Desertification and salinization are expected to increase in the future, threatening crop production, food security, and plant biodiversity. Soil degradation and various other abiotic stresses severely affect plant growth and account for the vast majority of global loss of crop yield. Considering the projected increase of the global human population and the increasing demand for animal protein consumption as well as the severity of present and future abiotic stresses, a major challenge will be to preserve biodiversity while sustainably feeding the global population. One approach to close the yield gap in the future is to study the adaptative abilities of different crops to abiotic stresses. These abilities are key to breed for more resilient crops that have the potential to counter soil degenerative processes, mitigate climate change, and produce stable yields.

2Osmotic stress regulates xylem patterning and induces suberin formation. DEEPER ROOTING 1 (DRO1) increases the gravitropism of rice roots and promotes drought tolerance.Salt stress reduces the root apical zone size and increases the basal zone size of tomato plants grown in soil rhizotrons, in Arabidopsis CYP79B2 and HKT1 are associated with lateral root growth maintenance under salt stress.ABA is required for root growth and hydrotropism in drought conditions, while halotropism is dependent on auxin redistribution and internal Na+/K+ balance.Formation of ROL in roots is an important trait for flooding tolerance in plants.Root responses to warm temperatures require brassinosteroid and auxin signaling.

3Osmotic stress regulates xylem patterning and induces suberin formation. DEEPER ROOTING 1 (DRO1) increases the gravitropism of rice roots and promotes drought tolerance.

4Salt stress reduces the root apical zone size and increases the basal zone size of tomato plants grown in soil rhizotrons, in Arabidopsis CYP79B2 and HKT1 are associated with lateral root growth maintenance under salt stress.

5ABA is required for root growth and hydrotropism in drought conditions, while halotropism is dependent on auxin redistribution and internal Na+/K+ balance.

6Formation of ROL in roots is an important trait for flooding tolerance in plants.

7Root responses to warm temperatures require brassinosteroid and auxin signaling.

8Plant roots provide anchorage, uptake, storage and transport of minerals and water. Plants can communicate and interact with the soil microbiome and other plants via their roots. Roots show high developmental plasticity and often adapt to their environment. The spatiotemporal configurations of roots are referred to as their root system architecture (RSA). RSA has been defined as the geometric description of the shape (topology and distribution) of the root system. In this review, we include RSA traits such as root positioning, length, angle, branching, surface area (including root hairs), coverage, and diameter. Studying the RSA of crops can provide insights into the genetic background of root traits for abiotic stress tolerance. This knowledge can be applied to new breeding strategies for stress-tolerant crops with stable yields even in challenging environments. Moreover, understanding RSA plasticity can give insights into the adaptability of plant species, allowing for novel strategies for replanting plants with adapted root architecture in places with extensive soil degradation to revert this process and support ecological succession. This review is aimed at highlighting recent discoveries on the molecular and cellular mechanisms behind root developmental plasticity as well as its importance for the survival of plants under abiotic stresses.

9Drought and salt are some of the most widespread abiotic stresses for plants. In addition to drought caused by water deficit, water deficit may occur in saline and cold soils and even flooded soils; all conditions that limit plant water uptake. Drought directly hampers root growth and development, and low water uptake by the roots puts extra tension on xylem tissue. Without acclimation of the xylem, this may cause embolism of the xylem resulting in hydraulic failure. Drought stress also affects nutrient uptake as nutrient mobility and diffusion is hampered. It alters soil microbial populations and activity and reduces the penetrability for the root systems, adding additional abiotic stress, soil compaction. Finally, postdrought rewatering of plants may provoke additional oxidative stress.

10Similar to drought, soil salinity provokes water deficit and nutrient imbalance. The low water potential of saline soils makes it difficult for roots to take up water by osmosis and salt ions compete with enzymes involved in the uptake and translocation of essential nutrients within plants. Studies have shown that supplementation of plants with micronutrients (alone or in form of biostimulants) may help to alleviate salt stress, suggesting that micronutrients may be a limiting factor to regular growth and development in saline soils. Salt, like drought stress, also induce changes in the soil microbial populations.

11In addition to water and nutrient deficit, soil salinity also provides (ion) toxicity stress. Accumulation of salt ions leads to hampered cell cycles and cytotoxic effects. Although most toxicity effects are attributed to sodium, chloride ions can also be detrimental by inducing chlorosis, chlorophyll deficiency that hampers photosynthesis. Drought and salinity stress perception have been suggested to occur through osmotic signals, cell wall integrity, plasma membrane lipids and ROS sensors. In roots and shoots, the most well-described signal provoked by drought is the plant hormone abscisic acid (ABA). In roots, ABA signaling coupled with modulation of auxin biosynthesis and transport appears to mediate changes in root architecture, morphology and anatomy to minimize water loss and maximize water uptake.

12Under mild stress, architectural adaptations are tailored toward drought or salt avoidance (Figure 1). Roots grow toward areas of higher water availability, often away from the dry top-soil layers where heat and salinity stress are most severe. Drought generally induces a parsimonious root architecture with fewer axial/lateral roots and a generally deeper rooting structure. Directional root growth toward areas of higher water is realized by investment into an elongation of roots while increasing the gravitropism response—adjusting root angles downward. Deeper rooting allows for efficient water capture and thereby ameliorates drought stress. Root angle is controlled by columella cells, which contain amyloplasts that sediment in the direction of gravity in the root tips. The asymmetric distribution of amyloplasts directs auxin flow to the lower side of the root. Relatively low auxin levels on the upper side of the root allow for increased elongation and the downward bending of the main root. Lateral roots, crown roots, and adventitious roots (ARs) tend to grow less toward gravity. Recent insights indicate that cytokinin functions as a potent repressor of gravitropic response in these root types (Waidmann and Kleine‐Vehn, 2020).

13showed that certain alleles of DEEPER ROOTING 1 (DRO1) and its homologs increase the gravitropism of rice (Oryza sativa L.) roots, effectively benefitting drought stress avoidance. Both DRO1 and qSOR1 (quantitative trait locus for SOIL SURFACE ROOTING 1), belonging to the IGT gene family (named after their IGT domain), are negatively regulated by auxin. Although their molecular function is unclear at present, it has been suggested that DRO1 and qSOR1 may have a role in establishing auxin gradients in the root tips. DRO1 homologs have been identified in several plant families including Arabidopsis and Prunus, and DRO1 clearly promotes deeper rooting and lateral root angle in these species.

14Positive hydrotropism, the bending of roots toward patches of water is another factor that influences RSA and drought tolerance. ABA was shown to be involved in the hydrotropism response of roots. ABA signaling subclass III Snf1-related kinases (SnRK2s) as well as MIZU KUSSEI1 (MIZ1) specifically expressed in the root cortex of the elongation zone are required for hydrotropism. Heterogeneous water presence at the root tip allows MIZ1 to generate a Ca2+ signal. The Ca2+ wave travels through the phloem to the elongation zone, at which point Ca2+ becomes asymmetrically distributed according to the water gradient. Interestingly cytokinin is also asymmetrically distributed during the hydrotropism response (; Figure 1). MIZ1 is also required for the hydrotropism-related asymmetric cytokinin redistribution. Furthermore, low ABA concentrations can induce root growth and promote hydrotropism by inhibiting the activity of PP2C phosphatases and enhancing the root apoplastic H+ efflux via H+-ATPase2 in both salt and drought conditions.

15Another drought-avoidance strategy involves the control of lateral root emergence under drought through hydropatterning and xerobranching. Hydropatterning is the preferential branching of roots into areas with high water content. Hydropatterning is independent of the ABA signaling, but it is dependent on AUXIN RESPONSE FACTOR 7 (ARF7). ARF7 is SUMOylated specifically on the side of the root in contact with a dry environment. SUMOylation of ARF7 enhances its interaction with its repressor, IAA3 (indole-3-acetic acid). Inhibition of ARF7 by IAA3 prevents the expression of lateral root initiation genes and lateral root initiation. Xerobranching is the strong repression of lateral root formation under drought when the roots are in aerial pores in the soil. When roots lack water contact in such soil macropores, ABA accumulates. The ABA binds to signaling PYR/PYL receptors, resulting in local auxin decrease. The ABA-induced auxin reduction could lead to the inhibition of lateral root formation. However, whether ABA signaling also plays a role in lateral root formation during xerobranching remains unknown.

16A marked response of the main root influencing root architecture in saline soils is halotropism (Figure 1). In roots of salt-sensitive, glycophyte species, including Arabidopsis, tomato and Sorghum, negative halotropism (root bending away from salty environments) is a key strategy to avoid salt stress. Halotropism is dependent on auxin redistribution in the root tip. The plasma membrane auxin transporter PIN2 relocalizes in a polar manner upon encountering salt. PIN2 promotes a relative reduction in auxin levels on the saline side of the root and enhanced bending away from salinity. PIN2 relocalization is associated with clathrin-mediated endocytosis and controlled by phospholipase PLDζ2. A Genome-Wide Association Study (GWAS) into natural variation of halotropism within Arabidopsis identified AtDOB1 and AtCHX13 as additional players in the response. Both genes are upregulated under salt stress, and both appear to be involved in Na+/K+ homeostasis, suggesting that internal ion homeostasis is likely a key factor underlying the halotropism response. Interestingly, several salt-tolerant, halophyte species such as Brassica indica and Limonium bicolor, show positive halotropism in heterogenous mild saline soils. It remains unknown whether similar molecular mechanisms regulate halotropism in the roots of these species.

17When challenged with high salt stress, the growth of primary and lateral roots is arrested. This arrest shows interesting temporal dynamics. Both root types first enter a quiescent phase (QP). In Arabidopsis, the QP generally lasts longer in lateral roots than primary roots (PRs) and is established by ABA-dependent inhibition of gibberellic acid (GA) and brassinosteroid (BR) signaling. Following the QP (lasting hours to several days), is a recovery phase with increased GA, BR and JA signaling and reduced ABA signaling, and this leads to a partial recovery of growth during salt stress. This partial growth recovery is likely due to the decrease of root meristem size. Upon salt stress, ROS accumulation is linked to the programmed cell death at vital meristematic tissues in the root tips and it is thought that this acts to protect the quiescent center from damage. A large-scale natural variation study in Arabidopsis, indicated that salt stress increases the variance in primary and lateral root growth between accessions. Subsequent GWAS studies indicated that natural variation in CYP79B2 and HKT1 (high-affinity Potassium Transporter 1) is associated with lateral root growth maintenance under salt stress. HKT1 is a sodium transporter that had been previously associated with salt tolerance in several plant species. While high HKT1 expression is generally considered positive for salt stress tolerance in crops, it can be detrimental to root growth in young seedlings, due to the accumulation of toxic Na+ ions in their roots. CYP79B2 on the other hand promotes the biosynthesis of IAOx, a precursor of the plant hormone auxin (IAA; ). CYP79B2 is expressed in root zones where lateral roots emerge, and mutant lines lacking both CYP79B2 and its homolog CYP79B3 have shorter and less dense lateral roots, specifically under high salt conditions.

18Defining a salt tolerance root ideotype is difficult. In a study with a limited set of Arabidopsis accessions, root systems with many, short lateral roots resulted in a lower internal shoot Na+/K+ ratio. In a more natural soil-rhizotron setup, salt stress was shown to significantly reduce the root apical zone size and strongly increased the basal zone size of tomato, resulting in the placement of lateral roots in the deeper zones of the soil with lower salt accumulation. Interestingly, a positive association between the root branched zone and the root K+/Na+ ratio was observed. In soil conditions, it is likely that the best adapted root system is the one that efficiently avoids saline environments by both root direction and placement and outgrowth of lateral roots. On the other hand, showed that a shallower root growth angle could be beneficial for salt tolerance in rice based on the qSOR1 loss-of-function mutants. Studying the molecular and cellular basis behind these changes may provide further insights into how plants cope with heterogeneous salt environments.

19Drought and salt induce also anatomical changes in the roots. For example under drought, cortical tissue with fewer, but large cell files is beneficial anatomy conferring tolerance. Cortical tissues can be converted into porous aerenchyma tissue in which cortical cells are lysed, creating an intercellular cell-less space that requires little energy to maintain. This process also releases nutrients to the surrounding cells and is prevalent in older roots that are no longer taking up water efficiently. The formation of lysigenous aerenchyma is also stimulated under salt stress.

20Under both drought and salt stress, the biosynthesis and deposition of suberin is stimulated in PRs, in particular in the endodermis and exodermis layers where suberin limits radial water loss. Studies in the grape show that generally enhanced suberin biosynthesis of the root system are associated with increased drought tolerance, while suberin layers in fine roots (roots ≤ 2 mm) may increase susceptibility to drought. The benefit of suberin may therefore be root-type specific. Studies comparing wild barley with domesticated cultivars indicate that wild barley has more suberin deposition in the exodermis under drought, similar to other drought-adapted species. Suberin was shown to function in salt exclusion, as a barrier in the endodermis. The suberin deficient mutant cyp86a1 is salt-sensitive compared with the wild-type and accumulates more Na+ ions. The most well-described TFs controlling suberization belong to the MYB family. MYB41 is upregulated by drought stress, salt stress and ABA, and stimulates suberin biosynthesis and deposition in Arabidopsis and grapevine. MYB41 regulates the expression of genes associated with the biosynthesis pathways of suberin and other waxy compounds that prevent water loss during salt stress. Another salt stress-responding MYB TF, SUBERMAN (MYB39) enhances suberin deposition in the endodermis. Other salt/drought stress induced TFs such as NACs and WRKYs have also been shown to stimulate the suberin biosynthesis pathway. ABA appears to promote suberization whereas ethylene represses this process.

21Lignin deposition is widely reported to enhance drought tolerance by forming a water-resistant barrier around mature xylem tissue. Interestingly, mutants overexpressing lignin biosynthesis genes often additionally show longer PRs. Like suberin, lignin biosynthesis is regulated by MYB TFs. During drought stress, xylem vessel size was shown to increase, and these large xylem vessels are responsible for increased root conductivity. Such root xylem distributions have been proposed to provide high hydraulic conductance while reducing the risk of hydraulic failure. Large xylem cells with high conductivity can allow for deeper rooting, but under prolonged stress, most drought-tolerant crops opt for numerous small xylem vessels, which can have big consequences for plant survival under drought. In poplar salt stress resulted in reduced xylem cells and vessel diameters, while in tomato roots lignified xylem cells increased under salt stress. In Arabidopsis, showed that in a thermospermine-deficient mutant salt hypersensitivity is linked to excessive xylem development, which suggests an opposite effect of salt compared with drought stress on xylem formation.

22The development of the xylem in the roots is controlled also by ABA. Drought-induced ABA accumulation activates microRNAs 165 (miR165) and miR166 to repress class III HD-ZIP TFs. Class III HD-ZIPs repress xylem formation and so their inhibition leads to the additional proto-xylem formation during drought stress.

23In olive trees, salt induces thickening of the high suberin cork layer in roots. This cork (periderm) layer strongly accumulates salts and reduces salt levels in the inner, salt-susceptible layers of the roots. Many species have the ability and the molecular framework to develop periderm tissue. Yet, little is known about the potential contribution of the periderm to abiotic stresses such as salt in non-woody plants. In addition to promoting root thickening, salt also accelerates root differentiation. In salt-treated plants, the formation of the endodermis, Casparian strip, and exodermis layers starts closer to the root tip.

24In addition to the adjustment of primary and lateral roots, recent research indicates the importance of root hair growth and development under drought and salt. Enhancement of root hair length and density has been reported to be a key factor in conferring drought tolerance in crops. Root hairs enhance the root surface area and may mediate higher penetrability on harder substrates (reviewed by ). Several genes influencing root hair formation under droughts such as EXPB7 and WOX11 also affect multiple traits conferring drought tolerance. The GLABRA2 TF negatively regulates root hair growth in response to osmotic stress. Under salt stress, both root hair length and density were shown to be decreased. It has been proposed that the Salt Overly Sensitive (SOS) pathway is involved in salt-responsive root hair modulation. sos1-3 lines show dramatically reduced root hair length or root hair density under salt. Overexpression of Triptychon (TRY) TFs from the halophyte Limonium bicolor in Arabidopsis showed their involvement in the salt tolerance root hair development pathway.

25For every species of plant, there is a range of temperatures at which growth is permitted. Temperatures above this range (heat stress) and temperatures below this range (cold stress) generally inhibit growth. Thermomorphogenesis is the effect of ambient (mild) temperatures on plant morphology. In Arabidopsis, growth temperatures of around 12°C to 28°C are typically considered as thermomorphogenic. Ambient temperature perception in the shoot is relatively well understood. Shoot thermomorphogenesis is controlled through the temperature-sensitive function of the phytochrome B photoreceptor. Given that phytochrome B requires light for its activation and the (mature) root is located underground, it is probable that other temperature sensors are utilized in the root. Recently, it was shown that the circadian clock component ELF3 also functions as a shoot temperature sensor. At warm temperatures, ELF3 undergoes phase separation to an inactive state. This process is presumably independent of light and so could conceptually play a role in root thermomorphogenesis. Another recent article showed a temperature signaling mechanism that requires the mitogen-activated protein kinase kinase kinase kinase4 (MAP4K4), TOT3. The TOT3 pathway is independent of phyB and also has the potential to act in the root. There appears to be a genetic linkage between shoot and root elongation at warm temperatures, but dissected roots are also capable of responding to temperature cues. This suggests that root elongation at ambient warm temperatures may be governed both directly by signaling events in the root, and indirectly through signaling events in the shoot.

26Outside of the ambient temperature range (during heat or cold stress), there are numerous potential sensors. Heat stress interferes with protein folding, ion channel activity, cell membrane integrity and enzyme function. All of these signals could conceivably contribute to root growth arrest during heat stress. In Arabidopsis shoots, sudden exposure to heat stress is associated with Ca2+ and ROS waves. Ca2+ and ROS waves are observed in response to multiple environmental stresses, and it is feasible that they are involved in the inhibition of root growth under heat stress. Recently two cold sensing mechanisms were identified. In Arabidopsis shoots, mRNA translation rates drop dramatically on exposure to cold temperatures. The inhibition of translation is coupled with an increase in intracellular free Ca2+. Intracellular Ca2+ activates CAMTA transcription factors and leads to the induction of cold-induced genes. Strikingly, chemical inhibition of translation has a similar effect on intracellular free Ca2+ and CAMTA-dependent gene expression. It has been proposed that cold temperatures reduce the translational efficiency of ribosomes and this promotes Ca2+ release and downstream signaling events. This work was based on whole seedlings, but given that cold stress also provokes transient increases in intracellular Ca2+ in the root, a similar mechanism may play a role in cold stress-mediated root inhibition.

27Another recent study found that reduced growth rates at cold temperatures can act as a signal itself. NTL8 (a transcription factor that promotes vernalization) accumulates in cold grown roots, without changes in gene expression or protein stability. Modeling approaches demonstrated that reduced cell elongation at cool temperatures reduces the cellular dilution of NTL8 in the root tip. This conclusion was supported by the fact that several pharmacological agents that supress root growth also led to NTL8 accumulation. It is not clear whether NTL8 accumulation plays a role in repressing root elongation at cool temperatures, but the same concept would likely hold for any long-lived protein. Moreover, it’s feasible that a similar mechanism contributes to root morphology under any stress that reduces root elongation.

28At cool temperatures (around 12°C–20°C) Arabidopsis roots develop a compact structure, whereas at warm temperatures (around 21°C–28°C) roots increasingly adopt an elongated, open architecture. Both heat and cold stress generally inhibit root elongation, but in field conditions, they are unlikely to result in the same root architecture. Temperature extremes are normally preceded by warm or cool periods through which root growth is permitted. A heat-stressed root is, therefore, more likely to have an elongated structure and cold stressed root is more likely to be compact.

29Warm ambient temperatures promote primary/seminal root elongation in diverse monocots and dicots (;;; Figure 1). In Arabidopsis and maize, warm temperature increases cell elongation rates in the root elongation zone, and reduces root meristem size. Arabidopsis main roots are slightly thinner at warm temperatures, but in maize, the opposite trend has been observed. Warm temperature promotes lateral root development in many species, but its effect on lateral root elongation is species-specific. Lateral root elongation was enhanced at warm temperatures in cotton and sunflower, but not affected in maize. In soybean and oilseed rape, warm temperatures increased the angle between primary and lateral roots, resulting in a more open structure. In Arabidopsis, warm temperatures promoted lateral root gravitropism, resulting in a deeper and more vertically oriented root system.

30The adaptive benefit of RSA changes at warm temperature effects is an open question. There is a negative correlation between temperature and water availability. High temperature increases evaporation from soils and evapotranspiration through plants. The reduced transpiration of plants during drought stress may induce also heat stress in the leaves. It may be that the elongated structure adopted by roots at warm temperature serves to enhance water uptake. Intriguingly, mild drought has a similar effect on root architecture as ambient warm temperatures. It has even been postulated, that temperature sensing in the roots could have derived from a drought sensing pathway, although experimental evidence of this is currently lacking.

31Temperature extremes are predicted to become more common in the future and optimizing the RSA of crops may help to increase their heat tolerance. A recent study on the temperature-stress resilience of plants on a global scale found that (as with animals) there is more variation in the ability of plants to survive cold stress than heat stress. The authors found that there is much more variation in cold stress tolerance than warm stress tolerance in plants. This suggests that there are many different pathways that plants can acquire cold tolerance, but that the development of heat tolerance is more difficult. Breeding plants for heat tolerance may therefore present a sizable challenge.

32PR elongation in Arabidopsis is the most well-characterized root response to ambient warm temperature. Even so, there is still only limited information on how this developmental process is regulated. Warm temperatures promote auxin signaling at the root tip. It appears that brassinosteroid signaling is also involved, but its directionality is debated. Some evidence implies that brassinosteroid signaling is reduced at warm temperature, whereas evidence from other studies implies that brassinosteroid signaling is increased. These conflicting results could be explained by the tissue-specific nature of brassinosteroid signaling. In the epidermis, brassinosteroid promotes PR elongation, whereas in the stele brassinosteroid represses elongation. Investigation of the tissue-specific effects of temperature on brassinosteroid signaling may help to resolve this point. Warm temperatures promote the transcription of heat shock protein (HSP) chaperones. HSP90.1 has been shown to promote the stability of the auxin receptor TIR1 and the negative regulator of brassinosteroid signaling BIN2 and so HSP90.1 probably contributes to ambient temperature signaling in the root.

33Currently, very little is known about how warm temperatures promote lateral root development. It is feasible that (as in the PR tip) increased auxin signaling is required. Lateral root initiation requires the rephasing of the circadian clock and so the warm temperature-mediated inactivation of clock-component ELF3 could well play a role. To our knowledge, there are no studies on the mechanism of warm temperature-mediated inhibition of root gravitropism. Further investigation into this phenotype may yield interesting insights into the control of root thermomorphogenesis.

34Flooding is the collective term of two distinct abiotic stresses; soil waterlogging and submergence. Flooding has a multitude of detrimental effects on plant growth and development (reviewed by ). One of the predominant stress factors in a flooded environment is the inhibition of gas diffusion, leading to oxygen deficiency (hypoxia). Hypoxia hampers respiration and limits energy production. Reduced energy production leads to reduced uptake of nutrients, and water, and metabolic imbalance. Hypoxia also inhibits root hydraulic conductivity, restricting water uptake despite environmental excess. Following flooding, re-exposure of plants to oxygen additionally results in oxidative damage.

35One of the first signals of hypoxia is the rapid accumulation of ethylene around the roots, due to reduced gas diffusion. The accumulation of ethylene acts to promote root meristem hypoxia tolerance. During postflooding recovery the hormone jasmonate (JA) accumulates rapidly in Arabidopsis rosettes. The transcription factor MYC2 is upregulated upon JA accumulation, which in turn stimulates genes involved in antioxidant synthesis pathways. JA-mediated antioxidant synthesis likely limits oxidative damage in these conditions. Curiously, during post-flooding recovery, ethylene seems to act as a negative regulator of the recovery by enhancing chlorophyll breakdown, water loss and senescence. It is currently unclear if these signaling pathways in rosettes also apply to the root. Considering that the JA has a well-established role in defense against biotic stress, it is likely that the reoxygenation response overlaps with known biotic defense responses.

36The majority of RSA adaptations during flooding are directly related to maximizing oxygen uptake, controlling oxygen loss. The first response to hypoxia includes a stop in both the formation and elongation of lateral roots. These responses are driven by ethylene signaling. The formation of lateral roots is repressed by ERF-TFs. RAP2.12 and HRE2 have been shown to bind and repress the expression of genes involved in lateral root primordia formation, such as LBD16, interfering with local auxin signaling that promote lateral root formation.

37Under flooding stress, plants also invest in ARs formation. ARs are roots that are formed post-embryonically from organs other than the root, such as the stem. Although certain plants can form ARs constitutively, de novo AR formation is particularly stimulated under flooding. AR formation and elongation allows the root system to grow toward oxygen-rich surfaces or even the atmosphere (aerial AR), as AR growth angles differ from regular root types. In rice, ARs have been reported to grow toward the surface enabling ethylene venting and re-aeration (Figure 1). Polar auxin redistribution by PIN1 and PIN2 in the root tip of ARs are involved in this process. Moreover, ARs provide additional anchorage post-flooding and benefit nutrient uptake. Anatomically, flood induced ARs are relatively cost-efficient due to their low density of energy-demanding cells; they contain more aerenchyma, which improves internal aeration within roots. In extreme cases of flooding, a plant’s original root system may be entirely substituted for an AR root system. Studies in flood-tolerant species indicate mechanistic variation underlying AR formation: ethylene has been reported to promote AR formation in rice while in Arabidopsis ethylene was found to inhibit AR formation. It is likely that due to evolutionary selection, flooding tolerant plants have evolved a different AR induction system. Plants can also alter their original roots angles and anatomy during flooding conditions. Hypoxic treatment induced Arabidopsis PR bending almost perpendicular to the gravity vector. After the re-establishment of normal oxygen conditions, the effect was reversed. In addition, it was shown that both RAP2.12 and HRE2 TFs negatively regulate hypoxia-driven root bending. Many questions remain to be answered regarding the root bending response, including the mechanism and adaptations that aquatic and wetland plants use in the regulation of hypoxia-driven root bending.

38The most well-described adaptations to flooding include the formation of aerenchyma and the formation of oxygen loss barriers. The formation of aerenchyma is regulated by ethylene and high concentrations of ethylene stimulate ROS production in the root cortex which results in controlled programmed cell death (Yamauchi et al.,, ). As with AR formation, ethylene is involved in the induction of aerenchyma formation, but auxin signaling and transport is needed for constitutive aerenchyma formation in rice (Yamauchi et al.,, ). Plants have evolved root adaptations to inhibit oxygen loss during floods through the synthesis of physical barriers, Radial Oxygen Loss (ROL) barriers. showed that ROL at the root tips appears to be a positive trait that correlated with biomass and nutrient uptake across 35 plant species. ROL barriers are generally formed 20–30 mm behind the root tips and are characterized by an increase in suberization of epidermal root cells. Importantly, ROL barriers which can be formed from the cortex layer to the rhizosphere (outer cell layers) of the root do not seem to hamper water or nutrient transport. Besides ROL barriers preventing oxygen loss, they may also allow oxygen flow to root tips. Under anoxic conditions, anaerobic microorganisms secrete organic acids, many of which are phytotoxic, and hamper nutrient availability for plant roots. These toxic organic acids appear to be the major environmental stimulus for ROL barrier formation. ROL barriers are predominantly reported to be formed in ARs of wetland plants. found ROL formation in lateral roots in teosinte (Zea nicaraguensis), a flooding-tolerant plant. In the future, the genetic background for this trait might provide important insights on flood tolerance through ROL barrier development.

39In the recent years, many discoveries have been made concerning the molecular mechanisms and signaling of abiotic stresses perception in plants. How abiotic stress perception impacts root plasticity is still an open question. Recently, several advances have been reported, including the discovery of DRO1 as a regulator of root angle, ABA controlled root growth, molecular mechanisms affecting halotropism and hydrotropism under salt and drought stress, ABA-mediated changes in xylem patterning during osmotic stress, the role of ROL barriers during flooding in teosinte and Glabra2- dependent root hair growth under drought and salt stress.

40Some of the molecular regulations involved in the root tropisms under different stresses are less understood. An example is the interaction between ABA-dependent and cytokinin-dependent hydrotropism. It was shown that MIZ1 is induced by both ABA and cytokinin and thus could be the link between the two pathways regulating PR hydrotropism response. The role of ABA signaling in lateral root development during xerobranching needs to be addressed as well.

41Furthermore, little is known about the molecular control of root thermomorphogenesis as well as on the mechanism of warm temperature-mediated inhibition of root gravitropism. In natural soils under drought stress, roots need to adapt their architecture and respond to drought, heat, and even soil compaction stresses at the same time. The links and molecular interaction between these soil stresses need further investigation.

42So far only a handful of GWAS studies have been performed to identify root traits related to abiotic stress resilience. Moreover, this knowledge is restricted mainly to the model species Arabidopsis and performed in vitro and in controlled climate conditions. An interesting question is how the RSA plasticity of different crops contributes to their survival under abiotic stress conditions. For example, although tuber plants like potatoes are very important crops agronomically, research on the importance of their RSA for the resilience to abiotic stresses is limited. To identify whether the gene regulatory networks controlling root architecture under different abiotic stresses are conserved between species or translatable from the model plant Arabidopsis into crops species, it will be interesting to compare if the hydrotropism and other root tropism responses are regulated by the same molecular mechanisms and hormonal cross talks like shown for the model species Arabidopsis. The discovery of root traits in crops associated with resilience to abiotic stress(es) will lead to new breeding strategies and selected genotypes that can grow and produce a stable yield in less favorable or changing environmental conditions. These robust crops could grow better in salinized or dry soil with fewer nutrients which will help to close the yield gap in the future and reduce the use of freshwater resources. The recent emergence of molecular technologies including single-cell sequencing, CRISPR/CAS9 genome editing as well as tissue- and cell-specific promoters studies for imaging of cellular processes will greatly contribute to our understanding of crop root plasticity under stress.

43In the field, crops are grown in soil and experience different mild or severe stresses at the same time. However, little is known about how the soil quality, soil type and availability of nutrients and soil structure influences plant root traits (bending of the roots, root angle) and adaptations in crops (see Outstanding Questions). Recently it was shown that the growth of roots in compact soils is inhibited due to the accumulation of ethylene, mirroring the pathway controlling hypocotyl emergence from compact soil. In addition, the root phenotype Multiseriate cortical sclerenchyma (MCS) associated with the ability to penetrate compacted soils was identified in maize and wheat. Interestingly MCS formation could be induced by exogenous ethylene. Another potential root adaptive mechanism, root circumnutation (the ability of the root to undergo helical movement) and its molecular regulation were recently revealed. Root circumnutation was proposed to serve as an adaptation of the PR to penetrate hard soils and to avoid obstacles in the soil. In rice, HK1 (histidine kinase-1 gene) was shown to be involved in the regulation of root circumnutation. Interestingly and in line with the proposed role of root circumnutation, the hk1 mutant is unable to explore/penetrate efficiently artificial solid surfaces or clay particles compared with the wild type rice roots.

44Although it has been shown that abiotic stresses like drought and salt can change the rhizosphere community of the roots in different crops, how RSA could influence the recruitment of beneficial root microbiome under abiotic stress remains to be discovered (see Outstanding questions). Another important direction of research is to understand the molecular mechanism of root-microbial interactions, the role of root exudates in these interactions in presence of abiotic stress or a combination of stresses. Future research should address the question of how crop RSA modulation interacts with the soil microbiome under stress. In summary, to understand the underlying mechanisms of plant root plasticity for the survival of crops under abiotic stresses, further research is needed to study root adaptations to single stresses in different environments (soil type, quality, and microbiome) and to multiple simultaneous stresses.

45How do plant roots recruit a beneficial rhizobiome under abiotic stress and what is the role of root exudates in this interaction?How do plants shape their root architecture under a combination of different stresses?Is there an interaction between soil type and root system plasticity of crops under abiotic stress?How does soil compaction affect the RSA of different crops?What is the contribution of the RSA plasticity of agronomically important tuber crops for their ability to survive under abiotic stress?What is the effect of abiotic stresses on alternative, less conventional plants not used in high input agroecosystems?

46How do plant roots recruit a beneficial rhizobiome under abiotic stress and what is the role of root exudates in this interaction?

47How do plants shape their root architecture under a combination of different stresses?

48Is there an interaction between soil type and root system plasticity of crops under abiotic stress?

49How does soil compaction affect the RSA of different crops?

50What is the contribution of the RSA plasticity of agronomically important tuber crops for their ability to survive under abiotic stress?

51What is the effect of abiotic stresses on alternative, less conventional plants not used in high input agroecosystems?

52This work was supported by the Dutch Research Council (NWO/OCW), as part of the MiCRop Consortium Programme, Harnessing the second genome of plants (grant number 024.004.014) and by NWO-TTW-H.I.P. (grant 16893 to C.T). We also acknowledge support by the European Union's Horizon 2020 Research and Innovation Programme under grant agreement No. 771134, ERA-NET Cofund SusCrop grant, being part of the Joint Programming Initiative on Agriculture, Food Security and Climate Change (FACCE-JPI) to C.T. and R.K., and a Wageningen Graduate Schools Grant/Award: Postdoctoral Talent Programme to S.H.

53Conflict of interest statement. The authors declare that there is no conflict of interest.