Roots are axial multicelular structures of sporophytes of vascular plants which usually occurs underground, have strictly apical elongation growth, and generally have gravitropic responses which range from positive gravitropism to diagravitropism, combined with negative phototropism 55. Root growth regulation, and its response to changing environmental conditions, is a highly complicated process that is controlled at many different levels by complex actions of gene networks in both time and space 35. Root growth relies on a specific set of signals involving hormones, nutrients and carbon supply 37. They generated a fractal-based model for root development that accounts for specific interactions between ethylene levels, nitrogen availability and energy supply.

Root system architecture (RSA) refers to the spatial configuration of the root system or the explicit deployment of root axes 43. Under poorly understood genetic control, RSA exhibits plasticity and responds to external environmental conditions such as soil moisture, nutrients, temperature, pH, and microbial communities 4. The study of RSA is important for agricultural productivity because most soils have uneven distribution of resources and/or localized depletions that make spatial distribution of the root system an important determinant of a plant’s ability to exploit these resources 43.Roots are essential for plant productivity and serve a variety of functions, such as water and nutrient uptake, forming symbioses with other microorganisms in the rhizosphere, anchoring the plant to the soil, and acting as storage organs. The different interactions of a root with its environment depend on its organization and structure, from the cellular to whole-plant level. The root contains a stele, comprised of the xylem, the phloem, and the pericycle 66.

The main functions of a root system are anchorage and uptake of water and nutrients. In trees and other woody species, extensive belowground structures whose main role is to provide support rather than nutrient acquisition are required but in smaller plant species anchorage occurs largely as a secondary function of root growth and development in soil 28. The overall form or ‘architecture’ of the root system is also important for anchorage and water-nutrient uptake. Root system architecture is very varied among different plant species but within species architecture is flexible and can alter as a result of prevailing soil conditions. This flexibility arises due to the modular structure of roots which enables root deployment in zones or patches rich in moisture or nutrients 28.

A major difference between plant and animal development is that positional information rather than cell lineage determines cell fate in plants 65. Post-embryonically, plant development is essentially driven by stem cells localized in apical regions of shoots and roots, and referred to as apical meristems. This particular characteristic allows plants, which are sessile organisms, to adapt their morphology and organ development to the encountered environmental conditions. The spatial configuration of the root system (number and length of lateral organs), so-called root architecture, vary greatly depending on the plant species, soil composition, and particularly on water and mineral nutrients availability 45. Plants can optimize their root architecture by initiating lateral root primordia and influencing growth of primary or lateral roots. The root system results from the coordinated control of both genetic endogenous programs (regulating growth and organogenesis) and the action of abiotic and biotic environmental stimuli 45. The interactions between these extrinsic and intrinsic signals however complicate the dissection of specific transduction pathways. Such complex traits likely depending on multiple genes may be analyzed through quantitative genetics via the identification of quantitative trait loci (QTL) linked to root architecture 19. Understanding the molecular mechanisms governing such developmental plasticity is therefore likely to be crucial for crop improvement in sustainable agriculture. The embryonic root apical meristem (RAM) specification occurs very early in embryo development 6. The RAM constitutes the stem cell niche that eventually produces all below-ground organs, including lateral roots 58.

The different stages of root development are controlled and regulated by various phytohormones with auxin playing a major role 40. In roots, auxin is involved in lateral root formation, maintenance of apical dominance and adventitious root formation. Auxin also plays a major role in lateral root initiation and development. Lateral root development can be divided in different steps: primordium initiation and development, emergence, and meristems activation. Auxin local accumulation in Arabidopsis root pericycle cells adjacent to xylem vessels, triggers lateral root initiation by re-specifying these cells into lateral root founder cells 17. All these developmental events require correct auxin transport and signaling. Furthermore, it is also involved in the growth and organization of lateral root primordia and emergence from the parent root 36.Indeed, mutants or transgenic lines with elevated auxin biosynthesis and endogenous levels of IAA display significant increased root branching 64. Auxin transport into the regions where lateral root initiate also seems crucial for the regulation of root branching 11.

Breeding efforts to improve crop yield are in general focused on aboveground, shoot-related phenotypes, whereas the roots as ‘hidden half’ of the plant are still an under-utilized source of crop improvement 1269. Trials aimed to select for new cultivars with improved crop yield are in general performed under optimal nutrient concentrations, which has often led to selection for smaller and less plastic roots 73. Moreover, modern cultivars develop in general faster and the earlier initiation of shoot sinks stimulates the investment of biomass into the shoots rather than into the roots. Modern wheat cultivars indeed have smaller root sizes and root:shoot ratios than older ones 70. Given the crucial role roots play in the establishment and performance of plants, researchers have started ‘the second green revolution’ to explore the possibility of yield improvements through optimization of root systems 42. Because water and nutrients are not evenly distributed in the soil, the spatial arrangement of the root system is crucial for optimal use of the available resources. This spatial arrangement of the root and its components is referred to as root system architecture (RSA). Length, number, positioning, and angle of root together determine RSA. These traits determine the soil volume that is explored.

In addition, the root surface area depends on root hair development and root diameter. The ability to adjust RSA is an important aspect of plant performance and its plasticity to a large variety of abiotic conditions 67. Root development is guided by environmental information that is integrated into decisions regarding how fast and in which direction to grow, and where and when to develop new lateral roots 45. The limits of root system plasticity are determined by intrinsic pathways governed by genetic components 51662530. Understanding the development and architecture of roots, as well its plasticity, holds thus great potential for stabilizing the productivity under suboptimal conditions in the root environment 1275.

In light of growing concerns over the threat of water and nutrient stress facing terrestrial ecosystems, especially those used for agricultural production, increased emphasis has been placed on understanding how abiotic stress conditions influence the composition and functioning of the root microbiome and the ultimate consequences for plant health. However, the composition of the root microbiome under abiotic stress conditions will not only reflect shifts in the greater bulk soil microbial community from which plants recruit their root microbiome but also plant responses to abiotic stress, which include changes in root exudate profiles and morphology 27.

The bacterial and fungal members of the root microbiome can establish commensal, pathogenic, and beneficial associations with their host 53.A large body of evidence highlights the beneficial services provided by the root microbiome, particularly its importance in maintaining plant productivity by contributing to plant biotic and abiotic stress resistance and resilience via many mechanisms 5368.

Though root systems are genetically determined they can be strongly influenced by a wide range of abiotic and biotic factors, including the presence of soil microorganisms. In some cases the effect upon root growth and morphogenesis are clearly evident with the formation of visible novel organs (e.g. root nodules in the Rhizobium-legume symbioses), while in others the impact upon roots are much less evident 28.

Pathogenic fungi reduce plant growth and affect root architecture 28. In tomato plants infected by Rhizoctoniasolani, the root system is characterized by the scarcity of short adventitious roots and the emergence of many short laterals, leading to a more branched root system 60. R. solani and Pithium sp. have been shown to induce a more monopodial type of branching pattern, with fewer orders of branching than uninfected controls in tomato and Medicago sativa, respectively 60. Coralloid roots are characterized by dichotomous branching, forming coral-like shapes. Their development begins with the formation of young roots named precoralloids that, when mature, are invaded by cyanobacteria located between the cells of the root cortex 15. Coralloid roots infected by cyanobacteria are surrounded by a pronounced layer of mucilaginous material, where cyanobacteria occur as short hormogonial filaments, the infective units of the Nostoc species involved in the symbiotic association 26. Hormogonia penetrate the roots through breaks in the dermal layer and reach, through a cortical channel, the cyanobacterial zone, which is the structural and physiological site of the CycasCyanobacteria symbiosis.

Nodules are specialized root organs in which symbiotic bacteria (Rhizobia) are able to convert atmospheric nitrogen into ammonia as a nitrogen source. Establishment of the Rhizobium-legume symbiosis depends on a molecular dialogue: flavonoids excreted by host plant roots induce the expression of bacterial nod genes, which encode protein involved in the synthesis and excretion of specific lipochitooligosaccharide signalling molecules called nod factors, that in turn are recognised by host legumes 259. Responses to nod factors by root hairs include: altered ion fluxes and plasma membrane depolarisation, calcium spiking, root hair deformation (due to changes in the actin cytoskeleton), and early nodulin gene expression.

In cortical cells, nod factors induce nodulin gene expression and cell division leading to nodule primordium formation 2. In legumes Rhizobia induce two types of nodules: determinate and indeterminate 15. The latter are the most commonly formed on temperate legumes by Rhizobium species, while the former are induced by Bradyrhizobium (the name is associated with the slow growth of these bacteria) on tropical legumes. Nodule formation is a multistep process. Rhizobia move to roots by positive chemotaxis in response to root exudates. The bacteria then infect the host roots via root hairs, or via wounds and lesions, or through spaces occurring around root primordia or adventitious roots. In the case of root-hair infection, the attachment of Rhizobia leads to root hair curling, Rhizobia then enter the root by invagination of the plasma membrane, and induce formation of an infection thread, a growing tube with cell wall material filled with growing bacteria 59. Rhizobia move down the infection thread towards the root cortex, where cell division leads to the production of nodule primordia, functioning as a meristem 2.

In pea, the genes controlling nodule morphogenesis have been identified for plant tissue colonization and differentiation of bacteria into bacterioids and for the development of nodule tissue 10. The genetic system controlling nitrogen-fixing symbiosis development in plants likely evolved from the system controlling AM symbiosis 10. Rhizobia obtain carbon compounds, especially malate, from their host and in turn perform nitrogen fixation at the centre of the nodule in a microaerobic zone surrounded by a layer of very closely packed cells with few air spaces.

Ectomycorrhizal are formed by mutualistic interactions between soil fungi and the roots of woody plants. In Ectomycorrhizal plants, roots usually have very few, or no, root hairs and tend to be short and thick. Within the root, hyphae always remain apoplastic and can colonize the epidermal (angiosperms) and the cortical cell (gymnosperms) layers, forming the Hartig net, a complex branched structure, which mediates nutrient transfer between fungus and plant 66. The most evident root modifications are the early formation of lateral roots and a dichotomy of the apical meristems in a number of species. External hyphae extend out of the depletion root zones, to explore the soil substrate and are responsible for the nutrient capture and water uptake of the symbiotic tissues. The fungi may also acquire nutrients from more complex organic substrates, but large differences between different species and even among strains of the same fungus exist in accessing these complex substrates 56. The structure of ectomycorrhizal is essentially determined by the fungal species rather than the host plant, however there is considerable variation in the degree of host specificity among species and even among strains of ectomycorrhizal fungi 38.

Root system structure is also influenced by other beneficial soil micro-organisms such as the root colonizing “Plant Growth Promoting Rhizobacteria (PGPR). PGPR’s affect root architecture by increasing total root length and branching as a consequence of hormone production and improved plant mineral nutrition 9. In turn, these changes to the root system architecture likely impact upon microbial dynamics in the rhizosphere through altered rhizodeposition including changes in signalling molecules released 3.Plants with different root system structure and physiology, are differently dependent upon mycorrhization 18 while, in turn, colonisation by mycorrhizal fungi may impact upon root system structure 9.

Different researchers reported that how roots respond to abiotic stresses, including nutritional limitations, elemental toxicities, waterlogging and physical constraints. Soil acidity affects more than 30 % of arable land and continues to limit agricultural productivity globally. Aluminium and manganese toxicities are largely responsible for poor plant growth but nutrient deficiencies also contribute. Many species have evolved strategies to cope with these stresses, and Rao et al.,54 comprehensively review the adaptive changes in root structure and function that provide protection from these hostile soils. They encourage further breeding strategies to select for additional root traits. Liska et al. 41 demonstrate how exposure of roots to air, or to toxic metals such as cadmium, influences the development of suberin lamella. Suberin is a wax-like cell-wall polymer that provides a barrier to the movement of water and solutes. They find that suberin is preferentially deposited on the side of the root exposed to these treatments, presumably as a means of protecting the plant from these stresses.

Phenotypic screens for single, abiotic soil constraints, such as those in the studies summarized above, can reveal the genetic and physiological basis of tolerance mechanisms. Similar studies have identified many new membrane transport proteins that regulate the uptake of nutrients and the exclusion of toxic ions through specific root exudates 63. The next step will be to combine these treatments and score performance with the multiple stresses encountered in the field. This will accelerate progress towards improving agricultural production and provide management options for forestry and natural systems 57. Soil is the most complex of all environments containing liquid, gaseous and solid phases, the ratios of which can change depending on the prevailing conditions.

Roots are subject to mechanical impedance when the force required to displace soil particles as the root grows increases. As a result, root diameter behind the root tip increases and root elongation decreases with increasing soil strength. Compaction is another major soil constraint that affects root penetration and final rooting depth. Popova et al., 52 studied the effect of soil strength on elongation rate and diameter of maize (Zea mays) roots and finally revealed that how final root shape and tortuosity in compacted soil results not only from mechanical deflections but also from tropic responses via touch stimuli.

Generally, water is believed to be available for plant uptake at matric potentials greater than -1.5 MPa (the wilting point of many mesophytic plants), but root growth can be severely slowed by potentials greater than this value 7. Schenk and Jackson 62 surveyed the literature on root system sizes for individual plants from deserts, scrublands, grass. Plant lands and savannas all with ≤ 1,000 mm mean annual precipitation. They found that maximum rooting depth showed a strong positive relationship with mean annual precipitation for all plant growth forms, except shrubs and trees. Moreover, maximum rooting depth for all growth forms tended to be shallowest in arid regions and deepest in subhumid regions, which was thought to be the result of more restricted water infiltration depths in areas with lower precipitation. These results appear to contradict the widely held view that rooting depth increases in drier environments. However, as Schenk and Jackson 62 state, the distinction between relative and absolute rooting depths is critical. Thus, for a given canopy size herbaceous plants do have deeper maximum rooting depths in drier environments, but as canopy size increases so too does the absolute rooting depth. However, the relationship is not simply due to increased plant size as above– and below–ground allometrics also change with climate. Moreover, depths at which plants have 50% or 95% of their total root biomass are significantly deeper in drier than in humid environments 61. Water availability is not the only abiotic factor that influences rooting depth, soil texture, organic horizon size 61 and plant species composition will also dictate the rooting depth achieved.

Nutrient availability and salinity of the soil affect the growth and development of plant roots (Kawa et al., 2016). Salt has a distinct effect on root growth 22. Although, low salt concentrations up to 50 mM can promote plant growth in Arabidopsis 29, higher salt concentrations have severe negative effects. Both primary and lateral root growth is inhibited during salt stress 29. In addition, lateral root number specifically decreases in the root zone developed after exposure to salt stress 29. Most studies show no effect of salt stress on lateral root density, indicating that the decrease in number of lateral roots is related to the inhibition of primary root growth 29. Within seconds after exposure to salt stress, plant signaling is activated.

In addition, mature cell length is smaller in salt stressed roots. Quiescence is induced by abscisic acid (ABA), which is rapidly up-regulated under salt stress due to the decrease in osmotic potential 1623. ABA in general inhibits both gibberellin (GA) and brassinosteroid (BR) signaling 20 and stress-induced reduction of growth has been shown to benefit the plant 1. Galvan-Ampudia et al.,21 showed that plants can specifically redirect growth away from higher salt concentrations, a response called halotropism. This response was observed in Arabidopsis, tomato and sorghum seedlings, both on agar media and in soil. Similar to gravitropism, auxin redistribution is central in regulating halotropism. Endocytosis of PIN2, an auxin efflux carrier, at the side of high salt concentrations, redistributes auxin in the root 21. Part of the salinity response is also triggered by osmotic stress and shows overlap with drought responses.

Most crop species are highly sensitive to salinity. Tomato serves as a model crop that is widely used to study how salt tolerance can be enhanced in crop species. For a wide range of vegetables, including tomato, grafting is a very effective way to increase crop resistance to biotic and abiotic stresses, without affecting above ground characteristics. For several salt sensitive commercial tomato cultivars, grafting onto rootstocks of more tolerant cultivars has positive effects on productivity when exposed to high salinity 47. The Na⁺/K⁺ levels in the shoot (scions) indicated that the tolerant rootstocks prevented Na+ reaching the shoot, illustrating the importance of the root system for salt tolerance. Unfortunately, only little is known about RSA development of crops during salt stress. In rice, rye, and maize inhibition of root length has been observed under high salinity 48.

Among various environmental stresses, drought is one of the serious stresses which has a significant but negative impact on crop yield. To manage drought, different tools are used to enhance crop yield under drought scenarios. Roots are the main organs to respond, perceive and maintain crop yield under drought conditions. Plant root systems are essential for adaptation against different types of biotic and abiotic stresses. Apart from genotyping quantitative traits, phenotyping has been a major challenge for plant breeders to improve abiotic stress tolerance in crop plants. It includes genetically complex traits that are extremely difficult to measure, and would be ideal to assist plant breeders for using in breeding program (Sharma et al., 2016). Roots have been evolved to be responsive and extremely adaptive to the local environment, their morphology, growth and physiology are closely related with plant genotype and growth medium properties. For example, elongation rate and number of lateral roots can be decreased by high soil water content or soil density and this can also be associated with shoot growth reduction 7. The type of root distribution required for different crops depends on the target environment, as abiotic stresses experienced by roots have a significant effect on the crop yield 571. Strong root development is essential for survival of seedlings in soils which undergo rapid surface drying, while sufficient moisture remains available in deeper soil layers.Therefore, good understanding about plant responses to abiotic stresses might be helpful in the selection of more resistant crop varieties 12.