Genetic Diversity under Soil Compaction in Wheat: Root Number as a Promising Trait for Early Plant Vigor

The crucial role of lateral root angle in enhancing drought resilience in cotton

Introduction

Plant responses to drought stress are influenced by various factors, including the lateral root angle (LRA), stomatal regulation, canopy temperature, transpiration rate and yield. However, there is a lack of research that quantifies their interactions, especially among different cotton varieties.

Methods

This experiment included two water treatments: well-watered (75 ± 5% soil relative water content) and drought stress (50 ± 5% soil relative water content) starting from the three-leaf growth stage.

Results

The results revealed that different LRA varieties show genetic variation under drought stress. Among them, varieties with smaller root angles show greater drought tolerance. Varieties with smaller LRAs had significantly increased stomatal opening by 15% to 43%, transpiration rate by 61.24% and 62.00%, aboveground biomass by 54% to 64%, and increased seed cotton yield by 76% to 79%, and decreased canopy temperature by 9% to 12% under drought stress compared to the larger LRAs. Varieties with smaller LRAs had less yield loss under drought stress, which may be due to enhanced access to deeper soil water, compensating for heightened stomatal opening and elevated transpiration rates. The increase in transpiration rate promotes heat dissipation from leaves, thereby reducing leaf temperature and protecting leaves from damage.

Discussion

Demonstrating the advantages conferred by the development of a smaller LRA under drought stress conditions holds value in enhancing cotton's resilience and promoting its sustainable adaptation to abiotic stressors.

Uncovering root compaction response mechanisms: new insights and opportunities

Compaction disrupts soil structure, reducing root growth, nutrient and water uptake, gas exchange, and microbial growth. Root growth inhibition by soil compaction was originally thought to reflect the impact of mechanical impedance and reduced water availability. However, using a novel gas diffusion-based mechanism employing the hormone ethylene, recent research has revealed that plant roots sense soil compaction. Non-compacted soil features highly interconnected pore spaces that facilitate diffusion of gases such as ethylene which are released by root tips. In contrast, soil compaction stress disrupts the pore network, causing ethylene to accumulate around root tips and trigger growth arrest. Genetically disrupting ethylene signalling causes roots to become much less sensitive to compaction stress. Such new understanding about the molecular sensing mechanism and emerging root anatomical traits provides novel opportunities to develop crops resistant to soil compaction by targeting key genes and their signalling pathways. This expert view discusses these recent advances and the molecular mechanisms associated with root-soil compaction responses.

Dissecting chickpea genomic loci associated with the root penetration responsive traits in compacted soil

MAIN CONCLUSION

Soil compaction reduces root exploration in chickpea. We found genes related to root architectural traits in chickpea that can help understand and improve root growth in compacted soils. Soil compaction is a major concern for modern agriculture, as it constrains plant root growth, leading to reduced resource acquisition. Phenotypic variation for root system architecture (RSA) traits in compacted soils is present for various crops; however, studies on genetic associations with these traits are lacking. Therefore, we investigated RSA traits in different soil compaction levels and identified significant genomic associations in chickpea. We conducted a Genome-Wide Association Study (GWAS) of 210 chickpea accessions for 13 RSA traits under three bulk densities (BD) (1.1BD, 1.6BD, and 1.8BD). Soil compaction decreases root exploration by reducing 12 RSA traits, except average diameter (AD). Further, AD is negatively correlated with lateral root traits, and this correlation increases in 1.8BD, suggesting the negative effect of AD on lateral root traits. Interestingly, we identified probable candidate genes such as GLP3 and LRX for lateral root traits and CRF1-like for total length (TL) in 1.6BD soil. In heavy soil compaction, DGK2 is associated with lateral root traits. Reduction in laterals during soil compaction is mainly due to delayed seedling establishment, thus making lateral root number a critical trait. Interestingly, we also found a higher contribution of the  GxE component of the number of root tips (Tips) to the total variation than the other lateral traits. We also identified a pectin esterase, PPE8B, associated with Tips in high soil compaction and a significantly associated SNP with the relative change in Tips depicting a trade-off between Tips and AD. Identified genes and loci would help develop soil-compaction-resistant chickpea varieties.

Root growth and physiological responses in wheat to topsoil and subsoil compaction with or without artificial vertical macropores

The process of soil compaction can cause various stresses on roots, ultimately limiting their growth and development within the soil. Understanding this phenomenon in real-world conditions can be challenging since the growth of roots is influenced by the soil environment. To investigate this issue, four experiments were conducted to examine the impact of topsoil (two in pots: with clay loam and sandy loam soils under two soil water regimes) and subsoil (in rhizobox: one with clay loam soil and the other with sandy loam soil, containing artificial vertical macropores) compaction on the relationship between edaphic factors and the physiological response of wheat roots. The topsoil compaction reduced root length, volume, and weight by 30-50% and the root diameter by ∼15% compared to the non-compact soil. The effect was reduced in the soil with higher clay content (clay loam), especially under the limited soil water condition. Plant physiological responses were adversely affected by compaction with a reduction in plant height. The transpiration rate was highly impacted (21-47% reduction) with the build-up of intercellular CO2 content in leaves (13-31%), especially with limited water applications. Root growth was severely restricted (>60%) in the compact subsoil layer, although the surface area and volume of roots increased in the overlying non-compact layer. Naturally occurring or artificial vertical macropores acted as escape channels, facilitating the roots to pass through the compact subsoil and grow abundantly in the loose soil below. However, plants in field conditions encounter a mix of loose and compact soil zones. By studying how roots respond to this soil heterogeneity, we can develop strategies to reduce the negative effects of soil compaction.

A review of compaction effect on subsurface processes in soil: Implications on stormwater treatment in roadside compacted soil

Sustainable cities require spacious infrastructures such as roadways to serve multiple functions, including transportation and water treatment. This can be achieved by installing stormwater control measures (SCM) such as biofilters and swales on the roadside compacted soil, but compacted soil limits infiltration and other functions of SCM. Understanding the effect of compaction on subsurface processes could help design SCM that could alleviate the negative impacts of compaction. Therefore, we synthesize reported data on compaction effects on subsurface processes, including infiltration rate, plant health, root microbiome, and biochemical processes. The results show that compaction could reduce runoff infiltration rate, but adding sand to roadside soil could alleviate the negative impact of compaction. Compaction could decrease the oxygen diffusion rate in the root zone, thereby affecting plant root activities, vegetation establishment, and microbial functions in SCM. The impacts of compaction on carbon mineralization rate and root biomass vary widely based on soil type, aeration status, plant species, and inherent soil compaction level. As these processes are critical in maintaining the long-term functions of SCM, the analysis would help develop strategies to alleviate the negative impacts of compaction and turn road infrastructure into a water solution in sustainable cities.

Future roots for future soils

Mechanical impedance constrains root growth in most soils. Crop cultivation changed the impedance characteristics of native soils, through topsoil erosion, loss of organic matter, disruption of soil structure and loss of biopores. Increasing adoption of Conservation Agriculture in high-input agroecosystems is returning cultivated soils to the soil impedance characteristics of native soils, but in the low-input agroecosystems characteristic of developing nations, ongoing soil degradation is generating more challenging environments for root growth. We propose that root phenotypes have evolved to adapt to the altered impedance characteristics of cultivated soil during crop domestication. The diverging trajectories of soils under Conservation Agriculture and low-input agroecosystems have implications for strategies to develop crops to meet global needs under climate change. We present several root ideotypes as breeding targets under the impedance regimes of both high-input and low-input agroecosystems, as well as a set of root phenotypes that should be useful in both scenarios. We argue that a 'whole plant in whole soil' perspective will be useful in guiding the development of future crops for future soils.

Effects of soil compaction on grain yield of wheat depend on weather conditions

The use of heavy farm machinery has resulted in widespread soil compaction in many regions of the world. Compacted soil limits the access of crops to soil water and nutrients and is expected to reduce crop productivity, but the influence of weather conditions on the interactions between compacted soil and crop productivity is unclear. Furthermore, early vigor has been regarded as a promising trait for improving the yield of crops grown under edaphic stress such as soil compaction. We aimed to assess the combined effects of soil compaction and contrasting weather conditions on growth and grain yield of spring wheat, and to evaluate the association between early vigor and grain yield under temporal variations of the soil physical conditions. Nine spring wheat genotypes were grown on compacted and non-compacted soils during two cropping seasons with contrasting weather conditions in Central Sweden. Compared to the non-compacted treatment, soil compaction increased the relative growth rate of shoot biomass from sowing to stem elongation, and from stem elongation to flowering in the drier year (2018), but decreased the same traits in the wetter year (2019). The contrasting effects of soil compaction on shoot growth in the two years could be explained by soil moisture and penetration resistance associated with the interactive effects of soil compaction and weather condition. Higher early vigor, here indicated by higher relative growth rate from sowing to stem elongation, was associated with reduced grain yield under the progressively drying and hardening soil conditions during the entire cropping season of both years. We conclude that the interactive effects of soil physical and weather conditions need to be considered when evaluating the impact of soil compaction on crop growth and productivity. The potential of early vigor to increase grain yield is strongly influenced by the temporal dynamics of soil physical conditions.

Wheat growth responses to soil mechanical impedance are dependent on phosphorus supply

Increased mechanical impedance induced by soil drying or compaction causes reduction in plant growth and crop yield. However, how mechanical impedance interacts with nutrient stress has been largely unknown. Here, we investigated the effect of mechanical impedance on the growth of wheat seedlings under contrasting phosphorus (P) supply in a sand culture system which allows the mechanical impedance to be independent of water and nutrient availability. Two wheat genotypes containing the Rht-B1a (tall) or Rht-B1c (gibberellin-insensitive dwarf) alleles in the Cadenza background were used and their shoot and root traits were determined. Mechanical impedance caused a significant reduction in plant growth under sufficient P supply, including reduced shoot and root biomass, leaf area and total root length. By contrast, under low P supply, mechanical impedance did not affect biomass, tiller number, leaf length, and nodal root number in both wheat genotypes, indicating that the magnitude of the growth restriction imposed by mechanical impedance was dependent on P supply. The interaction effect between mechanical impedance and P level was significant on most plant traits except for axial and lateral root length, suggesting an evident physical and nutritional interaction. Our findings provide valuable insights into the integrated effects of plants in response to both soil physical and nutritional stresses. Understanding the response patterns is critical for optimizing soil tillage and nutrient management in the field.

Root Response of Moso Bamboo (Phyllostachys edulis (Carrière) J. Houz.) Seedlings to Drought with Different Intensities and Durations

The root of Moso bamboo (Phyllostachys edulis (Carrière) J. Houz.) develops extremely rapidly at seedling phase and is highly sensitive to water content in soil, but its response patterns and adaptation strategies of its root to drought are little known. The aim of this study was to investigate the response of root morphology and architecture of Moso bamboo to drought at seedling phase and then to explore the drought adaptation strategies of its root. One-year-old potted seedlings of Moso bamboo were planted under three drought treatments (control, moderate drought and severe drought) for three months. Seedling growth, specific root length (SRL), root architecture (fractal dimension (FD), root branching angle (RBA) and root topological index (TI)) and non-structural carbohydrate (NSC) concentrations in roots were measured every month. The results are as follows: (i) The dry weight of root and shoot decreased significantly under drought stress. (ii) The SRL decreased under drought stress in the early duration (the first month), and then increased in the late duration (the third month). Both FD and RBA decreased, while TI and the concentrations of NSCs increased under drought stress. (iii) The NSC concentrations were positively correlated with SRL and TI, but exhibited an inverse relationship to FD and RBA. Our results indicated that Moso bamboo seedlings formed a “steeper, simpler, expensive (low SRL and high TI)” root architecture to adapt to a short-term drought (one month), and formed a “cheaper (high SRL)” root to adapt to a long-term drought (three months). Increase of NSC concentrations supported the root architecture plasticity to some extent.

Same same, but different: growth responses of primary and lateral roots

The root system architecture describes the shape and spatial arrangement of roots within the soil. Its spatial distribution depends on growth and branching rates as well as directional organ growth. The embryonic primary root gives rise to lateral (secondary) roots, and the ratio of both root types changes over the life span of a plant. Most studies have focused on the growth of primary roots and the development of lateral root primordia. Comparably less is known about the growth regulation of secondary root organs. Here, we review similarities and differences between primary and lateral root organ growth, and emphasize particularly how external stimuli and internal signals differentially integrate root system growth.

A Deep Learning-Based Phenotypic Analysis of Rice Root Distribution from Field Images

Root distribution in the soil determines plants' nutrient and water uptake capacity. Therefore, root distribution is one of the most important factors in crop production. The trench profile method is used to observe the root distribution underground by making a rectangular hole close to the crop, providing informative images of the root distribution compared to other root phenotyping methods. However, much effort is required to segment the root area for quantification. In this study, we present a promising approach employing a convolutional neural network for root segmentation in trench profile images. We defined two parameters, Depth50 and Width50, representing the vertical and horizontal centroid of root distribution, respectively. Quantified parameters for root distribution in rice (Oryza sativa L.) predicted by the trained model were highly correlated with parameters calculated by manual tracing. These results indicated that this approach is useful for rapid quantification of the root distribution from the trench profile images. Using the trained model, we quantified the root distribution parameters among 60 rice accessions, revealing the phenotypic diversity of root distributions. We conclude that employing the trench profile method and a convolutional neural network is reliable for root phenotyping and it will furthermore facilitate the study of crop roots in the field.

Soil compaction and the architectural plasticity of root systems

Soil compaction is a serious global problem, and is a major cause of inadequate rooting and poor yield in crops around the world. Root system architecture (RSA) describes the spatial arrangement of root components within the soil and determines the plant's exploration of the soil. Soil strength restricts root growth and may slow down root system development. RSA plasticity may have an adaptive value, providing environmental tolerance to soil compaction. However, it is challenging to distinguish developmental retardation (apparent plasticity) or responses to severe stress from those root architectural changes that may provide an actual environmental tolerance (adaptive plasticity). In this review, we outline the consequences of soil compaction on the rooting environment and extensively review the various root responses reported in the literature. Finally, we discuss which responses enhance root exploration capabilities in tolerant genotypes, and to what extent these responses might be useful for breeding. We conclude that RSA plasticity in response to soil compaction is complex and can be targeted in breeding to increase the performance of crops under specific agronomical conditions.

Cortical Cell Diameter Is Key To Energy Costs of Root Growth in Wheat

Root growth requires substantial amounts of energy and thus carbohydrates. The energy costs of root growth are particularly high in both dry and compacted soil, due to high soil penetration resistance. Consequently, more carbon must be allocated from aboveground plant tissue to roots, which limits crop productivity. In this study, we tested the utility of root cortical cell diameter as a potential selection target to reduce the energy costs of root growth. Isothermal calorimetry was adopted for in situ quantification of the energy costs of root growth of 16 wheat (Triticum aestivum) genotypes under three levels of penetration resistance. We show that cortical cell diameter is a pivotal and heritable trait, which is strongly related to the energy costs of root growth. Genotypic diversity was found for cortical cell diameter and the energy costs of root growth. A large root cortical cell diameter correlated with reduced energy costs of root growth, particularly under high soil penetration resistance. Moreover, significant correlations were found between the ability to radially enlarge cortical cells upon greater penetration resistance (i.e. phenotypic plasticity) and the responsiveness in the energy costs of root growth. A higher degree of phenotypic plasticity in cortical cell diameter was associated with reduced energy costs of root growth as soil penetration resistance increased. We therefore suggest that genotypic diversity and phenotypic plasticity in cortical cell diameter should be harnessed to adapt crops to dry and compacted soils.

Diversity of a wall-associated kinase gene in wild and cultivated barley

Domestication of barley and other cereals was accompanied by an increase in seed size which has been ascribed to human selection, large seeds being preferred by early farmers or favoured by cultivation practices such as deep sowing. An alternative suggestion is that the increase in seed size was an indirect consequence of selection for plants with more vigorous growth. To begin to address the latter hypothesis we studied the diversity of HvWAK1, a wall-associated kinase gene involved in root proliferation, in 220 wild barley accessions and 200 domesticated landraces. A 3655-bp sequence comprising the gene and upstream region contained 69 single nucleotide polymorphisms (SNPs), one indel and four short tandem repeats. A network of 50 haplotypes revealed a complex evolutionary relationship, but with landraces largely restricted to two parts of the topology. SNPs in the HvWAK1 coding region resulted in nonsynonymous substitutions at nine positions in the translation product, but none of these changes were predicted to have a significant effect on the protein structure. In contrast, the region upstream of the coding sequence contained five SNPs that were invariant in the domesticated population, fixation of these SNPs decreasing the likelihood that the upstream of a pair of TATA boxes and transcription start sites would be used to promote transcription of HvWAK1. The sequence diversity therefore suggests that the cis-regulatory region of HvWAK1 might have been subject to selection during barley domestication. The extent of root proliferation has been linked with traits such as above-ground biomass, so selection for particular cis-regulatory variants of HvWAK1 would be consistent with the hypothesis that seed size increases during domestication were the indirect consequence of selection for plants with increased growth vigour.

Identification of QTL regions for seedling root traits and their effect on nitrogen use efficiency in wheat (Triticum aestivum L.)

QTL for a wheat ideotype root system and its plasticity to nitrogen deficiency were characterized. Root system architecture-related traits (RRTs) and their plasticity to nitrogen availability are important for nitrogen acquisition and yield formation in wheat (Triticum aestivum L.). In this study, quantitative trait loci (QTL) analysis was conducted under different nitrogen conditions, using the seedlings of 188 recombinant inbred lines derived from a cross between Kenong 9204 and Jing 411. Fifty-three QTL for seven RRTs and fourteen QTL for the plasticity of these RRTs to nitrogen deficiency were detected. Thirty of these QTL were mapped in nine clusters on chromosomes 2B, 2D, 3A, 3D, 6B, 6D, 7A and 7B. Six of these nine clusters were also colocated with loci for nitrogen use efficiency (NUE)-related traits (NRTs). Among them, three QTL clusters (C2B, C6D and C7B) were highlighted, considering that they individually harbored three stable robust QTL (i.e., QMrl-2B.1, QdRs-6D and QMrl-7B). C2B and C7B stably contributed to the optimal root system, and C6D greatly affected the plasticity of RRTs in response to nitrogen deficiency. However, strong artificial selection was only observed for C7B in 574 derivatives of Kenong 9204. Covariance analysis identified QMrl-7B as the major contributor in C7B that affected the investigated NRTs in mature plants. Phenotypic analysis indicated that thousand kernel weight might represent a "concomitant" above-ground trait of the "hidden" RRTs controlled by C7B, which are used for breeding selection. Dissecting these QTL regions with potential breeding value will ultimately facilitate the selection of donor lines with both high yield and NUE in wheat breeding programs.

Feedbacks between soil penetration resistance, root architecture and water uptake limit water accessibility and crop growth - A vicious circle

Water is the most limiting resource for global crop production. The projected increase of dry spells due to climate change will further increase the problem of water limited crop yields. Besides low water abundance and availability, water limitations also occur due to restricted water accessibility. Soil penetration resistance, which is largely influenced by soil moisture, is the major soil property regulating root elongation and water accessibility. Until now the interactions between soil penetration resistance, root system properties, water uptake and crop productivity are rarely investigated. In the current study we quantified how interactive effects between soil penetration resistance, root architecture and water uptake affect water accessibility and crop productivity in the field. Maize was grown on compacted and uncompacted soil that was either tilled or remained untilled after compaction, which resulted in four treatments with different topsoil penetration resistance. Higher topsoil penetration resistance caused root systems to be shallower. This resulted in increased water uptake from the topsoil and hence topsoil drying, which further increased the penetration resistance in the uppermost soil layer. As a consequence of this feedback, root growth into deeper soil layers, where water would have been available, was reduced and plant growth decreased. Our results demonstrate that soil penetration resistance, root architecture and water uptake are closely interrelated and thereby determine the potential of plants to access soil water pools. Hence, these interactions and their feedbacks on water accessibility and crop productivity have to be accounted for when developing strategies to alleviate water limitations in cropping systems.