Variation In Root Architecture Research Articles

Location: root architecture structures rhizosphere microbial associations.

Root architectural phenotypes are promising targets for crop breeding, but root architectural effects on microbial associations in agricultural fields are not well understood. Architecture determines the location of microbial associations within root systems, which, when integrated with soil vertical gradients, determines the functions and the metabolic capability of rhizosphere microbial communities. We argue that variation in root architecture in crops has important implications for root exudation, microbial recruitment and function, and the decomposition and fate of root tissues and exudates. Recent research has shown that the root microbiome changes along root axes and among root classes, that root tips have a unique microbiome, and that root exudates change within the root system depending on soil physicochemical conditions. Although fresh exudates are produced in larger amounts in root tips, the rhizosphere of mature root segments also plays a role in influencing soil vertical gradients. We argue that more research is needed to understand specific root phenotypes that structure microbial associations and discuss candidate root phenotypes that may determine the location of microbial hotspots within root systems with relevance to agricultural systems.

Functional characterization of the IGT gene family in wheat reveals conservation and variation in root architecture under drought condition

Plant architecture traits are a pivotal component in crop improvement and one of the key aspects of breeding programs for centuries. Among architecture traits, leaves and roots angle are most important whereas roots angle is considered to play a vital role in plant response to drought avoidance. Several genes regulating drought response reported in plants, such as LAZY1, Deeper Rooting 1 (DRO1), and Tiller angle control 1 (TAC1), belong to the IGT family. The wheat (Triticum aestivum L.) genome is complex because it consists of three subgenomes A, B, and D. A genome-wide (A, B, and D) identification and characterization of IGT family genes in wheat was reported in this study. A total of 12 IGT genes were identified and categorized based on phylogenetic reconstruction and gene structure analysis. These genes were distributed on chromosomes 2, 5, and 6 corresponding to the A, B, and D genomes of wheat. Most of the genes showed similar structures. Cis-regulatory elements in the promoter regions interpreted the presence of light, stress, development, and hormone-related elements. Five miRNAs (tae-miR9773, tae-miR531, tae-miR9678–3p, tae-miR9781, and tae-miR5049–3p) were predicted which target these TaIGT. Both the RNA-seq-based transcriptomic and real-time gene expression analysis suggested that all the genes are strongly expressed in roots, thus showing function conservation. 3D models and molecular docking of TaIGT were also carried out systematically, and binding patterns and the orientation of ligands in the active site of proteins were predicted. This study delves further into TaIGT genes and their expression patterns. The findings of this work are important for understanding the molecular control of root development and for future functional characterization of wheat root architecture genes. Key messageIGT gene family has not been identified and characterized and we identified 12 genes strongly expressing in roots. Furthermore, five miRNAs were predicted and could have a role in root conservation.

Growth Patterns in Seedling Roots of the Pincushion Cactus Mammillaria Reveal Trends of Intra- and Inter-Specific Variation.

Genetic mechanisms controlling root development are well-understood in plant model species, and emerging frontier research is currently dissecting how some of these mechanisms control root development in cacti. Here we show the patterns of root architecture development in a gradient of divergent lineages, from populations to species in Mammillaria. First, we show the patterns of variation in natural variants of the species Mammillaria haageana. Then we compare this variation to closely related species within the Series Supertexta in Mammillaria (diverging for the last 2.1 million years) in which M. haageana is inserted. Finally, we compared these patterns of variation to what is found in a set of Mammillaria species belonging to different Series (diverging for the last 8 million years). When plants were grown in controlled environments, we found that the variation in root architecture observed at the intra-specific level, partially recapitulates the variation observed at the inter-specific level. These phenotypic outcomes at different evolutionary time-scales can be interpreted as macroevolution being the cumulative outcome of microevolutionary phenotypic divergence, such as the one observed in Mammillaria accessions and species.

Root metaxylem and architecture phenotypes integrate to regulate water use under drought stress.

At the genus and species level, variation in root anatomy and architecture may interact to affect strategies of drought avoidance. To investigate this idea, root anatomy and architecture of the drought-sensitive common bean (Phaseolus vulgaris) and drought-adapted tepary bean (Phaseolus acutifolius) were analyzed in relation to water use under terminal drought. Intraspecific variation for metaxylem anatomy and axial conductance was found in the roots of both species. Genotypes with high-conductance root metaxylem phenotypes acquired and transpired more water per unit leaf area, shoot mass, and root mass than genotypes with low-conductance metaxylem phenotypes. Interspecific variation in root architecture and root depth was observed where P. acutifolius has a deeper distribution of root length than P. vulgaris. In the deeper-rooted P. acutifolius, genotypes with high root conductance were better able to exploit deep soil water than genotypes with low root axial conductance. Contrastingly, in the shallower-rooted P. vulgaris, genotypes with low root axial conductance had improved water status through conservation of soil moisture for sustained water capture later in the season. These results indicate that metaxylem morphology interacts with root system depth to determine a strategy of drought avoidance and illustrate synergism among architectural and anatomical phenotypes for root function.

The Key Role of Variety and Method of Sowing Selection in Pea Roots’ Parameters Development under Sustainable Practice

The selection of varieties is extremely important for decreasing fertilizer consumption. However, little attention is devoted to assessing the effectiveness of row spacing in tandem with types of varieties of pea on root development in the context of limited nutrition. As essential knowledge in this area is lacking, a study was conducted with two objectives using an ordinal regression model. (i): To determine whether qualitative variables (cultivar, fertilization, and row spacing) or quantitative variables (root parameters) affect the root dry mass density, and (ii): To assess the variation in root architecture of two pea cultivars (fodder vs. edible type) grown under different P supply levels (0, 45, and 90 kg P2O5) and row spacing (narrow—15 cm—and wide—30 cm). The ordinal regression model showed that row spacing and cultivar type are meaningful predictors of root dry mass density (RDMD). The root dry mass density increased at wider row spacing in the fodder pea cultivar. As root surface area density (RSAD) and SRL-specific root length (SRL) most accurately describe root mass, it was concluded that the cultivar type and row spacing are crucial factors for increasing root plasticity, which can improve soil utilization.

Relationships between Nutrient Heterogeneity, Root Growth, and Hormones: Evidence for Interspecific Variation.

(1) Background: Plant roots respond to nutrients through root architecture that is regulated by hormones. Strong inter-specific variation in root architecture has been well documented, but physiological mechanisms that may control the variation have not. (2) Methods: We examined correlations between root architecture and hormones to seek clues on mechanisms behind root foraging behavior. In the green house at Beijing Normal University, hydroponic culture experiments were used to examine the root responses of four species—Callistephus chinensis, Solidago canadensis, Ailanthus altissima, Oryza sativa—to two nitrogen types (NO3− or NH4+), three nitrogen concentrations (low, medium, and high concentrations of 0.2, 1, and 18 mM, respectively) and two ways of nitrogen application (stable vs. variable). The plants were harvested after 36 days to measure root mass, 1st order root length, seminal root length for O. sativa, density of the 1st order laterals, seminal root number for O. sativa, the inter-node length of the 1st order laterals, and root hormone contents of indole-3-acetic acid, abscisic acid, and cytokinins (zeatin + zeatinriboside). (3) Results: Species differed significantly in their root architecture responses to nitrogen treatments. They also differed significantly in hormone responses to the nitrogen treatments. Additionally, the correlations between root architecture and hormone responses were quite variable across the species. Each hormone had highly species-specific relationships with root responses. (4) Conclusions: Our finding implies that a particular root foraging behavior is probably not controlled by the same biochemical pathway in all species.

Root type is not an important driver of mycorrhizal colonisation in Brachypodium distachyon

Breeding for favourable root traits in food and energy crops should be considered in the context of interactions with soil biota, notably those that can increase the nutrient use efficiency of crops. Arbuscular mycorrhizal (AM) fungi can provide services to plants but a better understanding of the interactions between root traits and AM fungi is required to maximise these benefits.One source of intraspecific variation in root architecture is the allocation of resources to different root types. We hypothesized that different root types would have different traits and be colonised differently by AM fungi, either in the amount of colonisation or identity of colonisers. We studied communities colonising the seminal, coleoptile nodal and leaf nodal roots of seven Brachypodium distachyon accessions grown in three crop or pasture soils.Leaf nodal roots had low specific root length compared to coleoptile nodal and seminal roots, yet all three root types harboured similar AM fungal communities and levels of colonisation. Most of the variation in the AM fungal communities was explained by soil; significant proportions were explained by plant accession and root type but these effects were weak.Differential allocation of resources between root types is not a trait that could be selected to maximise beneficial interactions with AM fungi and we found no link between a root phenotypic trait (specific root length) and AM fungal colonisation. Accessions did vary in extent of colonisation by arbuscules, meaning B. distachyon may be a useful model to study mechanisms underlying the symbiotic interface and mycorrhizal growth response of cereals.

Interspecific variation of tree root architecture in a temperate agroforestry system characterized using ground-penetrating radar

Root system architecture regulates belowground access to soil resources. Variation in root architecture is important in agroforestry systems given management objectives to optimize resource acquisition between trees and crops. However, the distributions of live tree roots in agroforestry systems remain understudied due to methodological constraints. In this study, we used ground-penetrating radar (GPR) to describe variation in whole-plant root architecture among tree species at the same agricultural site, with a specific focus on vertical coarse and fine root distributions within the zone of competition with neighbouring crops. Using GPR, we detected coarse roots of five trees species (Quercus rubra L., Juglans nigra L., Populus deltoides × nigra DN177, Picea abies (L.) Karst, and Thuja occidentalis L.) at a tree-based intercropping system in southern Ontario, Canada. A subset of soil profiles were assessed for GPR accuracy. A cumulative root distribution function was used to estimate the rooting depth (D95) of coarse roots. We also measured tree coarse root distributions and fine root density distributions 2 m into the crop rows, in the zone of competition. GPR accurately detected approximately 58 % of coarse roots for each study tree. Coarse root architecture varied among species, with differences in D95 and rooting patterns. Fine root length density distribution also varied among species, but was consistently high at 0.10 and 0.20 m depths regardless of species. Our results suggest differential tree suitability for minimizing belowground competition with crops. Additionally, we illustrate the viability of GPR to characterize vertical profiles of live tree root systems, which is critical for improving our understanding of whole-plant functional traits and belowground plant interactions.

Morphological variability in tree root architecture indirectly affects coexistence among competitors in the understory.

Interactions between plants can have strong effects on community structure and function. Variability in the morphological, developmental, physiological, and biochemical traits of plants can influence the outcome of plant interactions and thus have important ecological consequences. However, the ecological ramifications of trait variability in plants are poorly understood and have rarely been tested in the field. We experimentally tested the effects of morphological variation in root architecture of Quercus douglasii trees in the field on interactions between understory plants and community composition. Our results indicate that variability among Q. douglasii tree root systems initiates a striking reversal in the competitive effects of dominant understory grass species on a less common species. Trees with a deep-rooted morphology facilitated exotic annual grasses and these annual grasses, in turn, competitively excluded the native perennial bunchgrass, Stipapulchra. In contrast, Q. douglasii trees with shallow-rooted morphologies directly suppressed the growth of exotic annual grasses and indirectly released S. pulchra individuals from competition with these annual grasses. Morphological variation in the root architecture of Q. douglasii created substantial conditionality in the outcomes of competition among species which enhanced the potential for indirect interactions to sustain coexistence and increase community diversity.

RootScape: A Landmark-Based System for Rapid Screening of Root Architecture in Arabidopsis

The architecture of plant roots affects essential functions including nutrient and water uptake, soil anchorage, and symbiotic interactions. Root architecture comprises many features that arise from the growth of the primary and lateral roots. These root features are dictated by the genetic background but are also highly responsive to the environment. Thus, root system architecture (RSA) represents an important and complex trait that is highly variable, affected by genotype × environment interactions, and relevant to survival/performance. Quantification of RSA in Arabidopsis (Arabidopsis thaliana) using plate-based tissue culture is a very common and relatively rapid assay, but quantifying RSA represents an experimental bottleneck when it comes to medium- or high-throughput approaches used in mutant or genotype screens. Here, we present RootScape, a landmark-based allometric method for rapid phenotyping of RSA using Arabidopsis as a case study. Using the software AAMToolbox, we created a 20-point landmark model that captures RSA as one integrated trait and used this model to quantify changes in the RSA of Arabidopsis (Columbia) wild-type plants grown under different hormone treatments. Principal component analysis was used to compare RootScape with conventional methods designed to measure root architecture. This analysis showed that RootScape efficiently captured nearly all the variation in root architecture detected by measuring individual root traits and is 5 to 10 times faster than conventional scoring. We validated RootScape by quantifying the plasticity of RSA in several mutant lines affected in hormone signaling. The RootScape analysis recapitulated previous results that described complex phenotypes in the mutants and identified novel gene × environment interactions.

Variation in root architecture among switchgrass cultivars impacts root decomposition rates

Roots regulate soil carbon (C) input, but fine root decomposition rates and root impacts on soil organic C turnover (SOC) are uncertain. This uncertainty is, partly, caused by the heterogeneity of root systems, which vary in diameter distributions and tissue chemistry. Here, we evaluated how root diameter distributions affect root and SOC decomposition. Roots from eight Panicum virgatum (switchgrass) cultivars were analyzed for root diameter size-class distribution and C:N ratio. Roots from each cultivar were mixed with C3 soil according to five root diameter treatments: (1) 0–0.5 mm, (2) 0.5–1 mm, (3) 1–2.5 mm, (4) a 1:1:1 mixture of roots from each diameter size class, and (5) a mixture combining diameter classes in proportions representing measured size distributions for each cultivar. All treatments were incubated for 90 days under laboratory conditions. Respired CO2 was measured throughout and the microbial community structure was measured at termination of the experiment. Carbon-13 isotope techniques were used to partition respiration into root-derived C versus native SOC-derived C. Results indicated: (1) specific root length differed among the cultivars, (2) root decomposition rates within the three size classes varied by cultivar, but were not correlated with cultivar differences in root C:N ratios, (3) root diameter size class affected root and SOC decomposition, and (4) mixing roots of different diameters did not lead to synergistic increases in decomposition. We conclude that intraspecific variation in root architecture is significant and that fine root diameter size class distribution is an important trait for shaping decomposition processes.

Genetic variation in root architecture and phosphorus efficiency in response to heterogeneous phosphorus deficiency in <I>Pinus massoniana</I> families

Genetic variation in root architecture and phosphorus efficiency in response to heterogeneous phosphorus deficiency in <I>Pinus massoniana</I> families

Diversity in root architecture and response to P deficiency in seedlings of Cucumis melo L.

Breeding for more phosphorus (P)-efficient crops is one strategy to reduce the use of P fertilizers, thus mitigating the environmental and economic impacts of agriculture. Variation in root architecture and the response to P deficiency were studied in C. melo. Forty accessions representing genetic diversity within the species were screened for their root systems in normal and deficient P conditions at the seedling stage. Various parameters of P-uptake and P-use were analyzed in a subset of accessions at 40 days. Significant differences in root architecture were observed, with the taproot systems prevailing among the wild and exotic accessions, and more branched root systems in cultivated stocks. Moreover, differences in the plastic response of roots to P starvation were observed. Variation in different P-use and -uptake traits correlated with the root architecture. Within ssp. melo, the inodorus and flexuosus landraces had larger and more branched roots and more efficient P-uptake, thereby providing a close genepool for breeding. Within ssp. agrestis, conomon and momordica accessions can be sources of interest for the enhancement of variation in root architecture and P-use efficiency into cultivated melons. Therefore, the diversity observed within C. melo species could be useful in breeding P-efficient melon cultivars.

Novel insights into the genomics of rice root adaptive development

Deciphering the genetic and molecular mechanisms controlling the development of the root system and its adaptive plasticity under adverse environments is of primary importance for the sustainable establishment of the rice crop. Rice displays a complex root structure comprising several root types mostly of postembryonic origin. The large natural variation in root architecture among cultivars reflects their adaptation to contrasting agro-environmental conditions. This article reviews the current knowledge on the organization and anatomy of the various types of roots of the fibrous root system of rice, the diversity and genetic basis of natural variation of root system architecture and performance, and the molecular mechanisms underlying constitutive and adaptive root development. This paper also throws light on how the integrated approach of new tools in high-resolution microscopy imaging, expression profiling, mutant screening, and reverse genetics could facilitate the rapid discovery and analysis of the key genes and regulatory networks involved in root architectural traits affecting plant performance under field conditions.

Genetics of Root System Architecture Using Near-isogenic Lines of Melon

The study of the genetic control of natural variation in the root architecture of Cucumis melo L. is complex due to the difficulties of root phenotyping and to the quantitative nature of root traits and their plasticity. A library of near-isogenic lines (NILs), constructed by introgressing the genome of the exotic Korean accession Shongwan Charmi [SC (PI161375)] into the genetic background of the cultivar Piel de Sapo (PS) has recently become available. In this work, we used this population to identify quantitative trait loci (QTLs) controlling variation in root growth and architecture. We studied separately the primary root and the secondary and tertiary root systems during a 15-day period. Heritabilities for the root traits were moderate. Correlation and principal component analysis showed independence among traits measuring root length and root branching level, indicating the possibility of modifying both traits independently. PS and SC clearly differed in plant size. Significant allometric relationships between vine biomass and some root traits were identified. The use of NILs with similar plant size of PS allowed us to avoid the inaccuracies caused by size-dependent variation of root traits. A total of 17 QTLs for root traits in seven linkage groups were identified: three QTLs for primary root length, three QTLs for the diameter of the primary root, three QTLs for secondary root density, three QTLs for the average length of the secondary roots, three QTLs for the percentage of secondary roots bearing tertiary roots, and two QTLs for tertiary root density. In most of these traits, transgressive variation was observed.

Bimodal root diameter distributions in Serengeti grasses exhibit plasticity in response to defoliation and soil texture: implications for nitrogen uptake

Summary 1The effects of soil texture (low or high sand) and defoliation (clipped or unclipped) on root diameter distributions and nitrogen uptake were studied in the Serengeti grasses Digitaria macroblephara (Hack.) Stapf and Themeda triandra Forssk. in glasshouse cultures. 2At the end of the experiment, plants were harvested and images of the washed roots were digitized using a scanner. Root size distributions were distinctly bimodal and were described with pairs of lognormal distributions with six parameters used as variables in subsequent analyses. To investigate N uptake, a nitrate solution containing 15N was added to the soil 5 days before final harvest. 3In both grasses, root diameter distributions were more responsive to defoliation than to soil texture. However, the two species diverged strongly in their investment in fine roots in the more sandy soils. 4For each species, linear relationships were found among root biomass, root surface area and specific root length, which suggests that variation in root architecture is genetically constrained in each species. Plasticity emerged because the soil texture and defoliation experienced by an individual determined the specific architecture that it expressed within these linear relationships. 5Root parameters obtained from the experiment and previously published root biomass and enzyme activities were used to predict 15N uptake of the two grasses. Root diameter distribution and enzyme activities were important predictors of N uptake in the fast-growing grazing tolerant D. macroblephara, whereas root system size and root diameter distribution predicted N uptake in the slower growing, taller-statured T. triandra. 6The differential responses of these grasses to variation in soils and defoliation are consistent with the hypothesis that habitat heterogeneity and herbivory interact to influence species coexistence in plant communities of African savannas.

A review of tree root conflicts with sidewalks, curbs, and roads

Literature relevant to tree root and urban infrastructure conflicts is reviewed. Although tree roots can conflict with many infrastructure elements, sidewalk and curb conflicts are the focus of this review. Construction protocols, urban soils, root growth, and causal factors (soil conditions, limited planting space, tree size, variation in root architecture, management practices, and construction materials) are discussed. Because costs related to sidewalk and curb damage are substantial, a review of research addressing repair, mitigation, prevention, and litigation costs is included. Finally, future research needs are discussed.