Regulating Root System Architecture Research Articles

Abiotic factors determine the root system architecture – review and update

Decades of root research have led to a deep understanding of the molecular and genetic mechanisms regulating root system architecture. This review provides past and present-day root research with a focus on abiotic factors, such as nutrient limitation, excess of nutrients, water, salinity, temperature, light, selected heavy metals, and hazardous contaminations which affected primary and lateral root growth. It also briefly summarized current knowledge about the molecular machinery involved in the modulation of RSA of the modern root system of dicot species, such as <i>Arabidopsis thaliana</i>.

Mining genes regulating root system architecture in maize based on data integration analysis

Mining genes regulating root system architecture in maize based on data integration analysis

AZG1 is a cytokinin transporter that interacts with auxin transporter PIN1 and regulates the root stress response.

An environmentally responsive root system is crucial for plant growth and crop yield, especially in sub-optimal soil conditions. This responsiveness enables the plant to exploit regions of high nutrient density whilst simultaneously minimizing abiotic stress. Despite the vital importance of root systems in regulating plant growth, significant gaps of knowledge exist in the mechanisms that regulate their architecture. Auxin defines both the frequency of lateral root (LR) initiation and the rate of LR outgrowth. Here we describe a search for proteins that regulate root system architecture by interacting directly with a key auxin transporter, PIN1. The native separation of Arabidopsis plasma membrane protein complexes identified several PIN1 co-purifying proteins. Among them, AZG1 was subsequently confirmed as a PIN1 interactor. Here we show that, in Arabidopsis, AZG1 is a cytokinin import protein that co-localizes with and stabilizes PIN1, linking auxin and cytokinin transport streams. AZG1 expression in LR primordia is sensitive to NaCl, and the frequency of LRs is AZG1-dependent under salt stress. This report therefore identifies a potential point for auxin:cytokinin crosstalk which shapes root system architecture in response to NaCl.

Association mapping uncovers maize ZmbZIP107 regulating root system architecture and lead absorption under lead stress.

Lead (Pb) is a highly toxic contaminant to living organisms and the environment. Excessive Pb in soils affects crop yield and quality, thus threatening human health via the food chain. Herein, we investigated Pb tolerance among a maize association panel using root bushiness (BSH) under Pb treatment as an indicator. Through a genome-wide association study of relative BSH, we identified four single nucleotide polymorphisms (SNPs) and 30 candidate genes associated with Pb tolerance in maize seedlings. Transcriptome analysis showed that four of the 30 genes were differentially responsive to Pb treatment between two maize lines with contrasting Pb tolerance. Among these, the ZmbZIP107 transcription factor was confirmed as the key gene controlling maize tolerance to Pb by using gene-based association studies. Two 5’ UTR_variants in ZmbZIP107 affected its expression level and Pb tolerance among different maize lines. ZmbZIP107 protein was specifically targeted to the nucleus and ZmbZIP107 mRNA showed the highest expression in maize seedling roots among different tissues. Heterologous expression of ZmbZIP107 enhanced rice tolerance to Pb stress and decreased Pb absorption in the roots. Our study provided the basis for revelation of the molecular mechanism underlying Pb tolerance and contributed to cultivation of Pb-tolerant varieties in maize.

The Physiological Role of Abscisic Acid in Regulating Root System Architecture of Alfalfa in Its Adaptation to Water Deficit

Alfalfa (Medicago sativa L.) is a perennial leguminous plant, with a strong tap root system that plays an important role in alfalfa’s adaptation to drought stress. However, a better understanding of root functional traits and how these root traits are related to whole plant responses in order to improve pasture productivity under water deficit. Two greenhouse experiments were conducted: Experiment 1 used three alfalfa cultivars and four levels of soil water content treatments to investigate herbage productivity, growth point density, residual shoot weight, and root weight. Experiment 2 assessed relationships among root-sourced abscisic acid (ABA), root system architecture and plant biomass in response to water deficit. The results demonstrated that root system was used as a useful tool to improve tolerant and adaptation when alfalfa copied with lower levels of soil water content. On average, maintaining 60–65% soil water-holding capacity alfalfa had the highest herbage accumulation (6.7 g DM pot-1), growing point density (46.5 pot-1), and residual shoot biomass (1.8 g DM pot-1). At the level of water stress, Medicago sativa L. cv Zhaodong (ZD) and cv Aohan (AH) tended to exhibit a herringbone branching pattern with less root tips, root forks, altitude, and magnitude than cv Golden empress (GE). Principal component analysis and structural equation modeling revealed that root-sourced ABA positively regulated the altitude and magnitude of root system architecture, root tips and root forks, and was closely associated with plant root biomass and herbage biomass. It was concluded that these findings can contribute to developing optimum irrigation strategies and help alfalfa breeders in the development of new cultivars with improved drought tolerance based on root system architecture, plant hormone, and plant growth.

Introducing melatonin to the horticultural industry: physiological roles, potential applications, and challenges.

Melatonin (N-acetyl-5-methoxytryptamine) is an emerging biomolecule that influences horticultural crop growth, flowering, fruit ripening, postharvest preservation, and stress protection. It functions as a plant growth regulator, preservative and antimicrobial agent to promote seed germination, regulate root system architecture, influence flowering and pollen germination, promote fruit production, ensure postharvest preservation, and increase resistance to abiotic and biotic stresses. Here, we highlight the potential applications of melatonin in multiple aspects of horticulture, including molecular breeding, vegetative reproduction, production of virus-free plants, food safety, and horticultural crop processing. We also discuss its effects on parthenocarpy, autophagy, and arbuscular mycorrhizal symbiosis. Together, these many features contribute to the promise of melatonin for improving horticultural crop production and food safety. Effective translation of melatonin to the horticultural industry requires an understanding of the challenges associated with its uses, including the development of economically viable sources.

Recognizing the hidden half in wheat: root system attributes associated with drought tolerance.

Improving drought tolerance in wheat is crucial for maintaining productivity and food security. Roots are responsible for the uptake of water from soil, and a number of root traits are associated with drought tolerance. Studies have revealed many quantitative trait loci and genes controlling root development in plants. However, the genetic dissection of root traits in response to drought in wheat is still unclear. Here, we review crop root traits associated with drought, key genes governing root development in plants, and quantitative trait loci and genes regulating root system architecture under water-limited conditions in wheat. Deep roots, optimal root length density and xylem diameter, and increased root surface area are traits contributing to drought tolerance. In view of the diverse environments in which wheat is grown, the balance among root and shoot traits, as well as individual and population performance, are discussed. The known functions of key genes provide information for the genetic dissection of root development of wheat in a wide range of conditions, and will be beneficial for molecular marker development, marker-assisted selection, and genetic improvement in breeding for drought tolerance.

Characterization of CYCLOPHILLIN38 shows that a photosynthesis-derived systemic signal controls lateral root emergence.

Photosynthesis in leaves generates fixed-carbon resources and essential metabolites that support sink tissues, such as roots. Two of these metabolites, sucrose and auxin, promote growth in root systems, but the explicit connection between photosynthetic activity and control of root architecture has not been explored. Through a mutant screen to identify pathways regulating root system architecture, we identified a mutation in the Arabidopsis thaliana CYCLOPHILIN 38 (CYP38) gene, which causes accumulation of pre-emergent stage lateral roots. CYP38 was previously reported to stabilize photosystem II (PSII) in chloroplasts. CYP38 expression is enriched in shoots, and grafting experiments show that the gene acts non-cell-autonomously to promote lateral root emergence. Growth of wild-type plants under low-light conditions phenocopies the cyp38 lateral root emergence defect, as does the inhibition of PSII-dependent electron transport or Nicotinamide adenine dinucleotide phosphate (NADPH) production. Importantly, these perturbations to photosynthetic activity rapidly suppress lateral root emergence, which is separate from their effects on shoot size. Supplementary exogenous sucrose largely rescued primary root (PR) growth in cyp38, but not lateral root growth. Auxin (indole-3-acetic acid (IAA)) biosynthesis from tryptophan is dependent on reductant generated during photosynthesis. Consistently, we found that wild-type seedlings grown under low light and cyp38 mutants have highly diminished levels of IAA in root tissues. IAA treatment rescued the cyp38 lateral root defect, revealing that photosynthesis promotes lateral root emergence partly through IAA biosynthesis. These data directly confirm the importance of CYP38-dependent photosynthetic activity in supporting root growth, and define the specific contributions of two metabolites in refining root architecture under light-limited conditions.

Strigolactones Interact With Nitric Oxide in Regulating Root System Architecture of Arabidopsis thaliana.

Both nitric oxide (NO) and strigolactone (SL) are growth regulating signal components in plants; however, regarding their possible interplay our knowledge is limited. Therefore, this study aims to provide new evidence for the signal interplay between NO and SL in the formation of root system architecture using complementary pharmacological and molecular biological approaches in the model Arabidopsis thaliana grown under stress-free conditions. Deficiency of SL synthesis or signaling (max1-1 and max2-1) resulted in elevated NO and S-nitrosothiol (SNO) levels due to decreased S-nitrosoglutathione (GSNO) reductase (GSNOR) protein abundance and activity indicating that there is a signal interaction between SLs and GSNOR-regulated levels of NO/SNO. This was further supported by the down-regulation of SL biosynthetic genes (CCD7, CCD8 and MAX1) in GSNOR-deficient gsnor1-3. Based on the more pronounced sensitivity of gsnor1-3 to exogenous SL (rac-GR24, 2 µM), we suspected that functional GSNOR is needed to control NO/SNO levels during SL-induced primary root (PR) elongation. Additionally, SLs may be involved in GSNO-regulated PR shortening as suggested by the relative insensitivity of max1-1 and max2-1 mutants to exogenous GSNO (250 µM). Collectively, our results indicate a connection between SL and GSNOR-regulated NO/SNO signals in roots of A. thaliana grown in stress-free environment. As this work used max2-1 mutant and rac-GR24 exerting unspecific effects to both SL and karrikin signaling, it cannot be ruled out that karrikins are partly responsible for the observed effects, and this issue needs further clarification in the future.

Control of root system architecture by phytohormones and environmental signals in rice

Drought and flooding are environmental extremes and major threats to crop production. Water uptake is achieved by plant roots which have to explore new soil spaces to alleviate water deficit during drought or to cope with water excess during flooding. Adaptation of the root system architecture helps plants cope with such extreme conditions and is crucial for plant health and survival. While for dicot plants the well studied model plant Arabidopsis thaliana has provided insight into the genetic and molecular regulation of the root system, less information is available for monocot species, which include the agronomically important cereal crops. Rice (Oryza sativa L.) is a semi-aquatic monocot plant that develops strong tolerance to flooding. Flooding tolerance of rice is closely linked to its adaptive root system. The functional root system of rice is mainly composed of crown roots and is shifted to nodal adventitious roots during flooding which allows rice to maintain oxygen supply to the roots and to survive longer periods of partial submergence as compared with other crops. Likewise, a number of drought-tolerance traits of rice are the result of an altered root system architecture. Hence, the structure of the root system adapts to, both, flooding and drought. Understanding the regulatory mechanisms that control root system adaptation to extreme environments is a key task for scientists to accelerate the breeding efforts for stress-tolerant crops. This review summarizes recently identified genes and molecular mechanisms that regulate root system architecture in rice in response to drought and flooding.

Signaling pathways underlying nitrogen-dependent changes in root system architecture: from model to crop species.

Among all essential mineral elements, nitrogen (N) is required in the largest amounts and thus is often a limiting factor for plant growth. N is taken up by plant roots in the form of water-soluble nitrate, ammonium, and, depending on abundance, low-molecular weight organic N. In soils, the availability and composition of these N forms can vary over space and time, which exposes roots to various local N signals that regulate root system architecture in combination with systemic signals reflecting the N nutritional status of the shoot. Uncovering the molecular mechanisms underlying N-dependent signaling provides great potential to optimize root system architecture for the sake of higher N uptake efficiency in crop breeding. In this review, we summarize prominent signaling mechanisms and their underlying molecular players that derive from external N forms or the internal N nutritional status and modulate root development including root hair formation and gravitropism. We also compare the current state of knowledge of these pathways between Arabidopsis and graminaceous plant species.

Disruption of <i>CYCLOPHILIN 38</i> Function Reveals a Photosynthesis-Dependent Systemic Signal Controlling Lateral Root Emergence

Photosynthesis in leaves generates the fixed-carbon resources and essential metabolites that support sink tissues, such as roots. One of these products, sucrose, is known to promote primary root growth, but it is not clear what other molecules may be involved and whether other stages of root system development are affected by photosynthate levels. Through a mutant screen to identify pathways regulating root system architecture, we identified a mutation in the CYCLOPHILIN 38 (CYP38) gene, which causes an accumulation of pre-emergent stage lateral roots, with a minor effect on primary root growth. CYP38 was previously reported to maintain the stability of Photosystem II (PSII) in chloroplasts. CYP38 expression is enriched in the shoot and grafting experiments show that the gene acts non-cell autonomously to promote lateral root emergence. Growth of wild-type plants under low light conditions phenocopied the cyp38 lateral root emergence phenotype as did the inhibition of PSII-dependent electron transport or NADPH production. Importantly, the cyp38 root phenotype is not rescued by exogenous sucrose, suggesting the involvement of another metabolite. Auxin (IAA) is an essential hormone promoting root growth and its biosynthesis from tryptophan is dependent on reductant generated during photosynthesis. Both WT seedlings grown under low light and cyp38 mutants have highly diminished levels of IAA in root tissues. The cyp38 lateral root defect is rescued by IAA treatment, revealing that photosynthesis promotes lateral root emergence partly through IAA biosynthesis. Metabolomic profiling shows that the accumulation of several defense-related metabolites are also photosynthesis-dependent, suggesting that the regulation of a number of energy-intensive pathways are down-regulated when light becomes limiting.

Low phosphate represses histone deacetylase complex1 to regulate root system architecture remodeling in Arabidopsis.

The mechanisms involved in the regulation of gene expression in response to phosphate (Pi) deficiency have been extensively studied, but their chromatin-level regulation remains poorly understood. We examined the role of histone acetylation in response to Pi deficiency by using the histone deacetylase complex1 (hdc1) mutant. Genes involved in root system architecture (RSA) remodeling were analyzed by quantitative real-time polymerase chain reaction (qPCR) and chromatin immunoprecipitation qPCR. We demonstrate that histone H3 acetylation increased under Pi deficiency, and the hdc1 mutant was hypersensitive to Pi deficiency, with primary root growth inhibition and increases in root hair number. Concomitantly, Pi deficiency repressed HDC1 protein abundances. Under Pi deficiency, hdc1 accumulated higher concentrations of Fe3+ in the root tips and had higher expression of genes involved in RSA remodeling, such as ALUMINUM-ACTIVATED MALATE TRANSPORTER1 (ALMT1), LOW PHOSPHATE ROOT1 (LPR1), and LPR2 compared with wild-type plants. Furthermore, Pi deficiency enriched the histone H3 acetylation of ALMT1 and LPR1. Finally, genetic evidence showed that LPR1/2 was epistatic to HDC1 in regulating RSA remodeling. Our results suggest a chromatin-level control of Pi starvation responses in which HDC1-mediated histone H3 deacetylation represses the transcriptional activation of genes involved in RSA remodeling in Arabidopsis.

Low Nitrogen Enhances Nitrogen Use Efficiency by Triggering NO3- Uptake and Its Long-Distance Translocation.

Nitrogen is essential for plant growth and crop productivity; however, nitrogen use efficiency (NUE) decreases with increasing N supply, resulting in a waste of resources. Molecular mechanisms underlying low-nitrogen (LN)-mediated enhancement of NUE are not clear. We used high-NUE Brassica napus genotype H (Xiangyou 15), low-NUE B. napus genotype L (814), and Arabidopsis mutant aux1 to elucidate the mechanism underlying the changes in NUE under different rates of N fertilizer application. NUE of B. napus increased under LN, which enhanced N uptake ability by regulating root system architecture and plasma membrane H+-ATPase activity; AUX1 was involved in this process. Additionally, BnNRT1.5 was upregulated and BnNRT1.8 was downregulated under LN, whereby more N was transferred to the shoot through enhanced N transport. Observed changes in photosynthesis under LN were associated with N assimilation efficiency. Our study provides new insights into the mechanisms of plant adaptation to the environment.

Interactive Effects of Nutrients and Bradyrhizobium japonicum on the Growth and Root Architecture of Soybean (Glycine max L.).

Understanding the symbiotic performance of rhizobia and responses of plant root systems to mineral nutrient supply will facilitate the development of strategies to enhance effective rhizobia-legume symbioses. Interactive effect of nitrogen (N), phosphorus (P), and magnesium (Mg) on the symbiotic performance of soybean (Glycine max L.) with Bradyrhizobium japonicum, nodulation, root architecture, and the N concentration in plant tissue under hydroponic conditions were studied. Plant growth was significantly higher under a high N supply combined with Mg (HNHMg) than in combination with P (HNHP), which was attributed to the interaction between N and Mg ions. The plants grown at a low N concentration combined with either high or low P or Mg (LNHP, LNHMg, LNLP, and LNLMg) showed a higher nodule dry weight compared to those grown under a high N supply. We observed that the N content in the roots and shoots of soybean plants was significantly lower under LNHP or LNLP, but it was higher under HNHMg or LNHMg, indicating that Mg promotes N acquisition by the plant tissues. Neither root nor shoot growth responded significantly to P availability regardless of the N supply. We observed significant positive relationships between the number of nodules, the N content in plant tissues and the root system architecture of soybean plants grown with a variable supply of Mg combined with N, which highlights the importance of N and Mg availability in the growth medium in regulating root system architecture and nodule formation. The number of rhizobial cells colonizing soybean roots was highest under the HNHMg treatment (6.78 × 104 CFUs/cm of root tip), followed by the HNLMg (4.72 × 104 CFUs/cm of root tip) and LNHMg (4.10 × 104 CFU/cm of root tip) treatments, and lowest under the LNLMg (1.84 × 104 CFUs/cm of root tip) nutrient conditions. The results of this study contribute to new insights for the improvement of the root system and the symbiotic performance of rhizobia inoculated on legumes, stressing the importance of a balanced supply of nutrients.

Cytokinin as a positional cue regulating lateral root spacing in Arabidopsis.

The root systems of plants have developed adaptive architectures to exploit soil resources. The formation of lateral roots (LRs) contributes to root system architecture. Roots of plants with a lower cytokinin status form LR primordia (LRP) in unusually close proximity, indicating a role for the hormone in regulating the positioning of LRs along the main root axis. Data obtained from cytokinin-synthesis mutants of Arabidopsis thaliana combined with gene expression analysis indicate that cytokinin synthesis by IPT5 and LOG4 occurring early during LRP initiation generates a local cytokinin signal abbreviating LRP formation in neighbouring pericycle cells. In addition, IPT3, IPT5, and IPT7 contribute to cytokinin synthesis in the vicinity of existing LRP, thus suppressing initiation of new LRs. Interestingly, mutation of CYP735A genes required for trans-zeatin biosynthesis caused strong defects in LR positioning, indicating an important role for this cytokinin metabolite in regulating LR spacing. Further it is shown that cytokinin and a known regulator of LR spacing, the receptor-like kinase ARABIDOPSIS CRINKLY4 (ACR4), operate in a non-hierarchical manner but might exert reciprocal control at the transcript level. Taken together, the results suggest that cytokinin acts as a paracrine hormonal signal in regulating root system architecture.

Auxins differentially regulate root system architecture and cell cycle protein levels in maize seedlings

Maize (Zea mays) root system architecture has a complex organization, with adventitious and lateral roots determining its overall absorptive capacity. To generate basic information about the earlier stages of root development, we compared the post-embryonic growth of maize seedlings germinated in water-embedded cotton beds with that of plants obtained from embryonic axes cultivated in liquid medium. In addition, the effect of four different auxins, namely indole-3-acetic acid (IAA), 1-naphthaleneacetic acid (NAA), indole-3-butyric acid (IBA) and 2,4-dichlorophenoxyacetic acid (2,4-D) on root architecture and levels of the heat shock protein HSP101 and the cell cycle proteins CKS1, CYCA1 and CDKA1 were analyzed. Our data show that during the first days after germination, maize seedlings develop several root types with a simultaneous and/or continuous growth. The post-embryonic root development started with the formation of the primary root (PR) and seminal scutellar roots (SSR) and then continued with the formation of adventitious crown roots (CR), brace roots (BR) and lateral roots (LR). Auxins affected root architecture in a dose-response fashion; whereas NAA and IBA mostly stimulated crown root formation, 2,4-D showed a strong repressing effect on growth. The levels of HSP101, CKS1, CYCA1 and CDKA in root and leaf tissues were differentially affected by auxins and interestingly, HSP101 registered an auxin-inducible and root specific expression pattern. Taken together, our results show the timing of early branching patterns of maize and indicate that auxins regulate root development likely through modulation of the HSP101 and cell cycle proteins.

Cytokinin as a mediator for regulating root system architecture in response to environmental cues

Root system architecture (RSA) is developmentally controlled by genetic pathways and their interaction with various environmental cues, in particular soil conditions. One important player in shaping RSA is the hormone cytokinin, which acts as a negative regulator of root elongation and branching. The redundant roles of cytokinin metabolism and signaling genes of Arabidopsis thaliana in regulating early stages of lateral root formation has recently been shown and it has been proposed that this redundancy reflects a role in mediating different environmental cues. Here we report that the transcript levels of cytokinin genes in the root responds to changes in nutrient availability in distinct ways. IPT3, IPT5, CYP735A2, LOG5, and CKX4 are particularly responsive cytokinin metabolism genes, genes encoding different type-A response regulators and the transcriptions factor genes ARR10 and CRF6 are among the most responsive signaling genes. This finding supports the hypothesis that environmental cues operate through fine-tuned transcriptional regulation of cytokinin genes to modulate root development.

Transcriptional regulation of phosphate acquisition by higher plants.

Phosphorus (P), an essential macronutrient required for plant growth and development, is often limiting in natural and agro-climatic environments. To cope with heterogeneous or low phosphate (Pi) availability, plants have evolved an array of adaptive responses facilitating optimal acquisition and distribution of Pi. The root system plays a pivotal role in Pi-deficiency-mediated adaptive responses that are regulated by a complex interplay of systemic and local Pi sensing. Cross-talk with sugar, phytohormones, and other nutrient signaling pathways further highlight the intricacies involved in maintaining Pi homeostasis. Transcriptional regulation of Pi-starvation responses is particularly intriguing and involves a host of transcription factors (TFs). Although PHR1 of Arabidopsis is an extensively studied MYB TF regulating subset of Pi-starvation responses, it is not induced during Pi deprivation. Genome-wide analyses of Arabidopsis have shown that low Pi stress triggers spatiotemporal expression of several genes encoding different TFs. Functional characterization of some of these TFs reveals their diverse roles in regulating root system architecture, and acquisition and utilization of Pi. Some of the TFs are also involved in phytohormone-mediated root responses to Pi starvation. The biological roles of these TFs in transcriptional regulation of Pi homeostasis in model plants Arabidopsis thaliana and Oryza sativa are presented in this review.

Intrinsic and environmental response pathways that regulate root system architecture

Root system development is an important agronomic trait. The right architecture in a given environment allows plants to survive periods of water of nutrient deficit, and compete effectively for resources. Root systems also provide an optimal system for studying developmental plasticity, a characteristic feature of plant growth. This review proposes a framework for describing the pathways regulating the development of complex structures such as root systems: intrinsic pathways determine the characteristic architecture of the root system in a given plant species, and define the limits for plasticity in that species. Response pathways co-ordinate environmental cues with development by modulating intrinsic pathways. The current literature describing the regulation of root system development is summarized here within this framework. Regulatory pathways are also organized based on their specific developmental effect in the root system. All the pathways affect lateral root formation, but some specifically target initiation of the lateral root, while others target the development and activation of the lateral root primordium, or the elongation of the lateral root. Finally, we discuss emerging approaches for understanding the regulation of root system architecture.