Arabidopsis lateral root development: an emerging story

Light at the end of the tunnel: integrating signaling pathways in the coordination of lateral root development

Root system architecture (RSA) encompasses a range of physical root attributes, including the lateral roots (LRs), root hairs and adventitious roots, in addition to the primary or main root. This overall structure is a crucial trait for efficient water and mineral capture alongside providing anchorage to the plant in the soil and is vital for plant productivity and fitness. RSA dynamics are dependent upon various environmental cues such as light, soil pH, water, mineral nutrition and the belowground microbiome. Among these factors, light signaling through HY5 significantly influences the flexibility of RSA by controlling different signaling pathways that converge at photoreceptors-mediated signaling, also present in the 'hidden half'. Furthermore, several phytohormones also drive the formation and emergence of LRs and are critical to harmonize intra and extracellular stimuli in this regard. This review endeavors to elucidate the impact of these interactions on RSA, with particular emphasis on LR development and to enhance our understanding of the fundamental mechanisms governing the light-regulation of LR growth and physiology.

Recent advances in response to environmental signals during Arabidopsis root development

Plants grow by anchoring their roots in the soil, acquiring essential water and nutrients for growth, and interacting with other signaling factors in the soil. Root systems are crucial for both the basic growth and development of plants and their response to external environmental stimuli. Under different environmental conditions, the configuration of root systems in plants can undergo significant changes, with their strength determining the plant's ability to adapt to the environment. Therefore, understanding the mechanisms by which environmental factors regulate root development is essential for crop root architecture improvement and breeding for stress resistance. This paper summarizes the research progress in genetic regulation of root development of the model plant Arabidopsis thaliana (L.) Heynh. amidst diverse environmental stimuli over the past five years. Specifically, it focuses on the regulatory networks of environmental signals, encompassing light, energy, temperature, water, nutrients, and reactive oxygen species, on root development. Furthermore, it provides prospects for the application of root architecture improvement in crop breeding for stress resistance and nutrient efficiency.

MYB2 and MYB108 regulate lateral root development by interacting with LBD29 in Arabidopsis thaliana

AUXIN RESPONSE FACTOR 7 (ARF7)-mediated auxin signaling plays a key role in lateral root (LR) development by regulating downstream LATERAL ORGAN BOUNDARIES DOMAIN (LBD) transcription factor genes, including LBD16, LBD18, and LBD29. LBD proteins are believed to regulate the transcription of downstream genes as homodimers or heterodimers. However, whether LBD29 forms dimers with other proteins to regulate LR development remains unknown. Here, we determined that the Arabidopsis thaliana (L.) Heynh. MYB transcription factors MYB2 and MYB108 interact with LBD29 and regulate auxin-induced LR development. Both MYB2 and MYB108 were induced by auxin in an ARF7-dependent manner. Disruption of MYB2 by fusion with an SRDX domain severely affected auxin-induced LR formation and the ability of LBD29 to induce LR development. By contrast, overexpression of MYB2 or MYB108 resulted in greater LR numbers, except in the lbd29 mutant background. These findings underscore the interdependence and importance of MYB2, MYB108, and LBD29 in regulating LR development. In addition, MYB2-LBD29 and MYB108-LBD29 complexes promoted the expression of CUTICLE DESTRUCTING FACTOR 1 (CDEF1), a member of the GDSL (Gly-Asp-Ser-Leu) lipase/esterase family involved in LR development. In summary, this study identified MYB2-LBD29 and MYB108-LBD29 regulatory modules that act downstream of ARF7 and intricately control auxin-mediated LR development.

Toward uncovering an operating system in plant organs

Molecular motifs can explain information processing within single cells, while how assemblies of cells collectively achieve this remains less well understood. Plant fitness and survival depend upon robust and accurate decision-making in their decentralised multicellular organ systems. Mobile agents, including hormones, metabolites, and RNAs, have a central role in coordinating multicellular collective decision-making, yet mechanisms describing how cell-cell communication scales to organ-level transitions is poorly understood. Here, we explore how unified outputs may emerge in plant organs by distributed information processing across different scales and using different modalities. Mathematical and computational representations of these events are also explored toward understanding how these events take place and are leveraged to manipulate plant development in response to the environment.

Effects of Cadmium Stress on Tartary Buckwheat Seedlings

Cadmium (Cd) is a naturally occurring toxic heavy metal that adversely affects plant germination, growth, and development. While the effects of Cd have been described on many crop species including rice, maize, wheat and barley, few studies are available on cadmium's effect on Tartary buckwheat which is a traditional grain in China. We examined nine genotypes and found that 30 µM of Cd reduced the root length in seedlings by between 4 and 44% and decreased the total biomass by 7 to 31%, compared with Cd-free controls. We identified a significant genotypic variation in sensitivity to Cd stress. Cd treatment decreased the total root length and the emergence and growth of lateral roots, and these changes were significantly greater in the Cd-sensitive genotypes than in tolerant genotypes. Cd resulted in greater wilting and discoloration in sensitive genotypes than in tolerant genotypes and caused more damage to the structure of root and leaf cells. Cd accumulated in the roots and shoots, but the concentrations in the sensitive genotypes were significantly greater than in the more tolerant genotypes. Cd treatment affected nutrient uptake, and the changes in the sensitive genotypes were greater than those in the tolerant genotypes, which could maintain their concentrations closer to the control levels. The induction of SOD, POD, and CAT activities in the roots and shoots was significantly greater in the tolerant genotypes than in the sensitive genotypes. We demonstrated that Cd stress reduced root and shoot growth, decreased plant biomass, disrupted nutrient uptake, altered cell structure, and managed Cd-induced oxidative stress differently in the sensitive and tolerant genotypes of Tartary buckwheat.

Enigmatic role of auxin response factors in plant growth and stress tolerance

Abiotic and biotic stresses globally constrain plant growth and impede the optimization of crop productivity. The phytohormone auxin is involved in nearly every aspect of plant development. Auxin acts as a chemical messenger that influences gene expression through a short nuclear pathway, mediated by a family of specific DNA-binding transcription factors known as Auxin Response Factors (ARFs). ARFs thus act as effectors of auxin response and translate chemical signals into the regulation of auxin responsive genes. Since the initial discovery of the first ARF in Arabidopsis, advancements in genetics, biochemistry, genomics, and structural biology have facilitated the development of models elucidating ARF action and their contributions to generating specific auxin responses. Yet, significant gaps persist in our understanding of ARF transcription factors despite these endeavors. Unraveling the functional roles of ARFs in regulating stress response, alongside elucidating their genetic and molecular mechanisms, is still in its nascent phase. Here, we review recent research outcomes on ARFs, detailing their involvement in regulating leaf, flower, and root organogenesis and development, as well as stress responses and their corresponding regulatory mechanisms: including gene expression patterns, functional characterization, transcriptional, post-transcriptional and post- translational regulation across diverse stress conditions. Furthermore, we delineate unresolved questions and forthcoming challenges in ARF research.

Effects of environmental metal and metalloid pollutants on plants and human health: exploring nano-remediation approach

Metal and metalloid pollutants severely threatens environmental ecosystems and human health, necessitating effective remediation strategies. Nanoparticle (NPs)-based approaches have gained significant attention as promising solutions for efficient removing heavy metals from various environmental matrices. The present review is focused on green synthesized NPs-mediated remediation such as the implementation of iron, carbon-based nanomaterials, metal oxides, and bio-based NPs. The review also explores the mechanisms of NPs interactions with heavy metals, including adsorption, precipitation, and redox reactions. Critical factors influencing the remediation efficiency, such as NPs size, surface charge, and composition, are systematically examined. Furthermore, the environmental fate, transport, and potential risks associated with the application of NPs are critically evaluated. The review also highlights various sources of metal and metalloid pollutants and their impact on human health and translocation in plant tissues. Prospects and challenges in translating NPs-based remediation from laboratory research to real-world applications are proposed. The current work will be helpful to direct future research endeavors and promote the sustainable implementation of metal and metalloid elimination.

Transcriptional changes during crown-root development and emergence in barley (Hordeum vulgare L.)

BACKGROUND

Roots play an important role during plant growth and development, ensuring water and nutrient uptake. Understanding the mechanisms regulating their initiation and development opens doors towards root system architecture engineering.

RESULTS

Here, we investigated by RNA-seq analysis the changes in gene expression in the barley stem base of 1 day-after-germination (DAG) and 10DAG seedlings when crown roots are formed. We identified 2,333 genes whose expression was lower in the stem base of 10DAG seedlings compared to 1DAG seedlings. Those genes were mostly related to basal cellular activity such as cell cycle organization, protein biosynthesis, chromatin organization, cytoskeleton organization or nucleotide metabolism. In opposite, 2,932 genes showed up-regulation in the stem base of 10DAG seedlings compared to 1DAG seedlings, and their function was related to phytohormone action, solute transport, redox homeostasis, protein modification, secondary metabolism. Our results highlighted genes that are likely involved in the different steps of crown root formation from initiation to primordia differentiation and emergence, and revealed the activation of different hormonal pathways during this process.

CONCLUSIONS

This whole transcriptomic study is the first study aiming at understanding the molecular mechanisms controlling crown root development in barley. The results shed light on crown root emergence that is likely associated with a strong cell wall modification, death of the cells covering the crown root primordium, and the production of defense molecules that might prevent pathogen infection at the site of root emergence.

Trichoderma-secreted anthranilic acid promotes lateral root development via auxin signaling and RBOHF-induced endodermal cell wall remodeling

Trichoderma spp. have evolved the capacity to communicate with plants by producing various secondary metabolites (SMs). Nonhormonal SMs play important roles in plant root development, while specific SMs from rhizosphere microbes and their underlying mechanisms to control plant root branching are still largely unknown. In this study, a compound, anthranilic acid (2-AA), is identified from T. guizhouense NJAU4742 to promote lateral root development. Further studies demonstrate that 2-AA positively regulates auxin signaling and transport in the canonical auxin pathway. 2-AA also partly rescues the lateral root numbers of CASP1pro:shy2-2, which regulates endodermal cell wall remodeling via an RBOHF-induced reactive oxygen species burst. In addition, our work reports another role for microbial 2-AA in the regulation of lateral root development, which is different from its better-known role in plant indole-3-acetic acid biosynthesis. In summary, this study identifies 2-AA from T. guizhouense NJAU4742, which plays versatile roles in regulating plant root development.

Mechanisms for plant growth promotion activated by Trichoderma in natural and managed terrestrial ecosystems

Trichoderma spp. are free-living fungi present in virtually all terrestrial ecosystems. These soil fungi can stimulate plant growth and increase plant nutrient acquisition of macro- and micronutrients and water uptake. Generally, plant growth promotion by Trichoderma is a consequence of the activity of potent fungal signaling metabolites diffused in soil with hormone-like activity, including indolic compounds as indole-3-acetic acid (IAA) produced at concentrations ranging from 14 to 234 μg l-1, and volatile organic compounds such as sesquiterpene isoprenoids (C15), 6-pentyl-2H-pyran-2-one (6-PP) and ethylene (ET) produced at levels from 10 to 120 ng over a period of six days, which in turn, might impact plant endogenous signaling mechanisms orchestrated by plant hormones. Plant growth stimulation occurs without the need of physical contact between both organisms and/or during root colonization. When associated with plants Trichoderma may cause significant biochemical changes in plant content of carbohydrates, amino acids, organic acids and lipids, as detected in Arabidopsis thaliana, maize (Zea mays), tomato (Lycopersicon esculentum) and barley (Hordeum vulgare), which may improve the plant health status during the complete life cycle. Trichoderma-induced plant beneficial effects such as mechanisms of defense and growth are likely to be inherited to the next generations. Depending on the environmental conditions perceived by the fungus during its interaction with plants, Trichoderma can reprogram and/or activate molecular mechanisms commonly modulated by IAA, ET and abscisic acid (ABA) to induce an adaptative physiological response to abiotic stress, including drought, salinity, or environmental pollution. This review, provides a state of the art overview focused on the canonical mechanisms of these beneficial fungi involved in plant growth promotion traits under different environmental scenarios and shows new insights on Trichoderma metabolites from different chemical classes that can modulate specific plant growth aspects. Also, we suggest new research directions on Trichoderma spp. and their secondary metabolites with biological activity on plant growth.

Over-expression of the BnVIT-L2 gene improves the lateral root development and biofortification under iron stress

The vacuolar iron transporter (VIT) family is responsible for absorbing and storing iron ions in vacuoles. Here, the BnVIT-L2 gene from Brassica napus has been cloned for the first time and was found to be expressed in multiple tissues and organs, induced by iron stress. The BnVIT-L2 protein is located in vacuolar membranes and has the ability to bind both iron and other bivalent metal ions. Over-expression of the BnVIT-L2 gene increased lateral root number and main root length, as well as chlorophyll and iron content in transgenic Arabidopsis plants (BnVIT-L2/At) exposed to iron stress, compared to wild type Col-0. Furthermore, over-expression of this gene improved the adaptability of transgenic B. napus plants (BnVIT-L2-OE) under iron stress. The regulation of plant tolerance under iron stress by BnVIT-L2 gene may involve in the signal of reactive oxygen species (ROS), as suggested by Ribosome profiling sequencing (Ribo-seq). This study provides a reference for investigating plant growth and biofortification under iron stress through the BnVIT-L2 gene.

Lateral root primordium: Formation, influencing factors and regulation

Roots are the primary determinants of water and nutrient uptake by plants. The structure of roots is largely determined by the repeated formation of new lateral roots (LR). A new lateral root primordium (LRP) is formed between the beginning and appearance of LR, which defines the organization and function of LR. Therefore, proper LRP morphogenesis is a crucial process for lateral root formation. The development of LRP is regulated by multiple factors, including hormone and environmental signals. Roots integrate signals and regulate growth and development. At the molecular level, many genes regulate the growth and development of root organs to ensure stable development plans, while also being influenced by various environmental factors. To gain a better understanding of the LRP formation and its influencing factors, this study summarizes previous research. The cell cycle involved in LRP formation, as well as the roles of ROS, auxin, other auxin-related plant hormones, and genetic regulation, are discussed in detail. Additionally, the effects of gravity, mechanical stress, and cell death on LRP formation are explored. Throughout the text unanswered or poorly understood questions are identified to guide future research in this area.

A GARP transcription factor SlGCC positively regulates lateral root development in tomato via auxin-ethylene interplay

MAIN CONCLUSION

SlGCC, a GARP transcription factor, functions as a root-related transcriptional repressor. SlGCC synchronizes auxin and ethylene signaling involving SlPIN3 and SlIAA3 as intermediate targets sketching a molecular map for lateral root development in tomato. The root system is crucial for growth and development of plants as it performs basic functions such as providing mechanical support, nutrients and water uptake, pathogen resistance and responds to various stresses. SlGCC, a GARP family transcription factor (TF), exhibited predominant expression in age-dependent (initial to mature stages) tomato root. SlGCC is a transcriptional repressor and is regulated at a transcriptional and translational level by auxin and ethylene. Auxin and ethylene mediated SlGCC protein stability is governed via proteasome degradation pathway during lateral root (LR) growth development. SlGCC over-expressor (OE) and under-expressed (UE) tomato transgenic lines demonstrate its role in LR development. This study is an attempt to unravel the vital role of SlGCC in regulating tomato LR architecture.

Age-dependent analysis dissects the stepwise control of auxin-mediated lateral root development in rice

As root elongation rates are different among each individual root, the distance from the root apices does not always reflect the age of root cells. Thus, methods for correcting variations in elongation rates are needed to accurately evaluate the root developmental process. Here, we show that modeling-based age-dependent analysis is effective for dissecting stepwise lateral root (LR) development in rice (Oryza sativa). First, we measured the increases in LR and LR primordium (LRP) numbers, diameters, and lengths in wild type and an auxin-signaling-defective mutant, which has a faster main (crown) root elongation rate caused by the mutation in the gene encoding AUXIN/INDOLE-3-ACETIC ACID protein 13 (IAA13). The longitudinal patterns of these parameters were fitted by the appropriate models and the age-dependent patterns were identified using the root elongation rates. As a result, we found that LR and LRP numbers and lengths were reduced in iaa13. We also found that the duration of the increases in LR and LRP diameters were prolonged in iaa13. Subsequent age-dependent comparisons with gene expression patterns suggest that AUXIN RESPONSE FACTOR11 (ARF11), the homolog of MONOPTEROS (MP)/ARF5 in Arabidopsis (Arabidopsis thaliana), is involved in the initiation and growth of LR(P). Indeed, the arf11 mutant showed a reduction of LR and LRP numbers and lengths. Our results also suggest that PINOID-dependent rootward-to-shootward shift of auxin flux contributes to the increase in LR and LRP diameters. Together, we propose that modeling-based age-dependent analysis is useful for root developmental studies by enabling accurate evaluation of root traits' expression.

Auxin synthesis promotes N metabolism and optimizes root structure enhancing N acquirement in maize (Zea mays L.)

MAIN CONCLUSION

Foliar NAA increases photosynthate supplied by enhancing photosynthesis, to strengthen root activity and provide a large sink for root carbohydrate accumulation, which is beneficial to acquire more nitrogen. The improvement of grain yield is an effective component in the food security. Auxin acts as a well-known plant hormone, plays an important role in maize growth and nutrient uptake. In this study, with maize variety Zhengdan 958 (ZD958) as material, the effects of auxin on nitrogen (N) uptake and assimilation of seedling maize were studied by hydroponic experiments. With water as the control, naphthalene acetic acid (NAA, 0.1 mmol/L) and aminoethoxyvinylglycine (AVG, 0.1 mmol/L, an auxin synthesis inhibitor) were used for foliar spraying. The results showed that NAA significantly improved photosynthetic rate and plant biomass by 58.6% and 91.7%, respectively, while the effect of AVG was opposite to that of NAA. At the same time, key enzymes activities related N assimilation in NAA leaves were significantly increased, and the activities of nitrate reductase (NR), glutamine synthetase (GS) and glutamate synthase (GOGAT) were increased by 32.3%, 22.9%, and 16.2% in new leaves. Furthermore, NAA treatment promoted underground growth. When compared with control, total root length, root surface area, root tip number, branch number and root activity were significantly increased by 37.8%, 22.2%, 35.1%, 28.8% and 21.2%. Root growth is beneficial to N capture in maize. Ultimately, the total N accumulation of NAA treatment was significantly increased by 74.5%, as compared to the control. In conclusion, NAA foliar spraying increased endogenous IAA content, and enhanced the activity of N assimilation-related enzymes and photosynthesis rate, in order to build a large sink for carbohydrate accumulation. In addition, NAA strengthened root activity and regulated root morphology and architecture, which facilitated further N uptake and plant growth.

Revealing the phosphate-solubilizing characteristics and mechanisms of the plant growth-promoting bacterium Agrobacterium deltaense C1

AIMS

This study explores the phosphate (Pi)-solubilizing characteristics and mechanisms of a novel phosphate-solubilizing bacterium, Agrobacterium deltaense C1 (C1 hereafter).

METHODS AND RESULTS

The growth-promoting effects of C1 were investigated by gnotobiotic experiments, and the Pi-solubilizing mechanism was revealed by extracellular metabolomics, liquid chromatography analysis, and reverse transcription quantitative polymerase chain reaction. Results showed that C1 significantly increased Arabidopsis biomass and total phosphorus (P) content under P deficiency. Under Ca3(PO4)2 condition, the presence of C1 resulted in a significant and negative correlation between available P content and medium pH changes, implying that Pi dissolution occurs through acid release. Metabolomics revealed C1's ability to release 99 organic acids, with gluconic acid (GA), citric acid, and α-ketoglutaric acid contributing 64.86%, 9.58%, and 0.94%, respectively, to Pi solubilization. These acids were significantly induced by P deficiency. Moreover, C1's Pi solubilization may remain significant even in the presence of available P, as evidenced by substantial pH reduction and high gcd gene expression. Additionally, C1 produced over 10 plant growth-promoting substances.

CONCLUSIONS

C1 dissolves Pi primarily by releasing GA, which enhances plant growth under P deficiency. Notably, its Pi solubilization effect is not significantly limited by available Pi.

Plant KASH proteins SINE1 and SINE2 have synergistic and antagonistic interactions with actin-branching and actin-bundling factors

Linker of nucleoskeleton and cytoskeleton (LINC) complexes consist of outer nuclear membrane KASH proteins, interacting in the nuclear envelope lumen with inner nuclear membrane SUN proteins and connecting the nucleus and cytoskeleton. The paralogous Arabidopsis KASH proteins SINE1 and SINE2 function during stomatal dynamics induced by light-dark transitions and abscisic acid (ABA), which requires F-actin reorganization. SINE2 influences actin depolymerization and SINE1 actin repolymerization. The actin-related protein 2/3 (ARP2/3) complex, an actin nucleator, and the plant actin-bundling and -stabilizing factor SCAB1 are involved in stomatal aperture control. Here, we have tested the genetic interaction of SINE1 and SINE2 with SCAB1 and the ARP2/3 complex. We show that SINE1 and the ARP2/3 complex function in the same pathway during ABA-induced stomatal closure, while SINE2 and the ARP2/3 complex play opposing roles. The actin repolymerization defect observed in sine1-1 is partially rescued in scab1-2 sine1-1, while SINE2 is epistatic to SCAB1. In addition, SINE1 and ARP2/3 act synergistically in lateral root development. The absence of SINE2 renders trichome development independent of the ARP2/3 complex. Together, these data reveal complex and differential interactions of the two KASH proteins with the actin-remodeling apparatus and add evidence to the proposed differential role of SINE1 and SINE2 in actin dynamics.

Genetic regulation of lateral root development

Lateral roots (LRs) are an important part of plant root systems. In dicots, for example, after plants adapted from aquatic to terrestrial environments, filamentous pseudorhizae evolved to allow nutrient absorption. A typical plant root system comprises a primary root, LRs, root hairs, and a root cap. Classical plant roots exhibit geotropism (the tendency to grow downward into the ground) and can synthesize plant hormones and other essential substances. Root vascular bundles and complex spatial structures enable plants to absorb water and nutrients to meet their nutrient quotas and grow. The primary root carries out most functions during early growth stages but is later overtaken by LRs, underscoring the importance of LR development water and mineral uptake and the soil fixation capacity of the root. LR development is modulated by endogenous plant hormones and external environmental factors, and its underlying mechanisms have been dissected in great detail in Arabidopsis, thanks to its simple root anatomy and the ease of obtaining mutants. This review comprehensively and systematically summarizes past research (largely in Arabidopsis) on LR basic structure, development stages, and molecular mechanisms regulated by different factors, as well as future prospects in LR research, to provide broad background knowledge for root researchers.

The MADS-box family gene PtrANR1 encodes a transcription activator promoting root growth and enhancing plant tolerance to drought stress

KEY MESSAGE

PtrANR1 positively regulates plant drought tolerance by increasing proline level and reducing ROS accumulation. PtrANR1 directly activates PtrAUX1 expression to promote root growth and improve plant drought tolerance. Citrus quality and yield are severely declined under drought stress. To date, the effects of MADS-box family transcription factors (TFs) on plant drought resistance have made some progress. However, whether MADS-box family TFs are associated with citrus drought response has remained unclear. The current paper identified a MADS-box family gene PtrANR1 encoding anthocyanidin reductase from trifoliate orange. PtrANR1 exhibits high identities with ANR1 proteins found in various plants. PtrANR1 possesses two conserved domains known as MADS and kertanin-like domains. PtrANR1 is a nuclear protein which has transactivation activity. A significant induction of PtrANR1 transcript was detected in leaves and roots of trifoliate orange treated with PEG6000 and ABA. Under drought stress, Arabidopsis ectopic overexpressing PtrANR1 exhibited obviously elevated contents of proline, ABA and IAA, better developed root, enhanced antioxidant enzyme activities, as well as notably reduced accumulation of malondialdehyde (MDA) and reactive oxygen species (ROS) compared with WT plants. However, opposite change trends of these physiological indices were detected in PtrANR1 homolog silencing lemon. Furthermore, transgenic Arabidopsis displayed significantly increased expression levels in genes associated with ABA, IAA and proline production, IAA polar transport, ROS elimination and drought response. However, these genes exhibited noticeably decreased transcript levels in PtrANR1 homolog silencing lemon. Moreover, PtrANR1 could increase IAA content and promote root growth by binding to GArG-box in the promoter of PtrAUX1 to activate its transcript. These findings indicated that PtrANR1 had a beneficial impact on plant drought resistance through promoting root development, increasing proline accumulation and scavenging of ROS.

Auxin is involved in cadmium accumulation in rice through controlling nitric oxide production and the ability of cell walls to bind cadmium

Although auxin has been linked to plants' responses to cadmium (Cd) stress, the exact mechanism is yet elusive. The objective of the current investigation was to determine the role and the mechanism of auxin in controlling rice's Cd accumulation. Rice roots with Cd stress have higher endogenous auxin levels, and exogenous auxin combined Cd treatment could reduce root cell wall's hemicellulose content when compared with Cd treatment alone, which in turn reduced its fixation of Cd, as well as decreased the expression of OsCd1 (a major facilitator superfamily gene), OsNRAMP1/5 (Natural Resistance-Associated Macrophage Protein 1/5), OsZIP5/9 (Zinc Transporter 5/9), and OsHMA2 (Heavy Metal ATPase 2) that participated in Cd uptake and root to shoot translocation. Furthermore, less Cd accumulated in the shoots as a result of auxin's impact in increasing the expression of OsCAL1 (Cadmium accumulation in Leaf 1), OsABCG36/OsPDR9 (G-type ATP-binding cassette transporter/Pleiotropic drug resistance 9), and OsHMA3, which were in charge of Cd efflux and sequestering into vacuoles, respectively. Additionally, auxin decreased endogenous nitric oxide (NO) levels and antioxidant enzyme activity, while treatment of a NO scavenger-cPTIO-reduced auxin's alleviatory effects. In conclusion, the rice's ability to tolerate Cd toxicity was likely increased by the auxin-accelerated cell wall Cd exclusion mechanism, a pathway that controlled by the buildup of NO.

Maximizing trace metal phytoextraction through planting methods: Role of rhizosphere fertility and microbial activities

Brownfields are a widespread problem in the world. The poor quality of these soils and the potential presence of contaminants can pose a significant threat to plant establishment and growth. However, it may be possible to improve their establishment with an appropriate agricultural practice. In this paper, the effects of two common planting strategies, seeding and transplanting, on the establishment and growth of the hyperaccumulator species Noccaea caerulescens and on its phytoextraction capacity were investigated. A field experiment was conducted by direct sowing of N. caerulescens seeds on a plot of contaminated Technosols in Jeandelaincourt, France. At the same time, seeds were sown on potting soil under controlled conditions. One month later, the seedlings were transplanted to the field. One year later, the results showed that transplanting improved the establishment and growth of N. caerulescens. This was due to a decrease in soil pH in the rhizosphere, which subsequently increased nutrient availability. This change in rhizosphere properties also appeared to be the key that improved microbial activities in the rhizosphere soil of transplanted plants. The observed improvement in both rhizosphere nutrient availability and microbial activities, in turn, increased auxin concentrations in the rhizosphere and consequently a more developed root system was observed in the transplanted plants. Furthermore, the Cd and Zn phytoextraction yield of transplanted plants is 2.5 and 5 times higher, respectively, than that of sown plants. In conclusion, N. caerulescens transplantation on contaminated sites seems to be an adequate strategy to improve plant growth and enhance trace metal phytoextraction.

Genetic Interaction between Arabidopsis SUR2/CYP83B1 and GNOM Indicates the Importance of Stabilizing Local Auxin Accumulation in Lateral Root Initiation

Lateral root (LR) formation is an important developmental event for the establishment of the root system in most vascular plants. In Arabidopsis thaliana, the fewer roots (fwr) mutation in the GNOM gene, encoding a guanine nucleotide exchange factor of ADP ribosylation factor that regulates vesicle trafficking, severely inhibits LR formation. Local accumulation of auxin response for LR initiation is severely affected in fwr. To better understand how local accumulation of auxin response for LR initiation is regulated, we identified a mutation, fewer roots suppressor1 (fsp1), that partially restores LR formation in fwr. The gene responsible for fsp1 was identified as SUPERROOT2 (SUR2), encoding CYP83B1 that positions at the metabolic branch point in the biosynthesis of auxin/indole-3-acetic acid (IAA) and indole glucosinolate. The fsp1 mutation increases both endogenous IAA levels and the number of the sites where auxin response locally accumulates prior to LR formation in fwr. SUR2 is expressed in the pericycle of the differentiation zone and in the apical meristem in roots. Time-lapse imaging of the auxin response revealed that local accumulation of auxin response is more stable in fsp1. These results suggest that SUR2/CYP83B1 affects LR founder cell formation at the xylem pole pericycle cells where auxin accumulates. Analysis of the genetic interaction between SUR2 and GNOM indicates the importance of stabilization of local auxin accumulation sites for LR initiation.

Salinity stress and nanoparticles: Insights into antioxidative enzymatic resistance, signaling, and defense mechanisms

Salinized land is slowly spreading across the world. Reduced crop yields and quality due to salt stress threaten the ability to feed a growing population. We discussed the mechanisms behind nano-enabled antioxidant enzyme-mediated plant tolerance, such as maintaining reactive oxygen species (ROS) homeostasis, enhancing the capacity of plants to retain K+ and eliminate Na+, increasing the production of nitric oxide, involving signaling pathways, and lowering lipoxygenase activities to lessen oxidative damage to membranes. Frequently used techniques were highlighted like protecting cells from oxidative stress and keeping balance in ionic state. Salt tolerance in plants enabled by nanotechnology is also discussed, along with the potential role of physiobiochemical and molecular mechanisms. As a whole, the goal of this review is meant to aid researchers in fields as diverse as plant science and nanoscience in better-comprehending potential with novel solutions to addressing salinity issues for sustainable agriculture.

An artificial intelligence-integrated analysis of the effect of drought stress on root traits of "modern" and "ancient" wheat varieties

Due to drought stress, durum wheat production in the Mediterranean basin will be severely affected in the coming years. Durum wheat cultivation relies on a few genetically uniform "modern" varieties, more productive but less tolerant to stresses, and "traditional" varieties, still representing a source of genetic biodiversity for drought tolerance. Root architecture plasticity is crucial for plant adaptation to drought stress and the relationship linking root structures to drought is complex and still largely under-explored. In this study, we examined the effect of drought stress on the roots' characteristics of the "traditional" Saragolla cultivar and the "modern" Svevo. By means of "SmartRoot" software, we demonstrated that drought stress affected primary and lateral roots as well as root hair at different extents in Saragolla and Svevo cultivars. Indeed, we observed that under drought stress Saragolla possibly revamped its root architecture, by significantly increasing the length of lateral roots, and the length/density of root hairs compared to the Svevo cultivar. Scanning Electron Microscopy analysis of root anatomical traits demonstrated that under drought stress a greater stele area and an increase of the xylem lumen size vessel occurred in Saragolla, indicating that the Saragolla variety had a more efficient adaptive response to osmotic stress than the Svevo. Furthermore, for the analysis of root structural data, Artificial Intelligence (AI) algorithms have been used: Their application allowed to predict from root structural traits modified by the osmotic stress the type of cultivar observed and to infer the relationship stress-cultivar type, thus demonstrating that root structural traits are clear and incontrovertible indicators of the higher tolerance to osmotic stress of the Saragolla cultivar. Finally, to obtain an integrated view of root morphogenesis, phytohormone levels were investigated. According to the phenotypic effects, under drought stress,a larger increase in IAA and ABA levels, as well as a more pronounced reduction in GA levels occurred in Saragolla as compared to Svevo. In conclusion, these results show that the root growth and hormonal profile of Saragolla are less affected by osmotic stress than those of Svevo, demonstrating the great potential of ancient varieties as reservoirs of genetic variability for improving crop responses to environmental stresses.

Enhancing Biocrust Development and Plant Growth through Inoculation of Desiccation-Tolerant Cyanobacteria in Different Textured Soils

In recent years, there has been a burgeoning interest in the utilization of cyanobacteria for the purpose of land rehabilitation via enhancements in soil fertility, prevent erosion, and counter desertification. This study evaluated the ability of Nostoc calcicola BOT1, Scytonema sp. BOT2, and their consortia to form biocrusts on the substrate of coarse sand, fine sand, and loamy soil. A nutrient- and water-deficient substrate was inoculated with cyanobacteria to facilitate biocrust formation and evaluate their impact on agriculture. Cyanobacteria inoculation resulted in significant improvements in soil fertility, especially in coarse and fine sand, which initially had the lowest fertility. The findings of this investigation underscore that the consortium of cyanobacteria exhibited greater efficacy than individual strains in enhancing soil fertility and stimulating plant growth. The loamy soil treated with the consortium had the highest plant growth across all soil types, in contrast to the individual strains. The consortium of cyanobacteria showed promising results in promoting biocrust formation and fostering rice seedling growth in fine sand. This study provides empirical evidence supporting the potential utility of cyanobacterial consortia as a valuable tool for the rehabilitation of degraded land. Furthermore, the results indicate that cyanobacterial species can persist in soil environments even following prolonged periods of desiccation.

Turning up the volume: How root branching adaptive responses aid water foraging

Access to water is critical for all forms of life. Plants primarily access water through their roots. Root traits such as branching are highly sensitive to water availability, enabling plants to adapt their root architecture to match soil moisture distribution. Lateral root adaptive responses hydropatterning and xerobranching ensure new branches only form when roots are in direct contact with moist soil. Root traits are also strongly influenced by atmospheric humidity, where a rapid drop leads to a promotion of root growth and branching. The plant hormones auxin and/or abscisic acid (ABA) play key roles in regulating these adaptive responses. We discuss how these signals are part of a novel "water-sensing" mechanism that couples hormone movement with hydrodynamics to orchestrate root branching responses.

Chemical transformations of arsenic in the rhizosphere-root interface of Pityrogramma calomelanos and Pteris vittata

Pityrogramma calomelanos and Pteris vittata are cosmopolitan fern species that are the strongest known arsenic (As) hyperaccumulators, with potential to be used in the remediation of arsenic-contaminated mine tailings. However, it is currently unknown what chemical processes lead to uptake of As in the roots. This information is critical to identify As-contaminated soils that can be phytoremediated, or to improve the phytoremediation process. Therefore, this study identified the in situ distribution of As in the root interface leading to uptake in P. calomelanos and P. vittata, using a combination of synchrotron micro-X-ray fluorescence spectroscopy and X-ray absorption near-edge structure imaging to reveal chemical transformations of arsenic in the rhizosphere-root interface of these ferns. The dominant form of As in soils was As(V), even in As(III)-dosed soils, and the major form in P. calomelanos roots was As(III), while it was As(V) in P. vittata roots. Arsenic was cycled from roots growing in As-rich soil to roots growing in control soil. This study combined novel analytical approaches to elucidate the As cycling in the rhizosphere and roots enabling insights for further application in phytotechnologies to remediated As-polluted soils.

Spatially activated conserved auxin-transcription factor regulatory module controls de novo root organogenesis in rice

MAIN CONCLUSION

This study reveals that the process of crown root development and auxin-induced de novo root organogenesis during in vitro plantlet regeneration share a common auxin-OsWOX10 regulatory module in rice. In the fibrous-type root system of rice, the crown roots (CR) are developed naturally from the shoot tissues. Generation of robust auxin response, followed by activation of downstream cell fate determinants and signaling pathways at the onset of crown root primordia (CRP) establishment is essential for new root initiation. During rice tissue culture, embryonic calli are induced to regenerate shoots in vitro which undergo de novo root organogenesis on an exogenous auxin-supplemented medium, but the mechanism underlying spatially restricted root organogenesis remains unknown. Here, we reveal the dynamics of progressive activation of genes involved in auxin homeostasis and signaling during initiation and outgrowth of rice crown root primordia. By comparative global dataset analysis, we identify the crown root primordia-expressed genes whose expression is also regulated by auxin signaling. In-depth spatio-temporal expression pattern analysis shows that the exogenous application of auxin induces a set of key transcription factors exclusively in the spatially positioned CRP. Further, functional analysis of rice WUSCHEL-RELATED HOMEOBOX 10 (OsWOX10) during in vitro plantlet regeneration from embryogenic calli shows that it promotes de novo root organogenesis from regenerated shoots. Expression of rice OsWOX10 also induces adventitious roots (AR) in Arabidopsis, independent of homologous endogenous Arabidopsis genes. Together, our findings reveal that a common auxin-transcription factor regulatory module is involved in root organogenesis under different conditions.

CdWRKY2 transcription factor modulates salt oversensitivity in bermudagrass [Cynodon dactylon (L.) Pers.]

Common bermudagrass [Cynodon dactylon (L.) Pers.] has higher utilization potential on saline soil due to its high yield potential and excellent stress tolerance. However, key functional genes have not been well studied partly due to its hard transformation. Here, bermudagrass "Wrangler" successfully overexpressing CdWRKY2 exhibited significantly enhanced salt and ABA sensitivity with severe inhibition of shoot and root growth compared to the transgenic negative line. The reduced auxin accumulation and higher ABA sensitivity of the lateral roots (LR) under salt stress were observed in CdWRKY2 overexpression Arabidopsis lines. IAA application could rescue or partially rescue the salt hypersensitivity of root growth inhibition in CdWRKY2-overexpressing Arabidopsis and bermudagrass, respectively. Subsequent experiments in Arabidopsis indicated that CdWRKY2 could directly bind to the promoter region of AtWRKY46 and downregulated its expression to further upregulate the expression of ABA and auxin pathway-related genes. Moreover, CdWRKY2 overexpression in mapk3 background Arabidopsis could partly rescue the salt-inhibited LR growth caused by CdWRKY2 overexpression. These results indicated that CdWRKY2 could negatively regulate LR growth under salt stress via the regulation of ABA signaling and auxin homeostasis, which partly rely on AtMAPK3 function. CdWRKY2 and its homologue genes could also be useful targets for genetic engineering of salinity-tolerance plants.

The ABI3-ERF1 module mediates ABA-auxin crosstalk to regulate lateral root emergence

Abscisic acid (ABA) is involved in lateral root (LR) development, but how ABA signaling interacts with auxin signaling to regulate LR formation is not well understood. Here, we report that ABA-responsive ERF1 mediates the crosstalk between ABA and auxin signaling to regulate Arabidopsis LR emergence. ABI3 is a negative factor in LR emergence and transcriptionally activates ERF1 by binding to its promoter, and reciprocally, ERF1 activates ABI3, which forms a regulatory loop that enables rapid signal amplification. Notably, ABI3 physically interacts with ERF1, reducing the cis element-binding activities of both ERF1 and ABI3 and thus attenuating the expression of ERF1-/ABI3-regulated genes involved in LR emergence and ABA signaling, such as PIN1, AUX1, ARF7, and ABI5, which may provide a molecular rheostat to avoid overamplification of auxin and ABA signaling. Taken together, our findings identify the role of the ABI3-ERF1 module in mediating crosstalk between ABA and auxin signaling in LR emergence.

ERF1 inhibits lateral root emergence by promoting local auxin accumulation and repressing ARF7 expression

Lateral roots (LRs) are crucial for plants to sense environmental signals in addition to water and nutrient absorption. Auxin is key for LR formation, but the underlying mechanisms are not fully understood. Here, we report that Arabidopsis ERF1 inhibits LR emergence by promoting local auxin accumulation with altered distribution and regulating auxin signaling. Loss of ERF1 increases LR density compared with the wild type, whereas ERF1 overexpression causes the opposite phenotype. ERF1 enhances auxin transport by upregulating PIN1 and AUX1, resulting in excessive auxin accumulation in the endodermal, cortical, and epidermal cells surrounding LR primordia. Furthermore, ERF1 represses ARF7 transcription, thereby downregulating the expression of cell-wall remodeling genes that facilitate LR emergence. Together, our study reveals that ERF1 integrates environmental signals to promote local auxin accumulation with altered distribution and repress ARF7, consequently inhibiting LR emergence in adaptation to fluctuating environments.

DNA hypomethylation of the host tree impairs interaction with mutualistic ectomycorrhizal fungus

Ectomycorrhizas are an intrinsic component of tree nutrition and responses to environmental variations. How epigenetic mechanisms might regulate these mutualistic interactions is unknown. By manipulating the level of expression of the chromatin remodeler DECREASE IN DNA METHYLATION 1 (DDM1) and two demethylases DEMETER-LIKE (DML) in Populus tremula × Populus alba lines, we examined how host DNA methylation modulates multiple parameters of the responses to root colonization with the mutualistic fungus Laccaria bicolor. We compared the ectomycorrhizas formed between transgenic and wild-type (WT) trees and analyzed their methylomes and transcriptomes. The poplar lines displaying lower mycorrhiza formation rate corresponded to hypomethylated overexpressing DML or RNAi-ddm1 lines. We found 86 genes and 288 transposable elements (TEs) differentially methylated between WT and hypomethylated lines (common to both OX-dml and RNAi-ddm1) and 120 genes/1441 TEs in the fungal genome suggesting a host-induced remodeling of the fungal methylome. Hypomethylated poplar lines displayed 205 differentially expressed genes (cis and trans effects) in common with 17 being differentially methylated (cis). Our findings suggest a central role of host and fungal DNA methylation in the ability to form ectomycorrhizas including not only poplar genes involved in root initiation, ethylene and jasmonate-mediated pathways, and immune response but also terpenoid metabolism.

A cryptic natural variant allele of BYPASS2 suppresses the bypass1 mutant phenotype

The Arabidopsis (Arabidopsis thaliana) BYPASS1 (BPS1) gene encodes a protein with no functionally characterized domains, and loss-of-function mutants (e.g. bps1-2 in Col-0) present a severe growth arrest phenotype that is evoked by a root-derived graft-transmissible small molecule that we call dalekin. The root-to-shoot nature of dalekin signaling suggests it could be an endogenous signaling molecule. Here, we report a natural variant screen that allowed us to identify enhancers and suppressors of the bps1-2 mutant phenotype (in Col-0). We identified a strong semi-dominant suppressor in the Apost-1 accession that largely restored shoot development in bps1 and yet continued to overproduce dalekin. Using bulked segregant analysis and allele-specific transgenic complementation, we showed that the suppressor is the Apost-1 allele of a BPS1 paralog, BYPASS2 (BPS2). BPS2 is one of four members of the BPS gene family in Arabidopsis, and phylogenetic analysis demonstrated that the BPS family is conserved in land plants and the four Arabidopsis paralogs are retained duplicates from whole genome duplications. The strong conservation of BPS1 and paralogous proteins throughout land plants, and the similar functions of paralogs in Arabidopsis, suggests that dalekin signaling might be retained across land plants.

SlGH3.15, a member of the GH3 gene family, regulates lateral root development and gravitropism response by modulating auxin homeostasis in tomato

Multiple Gretchen Hagen 3 (GH3) genes have been implicated in a range of processes in plant growth and development through their roles in maintaining hormonal homeostasis. However, there has only been limited study on the functions of GH3 genes in tomato (Solanum lycopersicum). In this work, we investigated the important function of SlGH3.15, a member of the GH3 gene family in tomato. Overexpression of SlGH3.15 led to severe dwarfism in both the above- and below-ground sections of the plant, accompanied by a substantial decrease in free IAA content and reduction in the expression of SlGH3.9, a paralog of SlGH3.15. Exogenous supply of IAA negatively affected the elongation of the primary root and partially restored the gravitropism defects in SlGH3.15-overexpression lines. While no phenotypic change was observed in the SlGH3.15 RNAi lines, double knockout lines of SlGH3.15 and SlGH3.9 were less sensitive to treatments with the auxin polar transport inhibitor. Overall, these findings revealed important roles of SlGH3.15 in IAA homeostasis and as a negative regulator of free IAA accumulation and lateral root formation in tomato.

Nanoparticles in Plants: Uptake, Transport and Physiological Activity in Leaf and Root

Due to their unique characteristics, nanoparticles are increasingly used in agricultural production through foliage spraying and soil application. The use of nanoparticles can improve the efficiency of agricultural chemicals and reduce the pollution caused by the use of agricultural chemicals. However, introducing nanoparticles into agricultural production may pose risks to the environment, food and even human health. Therefore, it is crucial to pay attention to the absorption migration, and transformation in crops, and to the interaction with higher plants and plant toxicity of nanoparticles in agriculture. Research shows that nanoparticles can be absorbed by plants and have an impact on plant physiological activities, but the absorption and transport mechanism of nanoparticles is still unclear. This paper summarizes the research progress of the absorption and transportation of nanoparticles in plants, especially the effect of size, surface charge and chemical composition of nanoparticle on the absorption and transportation in leaf and root through different ways. This paper also reviews the impact of nanoparticles on plant physiological activity. The content of the paper is helpful to guide the rational application of nanoparticles in agricultural production and ensure the sustainability of nanoparticles in agricultural production.

Auxin-cytokinin interplay shapes root functionality under low-temperature stress

Low-temperature stress alters root system architecture. In particular, changes in the levels and response to auxin and cytokinin determine the fate of root architecture and function under stress because of their vital roles in regulating root cell division, differentiation, and elongation. An intricate nexus of genes encoding components of auxin and cytokinin biosynthesis, signaling, and transport components operate to counteract stress and facilitate optimum development. We review the role of auxin transport and signaling and its regulation by cytokinin during root development and stem cell maintenance under low-temperature stress. We highlight intricate mechanisms operating in root stem cells to minimize DNA damage by altering phytohormone levels, and discuss a working model for cytokinin in low-temperatures stress response.

Long term nitrogen deficiency alters expression of miRNAs and alters nitrogen metabolism and root architecture in Indian dwarf wheat (Triticum sphaerococcum Perc.) genotypes

The important roles of plant microRNAs (miRNAs) in adaptation to nitrogen (N) deficiency in different crop species especially cereals (rice, wheat, maize) have been under discussion since last decade with little focus on potential wild relatives and landraces. Indian dwarf wheat (Triticum sphaerococcum Percival) is an important landrace native to the Indian subcontinent. Several unique features, especially high protein content and resistance to drought and yellow rust, make it a very potent landrace for breeding. Our aim in this study is to identify the contrasting Indian dwarf wheat genotypes based on nitrogen use efficiency (NUE) and nitrogen deficiency tolerance (NDT) traits and the associated miRNAs differentially expressed under N deficiency in selected genotypes. Eleven Indian dwarf wheat genotypes and a high NUE bread wheat genotype (for comparison) were evaluated for NUE under control and N deficit field conditions. Based on NUE, selected genotypes were further evaluated under hydroponics and miRNome was compared by miRNAseq under control and N deficit conditions. Among the identified, differentially expressed miRNAs in control and N starved seedlings, the target gene functions were associated with N metabolism, root development, secondary metabolism and cell-cycle associated pathways. The key findings on miRNA expression, changes in root architecture, root auxin abundance and changes in N metabolism reveal new information on the N deficiency response of Indian dwarf wheat and targets for genetic improvement of NUE.

HY5 inhibits lateral root initiation in Arabidopsis through negative regulation of the microtubule-stabilizing protein TPXL5

Tight control of lateral root (LR) initiation is vital for root system architecture and function. Regulation of cortical microtubule reorganization is involved in the asymmetric radial expansion of founder cells during LR initiation in Arabidopsis (Arabidopsis thaliana). However, critical genetic evidence on the role of microtubules in LR initiation is lacking and the mechanisms underlying this regulation are poorly understood. Here, we found that the previously uncharacterized microtubule-stabilizing protein TPX2-LIKE5 (TPXL5) participates in LR initiation, which is finely regulated by the transcription factor ELONGATED HYPOCOTYL5 (HY5). In tpxl5 mutants, LR density was decreased and more LR primordia (LRPs) remained in stage I, indicating delayed LR initiation. In particular, the cell width in the peripheral domain of LR founder cells after the first asymmetric cell division was larger in tpxl5 mutants than in the wild-type. Consistently, ordered transverse cortical microtubule arrays were not well generated in tpxl5 mutants. In addition, HY5 directly targeted the promoter of TPXL5 and downregulated TPXL5 expression. The hy5 mutant exhibited higher LR density and fewer stage I LRPs, indicating accelerated LR initiation. Such phenotypes were partially suppressed by TPXL5 knockout. Taken together, our data provide genetic evidence supporting the notion that cortical microtubules are essential for LR initiation and unravel a molecular mechanism underlying HY5 regulation of TPXL5-mediated microtubule reorganization and cell remodeling during LR initiation.

Identification of a pluripotency-inducing small compound, PLU, that induces callus formation via Heat Shock Protein 90-mediated activation of auxin signaling

Plants retain the ability to generate a pluripotent tissue called callus by dedifferentiating somatic cells. A pluripotent callus can also be artificially induced by culturing explants with hormone mixtures of auxin and cytokinin, and an entire body can then be regenerated from the callus. Here we identified a pluripotency-inducing small compound, PLU, that induces the formation of callus with tissue regeneration potency without the external application of either auxin or cytokinin. The PLU-induced callus expressed several marker genes related to pluripotency acquisition via lateral root initiation processes. PLU-induced callus formation required activation of the auxin signaling pathway though the amount of active auxin was reduced by PLU treatment. RNA-seq analysis and subsequent experiments revealed that Heat Shock Protein 90 (HSP90) mediates a significant part of the PLU-initiated early events. We also showed that HSP90-dependent induction of TRANSPORT INHIBITOR RESPONSE 1, an auxin receptor gene, is required for the callus formation by PLU. Collectively, this study provides a new tool for manipulating and investigating the induction of plant pluripotency from a different angle from the conventional method with the external application of hormone mixtures.

Positional cloning and characterization reveal the role of a miRNA precursor gene ZmLRT in the regulation of lateral root number and drought tolerance in maize

Lateral roots play essential roles in drought tolerance in maize (Zea mays L.). However, the genetic basis for the variation in the number of lateral roots in maize remains elusive. Here, we identified a major quantitative trait locus (QTL), qLRT5-1, controlling lateral root number using a recombinant inbred population from a cross between the maize lines Zong3 (with many lateral roots) and 87-1 (with few lateral roots). Fine-mapping and functional analysis determined that the candidate gene for qLRT5-1, ZmLRT, expresses the primary transcript for the microRNA miR166a. ZmLRT was highly expressed in root tips and lateral root primordia, and knockout and overexpression of ZmLRT increased and decreased lateral root number, respectively. Compared with 87-1, the ZmLRT gene model of Zong3 lacked the second and third exons and contained a 14 bp deletion at the junction between the first exon and intron, which altered the splicing site. In addition, ZmLRT expression was significantly lower in Zong3 than in 87-1, which might be attributed to the insertions of a transposon and over large DNA fragments in the Zong3 ZmLRT promoter region. These mutations decreased the abundance of mature miR166a in Zong3, resulting in increased lateral roots at the seedling stage. Furthermore, miR166a post-transcriptionally repressed five development-related class-III homeodomain-leucine zipper genes. Moreover, knockout of ZmLRT enhanced drought tolerance of maize seedlings. Our study furthers our understanding of the genetic basis of lateral root number variation in maize and highlights ZmLRT as a target for improving drought tolerance in maize.

Advances in structure and function of auxin response factor in plants

Auxin is a crucial phytohormone that has various effects on the regulators of plant growth and development. Auxin signal transduction is mainly controlled by two gene families: auxin response factor (ARF) and auxin/indole-3-acetic acid (Aux/IAA). ARFs are plant-specific transcription factors that bind directly to auxin response elements in the promoters of auxin-responsive genes. ARF proteins contain three conserved regions: a conserved N-terminal B3 DNA-binding domain, a variable intermediate middle region domain that functions in activation or repression, and a C-terminal domain including the Phox and Bem1p region for dimerization, similar to the III and IV elements of Aux/IAA, which facilitate protein-protein interaction through homodimerization of ARF proteins or heterodimerization of ARF and Aux/IAA proteins. In the two decades following the identification of the first ARF, 23 ARF members have been identified and characterized in Arabidopsis. Using whole-genome sequencing, 22, 25, 23, 25, and 36 ARF genes have been identified in tomato, rice, wheat, sorghum, and maize, respectively, in addition to which the related biofunctions of some ARFs have been reported. ARFs play crucial roles in regulating the growth and development of roots, leaves, flowers, fruits, seeds, responses to biotic and abiotic stresses, and phytohormone signal crosstalk. In this review, we summarize the research progress on the structures and functions of ARFs in Arabidopsis, tomato, and cereal crops, to provide clues for future basic research on phytohormone signaling and the molecular design breeding of crops.

Role of lactoyl-glutathione lyase of Salmonella in the colonization of plants under salinity stress

Salmonella, a foodborne human pathogen, can colonize the members of the kingdom Plantae. However, the basis of the persistence of Salmonella in plants is largely unknown. Plants encounter various biotic and abiotic stress agents in soil. We conjectured that methylglyoxal (MG), one of the common metabolites that accumulate in plants during both biotic and abiotic stress, plays a role in regulating the plant-Salmonella interaction. The interaction of Salmonella Typhimurium with plants under salinity stress was investigated. It was observed that wild-type Salmonella Typhimurium can efficiently colonize the root, but mutant bacteria lacking MG detoxifying enzyme, lactoyl-glutathione lyase (Lgl), showed lower colonization in roots exclusively under salinity stress. This colonization defect is due to the poor viability of the mutated bacterial strains under these conditions. This is the first report to prove the role of MG-detoxification genes in the colonization of stressed plants and highlights the possible involvement of metabolic genes in the evolution of the plant-associated life of Salmonella.

Chromatin Remodeling Complex SWR1 Regulates Root Development by Affecting the Accumulation of Reactive Oxygen Species (ROS)

Reactive oxygen species (ROS), a type of oxygen monoelectronic reduction product, play integral roles in root growth and development. The epigenetic mechanism plays a critical role in gene transcription and expression; however, its regulation of ROS metabolism in root development is still limited. We found that the chromatin remodeling complex SWR1 regulates root length and lateral root formation in Arabidopsis. Our transcriptome results and gene ontology (GO) enrichment analysis showed that the oxidoreductase activity-related genes significantly changed in mutants for the Arabidopsis SWR1 complex components, such as arp6 and pie1, and histone variant H2A.Z triple mutant hta8 hta9 hta11. The three encoding genes in Arabidopsis are the three H2A.Z variants hta8, hta9, and hta11. Histochemical assays revealed that the SWR1 complex affects ROS accumulation in roots. Furthermore, chromatin immunoprecipitation quantitative real-time PCR (ChIP-qPCR) analysis showed that the reduced H2A.Z deposition in oxidoreductase activity-related genes caused ROS to accumulate in arp6, pie1, and hta8 hta9 hta11. H2A.Z deposition-deficient mutants decreased after the trimethylation of lysine 4 on histone H3 (H3K4me3) modifications and RNA polymerase II (Pol II) enrichment, and increased after the trimethylation of lysine 27 on histone H3 (H3K27me3) modifications, which may account for the expression change in oxidoreductase activity-related genes. In summary, our results revealed that the chromatin complex SWR1 regulates ROS accumulation in root development, highlighting the critical role of epigenetic mechanisms.

Endocytic trafficking induces lateral root founder cell specification in Arabidopsis thaliana in a process distinct from the auxin-induced pathway

Plants can modify their body structure, such as their root architecture, post-embryonically. For example, Arabidopsis thaliana can develop lateral roots as part of an endogenous program or in response to biotic and abiotic stimuli. Root pericycle cells are specified to become lateral root founder cells, initiating lateral root organogenesis. We used the endocytic trafficking inducer Sortin2 to examine the role of endomembrane trafficking in lateral root founder cell specification. Our results indicate that Sortin2 stimulation turns on a de novo program of lateral root primordium formation that is distinct from the endogenous program driven by auxin. In this distinctive mechanism, extracellular calcium uptake and endocytic trafficking toward the vacuole are required for lateral root founder cell specification upstream of the auxin module led by AUX/IAA28. The auxin-dependent TIR1/AFB F-boxes and auxin polar transport are dispensable for the endocytic trafficking-dependent lateral root founder cell specification; however, a different set of F-box proteins and a functional SCF complex are required. The endocytic trafficking could constitute a convenient strategy for organogenesis in response to environmental conditions.

An Experimental Rhizobox System for the Integrative Analysis of Root Development and Abiotic Stress Responses Under Water-Deficit Conditions

The study of root growth and plasticity in situ is rendered difficult by the opacity and mechanical barrier of soil substrates. Therefore, for the analysis of developmental processes and abiotic stress and development relationships, it is essential to set up cultivation systems that overcome these hindrances in a non-invasive and non-destructive manner. For this purpose, we have developed a useful and powerful rhizobox culture system, where the roots are separated from the soil substrate by a porous membrane with a mesh of such width that allows the exchange of water and solutes without allowing the roots to penetrate the soil. This system provides direct, easy, and quick access to the roots and allows to follow root growth and development, root system architecture, and root system plasticity at different stages of plant development and under various environmental conditions. Moreover, these rhizoboxes provide clean and intact roots that can be easily harvested to perform further physiological, biochemical, and molecular analyses at different stages of development and in response to various environmental constraints. This rhizobox method was validated by assessing root response plasticity of drought-stressed Arabidopsis and pea plants grown in soil displaying water content alterations. This rhizobox system is suitable for many types of abiotic stress-development studies, including the comparison of different stress intensities or of various mutants and genotypes.

Identification and function of miRNA-mRNA interaction pairs during lateral root development of hemi-parasitic Santalum album L. seedlings

Sandalwood (Santalum album L.) is a hemi-parasitic tree species famous for its santalol and santalene, which are extracted from its heartwood and roots. The ability to understand root functionality within its branched root system would benefit the regulation of sandalwood growth and enhance the commercial value of sandalwood. Phenotypic and anatomical evidence in this study indicated that seed germination stage 4 (SG4) seemed pivotal for lateral root (LR) morphogenesis. Small RNA (sRNA) high-throughput sequencing of root tissues at three sub-stages of SG4 (lateral root primordia initiation (LRPI), lateral root primordia development (LRPD), and lateral root primordia emergence (LRPE)) was performed to identify microRNAs (miRNAs) associated with LR development. A total of 135 miRNAs, including 70 differentially expressed miRNAs (DEMs), were screened. Ten DEMs were selected to investigate transcript abundance in different organs or developmental stages. Among 100 negative DEM-mRNA interaction pairs, four targets (Sa-miR166m_2, 408d, 858a, and novel_Sa-miR8) were selected for studying cleavage sites by 5' RLM-RACE validation. The expression mode of the four miRNA-mRNA pairs was investigated after indole-3-acetic acid (IAA) treatment. IAA enhanced the abundance of homeobox-leucine-zipper protein 32 (HOX32), laccase 12 (LAC12), myeloblastosis86 (MYB86), and pectin methylesterase inhibitor6 (PMEI6) target transcripts by reducing the expression of Sa-miR166m_2, 408d, 858a, and novel_Sa-miR8 in the first 10 min. A schematic model of miRNA-regulated LR development is proposed for this hemi-parasitic species. This novel genetic information for improving sandalwood root growth and development may allow for the cultivation of fast-growing and high-yielding plantations.

Exogenous brassinosteroids promotes root growth, enhances stress tolerance, and increases yield in maize

Brassinosteroids (BRs) regulate of maize (Zea mays L.) growth, but the underlying molecular mechanism remains unclear. In this study, we used a multi-disciplinary approach to determine how BRs regulate maize morphology and physiology during development. Treatment with the BRs promoted primary root the elongation and growth during germination, and the early development of lateral roots. BRs treatment during the middle growth stage increased the levels of various stress resistance factors, and enhanced resistance to lodging, likely by protecting the plant against stem rot and sheath rot. BRs had no significant effect on plant height during late growth, but it increased leaf angle and photosynthetic efficiency, as well as yield and quality traits. Our findings increase our understanding of the regulatory effects of BR on maize root growth and development and the mechanism by which BR improves disease resistance, which could further the potential for using BR to improve maize yield.

Primary Root Excision Induces ERF071, Which Mediates the Development of Lateral Roots in Makapuno Coconut (Cocos nucifera)

Coconut (Cocos nucifera L.) is widely recognized as one of nature's most beneficial plants. Makapuno, a special type of coconut with a soft, jelly-like endosperm, is a high-value commercial coconut and an expensive delicacy with a high cost of planting material. The embryo rescue technique is a very useful tool to support mass propagation of makapuno coconut. Nevertheless, transplanting the seedlings is a challenge due to poor root development, which results in the inability of the plant to acclimatize. In this study, primary root excision was used in makapuno to observe the effects of primary root excision on lateral root development. The overall results showed that seedlings with roots excised had a significantly higher number of lateral roots, and shoot length also increased significantly. Using de novo transcriptome assembly and differential gene expression analysis, we identified 512 differentially expressed genes in the excised and intact root samples. ERF071, encoding an ethylene-responsive transcription factor, was identified as a highly expressed gene in excised roots compared to intact roots, and was considered a candidate gene associated with lateral root formation induced by root excision in makapuno coconut. This study provides insight into the mechanism and candidate genes involved in the development of lateral roots in coconut, which may be useful for the future breeding and mass propagation of makapuno coconut through tissue culture.

Induction of Somatic Embryogenesis in Plants: Different Players and Focus on WUSCHEL and WUS-RELATED HOMEOBOX (WOX) Transcription Factors

In plants, other cells can express totipotency in addition to the zygote, thus resulting in embryo differentiation; this appears evident in apomictic and epiphyllous plants. According to Haberlandt's theory, all plant cells can regenerate a complete plant if the nucleus and the membrane system are intact. In fact, under in vitro conditions, ectopic embryos and adventitious shoots can develop from many organs of the mature plant body. We are beginning to understand how determination processes are regulated and how cell specialization occurs. However, we still need to unravel the mechanisms whereby a cell interprets its position, decides its fate, and communicates it to others. The induction of somatic embryogenesis might be based on a plant growth regulator signal (auxin) to determine an appropriate cellular environment and other factors, including stress and ectopic expression of embryo or meristem identity transcription factors (TFs). Still, we are far from having a complete view of the regulatory genes, their target genes, and their action hierarchy. As in animals, epigenetic reprogramming also plays an essential role in re-establishing the competence of differentiated cells to undergo somatic embryogenesis. Herein, we describe the functions of WUSCHEL-RELATED HOMEOBOX (WOX) transcription factors in regulating the differentiation-dedifferentiation cell process and in the developmental phase of in vitro regenerated adventitious structures.

Unraveling Genomic Regions Controlling Root Traits as a Function of Nitrogen Availability in the MAGIC Wheat Population WM-800

An ever-growing world population demands to be fed in the future and environmental protection and climate change need to be taken into account. An important factor here is nitrogen uptake efficiency (NUpE), which is influenced by the root system (the interface between plant and soil). To understand the natural variation of root system architecture (RSA) as a function of nitrogen (N) availability, a subset of the multiparent advanced generation intercross (MAGIC) winter wheat population WM-800 was phenotyped under two contrasting N treatments in a high-throughput phenotyping system at the seedling stage. Fourteen root and shoot traits were measured. Subsequently, these traits were genetically analyzed using 13,060 polymorphic haplotypes and SNPs in a genome-wide association study (GWAS). In total, 64 quantitative trait loci (QTL) were detected; 60 of them were N treatment specific. Candidate genes for the detected QTL included NRT1.1 and genes involved in stress signaling under N-, whereas candidate genes under N+ were more associated with general growth, such as mei2 and TaWOX11b. This finding may indicate (i) a disparity of the genetic control of root development under low and high N supply and, furthermore, (ii) the need for an N specific selection of genes and genotypes in breeding new wheat cultivars with improved NUpE.