Periodic root branching in Arabidopsis requires synthesis of an uncharacterized carotenoid derivative

Carotenoids: resources, knowledge, and emerging tools to advance apocarotenoid research

Carotenoids are a large class of isoprenoid compounds which are biosynthesized by plants, algae, along with certain fungi, bacteria and insects. In plants, carotenoids provide crucial functions in photosynthesis and photoprotection. Furthermore, carotenoids also serve as precursors to apocarotenoids, which are derived through enzymatic and non-enzymatic cleavage reactions. Apocarotenoids encompass a diverse set of compounds, including hormones, growth regulators, and signaling molecules which play vital roles in pathways associated with plant development, stress responses, and plant-organismic interactions. Regulation of carotenoid biosynthesis indirectly influences the formation of apocarotenoids and bioactive effects on target pathways. Recent discovery of a plethora of new bioactive apocarotenoids across kingdoms has increased interest in expanding knowledge of the breadth of apocarotenoid function and regulation. In this review, we provide insights into the regulation of carotenogenesis, specifically linked to the biosynthesis of apocarotenoid precursors. We highlight plant studies, including useful heterologous platforms and synthetic biology tools, which hold great value in expanding discoveries, knowledge and application of bioactive apocarotenoids for crop improvement and human health. Moreover, we discuss how this field has recently flourished with the discovery of diverse functions of apocarotenoids, thereby prompting us to propose new directions for future research.

Carotenoid-carbohydrate crosstalk: evidence for genetic and physiological interactions in storage tissues across crop species

Carotenoids play essential roles in photosynthesis, photoprotection, and human health. Efforts to increase carotenoid content in several staple crops have been successful through both conventional selection and genetic engineering methods. Interestingly, in some cases, altering carotenoid content has had unexpected effects on other aspects of plant metabolism, impacting traits like sugar content, dry matter percentage, fatty acid content, stress tolerance, and phytohormone concentrations. Studies across several diverse crop species have identified negative correlations between carotenoid and starch contents, as well as positive correlations between carotenoids and soluble sugars. Collectively, these reports suggest a metabolic interaction between carotenoids and carbohydrates. We synthesize evidence pointing to four hypothesized mechanisms: (1) direct competition for precursors; (2) physical interactions in plastids; (3) influences of sugar or apocarotenoid signaling networks; and (4) nonmechanistic population or statistical sources of correlations. Though the carotenoid biosynthesis pathway is well understood, the regulation and interactions of carotenoids, especially in nonphotosynthetic tissues, remain unclear. This topic represents an underexplored interplay between primary and secondary metabolism where further research is needed.

β-Carotene and its derivatives regulate pollen fertility in tomato

β-carotene promotes pollen germination and tube growth via a mechanism that regulates reactive oxygen species homeostasis in tomato.

Gibberellin dynamics governing nodulation revealed using GIBBERELLIN PERCEPTION SENSOR 2 in Medicago truncatula lateral organs

During nutrient scarcity, plants can adapt their developmental strategy to maximize their chance of survival. Such plasticity in development is underpinned by hormonal regulation, which mediates the relationship between environmental cues and developmental outputs. In legumes, endosymbiosis with nitrogen-fixing bacteria (rhizobia) is a key adaptation for supplying the plant with nitrogen in the form of ammonium. Rhizobia are housed in lateral root-derived organs termed nodules that maintain an environment conducive to Nitrogenase in these bacteria. Several phytohormones are important for regulating the formation of nodules, with both positive and negative roles proposed for gibberellin (GA). In this study, we determine the cellular location and function of bioactive GA during nodule organogenesis using a genetically encoded second-generation GA biosensor, GIBBERELLIN PERCEPTION SENSOR 2 in Medicago truncatula. We find endogenous bioactive GA accumulates locally at the site of nodule primordia, increasing dramatically in the cortical cell layers, persisting through cell divisions, and maintaining accumulation in the mature nodule meristem. We show, through misexpression of GA-catabolic enzymes that suppress GA accumulation, that GA acts as a positive regulator of nodule growth and development. Furthermore, increasing or decreasing GA through perturbation of biosynthesis gene expression can increase or decrease the size of nodules, respectively. This is unique from lateral root formation, a developmental program that shares common organogenesis regulators. We link GA to a wider gene regulatory program by showing that nodule-identity genes induce and sustain GA accumulation necessary for proper nodule formation.

Shaping root architecture: towards understanding the mechanisms involved in lateral root development

Plants have an amazing ability to adapt to their environment, and this extends beyond biochemical responses and includes developmental changes that help them better exploit resources and survive. The plasticity observed in individual plant morphology is associated with robust developmental pathways that are influenced by environmental factors. However, there is still much to learn about the mechanisms behind the formation of the root system. In Arabidopsis thaliana, the root system displays a hierarchical structure with primary and secondary roots. The process of lateral root (LR) organogenesis involves multiple steps, including LR pre-patterning, LR initiation, LR outgrowth, and LR emergence. The study of root developmental plasticity in Arabidopsis has led to significant progress in understanding the mechanisms governing lateral root formation. The importance of root system architecture lies in its ability to shape the distribution of roots in the soil, which affects the plant's ability to acquire nutrients and water. In Arabidopsis, lateral roots originate from pericycle cells adjacent to the xylem poles known as the xylem-pole-pericycle (XPP). The positioning of LRs along the primary root is underpinned by a repetitive pre-patterning mechanism that establishes primed sites for future lateral root formation. In a subset of primed cells, the memory of a transient priming stimulus leads to the formation of stable pre-branch sites and the establishment of founder cell identity. These founder cells undergo a series of highly organized periclinal and anticlinal cell divisions and expansion to form lateral root primordia. Subsequently, LRP emerges through three overlying cell layers of the primary root, giving rise to fully developed LRs. In addition to LRs Arabidopsis can also develop adventitious lateral roots from the primary root in response to specific stress signals such as wounding or environmental cues. Overall, this review creates an overview of the mechanisms governing root lateral root formation which can be a stepping stone to improved crop yields and a better understanding of plant adaptation to changing environments.

Exogenous application of the apocarotenoid retinaldehyde negatively regulates auxin-mediated root growth

Root development is essential for plant survival. The lack of carotenoid biosynthesis in the phytoene desaturase 3 (pds3) mutant results in short primary roots (PRs) and reduced lateral root formation. In this study, we showed that short-term inhibition of PDS by fluridone suppresses PR growth in wild type, but to a lesser extent in auxin mutants of Arabidopsis (Arabidopsis thaliana). Such an inhibition of PDS activity increased endogenous indole-3-acetic acid levels, promoted auxin signaling, and partially complemented the PR growth of an auxin-deficient mutant, the YUCCA 3 5 7 8 9 quadruple mutant (yucQ). The exogenous application of retinaldehyde (retinal), an apocarotenoid derived from β-carotene, complemented the fluridone-induced suppression of root growth, as well as the short roots of the pds3 mutant. Retinal also partially complemented the auxin-induced suppression of root growth. These results suggest that retinal may play a role in regulating root growth by modulating endogenous auxin levels.

Jasmonic Acid and Salicylic Acid improved resistance against Spodoptera frugiperda Infestation in maize by modulating growth and regulating redox homeostasis

Exploring host plant resistance and elevating plant defense mechanisms through the application of exogenous elicitors stands as a promising strategy for integrated pest management. The fall armyworm, a pernicious menace to grain crops in tropical and subtropical regions, stands as a formidable threat due to its capacity for devastation and a wide-ranging spectrum of host plants. There is no literature regarding artificially induced resistance in maize against fall armyworm (Spodoptera frugiperda) by exogenous application of phytohormones. The present investigation was performed to evaluate the role of jasmonic acid (JA) and salicylic acid (SA) on two maize hybrids namely FH-1046 and YH-1898 against fall armyworm. Results showed that plant height, biomass and lengths, fresh and dry weight of root shoot which decreased with armyworm infestation improved with phytohormonal application. JA treatment resulted in a higher increase in all attributes as compared to SA treatment. Improvement in relative water contents, photosynthetic pigments and pronounced levels of phenol and proline accumulation were observed in infested plants after JA treatment. Infested plants recovered from oxidative stress as JA application activated and increased the antioxidant enzyme activity of superoxide dismutase, peroxidase and polyphenol oxidase activity in both FH-1046 and YH-1898 . The oxidative stress reduction in infested plants after JA treatment was also evident from a fair decrease in MDA and H2O2 in both varieties. The SA and JA mediated genes expression was studied and it was found that in FH1046 maize cultivar, JA dependent genes, particularly marker genes PR1 and Lox5 were highly expressed along with TPS10 and BBT12. Whereas SPI, WRKY28, ICS and PAL were shown to be activated upon SA application. Evidently, both JA and SA elicited a robust defensive response within the maize plants against the voracious S. frugiperda, which in consequence exerted a discernible influence over the pest's developmental trajectory and physiological dynamics. A decrease in detoxification enzyme activity of the insects was observed after feeding on treated plants. Moreover, it was recorded that the survival and weight gain of FAW feeding on phytohormone treated maize plants also decelerated. In conclusion, FH-1046 was found to be more tolerant than YH-1898 against fall armyworm infestation and 1 mM JA was more effective than 1 mM SA for alleviation of fall armyworm stress. Therefore, it was inferred that phytohormones regulated redox homeostasis to circumvent oxidative damage and mediate essential metabolic events in maize under stress. To our current understanding, this study is the very first presentation of induced resistance in maize against S. frugiperda with the phytohormonal application (JA and SA).

In vitro assay and inhibition of 9-cis-epoxycarotenoid dioxygenase (NCED) from Solanum lycopersicum and Zea mays

The article reports methods for the expression and assay of 9-cis-epoxycarotenoid cleavage dioxygenase (NCED), an enzyme involved in the biosynthesis of phytohormone abscisic acid in plants. A method for the preparation of the unstable substrate 9'-cis-neoxanthin from fresh spinach is described. The inhibition of Solanum lycopersicum NCED by a series of aryl hydroxamic acid inhibitors is illustrated, and inhibitors D2 and D4 are assayed against NCED isozymes from Zea mays.

Increased drought resistance in state transition mutants is linked to modified plastoquinone pool redox state

Identifying traits that exhibit improved drought resistance is highly important to cope with the challenges of predicted climate change. We investigated the response of state transition mutants to drought. Compared with the wild type, state transition mutants were less affected by drought. Photosynthetic parameters in leaves probed by chlorophyll fluorescence confirmed that mutants possess a more reduced plastoquinone (PQ) pool, as expected due to the absence of state transitions. Seedlings of the mutants showed an enhanced growth of the primary root and more lateral root formation. The photosystem II inhibitor 3-(3,4-dichlorophenyl)-1,1-dimethylurea, leading to an oxidised PQ pool, inhibited primary root growth in wild type and mutants, while the cytochrome b6 f complex inhibitor 2,5-dibromo-3-methyl-6-isopropylbenzoquinone, leading to a reduced PQ pool, stimulated root growth. A more reduced state of the PQ pool was associated with a slight but significant increase in singlet oxygen production. Singlet oxygen may trigger a, yet unknown, signalling cascade promoting root growth. We propose that photosynthetic mutants with a deregulated ratio of photosystem II to photosystem I activity can provide a novel path for improving crop drought resistance.

Tunable recurrent priming of lateral roots in Arabidopsis: More than just a clock?

Lateral root (LR) formation in Arabidopsis is a continuous, repetitive, post-embryonic process regulated by a series of coordinated events and tuned by the environment. It shapes the root system, enabling plants to efficiently explore soil resources and adapt to changing environmental conditions. Although the auxin-regulated modules responsible for LR morphogenesis and emergence are well documented, less is known about the initial priming. Priming is characterised by recurring peaks of auxin signalling, which, once memorised, earmark cells to form the new LR. We review the recent experimental and modelling approaches to understand the molecular processes underlying the recurring LR formation. We argue that the intermittent priming of LR results from interweaving the pattern of auxin flow and root growth together with an oscillatory auxin-modulated transcriptional mechanism and illustrate its long-range sugar-mediated tuning by light.

Interactions between phenanthrene and polystyrene micro/nano plastics: Implications for rice (Oryza sativa L.) toxicity

Micro/nano plastics (MPs/NPs) are widely distributed and are one of the global pollutants of current concern. Micro/nano plastics can adsorb a variety of persistent organic pollutants, and different particle sizes and surface charges affect the biological effects of MPs/NPs. Therefore, how the compound pollution of MPs/NPs with different particle sizes and organic pollutants produces toxic effects on plants needs to be further studied. We investigated the toxic effects of phenanthrene (Phe) and amino-modified PS (PS-NH2) with two particle sizes (50 nm, 5 μm) on rice. The stress mechanism of PS-NH2 was different between the two particle sizes. Moreover, 50 nm PS-NH2 inhibited stomatal conductance and transpiration rate, reduced photosynthetic rate, significantly enriched GO functions such as "DNA repair" and "DNA double-strand break," and caused severe DNA damage in rice. Notably, 5 μm PS-NH2 affected the gene expression of "photosynthetic lighting" and "photosynthetic antenna protein" in rice, decreased chlorophyll content, and inhibited rice growth. The toxicity of 50 nm PS-NH2 was stronger. In addition, we found that Phe reduced the toxicity of PS-NH2 with different particle sizes, and the relief effect of 50 nm PS-NH2+Phe was more evident. Further, 50 nm PS-NH2+Phe alleviated the toxicity by stimulating the activities of antioxidant enzymes, reducing oxidative damage to chloroplasts, and inhibiting photosynthesis. However, 5 μm PS-NH2+Phe can reduce the stress by reducing the degree of membrane lipid peroxidation, activating metabolic pathways related to the cell wall and cell membrane formation, and plant antitoxin biosynthesis. The results contribute to the understanding of the mechanism of toxicity of MPs/NPs and polycyclic aromatic hydrocarbons (PAHs) to crops.

Natural overexpression of CAROTENOID CLEAVAGE DIOXYGENASE 4 in tomato alters carotenoid flux

Carotenoids and apocarotenoids function as pigments and flavor volatiles in plants that enhance consumer appeal and offer health benefits. Tomato (Solanum lycopersicum.) fruit, especially those of wild species, exhibit a high degree of natural variation in carotenoid and apocarotenoid contents. Using positional cloning and an introgression line (IL) of Solanum habrochaites "LA1777', IL8A, we identified carotenoid cleavage dioxygenase 4 (CCD4) as the factor responsible for controlling the dark orange fruit color. CCD4b expression in ripe fruit of IL8A plants was ∼8,000 times greater than that in the wild type, presumably due to 5' cis-regulatory changes. The ShCCD4b-GFP fusion protein localized in the plastid. Phytoene, ζ-carotene, and neurosporene levels increased in ShCCD4b-overexpressing ripe fruit, whereas trans-lycopene, β-carotene, and lutein levels were reduced, suggestive of feedback regulation in the carotenoid pathway by an unknown apocarotenoid. Solid-phase microextraction-gas chromatography-mass spectrometry analysis showed increased levels of geranylacetone and β-ionone in ShCCD4b-overexpressing ripe fruit coupled with a β-cyclocitral deficiency. In carotenoid-accumulating Escherichia coli strains, ShCCD4b cleaved both ζ-carotene and β-carotene at the C9-C10 (C9'-C10') positions to produce geranylacetone and β-ionone, respectively. Exogenous β-cyclocitral decreased carotenoid synthesis in the ripening fruit of tomato and pepper (Capsicum annuum), suggesting feedback inhibition in the pathway. Our findings will be helpful for enhancing the aesthetic and nutritional value of tomato and for understanding the complex regulatory mechanisms of carotenoid and apocarotenoid biogenesis.

Cellular and gene expression patterns associated with root bifurcation in Selaginella

The roots of lycophytes branch through dichotomy or bifurcation, during which the root apex splits into two daughter roots. This is morphologically distinct from lateral root (LR) branching in the extant euphyllophytes, with LRs developing along the root axis at different distances from the apex. Although the process of root bifurcation is poorly understood, such knowledge can be important, because it may represent an evolutionarily ancient strategy that roots recruited to form new stem cells or meristems. In this study, we examined root bifurcation in the lycophyte Selaginella moellendorffii. We characterized an in vitro developmental time frame based on repetitive apex bifurcations, allowing us to sample different stages of dichotomous root branching and analyze the root meristem and root branching in S. moellendorffii at the microscopic and transcriptomic level. Our results showed that, in contrast to previous assumptions, initial cells (ICs) in the root meristem are mostly not tetrahedral but rather show an irregular shape. Tracking down the early stages of root branching argues for the occurrence of a symmetric division of the single IC, resulting in two apical stem cells that initiate root meristem bifurcation. Moreover, we generated a S. moellendorffii root branching transcriptome that resulted in the delineation of a subset of core meristem genes. The occurrence of multiple putative orthologs of meristem genes in this dataset suggests the presence of conserved pathways in the control of meristem and root stem cell establishment or maintenance.

The role of carotenoids as a source of retrograde signals: impact on plant development and stress responses

Communication from plastids to the nucleus via retrograde signal cascades is essential to modulate nuclear gene expression, impacting plant development and environmental responses. Recently, a new class of plastid retrograde signals has emerged, consisting of acyclic and cyclic carotenoids and/or their degradation products, apocarotenoids. Although the biochemical identity of many of the apocarotenoid signals is still under current investigation, the examples described herein demonstrate the central roles that these carotenoid-derived signals play in ensuring plant development and survival. We present recent advances in the discovery of apocarotenoid signals and their role in various plant developmental transitions and environmental stress responses. Moreover, we highlight the emerging data exposing the highly complex signal transduction pathways underlying plastid to nucleus apocarotenoid retrograde signaling cascades. Altogether, this review summarizes the central role of the carotenoid pathway as a major source of retrograde signals in plants.

Carotenoid-derived bioactive metabolites shape plant root architecture to adapt to the rhizospheric environments

Roots are important plant organs for the uptake of water and nutrient elements. Plant root development is finely regulated by endogenous signals and environmental cues, which shapes the root system architecture to optimize the plant growth and adapt to the rhizospheric environments. Carotenoids are precursors of plant hormones strigolactones (SLs) and ABA, as well as multiple bioactive molecules. Numerous studies have demonstrated SLs and ABA as essential regulators of plant root growth and development. In addition, a lot carotenoid-derived bioactive metabolites are recently identified as plant root growth regulators, such as anchorene, β-cyclocitral, retinal and zaxinone. However, our knowledge on how these metabolites affect the root architecture to cope with various stressors and how they interact with each other during these processes is still quite limited. In the present review, we will briefly introduce the biosynthesis of carotenoid-derived root regulators and elaborate their biological functions on root development and architecture, focusing on their contribution to the rhizospheric environmental adaption of plants.

Overexpression of Sweet Potato Carotenoid Cleavage Dioxygenase 4 (IbCCD4) Decreased Salt Tolerance in Arabidopsis thaliana

Salt stress has a serious impact on normal plant growth and yield. Carotenoid cleavage dioxygenase (CCD) degrades carotenoids to produce apocarotenoids, which are involved in plant responses to biotic and abiotic stresses. This study shows that the expression of sweet potato IbCCD4 was significantly induced by salt and dehydration stress. The heterologous expression of IbCCD4 in Arabidopsis was induced to confirm its salt tolerance. Under 200 mM NaCl treatment, compared to wild-type plants, the rosette leaves of IbCCD4-overexpressing Arabidopsis showed increased anthocyanins and carotenoid contents, an increased expression of most genes in the carotenoid metabolic pathway, and increased malondialdehyde (MDA) levels. IbCCD4-overexpressing lines also showed a decreased expression of resistance-related genes and a lower activity of three antioxidant enzymes: peroxidase (POD), superoxide dismutase (SOD), and catalase (CAT). These results indicate that IbCCD4 reduced salt tolerance in Arabidopsis, which contributes to the understanding of the role of IbCCD4 in salt stress.

Effects of polystyrene nanoplastics with different functional groups on rice (Oryza sativa L.) seedlings: Combined transcriptome, enzymology, and physiology

Plastic particles originate from the daily use of plastics and have become a new form of pollutant. However, the effects of nanoplastics (NPs) on higher plants remain largely unclear, thus requiring further research. In this study, rice plants were exposed to polystyrene (PS) NPs with different functional groups to determine their toxicity. The presence of NPs reduced the biomass and photosynthetic capacity of rice. Compared with control (CK), the heights of rice plants exposed to no-modified PS, carboxyl-modified PS (PS-COOH) and amino-modified PS (PS-NH₂) groups decreased by 13.59%, 26.61%, and 42.71%, while the dry shoot weight decreased by 47.46%, 50.09%, and 71.04%, respectively. All treatments activated the antioxidant levels of rice and reduced photosynthesis. Transcriptome analysis showed that NPs induced the expression of genes related to antioxidant enzyme activity in rice roots. Rice could partially reduce the xenobiotic toxicity caused by external sources by regulating phenylpropane biosynthesis and the processes involved in cell detoxification. PS mainly affected the process of RNA metabolism, while PS-COOH mainly affected ion transport, and PS-NH₂ mainly affected the synthesis of macromolecular protein, which had different effects on rice growth.

The Root Clock as a Signal Integrator System: Ensuring Balance for Survival

The root system is essential for the survival of terrestrial plants, plant development, and adaptation to changing environments. The development of the root system relies on post-embryonic organogenesis and more specifically on the formation and growth of lateral roots (LR). The spacing of LR along the main root is underpinned by a precise prepatterning mechanism called the Root Clock. In Arabidopsis, the primary output of this mechanism involves the generation of periodic gene expression oscillations in a zone close to the root tip called the Oscillation Zone (OZ). Because of these oscillations, pre-branch sites (PBS) are established in the positions from which LR will emerge, although the oscillations can also possibly regulate the root wavy pattern and growth. Furthermore, we show that the Root Clock is present in LR. In this review, we describe the recent advances unraveling the inner machinery of Root Clock as well as the new tools to track the Root Clock activity. Moreover, we discuss the basis of how Arabidopsis can balance the creation of a repetitive pattern while integrating both endogenous and exogenous signals to adapt to changing environmental conditions. These signals can work as entrainment signals, but in occasions they also affect the periodicity and amplitude of the oscillatory dynamics in gene expression. Finally, we identify similarities with the Segmentation Clock of vertebrates and postulate the existence of a determination front delimiting the end of the oscillations in gene expression and initiating LR organogenesis through the activation of PBS in an ARF7 dependent-manner.

The hidden half comes into the spotlight: Peeking inside the black box of root developmental phases

Efficient use of natural resources (e.g., light, water, and nutrients) can be improved with a tailored developmental program that maximizes the lifetime and fitness of plants. In plant shoots, a developmental phase represents a time window in which the meristem triggers the development of unique morphological and physiological traits, leading to the emergence of leaves, flowers, and fruits. Whereas developmental phases in plant shoots have been shown to enhance food production in crops, this phenomenon has remained poorly investigated in roots. In light of recent advances, we suggest that root development occurs in three main phases: root apical meristem appearance, foraging, and senescence. We provide compelling evidence suggesting that these phases are regulated by at least four developmental pathways: autonomous, non-autonomous, hormonal, and periodic. Root developmental pathways differentially coordinate organ plasticity, promoting morphological alterations, tissue regeneration, and cell death regulation. Furthermore, we suggest how nutritional checkpoints may allow progression through the developmental phases, thus completing the root life cycle. These insights highlight novel and exciting advances in root biology that may help maximize the productivity of crops through more sustainable agriculture and the reduced use of chemical fertilizers.

A plant lipocalin promotes retinal-mediated oscillatory lateral root initiation

[Figure: see text].

Periodic root branching is influenced by light through an HY1-HY5-auxin pathway

The spacing of lateral roots (LRs) along the main root in plants is driven by an oscillatory signal, often referred to as the "root clock" that represents a pre-patterning mechanism that can be influenced by environmental signals. Light is an important environmental factor that has been previously reported to be capable of modulating the root clock, although the effect of light signaling on the LR pre-patterning has not yet been fully investigated. In this study, we reveal that light can activate the transcription of a photomorphogenic gene HY1 to maintain high frequency and amplitude of the oscillation signal, leading to the repetitive formation of pre-branch sites. By grafting and tissue-specific complementation experiments, we demonstrated that HY1 generated in the shoot or locally in xylem pole pericycle cells was sufficient to regulate LR branching. We further found that HY1 can induce the expression of HY5 and its homolog HYH, and act as a signalosome to modulate the intracellular localization and expression of auxin transporters, in turn promoting auxin accumulation in the oscillation zone to stimulate LR branching. These fundamental mechanistic insights improve our understanding of the molecular basis of light-controlled LR formation and provide a genetic interconnection between shoot- and root-derived signals in regulating periodic LR branching.

Iso-anchorene is an endogenous metabolite that inhibits primary root growth in Arabidopsis

Carotenoid-derived regulatory metabolites and hormones are generally known to arise through the oxidative cleavage of a single double bond in the carotenoid backbone, which yields mono-carbonyl products called apocarotenoids. However, the extended conjugated double bond system of these pigments predestines them also to repeated cleavage forming dialdehyde products, diapocarotenoids, which have been less investigated due to their instability and low abundance. Recently, we reported on the short diapocarotenoid anchorene as an endogenous Arabidopsis metabolite and specific signaling molecule that promotes anchor root formation. In this work, we investigated the biological activity of a synthetic isomer of anchorene, iso-anchorene, which can be derived from repeated carotenoid cleavage. We show that iso-anchorene is a growth inhibitor that specifically inhibits primary root growth by reducing cell division rates in the root apical meristem. Using auxin efflux transporter marker lines, we also show that the effect of iso-anchorene on primary root growth involves the modulation of auxin homeostasis. Moreover, by using liquid chromatography-mass spectrometry analysis, we demonstrate that iso-anchorene is a natural Arabidopsis metabolite. Chemical inhibition of carotenoid biosynthesis led to a significant decrease in the iso-anchorene level, indicating that it originates from this metabolic pathway. Taken together, our results reveal a novel carotenoid-derived regulatory metabolite with a specific biological function that affects root growth, manifesting the biological importance of diapocarotenoids.

Transformation of Long-Lived Albino Epipremnum aureum 'Golden Pothos' and Restoring Chloroplast Development

Chloroplasts are organelles responsible for chlorophyll biosynthesis, photosynthesis, and biosynthesis of many metabolites, which are one of key targets for crop improvement. Elucidating and engineering genes involved in chloroplast development are important approaches for studying chloroplast functions as well as developing new crops. In this study, we report a long-lived albino mutant derived from a popular ornamental plant Epipremnum aureum 'Golden Pothos' which could be used as a model for analyzing the function of genes involved in chloroplast development and generating colorful plants. Albino mutant plants were isolated from regenerated populations of variegated 'Golden Pothos' whose albino phenotype was previously found to be due to impaired expression of EaZIP, encoding Mg-protoporphyrin IX monomethyl ester cyclase. Using petioles of the mutant plants as explants with a traceable sGFP gene, an efficient transformation system was developed. Expressing Arabidopsis CHL27 (a homolog of EaZIP) but not EaZIP in albino plants restored green color and chloroplast development. Interestingly, in addition to the occurrence of plants with solid green color, plants with variegated leaves and pale-yellow leaves were also obtained in the regenerated populations. Nevertheless, our study shows that these long-lived albino plants along with the established efficient transformation system could be used for creating colorful ornamental plants. This system could also potentially be used for investigating physiological processes associated with chlorophyll levels and chloroplast development as well as certain biological activities, which are difficult to achieve using green plants.

GUN control in retrograde signaling: How GENOMES UNCOUPLED proteins adjust nuclear gene expression to plastid biogenesis

Communication between cellular compartments is vital for development and environmental adaptation. Signals emanating from organelles, so-called retrograde signals, coordinate nuclear gene expression with the developmental stage and/or the functional status of the organelle. Plastids (best known in their green photosynthesizing differentiated form, the chloroplasts) are the primary energy-producing compartment of plant cells, and the site for the biosynthesis of many metabolites, including fatty acids, amino acids, nucleotides, isoprenoids, tetrapyrroles, vitamins, and phytohormone precursors. Signals derived from plastids regulate the accumulation of a large set of nucleus-encoded proteins, many of which localize to plastids. A set of mutants defective in retrograde signaling (genomes uncoupled, or gun) was isolated over 25 years ago. While most GUN genes act in tetrapyrrole biosynthesis, resolving the molecular function of GUN1, the proposed integrator of multiple retrograde signals, has turned out to be particularly challenging. Based on its amino acid sequence, GUN1 was initially predicted to be a plastid-localized nucleic acid-binding protein. Only recently, mechanistic information on the function of GUN1 has been obtained, pointing to a role in plastid protein homeostasis. This review article summarizes our current understanding of GUN-related retrograde signaling and provides a critical appraisal of the various proposed roles for GUNs and their respective pathways.

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.

A quick protocol for the identification and characterization of early growth mutants in tomato

Root system architecture (RSA) manipulation may improve water and nutrient capture by plants under normal and extreme climate conditions. With the aim of initiating the genetic dissection of RSA in tomato, we established a defined ontology that allowed the curated annotation of the observed phenotypes on 12 traits at four consecutive growth stages. In addition, we established a quick approach for the molecular identification of the mutations associated with the trait-of-interest by using a whole-genome sequencing approach that does not require the building of an additional mapping population. As a proof-of-concept, we screened 4543 seedlings from 300 tomato M₃ lines (Solanum lycopersicum L. cv. Micro-Tom) generated by chemical mutagenesis with ethyl methanesulfonate. We studied the growth and early development of both the root system (primary and lateral roots) and the aerial part of the seedlings as well as the wound-induced adventitious roots emerging from the hypocotyl. We identified 659 individuals (belonging to 203 M₃ lines) whose early seedling and RSA phenotypes differed from those of their reference background. We confirmed the genetic segregation of the mutant phenotypes affecting primary root length, seedling viability and early RSA in 31 M₄ families derived from 15 M₃ lines selected in our screen. Finally, we identified a missense mutation in the SlCESA3 gene causing a seedling-lethal phenotype with short roots. Our results validated the experimental approach used for the identification of tomato mutants during early growth, which will allow the molecular identification of the genes involved.

Recent progress in the chemistry and biochemistry of strigolactones

Strigolactones (SLs) are plant secondary metabolites derived from carotenoids. SLs play important roles in the regulation of plant growth and development in planta and coordinate interactions between plants and other organisms including root parasitic plants, and symbiotic and pathogenic microbes in the rhizosphere. In the 50 years since the discovery of the first SL, strigol, our knowledge about the chemistry and biochemistry of SLs has advanced explosively, especially over the last two decades. In this review, recent advances in the chemistry and biology of SLs are summarized and possible future outcomes are discussed.

The dynamic nature and regulation of the root clock

Plants explore the soil by continuously expanding their root system, a process that depends on the production of lateral roots (LRs). Sites where LRs can be produced are specified in the primary root axis through a pre-patterning mechanism, determined by a biological clock that is coordinated by temporal signals and positional cues. This ‘root clock’ generates an oscillatory signal that is translated into a developmental cue to specify a set of founder cells for LR formation. In this Review, we summarize recent findings that shed light on the mechanisms underlying the oscillatory signal and discuss how a periodic signal contributes to the conversion of founder cells into LR primordia. We also provide an overview of the phases of the root clock that may be influenced by endogenous factors, such as the plant hormone auxin, and by exogenous environmental cues. Finally, we discuss additional aspects of the root-branching process that act independently of the root clock.

A cis-carotene derived apocarotenoid regulates etioplast and chloroplast development

Carotenoids are a core plastid component and yet their regulatory function during plastid biogenesis remains enigmatic. A unique carotenoid biosynthesis mutant, carotenoid chloroplast regulation 2 (ccr2), that has no prolamellar body (PLB) and normal PROTOCHLOROPHYLLIDE OXIDOREDUCTASE (POR) levels, was used to demonstrate a regulatory function for carotenoids and their derivatives under varied dark-light regimes. A forward genetics approach revealed how an epistatic interaction between a ζ-carotene isomerase mutant (ziso-155) and ccr2 blocked the biosynthesis of specific cis-carotenes and restored PLB formation in etioplasts. We attributed this to a novel apocarotenoid retrograde signal, as chemical inhibition of carotenoid cleavage dioxygenase activity restored PLB formation in ccr2 etioplasts during skotomorphogenesis. The apocarotenoid acted in parallel to the repressor of photomorphogenesis, DEETIOLATED1 (DET1), to transcriptionally regulate PROTOCHLOROPHYLLIDE OXIDOREDUCTASE (POR), PHYTOCHROME INTERACTING FACTOR3 (PIF3) and ELONGATED HYPOCOTYL5 (HY5). The unknown apocarotenoid signal restored POR protein levels and PLB formation in det1, thereby controlling plastid development.

cis/trans Carotenoid Extraction, Purification, Detection, Quantification, and Profiling in Plant Tissues

Reverse phase high-performance liquid chromatography (HPLC) is the method of choice used in biological, health, and food research to identify, quantify, and profile carotenoid species. The identification and quantification of cis- and/or trans-carotene and xanthophyll isomers in plant tissues can be affected by the method of sample preparation and extraction, as well as the HPLC column chemistry and the solvent gradient. There is a high degree of heterogeneity in existing methods in terms of their ease, efficiency, and accuracy. We describe a simple carotenoid extraction method and two different optimised HPLC methods utilizing C18 or C30 reverse-phase columns. We outline applications, advantages, and disadvantages for using these reverse phase columns to detect xanthophylls and cis-carotenes in wild-type photosynthetic leaves and mutant dark-grown etiolated seedlings, respectively. Resources are provided to profile individual species based upon their spectral properties and retention time, as well as quantify carotenoids by their composition and absolute levels in different plant tissues.

Pathways for Carotenoid Biosynthesis, Degradation, and Storage

Carotenoids are isoprenoid compounds synthesized de novo in all photosynthetic organisms as well as in some nonphotosynthetic bacteria and fungi. In plants, carotenoids are essential for light harvesting and photoprotection. They contribute to the vivid color found in many plant organs. The cleavage of carotenoids produces small molecules (apocarotenoids) that serve as aroma compounds, as well as phytohormones and signals to affect plant growth and development. Since carotenoids provide valuable nutrition and health benefits for humans, understanding of carotenoid biosynthesis, catabolism and storage is important for biofortification of crops with improved nutritional quality. This chapter primarily introduces our current knowledge about carotenoid biosynthesis and degradation pathways as well as carotenoid storage in plants.

The Apocarotenoid Zaxinone Is a Positive Regulator of Strigolactone and Abscisic Acid Biosynthesis in Arabidopsis Roots

Carotenoids are ubiquitous precursors of important metabolites including hormones, such as strigolactones (SLs) and abscisic acid (ABA), and signaling and regulatory molecules, such as the recently discovered zaxinone. Strigolactones and ABA are key regulators of plant growth and development, adaptation to environmental changes and response to biotic and abiotic stress. Previously, we have shown that zaxinone, an apocarotenoid produced in rice by the enzyme zaxinone synthase (ZAS) that is common in mycorrhizal plants, is required for normal rice growth and development, and a negative regulator of SL biosynthesis. Zaxinone is also formed in Arabidopsis, which lacks ZAS, via an unknown route. In the present study, we investigated the biological activity of zaxinone in Arabidopsis, focusing on its effect on SL and ABA biosynthesis. For this purpose, we quantified the content of both hormones and determined the levels of related transcripts in Arabidopsis (Arabidopsis thaliana), roots upon zaxinone treatment. For SL quantification, we also employed Striga seed germination bioassay. Results obtained show that zaxinone application to hydroponically grown Arabidopsis seedlings enhanced transcript levels of key biosynthetic genes of both hormones, led to higher root ABA and SL (methyl carlactonoate, MeCLA) content, and increased SL release, even under sufficient phosphate supply. Using the SL insensitive (max2-1) and the ABA deficient (aba1-6, aba2-1, and nced3) mutants, we also show that zaxinone application reduced hypocotyl growth and that this effect is caused by increasing ABA content. Our results suggest that zaxinone is a regulatory metabolite also in Arabidopsis, which triggers the biosynthesis of both carotenoid-derived hormones, SLs and ABA, in roots. In the non-mycotrophic plant Arabidopsis, zaxinone does not increase growth and may be perceived as a stress signal, while it acts as a growth-promoting metabolite and suppressor of SL biosynthesis in rice.

Cadmium stress suppresses lateral root formation by interfering with the root clock

A biological clock activated by oscillating signals, known as root clock, has been linked to lateral root (LR) formation and is essential for regular LR spacing along the primary root. However, it remains unclear how this internal mechanism is influenced by environmental factors known to affect the LR pattern. Here, we report that excessive cadmium (Cd) inhibits LR formation by disrupting the lateral root cap (LRC)-programmed cell death (PCD)-regulated root clock. Cd restricts the frequency of the oscillating signal rather than its amplitude. This could be attributed to the inhibition on meristematic activity by Cd, which resulted in decreased LRC cell number and LRC-PCD frequency. Genetic evidence further showed that LRC cell number is positively correlated with root resistance to Cd. Our study reveals root cap dynamics as a novel mechanism mediating root responses to Cd, providing insight into the signalling pathways of the root clock responding to environmental cues.

Anchorene is a carotenoid-derived regulatory metabolite required for anchor root formation in Arabidopsis

Anchor roots (ANRs) arise at the root-shoot junction and are the least investigated type of Arabidopsis root. Here, we show that ANRs originate from pericycle cells in an auxin-dependent manner and a carotenogenic signal to emerge. By screening known and assumed carotenoid derivatives, we identified anchorene, a presumed carotenoid-derived dialdehyde (diapocarotenoid), as the specific signal needed for ANR formation. We demonstrate that anchorene is an Arabidopsis metabolite and that its exogenous application rescues the ANR phenotype in carotenoid-deficient plants and promotes the growth of normal seedlings. Nitrogen deficiency resulted in enhanced anchorene content and an increased number of ANRs, suggesting a role of this nutrient in determining anchorene content and ANR formation. Transcriptome analysis and treatment of auxin reporter lines indicate that anchorene triggers ANR formation by modulating auxin homeostasis. Together, our work reveals a growth regulator with potential application to agriculture and a new carotenoid-derived signaling molecule.

Trichoplusia ni (Lepidoptera: Noctuidae) Qualitative and Quantitative Sequestration of Host Plant Carotenoids

Carotenoids are fundamental precursors for hormones and antioxidants, and insects must acquire carotenoids from their diet. Previous research has shown that insects can selectively absorb dietary carotenoids, often modifying them qualitatively or quantitatively, and quantities may be proportional to those found in the diet. Trichoplusia ni Hübner is a generalist herbivore with host plants varying greatly in carotenoid profiles and concentrations. Larvae sequester carotenoids in their hemolymph, and carotenoid sequestration contributes to their cryptic green coloration. Our objectives were to compare the types of carotenoids found in T. ni and their host plants to determine whether qualitative changes occurred, and compare the amounts of sequestered carotenoids in T. ni reared upon different host plants to determine whether quantitative variation influences sequestration. To fulfill these objectives, larvae were fed romaine lettuce (Lactuca sativa L. [Asterales: Asteraceae] var. longifolia) or kale (Brassica oleracea L. [Brassicales: Brassicaceae] var. sabellica) for a period of 5 d, and sequestered carotenoids from the entire insect were resolved with thin-layer chromatography and measured with spectrophotometer. All carotenoids resolved from plants were also resolved from larvae, and although the carotenoids of plants differed quantitatively, the sequestered carotenoids did not differ between host plants. Regardless of host plant species, T. ni sequestered carotenoids at concentrations up to 20 times higher than the concentrations found in the plants. Future research may be able to explicitly identify enzyme systems involved in the transport and modification of carotenoids in T. ni and other animals.

β-Cyclocitral is a conserved root growth regulator

Natural compounds capable of increasing root depth and branching are desirable tools for enhancing stress tolerance in crops. We devised a sensitized screen to identify natural metabolites capable of regulating root traits in Arabidopsis β-Cyclocitral, an endogenous root compound, was found to promote cell divisions in root meristems and stimulate lateral root branching. β-Cyclocitral rescued meristematic cell divisions in ccd1ccd4 biosynthesis mutants, and β-cyclocitral-driven root growth was found to be independent of auxin, brassinosteroid, and reactive oxygen species signaling pathways. β-Cyclocitral had a conserved effect on root growth in tomato and rice and generated significantly more compact crown root systems in rice. Moreover, β-cyclocitral treatment enhanced plant vigor in rice plants exposed to salt-contaminated soil. These results indicate that β-cyclocitral is a broadly effective root growth promoter in both monocots and eudicots and could be a valuable tool to enhance crop vigor under environmental stress.

Volatile apocarotenoid discovery and quantification in Arabidopsis thaliana: optimized sensitive analysis via HS-SPME-GC/MS

INTRODUCTION

In the field of carotenoid metabolism researchers' focus has been directed recently toward the discovery and quantification of carotenoid cleavage products (i.e. apocarotenoids, excluding the well-studied carotenoid-derived hormones abscisic acid and strigolactones), due to their emerging roles as putative signaling molecules. Gas chromatography mass spectrometry (GC/MS) and sample preparation via headspace solid phase micro-extraction (HS-SPME) are widely used analytical techniques for broad untargeted metabolomics studies and until now, no optimized quantitative targeted HS-SPME-GC/MS method has been developed specifically for volatile apocarotenoids (VAs) in planta.

OBJECTIVES

Optimization and subsequent validation of the HS-SPME technique for extracting and quantifying volatile apocarotenoids in planta.

METHODS

Factors considered during method optimization were HS-SPME parameters; vial storage conditions; different adsorbent SPME fibre coating chemistries; plant tissue matrix effects; and fresh tissues to be analyzed.

RESULTS

Mean linear regression in planta calibration correlation coefficients (R²) for VAs was 0.974. The resultant method mean limits of detection (LOD) and lower limits of quantification (LLOQ) for VAs using in planta standard additions were 0.384 ± 0.139 and 0.640 ± 0.231 µg/L, respectively. VAs remained stable at elevated SPME incubation temperatures, with no observable effects of thermal and photo-stereoisomerisation and oxidation. The bipolar 50/30 µm divinylbenzene/carboxen on polydimethylsiloxane (PDMS/DVB/CAR) was identified as the optimal fibre for broad molecular weight range VA analysis.

CONCLUSIONS

An optimized HS-SPME-GC/MS method for VA detection and quantification was validated in vitro and in planta: based on biological replicates and stringent QA/QC approaches, thereby providing robust detection and quantification of VAs across a broad range of Arabidopsis tissues, fifteen of which were identified for the first time in Arabidopsis.

A Genome-Wide Association Study Identifies New Loci Involved in Wound-Induced Lateral Root Formation in Arabidopsis thaliana

Root systems can display variable architectures that contribute to nutrient foraging or to increase the tolerance of abiotic stress conditions. Root tip excision promotes the developmental progression of previously specified lateral root (LR) founder cells, which allows to easily measuring the branching capacity of a given root as regards its genotype and/or growth conditions. Here, we describe the natural variation among 120 Arabidopsis thaliana accessions in root system architecture (RSA) after root tip excision. Wound-induced changes in RSA were associated with 19 genomic loci using genome-wide association mapping. Three candidate loci associated with wound-induced LR formation were investigated. Sequence variation in the hypothetical protein encoded by the At4g01090 gene affected wound-induced LR development and its loss-of-function mutants displayed a reduced number of LRs after root tip excision. Changes in a histidine phosphotransfer protein putatively involved in cytokinin signaling were significantly associated with LR number variation after root tip excision. Our results provide a better understanding of some of the genetic components involved in LR capacity variation among accessions.

Changing Form and Function through Carotenoids and Synthetic Biology

The diverse structures and multifaceted roles of carotenoids make these colorful pigments attractive targets for synthetic biology.

In vitro plant regeneration and Agrobacterium tumefaciens-mediated transformation of Datura stramonium (Solanaceae)

PREMISE OF THE STUDY

Datura stramonium is a pharmacologically and evolutionarily important plant species in the family Solanaceae. Stable transformation methodology of this species would be advantageous for future genetic studies.

METHODS

In vitro plant regeneration and Agrobacterium tumefaciens-mediated transformation techniques were developed for D. stramonium based on methods reported for tomato. A binary vector containing pAtUBQ10::erGFP was used for transformation.

RESULTS

We recovered primary transformants harboring the green fluorescent protein (GFP) transgene that resulted in expression of fluorescence in all tissues analyzed. Transformants were allowed to self-pollinate, and two of five progeny contained the GFP transgene and displayed fluorescence identical to the primary transformants.

DISCUSSION

We have demonstrated the first stable transformation in the genus Datura. This is a key first step to study the genetic basis of traits in this evolutionarily interesting species.

HY5 Contributes to Light-Regulated Root System Architecture Under a Root-Covered Culture System

Light is essential for plant organogenesis and development. Light-regulated shoot morphogenesis has been extensively studied; however, the mechanisms by which plant roots perceive and respond to aboveground light are largely unknown, particularly because the roots of most terrestrial plants are usually located underground in darkness. To mimic natural root growth conditions, we developed a root-covered system (RCS) in which the shoots were illuminated and the plant roots could be either exposed to light or cultivated in darkness. Using the RCS, we observed that root growth of wild-type plants was significantly promoted when the roots were in darkness, whereas it was inhibited by direct light exposure. This growth change seems to be regulated by ELONGATED HYPOCOTYL 5 (HY5), a master regulator of photomorphogenesis. Light was found to regulate HY5 expression in the roots, while a HY5 deficiency partially abolished the inhibition of growth in roots directly exposed to light, suggesting that HY5 expression is induced by direct light exposure and inhibits root growth. However, no differences in HY5 expression were observed between illuminated and dark-grown cop1 roots, indicating that HY5 may be regulated by COP1-mediated proteasome degradation. We confirmed the crucial role of HY5 in regulating root development in response to light under soil-grown conditions. A transcriptomic analysis revealed that light controls the expression of numerous genes involved in phytohormone signaling, stress adaptation, and metabolic processes in a HY5-dependent manner. In combination with the results of the flavonol quantification and exogenous quercetin application, these findings suggested that HY5 regulates the root response to light through a complex network that integrates flavonol biosynthesis and reactive oxygen species signaling. Collectively, our results indicate that HY5 is a master regulator of root photomorphogenesis.

From in planta Function to Vitamin-Rich Food Crops: The ACE of Biofortification

Humans are highly dependent on plants to reach their dietary requirements, as plant products contribute both to energy and essential nutrients. For many decades, plant breeders have been able to gradually increase yields of several staple crops, thereby alleviating nutritional needs with varying degrees of success. However, many staple crops such as rice, wheat and corn, although delivering sufficient calories, fail to satisfy micronutrient demands, causing the so called 'hidden hunger.' Biofortification, the process of augmenting nutritional quality of food through the use of agricultural methodologies, is a pivotal asset in the fight against micronutrient malnutrition, mainly due to vitamin and mineral deficiencies. Several technical advances have led to recent breakthroughs. Nutritional genomics has come to fruition based on marker-assisted breeding enabling rapid identification of micronutrient related quantitative trait loci (QTL) in the germplasm of interest. As a complement to these breeding techniques, metabolic engineering approaches, relying on a continuously growing fundamental knowledge of plant metabolism, are able to overcome some of the inevitable pitfalls of breeding. Alteration of micronutrient levels does also require fundamental knowledge about their role and influence on plant growth and development. This review focuses on our knowledge about provitamin A (beta-carotene), vitamin C (ascorbate) and the vitamin E group (tocochromanols). We begin by providing an overview of the functions of these vitamins in planta, followed by highlighting some of the achievements in the nutritional enhancement of food crops via conventional breeding and genetic modification, concluding with an evaluation of the need for such biofortification interventions. The review further elaborates on the vast potential of creating nutritionally enhanced crops through multi-pathway engineering and the synergistic potential of conventional breeding in combination with genetic engineering, including the impact of novel genome editing technologies.

Morphological Characterization of Root System Architecture in Diverse Tomato Genotypes during Early Growth

Plant roots exploit morphological plasticity to adapt and respond to different soil environments. We characterized the root system architecture of nine wild tomato species and four cultivated tomato (Solanum lycopersicum L.) varieties during early growth in a controlled environment. Additionally, the root system architecture of six near-isogenic lines from the tomato 'Micro-Tom' mutant collection was also studied. These lines were affected in key genes of ethylene, abscisic acid, and anthocyanin pathways. We found extensive differences between the studied lines for a number of meaningful morphological traits, such as lateral root distribution, lateral root length or adventitious root development, which might represent adaptations to local soil conditions during speciation and subsequent domestication. Taken together, our results provide a general quantitative framework for comparing root system architecture in tomato seedlings and other related species.

Callus Initiation from Root Explants Employs Different Strategies in Rice and Arabidopsis

Callus formation in tissue culture follows the rooting pathway, and newly formed callus seems to be a group of root primordium-like cells. However, it is not clear whether there are multiple mechanisms of callus initiation in different species and in different organs. Here we show that the OsIAA11-mediated pathway is specifically and strictly required for callus initiation in the lateral root (LR) formation region of the primary root (PR) but not for callus initiation at the root tip or the stem base in rice. OsIAA11 and its Arabidopsis homolog AtIAA14 are key players in lateral rooting. However, the AtIAA14-mediated pathway is not strictly required for callus initiation in the LR formation region in Arabidopsis. LRs can be initiated through either the AtIAA14-mediated or AtWOX11-mediated pathway in the Arabidopsis PR, therefore providing optional pathways for callus initiation. In contrast, OsIAA11 is strictly required for lateral rooting in the rice PR, meaning that the OsIAA11 pathway is the only choice for callus initiation. Our study suggests that multiple pathways may converge to WOX5 activation during callus formation in different organs and different species.

A comparison of lateral root patterning among dicot and monocot plants

Lateral root branching along the primary root involves complex gene regulatory networks in model plant Arabidopsis. However, it is largely unclarified whether different plant species share a common mechanism to pattern the lateral root along the primary axis. In this study, we assessed the development pattern of lateral root among several dicot and monocot plants, including Arabidopsis, tomato, Medicago, Nicotiana, rice, and ryegrass by using an agar-gel culture system. Our results reveal a regular-spaced distribution pattern of lateral roots along the primary root axis of both dicot and monocot plants. Meanwhile, the root patterning is tightly controlled by root bending and the plant hormone auxin. However, nitrogen and phosphate starvations trigger distinguished root growth patterns among different plant species. Our studies strongly suggest a partially shared signaling pathway underlying root patterning of various plant species, and also provide a foundation for further identification of genes associated with root development.