AtML: An Arabidopsis thaliana root cell identity recognition tool for medicinal ingredient accumulation.

Arabidopsis thaliana synthesizes various medicinal compounds, and serves as a model plant for medicinal plant research. Single-cell transcriptomics technologies are essential for understanding the developmental trajectory of plant roots, facilitating the analysis of synthesis and accumulation patterns of medicinal compounds in different cell subpopulations. Although methods for interpreting single-cell transcriptomics data are rapidly advancing in Arabidopsis, challenges remain in precisely annotating cell identity due to the lack of marker genes for certain cell types. In this work, we trained a machine learning system, AtML, using sequencing datasets from six cell subpopulations, comprising a total of 6000 cells, to predict Arabidopsis root cell stages and identify biomarkers through complete model interpretability. Performance testing using an external dataset revealed that AtML achieved 96.50% accuracy and 96.51% recall. Through the interpretability provided by AtML, our model identified 160 important marker genes, contributing to the understanding of cell type annotations. In conclusion, we trained AtML to efficiently identify Arabidopsis root cell stages, providing a new tool for elucidating the mechanisms of medicinal compound accumulation in Arabidopsis roots.

BnaC4.BOR2 mediates boron uptake and translocation in Brassica napus under boron deficiency.

Boron (B) is an essential microelement in plant growth and development. However, the molecular mechanisms underlying B uptake and translocation in Brassica napus are poorly understood. Herein, we identified a low-B (LB)-inducible gene, namely BnaC4.BOR2, with high transcriptional activity in root tips, stele cells, leaves, and floral organs. The green fluorescence protein labelled BnaC4.BOR2 protein was localised to the plasma membrane to demonstrate the B efflux activity in yeast and Arabidopsis. BnaC4.BOR2 knockout considerably reduced B concentration in the root and xylem sap, and altered B distribution in different organs at low B supply, exacerbating B sensitivity at the vegetative and reproductive stages. Additionally, the grafting experiment showed that BnaC4.BOR2 expression in the roots contributed more to B deficiency adaptability than that in the shoots. The pot experiments with LB-soil revealed B concentration in leaves and siliques of BnaC4.BOR2 mutants were markedly reduced, showing an obvious B-deficient phenotype of 'flowering without seed setting' and a considerable reduction in seed yield in B-deficient soil. Altogether, the findings of this study highlight the crucial role of BnaC4.BOR2 in B uptake and translocation during B. napus growth and seed yield under LB conditions.

Comparative metabolomics of root-tips reveals distinct metabolic pathways conferring drought tolerance in contrasting genotypes of rice.

BACKGROUND: The mechanisms underlying rice root responses to drought during the early developmental stages are yet unknown. RESULTS: This study aimed to determine metabolic differences in IR64, a shallow-rooting, drought-susceptible genotype, and Azucena, a drought-tolerant and deep-rooting genotype under drought stress. The morphological evaluation revealed that Azucena might evade water stress by increasing the lateral root system growth, the root surface area, and length to access water. At the same time, IR64 may rely mainly on cell wall thickening to tolerate stress. Furthermore, significant differences were observed in 49 metabolites in IR64 and 80 metabolites in Azucena, for which most metabolites were implicated in secondary metabolism, amino acid metabolism, nucleotide acid metabolism and sugar and sugar alcohol metabolism. Among these metabolites, a significant positive correlation was found between allantoin, galactaric acid, gluconic acid, glucose, and drought tolerance. These metabolites may serve as markers of drought tolerance in genotype screening programs. Based on corresponding biological pathways analysis of the differentially abundant metabolites (DAMs), biosynthesis of alkaloid-derivatives of the shikimate pathway, fatty acid biosynthesis, purine metabolism, TCA cycle and amino acid biosynthesis were the most statistically enriched biological pathway in Azucena in drought response. However, in IR64, the differentially abundant metabolites of starch and sucrose metabolism were the most statistically enriched biological pathways. CONCLUSION: Metabolic marker candidates for drought tolerance were identified in both genotypes. Thus, these markers that were experimentally determined in distinct metabolic pathways can be used for the development or selection of drought-tolerant rice genotypes.

Contrasting dynamics and trait controls in first-order root compared with leaf litter decomposition.

Decomposition is a key component of the global carbon (C) cycle, yet current ecosystem C models do not adequately represent the contributions of plant roots and their mycorrhizae to this process. The understanding of decomposition dynamics and their control by traits is particularly limited for the most distal first-order roots. Here we followed decomposition of first-order roots and leaf litter from 35 woody plant species differing in mycorrhizal type over 6 years in a Chinese temperate forest. First-order roots decomposed more slowly (k = 0.11 ± 0.01 years-1) than did leaf litter (0.35 ± 0.02 years-1), losing only 35% of initial mass on average after 6 years of exposure in the field. In contrast to leaf litter, nonlignin root C chemistry (nonstructural carbohydrates, polyphenols) accounted for 82% of the large interspecific variation in first-order root decomposition. Leaf litter from ectomycorrhizal (EM) species decomposed more slowly than that from arbuscular mycorrhizal (AM) species, whereas first-order roots of EM species switched, after 2 years, from having slower to faster decomposition compared with those from AM species. The fundamentally different dynamics and control mechanisms of first-order root decomposition compared with those of leaf litter challenge current ecosystem C models, the recently suggested dichotomy between EM and AM plants, and the idea that common traits can predict decomposition across roots and leaves. Aspects of C chemistry unrelated to lignin or nitrogen, and not presently considered in decomposition models, controlled first-order root decomposition; thus, current paradigms of ecosystem C dynamics and model parameterization require revision.

Glyphosate treatments for weed control affect early stages of root colonization by Tuber melanosporum but not secondary colonization.

The cultivation of the ectomycorrhizal fungus Tuber melanosporum has considerably spread in recent years throughout the world. During the first years of truffle cultivation, weed control is a key practice to improve the establishment of host trees and the proliferation of the fungus in the soil. Glyphosate is nowadays the most commonly used herbicide in Spanish truffle orchards. We explored the effect of glyphosate on the proliferation of T. melanosporum mycorrhizae, on extraradical mycelium and on the inoculum potential of T. melanosporum spores in greenhouse experiments using Quercus ilex seedlings as host plants. No detrimental effect on the secondary infection of T. melanosporum was found after three sequential glyphosate applications in young seedlings during one vegetative period. Instead, a change in the distribution of fine roots and T. melanosporum mycorrhizae along soil depth was observed. On the other hand, results indicate that high application rates of glyphosate hinder the infectivity of T. melanosporum spore inoculum, without apparent impact on the host performance. Our results suggest that glyphosate has the potential to jeopardise the role of the soil spore bank as inoculum source for the colonisation of new roots, also raising the question of whether glyphosate could hinder the presumed role of spores in sexual mating.

How deep can ectomycorrhizas go? A case study on Pisolithus down to 4 meters in a Brazilian eucalypt plantation.

Despite the strong ecological importance of ectomycorrhizal (ECM) fungi, their vertical distribution remains poorly understood. To our knowledge, ECM structures associated with trees have never been reported in depths below 2 meters. In this study, fine roots and ECM root tips were sampled down to 4-m depth during the digging of two independent pits differing by their water availability. A meta-barcoding approach based on Illumina sequencing of internal transcribed spacers (ITS1 and ITS2) was carried out on DNA extracted from root samples (fine roots and ECM root tips separately). ECM fungi dominated the root-associated fungal community, with more than 90% of sequences assigned to the genus Pisolithus. The morphological and barcoding results demonstrated, for the first time, the presence of ECM symbiosis down to 4-m. The molecular diversity of Pisolithus spp. was strongly dependent on depth, with soil pH and soil water content as primary drivers of the Pisolithus spp. structure. Altogether, our results highlight the importance to consider the ECM symbiosis in deep soil layers to improve our understanding of fine roots functioning in tropical soils.

Nuclear Proteomics Reveals the Role of Protein Synthesis and Chromatin Structure in Root Tip of Soybean during the Initial Stage of Flooding Stress.

To identify the upstream events controlling the regulation of flooding-responsive proteins in soybean, proteomic analysis of nuclear proteins in root tip was performed. By using nuclear fractions, which were highly enriched, a total of 365 nuclear proteins were changed in soybean root tip at initial stage of flooding stress. Four exon-junction complex-related proteins and NOP1/NOP56, which function in upstream of 60S preribosome biogenesis, were decreased in flooded soybean. Furthermore, proteomic analysis of crude protein extract revealed that the protein translation was suppressed by continuous flooding stress. Seventeen chromatin structure-related nuclear proteins were decreased in response to flooding stress. Out of them, histone H3 was clearly decreased with protein abundance and mRNA expression levels at the initial flooding stress. Additionally, a number of protein synthesis-, RNA-, and DNA-related nuclear proteins were decreased in a time-dependent manner. mRNA expressions of genes encoding the significantly changed flooding-responsive nuclear proteins were inhibited by the transcriptional inhibitor, actinomycin D. These results suggest that protein translation is suppressed through inhibition of preribosome biogenesis- and mRNA processing-related proteins in nuclei of soybean root tip at initial flooding stress. In addition, flooding stress may regulate histone variants with gene expression in root tip.

Organellar genome copy number variation and integrity during moderate maturation of roots and leaves of maize seedlings.

Little information is available about organellar genome copy numbers and integrity in plant roots, although it was reported recently that the plastid and mitochondrial genomes were damaged under light, resulting in non-functional fragments in green seedling leaves in a maize line. In the present study, we investigated organellar genome copy numbers and integrity, after assessing the cellular ploidy, in seedling leaves and roots of two elite maize (Zea mays) cultivars using both long-fragment polymerase chain reaction (long-PCR) and real-time quantitative polymerase chain reaction (qPCR, a type of short-PCR). Since maize leaf and root cells are mainly diploid according to chromosome number counting and the literature, the DNA amount ratio between the organellar genomes and the nuclear genome could be used to estimate average organellar genome copy numbers per cell. In the present study, both long-PCR and qPCR analyses found that green leaves had dramatically more plastid DNA and less mitochondrial DNA than roots had in both cultivars. The similarity in results from long-PCR and qPCR suggests that green leaves and roots during moderate maturation have largely intact plastid and mitochondrial genomes. The high resolution of qPCR led to the detection of an increase in copies in the plastid genome and a decrease in copies in the analyzed mitochondrial sub-genomes during the moderate maturation of seedling leaves and roots. These results suggest that green seedling leaves and roots of these two maize cultivars during moderate maturation had essentially intact organellar genomes, an increased copy number of the plastid genome, and decreased copy numbers of certain mitochondrial sub-genomes.

Quantitative assessment of the differential impacts of arbuscular and ectomycorrhiza on soil carbon cycling.

A significant fraction of carbon stored in the Earth's soil moves through arbuscular mycorrhiza (AM) and ectomycorrhiza (EM). The impacts of AM and EM on the soil carbon budget are poorly understood. We propose a method to quantify the mycorrhizal contribution to carbon cycling, explicitly accounting for the abundance of plant-associated and extraradical mycorrhizal mycelium. We discuss the need to acquire additional data to use our method, and present our new global database holding information on plant species-by-site intensity of root colonization by mycorrhizas. We demonstrate that the degree of mycorrhizal fungal colonization has globally consistent patterns across plant species. This suggests that the level of plant species-specific root colonization can be used as a plant trait. To exemplify our method, we assessed the differential impacts of AM : EM ratio and EM shrub encroachment on carbon stocks in sub-arctic tundra. AM and EM affect tundra carbon stocks at different magnitudes, and via partly distinct dominant pathways: via extraradical mycelium (both EM and AM) and via mycorrhizal impacts on above- and belowground biomass carbon (mostly AM). Our method provides a powerful tool for the quantitative assessment of mycorrhizal impact on local and global carbon cycling processes, paving the way towards an improved understanding of the role of mycorrhizas in the Earth's carbon cycle.

Exogenous Cytokinin Induces Callus and Protocorm-Like-Bodies Formation in In Vitro Root Tips of Vanilla planifolia Andrews.

Vanilla is a popular flavouring essence derived from the pods of vanilla orchid plants. Due to the high demand for vanilla flavour, high yielding vanilla plantlets are necessary for establishing vanilla plantations. Clonal micropropagation is a viable technique for the mass production of high yielding vanilla plantlets. This study reports an efficient regeneration protocol by using cytokinin as the sole plant growth regulator to regenerate plantlets from the root tips of a commercial vanilla orchid species, Vanilla planifolia. Most studies to date have reported using seeds and nodes as starting explants for in vitro micropropagation of vanilla orchids. So far, regeneration from roots has not been very successful. Previous studies favoured the use of auxins only or high auxin to cytokinin ratios to induce callus, and sole cytokinins were used for direct shoot regeneration. However, it was sporadically observed in plantlets regeneration of V. planifolia that multiple shoots were regenerated from the tips of intact aerial roots submerged in media. This study therefore investigated the regeneration of excised vanilla root tips through the application of most commonly used auxins (1-naphthaleneacetic acid and 2,4-dichlorophenoxyacetic acid) and cytokinins (6-benzylaminopurine and thidiazuron). High auxin presence is known to promote callusing in in vitro plants. However, in this study, auxin treatment inhibits callusing in root tips. While cytokinin treatments, even at low levels, has promoted high rate of callusing. These callus cells regenerate into protocorm-like-body (PLB) shoots when cytokinin levels are increased to 0.5 mg/mL 6-benzylaminopurine (BAP) under light conditions. The findings of the study have the potential of providing large quantity of high yielding vanilla plantlets through clonal micropropagation.

Multiplex micro-respiratory measurements of Arabidopsis tissues.

Researchers often want to study the respiratory properties of individual parts of plants in response to a range of treatments. Arabidopsis is an obvious model for this work; however, because of its size, it represents a challenge for gas exchange measurements of respiration. The combination of micro-respiratory technologies with multiplex assays has the potential to bridge this gap, and make measurements possible in this model plant species. We show the adaptation of the commercial technology used for mammalian cell respiration analysis to study three critical tissues of interest: leaf sections, root tips and seeds. The measurement of respiration in single leaf discs has allowed the age dependence of the respiration rate in Arabidopsis leaves across the rosette to be observed. The oxygen consumption of single root tips from plate-grown seedlings shows the enhanced respiration of root tips and their time-dependent susceptibility to salinity. The monitoring of single Arabidopsis seeds shows the kinetics of respiration over 48 h post-imbibition, and the effect of the phytohormones gibberellic acid (GA3 ) and abscisic acid (ABA) on respiration during seed germination. These studies highlight the potential for multiplexed micro-respiratory assays to study oxygen consumption in Arabidopsis tissues, and open up new possibilities to screen and study mutants and to identify differences in ecotypes or populations of different plant species.

Proteomic and phosphoproteomic analysis of polyethylene glycol-induced osmotic stress in root tips of common bean (Phaseolus vulgaris L.).

Previous studies have shown that polyethylene glycol (PEG)-induced osmotic stress (OS) reduces cell-wall (CW) porosity and limits aluminium (Al) uptake by root tips of common bean (Phaseolus vulgaris L.). A subsequent transcriptomic study suggested that genes related to CW processes are involved in adjustment to OS. In this study, a proteomic and phosphoproteomic approach was applied to identify OS-induced protein regulation to further improve our understanding of how OS affects Al accumulation. Analysis of total soluble proteins in root tips indicated that, in total, 22 proteins were differentially regulated by OS; these proteins were functionally categorized. Seventy-seven per- cent of the total expressed proteins were involved in metabolic pathways, particularly of carbohydrate and amino acid metabolism. An analysis of the apoplastic proteome revealed that OS reduced the level of five proteins and increased that of seven proteins. Investigation of the total soluble phosphoproteome suggested that dehydrin responded to OS with an enhanced phosphorylation state without a change in abundance. A cellular immunolocalization analysis indicated that dehydrin was localized mainly in the CW. This suggests that dehydrin may play a major protective role in the OS-induced physical breakdown of the CW structure and thus maintenance of the reversibility of CW extensibility during recovery from OS. The proteomic and phosphoproteomic analyses provided novel insights into the complex mechanisms of OS-induced reduction of Al accumulation in the root tips of common bean and highlight a key role for modification of CW structure.

NRTPredictor: identifying rice root cell state in single-cell RNA-seq via ensemble learning.

BACKGROUND: Single-cell RNA sequencing (scRNA-seq) measurements of gene expression show great promise for studying the cellular heterogeneity of rice roots. How precisely annotating cell identity is a major unresolved problem in plant scRNA-seq analysis due to the inherent high dimensionality and sparsity. RESULTS: To address this challenge, we present NRTPredictor, an ensemble-learning system, to predict rice root cell stage and mine biomarkers through complete model interpretability. The performance of NRTPredictor was evaluated using a test dataset, with 98.01% accuracy and 95.45% recall. With the power of interpretability provided by NRTPredictor, our model recognizes 110 marker genes partially involved in phenylpropanoid biosynthesis. Expression patterns of rice root could be mapped by the above-mentioned candidate genes, showing the superiority of NRTPredictor. Integrated analysis of scRNA and bulk RNA-seq data revealed aberrant expression of Epidermis cell subpopulations in flooding, Pi, and salt stresses. CONCLUSION: Taken together, our results demonstrate that NRTPredictor is a useful tool for automated prediction of rice root cell stage and provides a valuable resource for deciphering the rice root cellular heterogeneity and the molecular mechanisms of flooding, Pi, and salt stresses. Based on the proposed model, a free webserver has been established, which is available at https://www.cgris.net/nrtp .

Influencing Factors of Bidens pilosa L. Hyperaccumulating Cadmium Explored by the Real-Time Uptake of Cd2+ Influx around Root Apexes under Different Exogenous Nutrient Ion Levels.

Though Bidens pilosa L. has been confirmed to be a potential Cd hyperaccumulator, the accumulation mechanism is not yet clear. The dynamic and real-time uptake of Cd2+ influx by B. pilosa root apexes was determined using non-invasive micro-test technology (NMT), which partly explored the influencing factors of the Cd hyperaccumulation mechanism under the conditions of different exogenous nutrient ions. The results indicated that Cd2+ influxes at 300 µm around the root tips decreased under Cd treatments with 16 mM Ca2+, 8 mM Mg2+, 0.5 mM Fe2+, 8 mM SO42- or 18 mM K+ compared to single Cd treatments. The Cd treatments with a high concentration of nutrient ions showed an antagonistic effect on Cd2+ uptake. However, Cd treatments with 1 mM Ca2+, 0.5 mM Mg2+, 0.5 mM SO42- or 2 mM K+ had no effect on the Cd2+ influxes as compared with single Cd treatments. It is worth noting that the Cd treatment with 0.05 mM Fe2+ markedly increased Cd2+ influxes. The addition of 0.05 mM Fe2+ exhibited a synergistic effect on Cd uptake, which could be low concentration Fe2+ rarely involved in blocking Cd2+ influx and often forming an oxide membrane on the root surface to help the Cd uptake by B. pilosa. The results also showed that Cd treatments with high concentration of nutrient ions significantly increased the concentrations of chlorophyll and carotenoid in leaves and the root vigor of B. pilosa relative to single Cd treatments. Our research provides novel perspectives with respect to Cd uptake dynamic characteristics by B. pilosa roots under different exogenous nutrient ion levels, and shows that the addition of 0.05 mM Fe2+ could promote the phytoremediation efficiency for B. pilosa.

Difference in Cd2+ flux around the root tips of different soybean (Glycine max L.) cultivars and physiological response under mild cadmium stress.

The purpose of the study was to compare differences in Cd2+ flux in the vicinity of root tips of 20 soybean cultivars under mild Cd stress conditions using non-invasive micro-test technology (NMT). The results indicated that Cd2+ influx to the root tips under mild Cd treatment was higher compared to controls. Cd2+ influx showed an obvious spatial distribution, with the highest Cd2+ influx measured 300 µm from the root tips, and a gradually decrease above and below this site. The cultivar Liaodou32 had a lower Cd uptake (3.40 pmol cm-2 s-1), while Liaodou23 had a relatively higher Cd uptake (66.37 pmol cm-2 s-1). Cluster analysis showed that the order of the average Cd2+ influx of the cultivars at a distance of 300 µm from the root tips was as follows: high-uptake cultivars (61.80 pmol cm-2 s-1)>medium-high-uptake cultivars (33.92 pmol cm-2 s-1)>medium-low-uptake cultivars (19.78 pmol cm-2 s-1)>low-uptake cultivars (4.84 pmol cm-2 s-1). We also analyzed physiological responses of different soybean cultivars to mild Cd stress. The results indicated that mild Cd stress could inhibit soluble protein production and root vigor among individual soybean cultivars. Moreover, stress increased SOD, CAT and POD activities and MDA content in root tissues. It should be noted that the physio-biochemical indicators of low-uptake cultivars did not change significantly after exposure to mild Cd stress compared to controls. Pearson's correlation analyses showed that all physio-biochemical indicators were significantly positively associated with influx, except of root SP and biomass. PCA analysis demonstrated that root vigor was a dominant factor causing the differences in Cd tolerance among different soybean seedling cultivars. NMT is of great significance for safe utilization of contaminated soil to distinguish the cultivars with different enrichment capacity for heavy metals from different crop cultivars.

Salicylic acid pre-treatment modulates Pb2+-induced DNA damage vis-à-vis oxidative stress in Allium cepa roots.

The current study investigated the putative role of salicylic acid (SA) in modulating Pb2+-induced DNA and oxidative damage in Allium cepa roots. Pb2+ exposure enhanced free radical generation and reduced DNA integrity and antioxidant machinery after 24 h; however, SA pre-treatment (for 24 h) ameliorated Pb2+ toxicity. Pb2+ exposure led to an increase in malondialdehyde (MDA) and hydrogen peroxide (H2O2) accumulation and enhanced superoxide radical and hydroxyl radical levels. SA improved the efficiency of enzymatic antioxidants (ascorbate and guaiacol peroxidases [APX, GPX], superoxide dismutases [SOD], and catalases [CAT]) at 50-µM Pb2+ concentration. However, SA pre-treatment could not improve the efficiency of CAT and APX at 500 µM of Pb2+ treatment. Elevated levels of ascorbate and glutathione were observed in A. cepa roots pre-treated with SA and exposed to 50 µM Pb2+ treatment, except for oxidized glutathione. Nuclear membrane integrity test demonstrated the ameliorating effect of SA by reducing the number of dark blue-stained nuclei as compared to Pb2+ alone treatments. SA was successful in reducing DNA damage in cell exposed to higher concentration of Pb2+ (500 µM) as observed through comet assay. The study concludes that SA played a major role in enhancing defense mechanism and protecting against DNA damage by acclimatizing the plant to Pb2+-induced toxicity.

S-nitrosated proteomic analysis reveals the regulatory roles of protein S-nitrosation and S-nitrosoglutathione reductase during Al-induced PCD in peanut root tips.

Nitric oxide-mediated S-nitrosation through S-nitrosoglutathione reductase (GSNOR) plays important roles in cellular processes and signaling of plants; however, the regulatory mechanism of programmed cell death (PCD) by S-nitrosation remains unclear. In this study, the S-nitrosated proteomic and functions of GSNOR during Al-induced PCD in peanut were investigated. Al stress induced an increase of S-nitrosothiol (SNO) content and GSNOR activity in Al-induced PCD. There was significant positive correlation between SNO content and hydrogen peroxide content. The S-nitrosated proteomic analysis identified 402 S-nitrosated proteins containing 551 S-nitrosated sites during Al-induced PCD in the root tips of peanut. These S-nitrosated proteins were involved in regulation of various biological processes including energy metabolism, maintenance of cell wall function and organic acid secretion. Among them, 128 S-nitrosated proteins were up-regulated and one was down-regulated after Al stress. Experiments with recombinant AhGSNOR revealed that activity of the enzyme was inhibited by its S-nitrosation, with a moderate decrease of 17.9 % after 100 µM GSNO incubation. These data provide novel insights to understanding the functional mechanism of NO-mediated S-nitrosation during plant PCD.

Nitric oxide inhibits aluminum-induced programmed cell death in peanut (Arachis hypoganea L.) root tips.

It had been reported that Aluminum (Al) stress altered nitric oxide (NO) concentration and induced programmed cell death (PCD) in plants. However, the relationship between NO and PCD occurrence under Al stress is unclear. The results showed that cell death induced by Al was significant negative correlation with the inhibition of Al on root elongation growth in peanut. AlCl3 at 100µmolL-1 induced DNA ladder, chromatin condensation, typical apoptotic chromatin condensation staining with DAPI, apoptosis related gene Hrs203j expression and caspase3-like protease activation in peanut root tip cells, and showed that Al-induced cell death in peanut root tip cells was a typical PCD. Exogenous NO donor sodium nitroprusside (SNP) at 200µmolL-1 inhibited Al-induced PCD occurrence, but NO specific scavenger cPTIO aggravated PCD production. It suggests that NO is a negative regulator of Al-induced PCD in peanut root tips.

Small RNA profiles in soybean primary root tips under water deficit.

BACKGROUND: Soybean (Glycine max) production is significantly hampered by frequent droughts in many regions of the world including the United States. Identifying microRNA (miRNA)-controlled posttranscriptional gene regulation under drought will enhance our understanding of molecular basis of drought tolerance in this important cash crop. Indeed, miRNA profiles in soybean exposed to drought were studied but not from the primary root tips, which is not only a main zone of water uptake but also critical for water stress sensing and signaling. METHODS: Here we report miRNA profiles specifically from well-watered and water-stressed primary root tips (0 to 8 mm from the root apex) of soybean. Small RNA sequencing confirmed the expression of vastly diverse miRNA (303 individual miRNAs) population, and, importantly several conserved miRNAs were abundantly expressed in primary root tips. RESULTS: Notably, 12 highly conserved miRNA families were differentially regulated in response to water-deficit; six were upregulated while six others were downregulated at least by one fold (log2) change. Differentially regulated soybean miRNAs are targeting genes include auxin response factors, Cu/Zn Superoxide dismutases, laccases and plantacyanin and several others. CONCLUSIONS: These results highlighted the importance of miRNAs in primary root tips both under control and water-deficit conditions; under control conditions, miRNAs could be important for cell division, cell elongation and maintenance of the root apical meristem activity including quiescent centre whereas under water stress differentially regulated miRNAs could decrease auxin signaling and oxidative stress as well as other metabolic processes that save energy and water.

Do ectomycorrhizal and arbuscular mycorrhizal temperate tree species systematically differ in root order-related fine root morphology and biomass?

While most temperate broad-leaved tree species form ectomycorrhizal (EM) symbioses, a few species have arbuscular mycorrhizas (AM). It is not known whether EM and AM tree species differ systematically with respect to fine root morphology, fine root system size and root functioning. In a species-rich temperate mixed forest, we studied the fine root morphology and biomass of three EM and three AM tree species from the genera Acer, Carpinus, Fagus, Fraxinus, and Tilia searching for principal differences between EM and AM trees. We further assessed the evidence of convergence or divergence in root traits among the six co-occurring species. Eight fine root morphological and chemical traits were investigated in root segments of the first to fourth root order in three different soil depths and the relative importance of the factors root order, tree species and soil depth for root morphology was determined. Root order was more influential than tree species while soil depth had only a small effect on root morphology All six species showed similar decreases in specific root length and specific root area from the 1st to the 4th root order, while the species patterns differed considerably in root tissue density, root N concentration, and particularly with respect to root tip abundance. Most root morphological traits were not significantly different between EM and AM species (except for specific root area that was larger in AM species), indicating that mycorrhiza type is not a key factor influencing fine root morphology in these species. The order-based root analysis detected species differences more clearly than the simple analysis of bulked fine root mass. Despite convergence in important root traits among AM and EM species, even congeneric species may differ in certain fine root morphological traits. This suggests that, in general, species identity has a larger influence on fine root morphology than mycorrhiza type.