Auxin and monocot development

Metabolism of 2,4-D in plants: comparative analysis of metabolic detoxification pathways in tolerant crops and resistant weeds

The commercialization of 2,4-D (2,4-dichlorophenoxyacetic acid) latifolicide in 1945 marked the beginning of the selective herbicide market, with this active ingredient playing a pivotal role among commercial herbicides due to the natural tolerance of monocots compared with dicots. Due to its intricate mode of action, involving interactions within endogenous auxin signaling networks, 2,4-D was initially considered a low-risk herbicide to evolve weed resistance. However, the intensification of 2,4-D use has contributed to the emergence of 2,4-D-resistant broadleaf weeds, challenging earlier beliefs. This review explores 2,4-D tolerance in crops and evolved resistance in weeds, emphasizing an in-depth understanding of 2,4-D metabolic detoxification. Nine confirmed 2,4-D-resistant weed species, driven by rapid metabolism, highlight cytochrome P450 monooxygenases in Phase I and glycosyltransferases in Phase II as key enzymes. Resistance to 2,4-D may also involve impaired translocation associated with mutations in auxin/indole-3-acetic acid (Aux/IAA) co-receptor genes. Moreover, temperature variations affect 2,4-D efficacy, with high temperatures increasing herbicide metabolism rates and reducing weed control, while drought stress did not affect 2,4-D efficacy. Research on 2,4-D resistance has primarily focused on non-target-site resistance (NTSR) mechanisms, including 2,4-D metabolic detoxification, with limited exploration of the inheritance and genetic basis underlying these traits. Resistance to 2,4-D in weeds is typically governed by a single gene, either dominant or incompletely dominant, raising questions about gain-of-function or loss-of-function mutations that confer resistance. Future research should unravel the physiological and molecular-genetic basis of 2,4-D NTSR, exploring potential cross-resistance patterns and assessing fitness costs that may affect future evolution of auxin-resistant weeds. © 2024 Society of Chemical Industry.

In Vitro Propagation Technology for the Endangered Aquatic Species Nymphoides coronata

Nymphoides coronata is an endangered aquatic plant species with significant medicinal and ecological importance. To preserve N. coronata from going extinct, we need to provide seedlings and efficient multiplication techniques so that it can be extensively studied. This study aimed to identify the most suitable sterilization treatment, growth medium, and substrate for the cultivation and propagation of N. coronata. Ethanol sterilization, fungicide treatment, and sterile water washing were the most important sterilization steps. A combination of 6-benzylaminopurine (6-BA) and indoleacetic acid (IAA) was the most suitable medium for bud induction and shoot proliferation. The use of α-naphthaleneacetic acid (NAA) increased the rooting rate and rooting time compared to indole-3-butyric acid (IBA). Increasing the concentration of NAA from 0.5 to 1.0 mg/L increased the rooting rate from 78 to 100% and reduced the rooting time from 7 to 5 days. The survival rate of N. coronata seedlings was 100% in a mixture of red soil and sand (1:1, w/w). As a result, the procedure mentioned above could potentially be used to safely propagate this rare species on a large scale. These findings provide valuable insights into the optimal conditions for the successful cultivation and propagation of N. coronata, which can contribute to the conservation and sustainable use of this important rare plant species.

A comprehensive comparative genomic analysis revealed that plant growth promoting traits are ubiquitous in strains of Stenotrophomonas

Stenotrophomonas strains, which are often described as plant growth promoting (PGP) bacteria, are ubiquitous in many environments. A total of 213 genomes of strains of Stenotrophomonas were analyzed using comparative genomics to better understand the ecological roles of these bacteria in the environment. The pan-genome of the 213 strains of Stenotrophomonas consists of 27,186 gene families, including 710 core gene families, 11,039 unique genes and 15,437 accessory genes. Nearly all strains of Stenotrophomonas harbor the genes for GH3-family cellulose degradation and GH2- and GH31-family hemicellulose hydrolase, as well as intact glycolysis and tricarboxylic acid cycle pathways. These abilities suggest that the strains of this genus can easily obtain carbon and energy from the environment. The Stenotrophomonas strains can respond to oxidative stress by synthesizing catalase, superoxide dismutase, methionine sulfoxide reductase, and disulfide isomerase, as well as managing their osmotic balance by accumulating potassium and synthesizing compatible solutes, such as betaine, trehalose, glutamate, and proline. Each Stenotrophomonas strain also contains many genes for resistance to antibiotics and heavy metals. These genes that mediate stress tolerance increase the ability of Stenotrophomonas strains to survive in extreme environments. In addition, many functional genes related to attachment and plant colonization, growth promotion and biocontrol were identified. In detail, the genes associated with flagellar assembly, motility, chemotaxis and biofilm formation enable the strains of Stenotrophomonas to effectively colonize host plants. The presence of genes for phosphate-solubilization and siderophore production and the polyamine, indole-3-acetic acid, and cytokinin biosynthetic pathways confer the ability to promote plant growth. These strains can produce antimicrobial compounds, chitinases, lipases and proteases. Each Stenotrophomonas genome contained 1-9 prophages and 17-60 genomic islands, and the genes related to antibiotic and heavy metal resistance and the biosynthesis of polyamines, indole-3-acetic acid, and cytokinin may be acquired by horizontal gene transfer. This study demonstrates that strains of Stenotrophomonas are highly adaptable for different environments and have strong potential for use as plant growth-promoting bacteria.

In situ seasonal patterns of root auxin concentrations and meristem length in an arctic sedge

Seasonal dynamics of root growth play an important role in large-scale ecosystem processes; they are largely governed by growth regulatory compounds and influenced by environmental conditions. Yet, our knowledge about physiological drivers of root growth is mostly limited to laboratory-based studies on model plant species. We sampled root tips of Eriophorum vaginatum and analyzed their auxin concentrations and meristem lengths biweekly over a growing season in situ in a subarctic peatland, both in surface soil and at the permafrost thawfront. Auxin concentrations were almost five times higher in surface than in thawfront soils and increased over the season, especially at the thawfront. Surprisingly, meristem length showed an opposite pattern and was almost double in thawfront compared with surface soils. Meristem length increased from peak to late season in the surface soils but decreased at the thawfront. Our study of in situ seasonal dynamics in root physiological parameters illustrates the potential for physiological methods to be applied in ecological studies and emphasizes the importance of in situ measurements. The strong effect of root location and the unexpected opposite patterns of meristem length and auxin concentrations likely show that auxin actively governs root growth to ensure a high potential for nutrient uptake at the thawfront.

Functional Genome Analysis of a Conditionally Pathogenic Rhizobacterial Strain, Pseudomonas putida AKMP7

This manuscript reports the whole genome sequence of a conditionally pathogenic rhizobacterial strain, Pseudomonas putida AKMP7, which has been previously reported by us to be beneficial to Arabidopsis thaliana under well-watered conditions and pathogenic to the plant under water stress. As part of a study to understand this unique behavior, the whole genome sequence of this strain was analyzed. Based on the results, it was identified that the total length of the AKMP7 genome is 5,764,016 base pairs, and the total GC content of the genome is 62.93% (typical of P. putida). Using RAST annotation pipeline, it was identified that the genome has 5605 coding sequences, 80 repeat regions, 71 tRNA genes, and 22 rRNA genes. A total of 4487 functional proteins and 1118 hypothetical proteins were identified. Phylogenetic analysis has classified it as P. putida species, with a P value of 0.03. In order to identify close relatives of this strain, comparative genomics was performed with 30 other P. putida strains, taken from publicly available genome databases, using Average Nucleotide Identity (ANI) analysis. Whole genome comparison with these strains reveals that AKMP7 possesses Type-IV Secretion System (T4SS) with conjugative transfer functionality. Interestingly, the T4SS feature is absent in all the beneficial/harmless strains of P. putida that we analyzed. All the plant pathogenic bacteria that were analyzed had the T4SS feature in their genome, indicating its role in pathogenesis. This study aims to address important gaps in understanding the molecular mechanisms involved in the conditional/opportunistic pathogenesis of plant-associated, beneficial soil bacteria, using genomics approaches.

Nitrogen fertilization application strategies improve yield of the rice cultivars with different yield types by regulating phytohormones

Rice (Oryza sativa L.) is the most important food crop worldwide, and its sustainable development is essential to ensure global food security. Panicle morphological and physiological characteristics plays an important role in rice yield formation. However, under different nitrogen (N) fertilization strategies, it is not clear whether the morphological and physiological state of panicles at panicle development stage affects the formation of yield. To understand how the panicle differentiation and development, and grain yield are affected by the N fertilization strategies, and clarify the relationship between related traits and yield in the process of panicle development in different cultivars. In this study consisted of no N fertilizer and four N fertilization strategies, a panicle weight type (PWT) rice cultivar, Dongfu 114 (DF114) and a panicle number type (PNT) rice cultivar, Longdao 11 (LD11) were grown in the field. The results showed that N fertilization strategies could improve the nitrogen use efficiency and yield of rice, but the response of different rice varieties to N fertilizer strategies was different. Different from the DF114, the further increase of panicle N fertilizer ratio could not further improve the yield of LD11, and the highest grain yield of DF114 and LD11 was obtained under N4 and N3 conditions, respectively. In addition, this study found that N fertilizer strategies can affect the content of phytohormones in rice at the panicle differentiation stage, and then regulate the differentiation and development of rice panicles to affect yield. It is of great significance to optimize the application mode of N fertilizer according to the characteristics of varieties to improve rice yield and ensure food security.

Allelopathic studies with furanocoumarins isolated from Ducrosia anethifolia. In vitro and in silico investigations to protect legumes, rice and grain crops

Six different furanocoumarins were isolated from the aerial parts of Ducrosia anethifolia and tested in vitro for plant cell elongation in etiolated wheat coleoptile. They were also tested for their ability to control three different weeds: ribwort plantain, annual ryegrass, and common purslane. These compounds exhibited strong inhibition of plant cell elongation. In the case of (+)-heraclenin, the IC50 was lower than 20 μM, indicating a better inhibition than the positive control Logran®. Computational experiments for docking and molecular dynamics revealed for the investigated furanocoumarins bearing an epoxide moiety an improved fitting and stronger interaction with the auxin-like TIR1 ubiquitin ligase. Furthermore, the formed inhibition complex remained also stable during dynamic evaluation. Bidental interaction at the active site, along with an extended hydrogen-bond lifetime, explained the enhanced activity of the epoxides. The in vitro weed bioassay results showed that Plantago lanceolata was the most affected weed for germination, root, and shoot development. In addition, (+)-heraclenin displayed better inhibition values than positive control even at 300 μM concentration.

Opposite Auxin Dynamics Determine the Gametophytic and Embryogenic Fates of the Microspore

The microspore can follow two different developmental pathways. In vivo microspores follow the gametophytic program to produce pollen grains. In vitro, isolated microspores can be reprogrammed by stress treatments and follow the embryogenic program, producing doubled-haploid embryos. In the present study, we analyzed the dynamics and role of endogenous auxin in microspore development during these two different scenarios, in Brassica napus. We analyzed auxin concentration, cellular accumulation, the expression of the TAA1 auxin biosynthesis gene, and the PIN1-like efflux carrier gene, as well as the effects of inhibiting auxin biosynthesis by kynurenine on microspore embryogenesis. During the gametophytic pathway, auxin levels and TAA1 and PIN1-like expression were high at early stages, in tetrads and tapetum, while they progressively decreased during gametogenesis in both pollen and tapetum cells. In contrast, in microspore embryogenesis, TAA1 and PIN1-like genes were upregulated, and auxin concentration increased from the first embryogenic divisions. Kynurenine treatment decreased both embryogenesis induction and embryo production, indicating that auxin biosynthesis is required for microspore embryogenesis initiation and progression. The findings indicate that auxin exhibits two opposite profiles during these two microspore developmental pathways, which determine the different cell fates of the microspore.

Studies Using Mutant Strains of Azospirillum brasilense Reveal That Atmospheric Nitrogen Fixation and Auxin Production Are Light Dependent Processes

As the use of microbial inoculants in agriculture rises, it becomes important to understand how the environment may influence microbial ability to promote plant growth. This work examines whether there are light dependencies in the biological functions of Azospirillum brasilense, a commercialized prolific grass-root colonizer. Though classically defined as non-phototrophic, A. brasilense possesses photoreceptors that could perceive light conducted through its host's roots. Here, we examined the light dependency of atmospheric biological nitrogen fixation (BNF) and auxin biosynthesis along with supporting processes including ATP biosynthesis, and iron and manganese uptake. Functional mutants of A. brasilense were studied in light and dark environments: HM053 (high BNF and auxin production), ipdC (capable of BNF, deficient in auxin production), and FP10 (capable of auxin production, deficient in BNF). HM053 exhibited the highest rate of nitrogenase activity with the greatest light dependency comparing iterations in light and dark environments. The ipdC mutant showed similar behavior with relatively lower nitrogenase activity observed, while FP10 did not show a light dependency. Auxin biosynthesis showed strong light dependencies in HM053 and FP10 strains, but not for ipdC. Ferrous iron is involved in BNF, and a light dependency was observed for microbial ⁵⁹Fe²⁺ uptake in HM053 and ipdC, but not FP10. Surprisingly, a light dependency for ⁵²Mn²⁺ uptake was only observed in ipdC. Finally, ATP biosynthesis was sensitive to light across all three mutants favoring blue light over red light compared to darkness with observed ATP levels in descending order for HM053 > ipdC > FP10.

Repurposed inhibitor of bacterial dihydrodipicolinate reductase exhibits effective herbicidal activity

Herbicide resistance represents one of the biggest threats to our natural environment and agricultural sector. Thus, new herbicides are urgently needed to tackle the rise in herbicide-resistant weeds. Here, we employed a novel strategy to repurpose a 'failed' antibiotic into a new and target-specific herbicidal compound. Specifically, we identified an inhibitor of bacterial dihydrodipicolinate reductase (DHDPR), an enzyme involved in lysine biosynthesis in plants and bacteria, that exhibited no antibacterial activity but severely attenuated germination of the plant Arabidopsis thaliana. We confirmed that the inhibitor targets plant DHDPR orthologues in vitro, and exhibits no toxic effects against human cell lines. A series of analogues were then synthesised with improved efficacy in germination assays and against soil-grown A. thaliana. We also showed that our lead compound is the first lysine biosynthesis inhibitor with activity against both monocotyledonous and dicotyledonous weed species, by demonstrating its effectiveness at reducing the germination and growth of Lolium rigidum (rigid ryegrass) and Raphanus raphanistrum (wild radish). These results provide proof-of-concept that DHDPR inhibition may represent a much-needed new herbicide mode of action. Furthermore, this study exemplifies the untapped potential of repurposing 'failed' antibiotic scaffolds to fast-track the development of herbicide candidates targeting the respective plant enzymes.

IAA-decorated CuO nanocarriers significantly improve Chickpea growth by increasing antioxidative activities

Plant growth regulators tagged on metallic oxide nanoparticles (NPs) may function as nanofertilizers with reduced toxicity of NPs. CuO NPs were synthesized to function as nanocarriers of Indole-3-acetic acid (IAA). Powder X-ray diffraction (XRD) and scanning electron microscopy (SEM) revealed 30.4 nm size of NPs and sheet-like structure, respectively, of CuO-IAA NPs. Fourier-transform infrared spectroscopy (FTIR) confirmed CuO-IAA formation. IAA-decorated CuO NPs enhanced the physiological parameters of Chickpea plants, i.e., root length, shoot length, and biomass compared to naked CuO NPs. The variation in physiological response was due to change of phytochemical contents in plants. Phenolic content increased up to 17.98 and 18.13 µgGAE/mg DW at 20 and 40 mg/L of CuO-IAA NPs, respectively. However, significant decrease in antioxidant enzymes' activity was recorded compared to control. Presence of CuO-IAA NPs increased the reducing potential of plants at higher concentration of NPs, while decrease in total antioxidant response was observed. This study concludes that IAA conjugation to CuO NPs reduces toxicity of NPs. Furthermore, NPs can be explored as nanocarriers for plant modulators and slow release in future studies.

Auxin Transporter OsPIN1b, a Novel Regulator of Leaf Inclination in Rice (Oryza sativa L.)

Leaf inclination is one of the most important components of the ideal architecture, which effects yield gain. Leaf inclination was shown that is mainly regulated by brassinosteroid (BR) and auxin signaling. Here, we reveal a novel regulator of leaf inclination, auxin transporter OsPIN1b. Two CRISPR-Cas9 homozygous mutants, ospin1b-1 and ospin1b-2, with smaller leaf inclination compared to the wild-type, Nipponbare (WT/NIP), while overexpression lines, OE-OsPIN1b-1 and OE-OsPIN1b-2 have opposite phenotype. Further cell biological observation showed that in the adaxial region, OE-OsPIN1b-1 has significant bulge compared to WT/NIP and ospin1b-1, indicating that the increase in the adaxial cell division results in the enlarging of the leaf inclination in OE-OsPIN1b-1. The OsPIN1b was localized on the plasma membrane, and the free IAA contents in the lamina joint of ospin1b mutants were significantly increased while they were decreased in OE-OsPIN1b lines, suggesting that OsPIN1b might action an auxin transporter such as AtPIN1 to alter IAA content and leaf inclination. Furthermore, the OsPIN1b expression was induced by exogenous epibrassinolide (24-eBL) and IAA, and ospin1b mutants are insensitive to BR or IAA treatment, indicating that the effecting leaf inclination is regulated by OsPIN1b. This study contributes a new gene resource for molecular design breeding of rice architecture.

The role of auxins and auxin-producing bacteria in the tolerance and accumulation of cadmium by plants

Cadmium (Cd) is one of the most toxic heavy metals for plant physiology and development. This review discusses Cd effects on auxin biosynthesis and homeostasis, and the strategies for restoring plant growth based on exogenous auxin application. First, the two well-characterized auxin biosynthesis pathways in plants are described, as well as the effect of exogenous auxin application on plant growth. Then, review describes the impacts of Cd on the content, biosynthesis, conjugation, and oxidation of endogenous auxins, which are related to a decrease in root development, photosynthesis, and biomass production. Finally, compelling evidence of the beneficial effects of auxin-producing rhizobacteria in plants exposed to Cd is showed, focusing on photosynthesis, oxidative stress, and production of antioxidant compounds and osmolytes that counteract Cd toxicity, favoring plant growth and improve phytoremediation efficiency. Expanding our understanding of the positive effects of exogenous auxins application and the interactions between bacteria and plants growing in Cd-polluted environments will allow us to propose phytoremediation strategies for restoring environments contaminated with this metal.

Architectural analysis of root system and phytohormone biosynthetic genes expression in wheat (Triticum aestivum L.) inoculated with Penicillium oxalicum

In this study, a fungal plant growth promoter Penicillium oxalicum T4 isolated from non-rhizosphere soil of Arunachal Pradesh, India, was screened for different plant growth promoting traits in a gnotobiotic study. Though inoculation improved the overall growth of the plants, critical differences were observed in root architecture. Confocal Laser Scanning Microscope, Scanning electron microscope and stereo microscopic study showed that inoculated wheat plants could develop profuse root hairs as compared to control. Root scanning indicated improvement in cumulative root length, root area, root volume, number of forks, links, crossings, and other parameters. Confocal scanning laser microscope indicated signs of endophytic colonization in wheat roots. Gene expression studies revealed that inoculation of T4 modulated the genes affecting root hair development. Significant differences were marked in the expression levels of TaRSL4, TaEXPB1, TaEXPB23, PIN-FORMED protein, kaurene oxidase, lipoxygenase, ACC synthase, ACC oxidase, 9-cis-epoxycarotenoid dioxygenase, and ABA 8'-hydroxylase genes. These genes contribute to early plant development and ultimately to biomass accumulation and yield. The results suggested that P. oxalicum T4 has potential for growth promotion in wheat and perhaps also in other cereals.

Abscisic Acid Induces Adventitious Rooting in Cucumber (Cucumis sativus L.) by Enhancing Sugar Synthesis

Abscisic acid (ABA) affects many important plant processes, such as seed germination, root elongation and stomatal movement. However, little information is available about the relationship between ABA and sugar synthesis during adventitious root formation. The aim of this study was to evaluate the effect of ABA on adventitious root formation in cucumber and whether the effect of this plant hormone on sugar synthesis could be included as a causative factor for adventitious root development. We determined the contents of glucose, sucrose, starch, total sugar and sugar-related enzymes, including sucrose synthase (SS), sucrose phosphate synthase (SPS), hexokinase (HK) and pyruvate kinase (PK) activities in ABA treatment. We also quantified the relative expression of sucrose or glucose synthesis genes during this process. Increasing ABA concentrations significantly improved adventitious root formation, with the most considerable effect at 0.05 μM. Compared to the control, ABA treatment showed higher glucose, sucrose, starch and total sugar contents. Moreover, ABA treatment increased glucose-6-phosphate (G6P), fructose-6-phosphate (F6P) and glucose-1-phosphate (G1P) contents in cucumber explants during adventitious root development, which was followed by an increase of activities of sucrose-related enzymes SS and SPS, glucose-related enzymes HK and PK. ABA, meanwhile, upregulated the expression levels of sucrose or glucose synthesis-related genes, including CsSuSy1, CsSuSy6, CsHK1 and CsHK3. These results suggest that ABA may promote adventitious root development by increasing the contents of glucose, sucrose, starch, total sugar, G6P, F6P and G1P, the activities of SS, SPS, HK, SPS and the expression levels of CsSuSy1, CsSuSy6, CsHK1 and CsHK3 genes. These findings provide evidence for the physiological role of ABA during adventitious root formation and provide a new understanding of the possible relationship between ABA and sugar synthesis during adventitious rooting in plants.

Auxin in Root Development

Root system architecture is an important determinant of below-ground resource capture and hence overall plant fitness. The plant hormone auxin plays a central role in almost every facet of root development from the cellular to the whole-root-system level. Here, using Arabidopsis as a model, we review the multiple gene signaling networks regulated by auxin biosynthesis, conjugation, and transport that underpin primary and lateral root development. We describe the role of auxin in establishing the root apical meristem and discuss how the tight spatiotemporal regulation of auxin distribution controls transitions between cell division, cell growth, and differentiation. This includes the localized reestablishment of mitotic activity required to elaborate the root system via the production of lateral roots. We also summarize recent discoveries on the effects of auxin and auxin signaling and transport on the control of lateral root gravitropic setpoint angle (GSA), a critical determinant of the overall shape of the root system. Finally, we discuss how environmental conditions influence root developmental plasticity by modulation of auxin biosynthesis, transport, and the canonical auxin signaling pathway.

Comparative analysis of buds transcriptome and identification of two florigen gene AkFTs in Amorphophallus konjac

Leaves and flowers of Amorphophallus konjac do not develop simultaneously thus unique features can be elucidated through study of flowering transformation in A. konjac. In this study, transcriptome libraries of A. konjac leaf buds (LB) and flower buds (FB) were constructed followed by high-throughput sequencing. A total of 68,906 unigenes with an average length of 920 bp were obtained after library assembly. Out of these genes, 24,622 unigenes had annotation information. A total of 6859 differentially expressed genes (DEGs) were identified through differential expression analysis using LB as control. Notably, 2415 DEGs were upregulated whereas 4444 DEGs were downregulated in the two transcriptomes. Go and KEGG analysis showed that the DEGs belonged to 44 functional categories and were implicated in 98 metabolic pathways and 38 DEGs involved in plant hormone signal transduction. Several genes were mined that may be involved in A. konjac flower bud differentiation and flower organ development. Eight DEGs were selected for verification of RNA-seq results using qRT-PCR analysis. Two FLOWERING LOCUS T (FT) genes named AkFT1 and AkFT2 were identified though homologous analysis may be the florigen gene implicated in modulation of A. konjac flowering. These genes were significantly upregulated in flower buds compared with the expression levels on leaf buds. Overexpression of AkFT genes though heterologous expression in Arabidopsis showed that the transgenics flowered at a very early stage relative to wild type plants. These findings indicate that AkFT1 and AkFT2 function as regulation genes in A. konjac flowering development and the two genes may present similar functions during flowering transition.

The wild grass Brachypodium distachyon as a developmental model system

The arrival of cheap and high-throughput sequencing paired with efficient gene editing technologies allows us to use non-traditional model systems and mechanistically approach biological phenomena beyond what was conceivable just a decade ago. Venturing into different model systems enables us to explore for example clade-specific environmental responses to changing climates or the genetics and development of clade-specific organs, tissues and cell types. We-both early career researchers working with the wild grass model Brachypodium distachyon-want to use this review to (1) highlight why we think B. distachyon is a fantastic grass developmental model system, (2) summarize the tools and resources that have enabled discoveries made in B. distachyon, and (3) discuss a handful of developmental biology vignettes made possible by using B. distachyon as a model system. Finally, we want to conclude by (4) relating our personal stories with this emerging model system and (5) share what we think is important to consider before starting work with an emerging model system.

Auxin Efflux Transporters OsPIN1c and OsPIN1d Function Redundantly in Regulating Rice (Oryza sativa L.) Panicle Development

The essential role of auxin in plant growth and development is well known. Pathways related to auxin synthesis, transport and signaling have been extensively studied in recent years, and the PIN-FORMED (PIN) protein family has been identified as being pivotal for polar auxin transport and distribution. However, research focused on the functional characterization of PIN proteins in rice is still lacking. In this study, we investigated the expression and function of OsPIN1c and OsPIN1d in the japonica rice variety (Nipponbare) using gene knockout and high-throughput RNA sequencing analysis. The results showed that OsPIN1c and OsPIN1d were mainly expressed in young panicles and exhibited a redundant function. Furthermore, OsPIN1c or OsPIN1d loss-of-function mutants presented a mild phenotype compared with the wild type. However, in addition to significantly decreased plant height and tiller number, panicle development was severely disrupted in double-mutant lines of OsPIN1c and OsPIN1d. Severe defects included smaller inflorescence meristem and panicle sizes, fewer primary branches, elongated bract leaves, non-degraded hair and no spikelet growth. Interestingly, ospin1cd-3, a double-mutant line with functional retention of OsPIN1d, showed milder defects than those observed in other mutants. Additionally, several critical regulators of reproductive development, such as OsPID, LAX1, OsMADS1 and OsSPL14/IPA1, were differentially expressed in ospin1c-1 ospin1d-1, supporting the hypothesis that OsPIN1c and OsPIN1d are involved in regulating panicle development. Therefore, this study provides novel insights into the auxin pathways that regulate plant reproductive development in monocots.

Insights into the molecular basis of hypergravity-induced root growth phenotype in bread wheat (Triticum aestivum L.)

Hypergravity is a condition where the force of gravity exceeds that on the surface of the Earth and can be simulated by centrifugation. Previously, a significant increase in root growth phenotype was observed when wheat seeds were exposed to hypergravity (10 g for 12 h). In the present study, we investigated the molecular basis of this change through root transcriptome. The data revealed a total of 3765 up-regulated and 2102 down-regulated transcripts in response to hypergravity. GO enrichment analysis revealed hormonal responses, cell division, and cell-wall-related terms were significantly enriched in hypergravity. The increased isoform level expression of transcripts involved in auxin biosynthesis, transport, and signaling was observed. Further, enhanced expression of cell division transcripts and down-regulation of cell number regulator genes suggests rapid cell division. Overexpression of cellulose and hemicellulose biosynthesis transcripts suggests demand for cell-wall constituents. Collectively, this study identified candidate genes associated with hypergravity-induced enhanced root growth.

Carbon-11 Radiotracing Reveals Physiological and Metabolic Responses of Maize Grown under Different Regimes of Boron Treatment

In agriculture, boron is known to play a critical role in healthy plant growth. To dissect the role of boron in maize metabolism, radioactive carbon-11 (t_½ 20.4 min) was used to examine the physiological and metabolic responses of 3-week-old B73 maize plants to different levels of boron spanning 0 mM, 0.05 mM, and 0.5 mM boric acid (BA) treatments. Growth behavior, of both shoots and roots, was recorded and correlated to plant physiological responses. ¹¹CO₂ fixation, leaf export of [¹¹C]-photosynthates, and their rate of transport increased systematically with increasing BA concentrations, while the fraction of [¹¹C]-photosynthates delivered to the roots under 0 mM and 0.5 mM BA treatments was lower than under 0.05 mM BA treatment, likely due to changes in root growth. Additionally, solid-phase extraction coupled with gamma counting, radio-fluorescence thin layer chromatography, and radio-fluorescence high-performance liquid chromatography techniques applied to tissue extracts provided insight into the effects of BA treatment on 'new' carbon (as ¹¹C) metabolism. Most notable was the strong influence reducing boron levels had on raising ¹¹C partitioning into glutamine, aspartic acid, and asparagine. Altogether, the growth of maize under different regimes of boron affected ¹¹CO₂ fixation, its metabolism and allocation belowground, and altered root growth. Finally, inductively coupled plasma mass spectrometry provided insight into the effects of BA treatment on plant uptake of other essential nutrients. Here, levels of boron and zinc systematically increased in foliar tissues with increasing BA concentration. However, levels of magnesium, potassium, calcium, manganese, and iron remained unaffected by treatment. The rise in foliar zinc levels with increased BA concentration may contribute to improved ¹¹CO₂ fixation under these conditions.

Adventitious root primordia formation and development in the stem of Ananas comosus var. bracteatus slip

There are about 4-6 slips on a fruit, and they are good materials for effective regeneration of Ananas comosus var. bracteatus. Adventitious root (AR) induction is essential for the propagation of Ananas comosus var. bracteatus slips. Growth regulator treatment, and culture medium are imperative factors that affect slip growth and rooting. In order to screen the optimal methods for slips rooting and reveal the anatomic procedure of slip rooting, this study induced slip rooting by different treatment of growth regulator, culture medium, observed the slip stem structure, AR origination and formation procedure through paraffin sections. The results showed that, slip cuttings treated with 100 mg/L of Aminobenzotriazole (ABT) for 6 hrs, cultured in river sand: coconut chaff: garden soil 2:2:1 medium is the optimal method for rooting. The proper supplementary of ABT can enhance the soluble sugar content, soluble protein content, polyphenol oxidase (PPO) activity and peroxidase (POD) enzyme activity, which resulted in the improvement of rooting. The slip stem structure is quite different from other monocots, which consists of epidermis, cortex, and stele with vascular tissues distributed in the cortex and stele. The AR primordia originates from the parenchyma cells located on the borderline between the cortex and stele. The vascular tissues in the AR develop and are connected with vascular tissue of the stem before the AR grew out the stem. The number of primary xylem poles in AR is about 30.

Overexpression of γ-glutamylcysteine synthetase gene from Caragana korshinskii decreases stomatal density and enhances drought tolerance

BACKGROUND

Gamma-glutamylcysteine synthetase (γ-ECS) is a rate-limiting enzyme in glutathione biosynthesis and plays a key role in plant stress responses. In this study, the endogenous expression of the Caragana korshinskii γ-ECS (Ckγ-ECS) gene was induced by PEG 6000-mediated drought stress in the leaves of C. korshinskii. and the Ckγ-ECS overexpressing transgenic Arabidopsis thaliana plants was constructed using the C. korshinskii. isolated γ-ECS.

RESULTS

Compared with the wildtype, the Ckγ-ECS overexpressing plants enhanced the γ-ECS activity, reduced the stomatal density and aperture sizes; they also had higher relative water content, lower water loss, and lower malondialdehyde content. At the same time, the mRNA expression of stomatal development-related gene EPF1 was increased and FAMA and STOMAGEN were decreased. Besides, the expression of auxin-relative signaling genes AXR3 and ARF5 were upregulated.

CONCLUSIONS

These changes suggest that transgenic Arabidopsis improved drought tolerance, and Ckγ-ECS may act as a negative regulator in stomatal development by regulating the mRNA expression of EPF1 and STOMAGEN through auxin signaling.

Overview of Approaches to Improve Rhizoremediation of Petroleum Hydrocarbon-Contaminated Soils

Soil contamination with petroleum hydrocarbons (PHCs) has become a global concern and has resulted from the intensification of industrial activities. This has created a serious environmental issue; therefore, there is a need to find solutions, including application of efficient remediation technologies or improvement of current techniques. Rhizoremediation is a green technology that has received global attention as a cost-effective and possibly efficient remediation technique for PHC-polluted soil. Rhizoremediation refers to the use of plants and their associated microbiota to clean up contaminated soils, where plant roots stimulate soil microbes to mineralize organic contaminants to H2O and CO2. However, this multipartite interaction is complicated because many biotic and abiotic factors can influence microbial processes in the soil, making the efficiency of rhizoremediation unpredictable. This review reports the current knowledge of rhizoremediation approaches that can accelerate the remediation of PHC-contaminated soil. Recent approaches discussed in this review include (1) selecting plants with desired characteristics suitable for rhizoremediation; (2) exploiting and manipulating the plant microbiome by using inoculants containing plant growth-promoting rhizobacteria (PGPR) or hydrocarbon-degrading microbes, or a combination of both types of organisms; (3) enhancing the understanding of how the host–plant assembles a beneficial microbiome, and how it functions, under pollutant stress. A better understanding of plant–microbiome interactions could lead to successful use of rhizoremediation for PHC-contaminated soil in the future.

Synthesis and regulation of auxin and abscisic acid in maize

Indole-3-acetic acid (IAA), the primary auxin in higher plants, and abscisic acid (ABA) play crucial roles in the ability of maize (Zea mays L.) to acclimatize to various environments by mediating growth, development, defense and nutrient allocation. Although understanding the biochemical reactions for IAA and ABA biosynthesis and signal transduction has progressed, the mechanisms by which auxin and ABA are synthesized and transduced in maize have not been fully elucidated to date. The synthesis and signal transduction pathway of IAA and ABA in maize can be analyzed using an existing model. This article focuses on the research progress toward understanding the synthesis and signaling pathways of IAA and ABA, as well as IAA and ABA regulation of maize growth, providing insight for future development and the significance of IAA and ABA for maize improvement.

grasviq: an image analysis framework for automatically quantifying vein number and morphology in grass leaves

Beyond facilitating transport and providing mechanical support to the leaf, veins have important roles in the performance and productivity of plants and the ecosystem. In recent decades, computational image analysis has accelerated the extraction and quantification of vein traits, benefiting fields of research from agriculture to climatology. However, most of the existing leaf vein image analysis programs have been developed for the reticulate venation found in dicots. Despite the agroeconomic importance of cereal grass crops, like Oryza sativa (rice) and Zea mays (maize), a dedicated image analysis program for the parallel venation found in monocots has yet to be developed. To address the need for an image-based vein phenotyping tool for model and agronomic grass species, we developed the grass vein image quantification (grasviq) framework. Designed specifically for parallel venation, this framework automatically segments and quantifies vein patterns from images of cleared leaf pieces using classical computer vision techniques. Using image data sets from maize inbred lines and auxin biosynthesis and transport mutants in maize, we demonstrate the utility of grasviq for quantifying important vein traits, including vein density, vein width and interveinal distance. Furthermore, we show that the framework can resolve quantitative differences and identify vein patterning defects, which is advantageous for genetic experiments and mutant screens. We report that grasviq can perform high-throughput vein quantification, with precision on a par with that of manual quantification. Therefore, we envision that grasviq will be adopted for vein phenomics in maize and other grass species.

Transcriptome and metabolite analysis related to branch development in two genotypes of Eucalyptus urophylla

Branching in long-lived plants can cause scarring at the base and affect wood density, which greatly inhibits wood yield and quality. Eucalyptus urophylla is one of the most important commercial forest tree species in South China, with diverse branch number and branch angles under different genetic backgrounds. However, the main elements and regulatory mechanisms associated with different branching traits in E. urophylla remain unclear. To identify the factors that may influence branching, the transcriptome and metabolome were performed on the shoot apex (SA), lateral shoot apex (LSA), and stem segment at the 5th axillary bud from the shoot apex (S1) in lines ZQUC14 (A) and LDUD26 (B), with A exhibiting a smaller Ba than B. A total of 307.3 million high-quality clean reads and nine hormones were identified from six libraries. Several differentially expressed regulatory factors were identified between the two genotypes of E. urophylla. The Kyoto Encyclopedia of Genes and Genomes pathways were enriched in plant hormone signal transduction, plant hormone biosynthesis and their transport pathways. Furthermore, gene expression pattern analysis identified genes that were significantly downregulated or upregulated in S1 relative to the SA and LSA segments, and the plant hormone signal transduction pathway was constructed to explain branching development. This study clarified the main plant hormones and genes underlying branch numbers and angles of E. urophylla, confirmed that ABA and SA could promote a larger branch angle and smaller branch number, while IAA has an opposite function. Numbers of key candidate genes involved in plant hormone signal transduction were found in the positive regulation of branch formation. These novel findings should aid molecular breeding of branching in Eucalyptus.

The auxin herbicide mecoprop-P in new light: Filling the data gap for dicotyledonous macrophytes

Mecoprop-P (MCPP-P) is an auxin herbicide which has been used against dicotyledonous weed plants since the 1980s. While fate and monitoring data of MCPP-P in the aquatic environment revealing concentrations up to 103 μg/L in freshwaters are well documented, only very few toxicity data and no studies with dicotyledonous macrophytes have been published in open literature so far. To fill up this essential data gap, a microcosm study was conducted in order to test the sensitivity of nine dicotyledonous and one Ceratophyllales macrophyte species. The plant species were exposed to seven MCPP-P concentrations ranging from 8 to 512 μg/L for 21/22 days in one microcosm per concentration, and two further microcosms served as controls. Plant preparation was adapted to each species and endpoints were measured to calculate growth rates. Data were generated to obtain effect concentrations (EC_X) which then were used to construct species sensitivity distribution curves (SSD). Eight species proved to be sensitive to MCPP-P in the tested concentration range with EC₅₀ values ranging from 46.9 μg/L for Ranunculus aquatilis to 656.4 μg/L MCPP-P for Ludwigia repens. Taking the EC₅₀ values of this study and published data for autotrophic organisms into account, a hazard concentration (HC₅) of 2.7 μg/L was derived from the SSD curve, while an SSD curve without dicotyledonous macrophytes resulted in an about 100 times higher HC₅ (360.8 μg/L MCCP-P). This confirms that a re-evaluation for old auxin herbicides by including dicotyledonous test species into the environmental risk assessment may be indicated. Furthermore, the use of MCPP-P in bitumen felts as protection against rooting by plants is not in the focus of any risk regulation so far. This application, however, can lead to high run-off concentrations that can enter surface waters easily, exceeding the new regulatory acceptable concentration values.

Functional analysis of auxin receptor OsTIR1/OsAFB family members in rice grain yield, tillering, plant height, root system, germination, and auxinic herbicide resistance

Auxin regulates almost every aspect of plant growth and development and is perceived by the TIR1/AFB auxin co-receptor proteins differentially acting in concert with specific Aux/IAA transcriptional repressors. Little is known about the diverse functions of TIR1/AFB family members in species other than Arabidopsis. We created targeted OsTIR1 and OsAFB2-5 mutations in rice using CRISPR/Cas9 genome editing, and functionally characterized the roles of these five members in plant growth and development and auxinic herbicide resistance. Our results demonstrated that functions of OsTIR1/AFB family members are partially redundant in grain yield, tillering, plant height, root system and germination. Ostir1, Osafb2 and Osafb4 mutants exhibited more severe phenotypes than Osafb3 and Osafb5. The Ostir1Osafb2 double mutant displays extremely severe defects in plant development. All five OsTIR1/AFB members interacted with OsIAA1 and OsIAA11 proteins in vivo. Root elongation assay showed that each Ostir1/afb2-5 mutant was resistant to 2,4-dichlorophenoxyacetic acid (2,4-D) treatment. Notably, only the Osafb4 mutants were strongly resistant to the herbicide picloram, suggesting that OsAFB4 is a unique auxin receptor in rice. Our findings demonstrate similarities and specificities of auxin receptor TIR1/AFB proteins in rice, and could offer the opportunity to modify effective herbicide-resistant alleles in agronomically important crops.

Regulation of Sixth Seminal Root Formation by Jasmonate in Triticum aestivum L

A well-developed root system is an important characteristic of crop plants, which largely determines their productivity, especially under conditions of water and nutrients deficiency. Being Poaceous, wheat has more than one seminal root. The number of grown seminal roots varies in different wheat accessions and is regulated by environmental factors. Currently, the molecular mechanisms determining the number of germinated seminal roots remain poorly understood. The analysis of the root system development in germinating seeds of genetically modified hexaploid wheat plants with altered activity of jasmonate biosynthesis pathway and seeds exogenously treated with methyl jasmonate revealed the role of jasmonates in the regulation of sixth seminal root development. This regulatory effect strongly depends on the jasmonate concentration and the duration of the exposure to this hormone. The maximum stimulatory effect of exogenously applied methyl jasmonate on the formation of the sixth seminal root was achieved at 200 μM concentration after 48 h of treatment. Further increase in concentration and exposure time does not increase the stimulating effect. While 95% of non-transgenic plants under non-stress conditions possess five or fewer seminal roots, the number of plants with developed sixth seminal root reaches up to 100% when selected transgenic lines are treated with methyl jasmonate.

Genetic dissection of the auxin response network

The expansion of gene families during evolution, which can generate functional overlap or specialization among their members, is a characteristic feature of signalling pathways in complex organisms. For example, families of transcriptional activators and repressors mediate responses to the plant hormone auxin. Although these regulators were identified more than 20 years ago, their overlapping functions and compensating negative feedbacks have hampered their functional analyses. Studies using loss-of-function approaches in basal land plants and gain-of-function approaches in angiosperms have in part overcome these issues but have still left an incomplete understanding. Here, we propose that renewed emphasis on genetic analysis of multiple mutants and species will shed light on the role of gene families in auxin response. Combining loss-of-function mutations in auxin-response activators and repressors can unravel complex outputs enabled by expanded gene families, such as fine-tuned developmental outcomes and robustness. Similar approaches and concepts may help to analyse other regulatory pathways whose components are also encoded by large gene families.

PINOID regulates floral organ development by modulating auxin transport and interacts with MADS16 in rice

In rice (Oryza sativa L.), floral organ development is an important trait. Although a role for PINOID in regulating floral organ development was reported recently, the underlying molecular mechanism remains unclear. Here, we isolated and characterized an abnormal floral organ mutant and mapped the causative gene through an improved MutMap method. Molecular study revealed that the observed phenotype is caused by a point mutation in OsPINOID (OsPID) gene; therefore, we named the mutation as ospid-4. Our data demonstrate that OsPID interacts with OsPIN1a and OsPIN1b to regulate polar auxin transport as shown previously. Additionally, OsPID also interacts with OsMADS16 to regulate transcription during floral organ development in rice. Together, we propose a model that OsPID regulates floral organ development by modulating auxin polar transport and interaction with OsMADS16 and/or LAX1 in rice. These results provide a novel insight into the role of OsPID in regulating floral organ development of rice, especially in stigma development, which would be useful for genetic improvement of high-yield breeding of rice.

A Synthetic Approach Allows Rapid Characterization of the Maize Nuclear Auxin Response Circuit

Auxin plays a key role across all land plants in growth and developmental processes. Although auxin signaling function has diverged and expanded, differences in the molecular functions of signaling components have largely been characterized in Arabidopsis (Arabidopsis thaliana). Here, we used the nuclear Auxin Response Circuit recapitulated in yeast (Saccharomyces cerevisiae) system to functionally annotate maize (Zea mays) auxin signaling components, focusing on genes expressed during the development of ear and tassel inflorescences. All 16 maize auxin/indole-3-acetic acid repressor proteins were degraded in response to auxin with rates that depended on both receptor and repressor identities. When fused to the maize TOPLESS homolog RAMOSA1 ENHANCER LOCUS2, maize auxin/indole-3-acetic acids were able to repress AUXIN RESPONSE FACTOR transcriptional activity. A complete auxin response circuit comprising all maize components, including the ZmAFB2/3 b1 maize AUXIN SIGNALING F-BOX (AFB) receptor, was fully functional. The ZmAFB2/3 b1 auxin receptor was more sensitive to hormone than AtAFB2 and allowed for rapid circuit activation upon auxin addition. These results validate the conserved role of predicted auxin response genes in maize as well as provide evidence that a synthetic approach can facilitate broader comparative studies across the wide range of species with sequenced genomes.

Arabidopsis PIC30 encodes a major facilitator superfamily transporter responsible for the uptake of picolinate herbicides

Picloram is an auxinic herbicide that is widely used for controlling broad leaf weeds. However, its mechanism of transport into plants is poorly understood. In a genetic screen for picloram resistance, we identified three Arabidopsis mutant alleles of PIC30 (PICLORAM RESISTANT30) that are specifically resistant to picolinates, but not to other auxins. PIC30 is a previously uncharacterized gene that encodes a major facilitator superfamily (MFS) transporter. Similar to most members of MFS, PIC30 contains 12 putative transmembrane domains, and PIC30-GFP fusion protein selectively localizes to the plasma membrane. In planta transport assays demonstrate that PIC30 specifically transports picloram, but not indole-3-acetic acid (IAA). Functional analysis of Xenopus laevis oocytes injected with PIC30 cRNA demonstrated PIC30 mediated transport of picloram and several anions, including nitrate and chloride. Consistent with these roles of PIC30, three allelic pic30 mutants are selectively insensitive to picolinate herbicides, while pic30-3 is also defective in chlorate (analogue of nitrate) transport and also shows reduced uptake of 15NO3- . Overexpression of PIC30 fully complements both picloram and chlorate insensitive phenotypes of pic30-3. Despite the continued use of picloram as an herbicide, a transporter for picloram was not known until now. This work provides insight into the mechanisms of plant resistance to picolinate herbicides and also shed light on the possible endogenous function of PIC30 protein.

The Effect of Auxin and Auxin-Producing Bacteria on the Growth, Essential Oil Yield, and Composition in Medicinal and Aromatic Plants

Aromatic plants had been used since ancient times for their preservative and medicinal properties, and to impart aroma and flavor to food. Also their secondary metabolites are economically important as drugs, flavor and fragrances, pharmaceuticals, agrochemicals, dye, and pigments, pesticides, cosmetics, food additives, other industrially biochemical, and also play a major role in the adaptation of plants to their environment. Indole acetıc acid-producing rhizobacteria inoculations increase in stomatal density and level of secondary metabolite and have a synergistic effect on monoterpene biosynthesis. Bacterial inoculation significantly affected and increased the chemical composition of essential oil, citronellol, and geraniol content in rose-scented geranium; essential oil composition and total phenolic content in marigold; density, number, and size of glandular trichomes in sweet wormwood and peppermint essential oil components such as geranyl acetate, limonene, and β-pinene in coriander; oil yield and content in calendula; yield of the herb in hyssop; oxygenated compounds, essential oil content and yield, anethol and changing the chemical composition in fennel; growth, number of glandular trichomes and essential oil yield, root branching and length, and total amount of essential oil, production of monoterpenes such as pulegone, menthol, menthone, menthofuran, and terpineol content, biosynthesis of secondary metabolites in peppermint; growth and essential oil yield in marjoram; glandular hair abundance, essential oil yield, and monoterpene biosynthesis in basil; phellandrene, limonene, borneol, and campor in rosemary; carvacrol, thymol, linalool, and borneol in oregano; and α-thujene, α-pinene, α-terpinene, p-simen, β-pinene, and γ-terpinene contents and essential oil yield in summer savory. Inoculation with IAA-producing bacteria medicinal roots increased the valerenic acid in valerian, essential oil and quality in vetiver, curcumin content in turmeric alkaloid and ginsenoside content in ginseng, and inulin content in Jerusalem artichoke.

In-Situ Metabolomic Analysis of Setaria viridis Roots Colonized by Beneficial Endophytic Bacteria

Over the past decades, crop yields have risen in parallel with increasing use of fossil fuel-derived nitrogen (N) fertilizers but with concomitant negative impacts on climate and water resources. There is a need for more sustainable agricultural practices, and biological nitrogen fixation (BNF) could be part of the solution. A variety of nitrogen-fixing, epiphytic, and endophytic plant growth-promoting bacteria (PGPB) are known to stimulate plant growth. However, compared with the rhizobium-legume symbiosis, little mechanistic information is available as to how PGPB affect plant metabolism. Therefore, we investigated the metabolic changes in roots of the model grass species Setaria viridis upon endophytic colonization by Herbaspirillum seropedicae SmR1 (fix⁺) or a fix^- mutant strain (SmR54) compared with uninoculated roots. Endophytic colonization of the root is highly localized and, hence, analysis of whole-root segments dilutes the metabolic signature of those few cells impacted by the bacteria. Therefore, we utilized in-situ laser ablation electrospray ionization mass spectrometry to sample only those root segments at or adjacent to the sites of bacterial colonization. Metabolites involved in purine, zeatin, and riboflavin pathways were significantly more abundant in inoculated plants, while metabolites indicative of nitrogen, starch, and sucrose metabolism were reduced in roots inoculated with the fix^- strain or uninoculated, presumably due to N limitation. Interestingly, compounds, involved in indole-alkaloid biosynthesis were more abundant in the roots colonized by the fix^- strain, perhaps reflecting a plant defense response.

Screening and Assessment of Potential Plant Growth-promoting Bacteria Associated with Allium cepa Linn

Plant growth-promoting bacteria (PGPB) are beneficial microbes that increase plant growth and yield. However, limited information is currently available on PGPB in onion (Allium cepa Linn.). The aims of the present study were to isolate and identify PGPB in onion and examine the effects of isolated PGPB on germination and growth during the vegetative stage in onion, pak choy (Brassica chinensis), and sweet pepper (Capsicum annuum). Twenty-three strains of PGPB were isolated from the roots, bulbs, and rhizosphere soil of onion. All isolated bacterial strains showed one or more PGP traits, including indole acetic acid production, phosphate solubilization ability, and 1-aminocyclopropane-1-carboxylate deaminase and nitrogenase activities; most of these traits were derived from Bacillus sp., Microbacterium sp., and Pseudomonas sp. Eight bacteria that exhibited strong abilities to produce indole acetic acid were selected for a Petri dish trial, soil pot test, and vermiculate pot test. The Petri dish trial showed that strains ORE8 and ORTB2 simultaneously increased radicle and hypocotyl lengths in onion, but inhibited growth in sweet pepper after 7 d. The soil pot experiment on onion revealed that strains ORE5, ORE8, and ORTB2 strongly promoted growth during the vegetative stage with only a half dose of chemical fertilizer. The present results indicate that ORE8 (Bacillus megaterium) and ORTB2 (Pantoea sp.) are the most promising biofertilizers of onion and may simultaneously inhibit the seedling growth of other plants.

Functional Divergence of PIN1 Paralogous Genes in Rice

Auxin is a phytohormone that plays an important role in plant growth and development by forming local concentration gradients. The regulation of auxin levels is determined by the activity of auxin efflux carrier protein PIN-formed (PIN). In Arabidopsis thaliana, PIN-formed1 (PIN1) functions in inflorescence and root development. In rice (Oryza sativa L.), there are four PIN1 homologs (OsPIN1a-1d), but their functions remain largely unexplored. Hence, in this study, we created mutant alleles of PIN1 gene-pin1a, pin1b, pin1c, pin1d, pin1a pin1b and pin1c pin1d- using CRISPR/Cas9 technology and used them to study the functions of the four OsPIN1 paralogs in rice. In wild-type rice, all four OsPIN1 genes were relatively highly expressed in the root than in other tissues. Compared with the wild type, the OsPIN1 single mutants had no dramatic phenotypes, but the pin1a pin1b double mutant had shorter shoots and primary roots, fewer crown roots, reduced root gravitropism, longer root hairs and larger panicle branch angle. Furthermore, the pin1c pin1d double mutant showed no observable phenotype at the seedling stage, but showed naked, pin-shape inflorescence at flowering. These data suggest that OsPIN1a and OsPIN1b are involved in root, shoot and inflorescence development in rice, whereas OsPIN1c and OsPIN1d mainly function in panicle formation. Our study provides basic knowledge that will facilitate the study of auxin transport and signaling in rice.

Stress-Induced Microspore Embryogenesis Requires Endogenous Auxin Synthesis and Polar Transport in Barley

Stress-induced microspore embryogenesis is a model in vitro system of cell reprogramming, totipotency acquisition, and embryo development. After induction, responsive microspores abandon their developmental program to follow an embryogenic pathway, leading to in vitro embryo formation. This process is widely used to produce doubled-haploid lines, essential players to create new materials in modern breeding programs, particularly in cereals, although its efficiency is still low in many crop species, because the regulating mechanisms are still elusive. Stress signaling and endogenous hormones, mainly auxin, have been proposed as determinant factors of microspore embryogenesis induction in some eudicot species; however, much less information is available in monocot plants. In this study, we have analyzed the dynamics and possible role of endogenous auxin during stress-induced microspore embryogenesis in the monocot Hordeum vulgare, barley. The results showed auxin accumulation in early proembryo cells, from embryogenesis initiation and a further increase with embryo development and differentiation, correlating with the induction and expression pattern of the auxin biosynthesis gene HvTAR2-like. Pharmacological treatments with kynurenine, inhibitor of auxin biosynthesis, and α-(p-chlorophenoxy)-isobutyric acid (PCIB), auxin antagonist, impaired embryogenesis initiation and development, indicating that de novo auxin synthesis and its activity were required for the process. Efflux carrier gene HvPIN1-like was also induced with embryogenesis initiation and progression; auxin transport inhibition by N-1-naphthylphthalamic acid significantly reduced embryo development at early and advanced stages. The results indicate activation of auxin biosynthesis with microspore embryogenesis initiation and progression, in parallel with the activation of polar auxin transport, and reveal a central role of auxin in the process in a monocot species. The findings give new insights into the complex regulation of stress-induced microspore embryogenesis, particularly in monocot plants for which information is still scarce, and suggest that manipulation of endogenous auxin content could be a target to improve in vitro embryo production.

Plant circadian rhythms regulate the effectiveness of a glyphosate-based herbicide

Herbicides increase crop yields by allowing weed control and harvest management. Glyphosate is the most widely-used herbicide active ingredient, with $11 billion spent annually on glyphosate-containing products applied to >350 million hectares worldwide, using about 8.6 billion kg of glyphosate. The herbicidal effectiveness of glyphosate can depend upon the time of day of spraying. Here, we show that the plant circadian clock regulates the effectiveness of glyphosate. We identify a daily and circadian rhythm in the inhibition of plant development by glyphosate, due to interaction between glyphosate activity, the circadian oscillator and potentially auxin signalling. We identify that the circadian clock controls the timing and extent of glyphosate-induced plant cell death. Furthermore, the clock controls a rhythm in the minimum effective dose of glyphosate. We propose the concept of agricultural chronotherapy, similar in principle to chronotherapy in medical practice. Our findings provide a platform to refine agrochemical use and development, conferring future economic and environmental benefits.

Establishing a role for environmental toxicant exposure induced epigenetic remodeling in malignant transformation

Humans are exposed to a wide variety of environmental exposures throughout their lifespan. These include both naturally occurring toxins and chemical toxicants like pesticides, herbicides, and industrial chemicals, many of which have been implicated as possible contributors to human disease susceptibility [1-3]. We, and others, have hypothesized that environmental exposures may cause adaptive epigenetic changes in regenerative cell populations and developing organisms, leading to abnormal gene expression and increased disease susceptibility later in life [3]. Common epigenetic changes include changes in miRNA expression, covalent histone modifications, and methylation of DNA. Importantly, due to their heritable nature, abnormal epigenetic modifications which occur within stem cells may be particularly deleterious. Abnormal epigenetic changes in regenerative cell linages can be passed onto a large population of daughter cells and can persist for long periods of time. It is well established that an accumulation of epigenetic changes can lead to many human diseases including cancer [4-6]. Subsequently, it is imperative that we increase our understanding of how common environmental toxins and toxicants can induce epigenetic changes, particularly in stem cell populations. In this review, we will discuss how common environmental exposures in the United States and around the world may lead to epigenetic changes and discuss potential links to human disease, including cancer.

Modulation of defence and iron homeostasis genes in rice roots by the diazotrophic endophyte Herbaspirillum seropedicae

Rice is staple food of nearly half the world’s population. Rice yields must therefore increase to feed ever larger populations. By colonising rice and other plants, Herbaspirillum spp. stimulate plant growth and productivity. However the molecular factors involved are largely unknown. To further explore this interaction, the transcription profiles of Nipponbare rice roots inoculated with Herbaspirillum seropedicae were determined by RNA-seq. Mapping the 104 million reads against the Oryza sativa cv. Nipponbare genome produced 65 million unique mapped reads that represented 13,840 transcripts each with at least two-times coverage. About 7.4% (1,014) genes were differentially regulated and of these 255 changed expression levels more than two times. Several of the repressed genes encoded proteins related to plant defence (e.g. a putative probenazole inducible protein), plant disease resistance as well as enzymes involved in flavonoid and isoprenoid synthesis. Genes related to the synthesis and efflux of phytosiderophores (PS) and transport of PS-iron complexes were induced by the bacteria. These data suggest that the bacterium represses the rice defence system while concomitantly activating iron uptake. Transcripts of H. seropedicae were also detected amongst which transcripts of genes involved in nitrogen fixation, cell motility and cell wall synthesis were the most expressed.

The plant growth-promoting potential of the mesophilic wood-rot mushroom Pleurotus pulmonarius

AIMS

To demonstrate the plant growth-promoting potential of a wood-decay mushroom.

METHODS AND RESULTS

A wild strain of a white rot fungus (Pleurotus pulmonarius) was found to convert 10 mmol l^-1 L-tryptophan (TRP) to approximately 15 μg ml^-1 indole-3-acetic acid (IAA) under the optimal growth conditions of 30°C and pH 5 for 15 days. Results of gas chromatography-mass spectrometry indicated IAA synthesis through the indole-3-pyruvic acid pathway when using cellulose as a sole carbon source. The mycelium as well as the culture filtrate promoted the growth and chlorophyll content of seedlings. In a monocotyledonous plant (rice), the number of lateral roots was increased experimentally, whereas in a dicotyledonous plant (tomato), the fungus led to an increased length of shoots and roots.

CONCLUSIONS

TRP-dependent IAA production was demonstrated for the first time for P. pulmonarius and may be responsible for enhancing plant growth in vitro.

SIGNIFICANCE AND IMPACT OF THE STUDY

Synthesis of IAA as the most prevalent phytohormone in plants has been demonstrated for soil microfungi. Pleurotus pulmonarius is reported as an IAA-producing wood-decay macrofungus. The higher temperature optimum of P. pulmonarius isolated from subtropical environment compared to other Pleurotus species from temperate regions makes it more suitable for application in subtropical/tropical regions.

Different knockout genotypes of OsIAA23 in rice using CRISPR/Cas9 generating different phenotypes

We have isolated several Osiaa23 rice mutants with different knockout genotypes, resulting in different phenotypes, which suggested that different genetic backgrounds or mutation types influence gene function. The Auxin/Indole-3-Acetic Acid (Aux/IAA) gene family performs critical roles in auxin signal transduction in plants. In rice, the gene OsIAA23 (Os06t0597000) is known to affect development of roots and shoots, but previous knockouts in OsIAA23 have been sterile and difficult for research continuously. Here, we isolate new Osiaa23 mutants using the CRISPR/Cas9 system in japonica (Wuyunjing24) and indica (Kasalath) rice, with extensive genome re-sequencing to confirm the absence of off-target effects. In Kasalath, mutants with a 13-amino acid deletion showed profoundly greater dwarfing, lateral root developmental disorder, and fertility deficiency, relative to mutants with a single amino acid deletion, demonstrating that those 13 amino acids in Kasalath are essential to gene function. In Wuyunjing24, we predicted that mutants with a single base-pair frameshift insertion would experience premature termination and strong phenotypic defects, but instead these lines exhibited negligible phenotypic difference and normal fertility. Through RNA-seq, we show here that new mosaic transcripts of OsIAA23 were produced de novo, which circumvented the premature termination and thereby preserved the wild-type phenotype. This finding is a notable demonstration in plants that mutants can mask loss of function CRISPR/Cas9 editing of the target gene through de novo changes in alternative splicing.

Auxin and GA signaling play important roles in the maize response to phosphate deficiency

Phytohormone signaling is involved in the low-phosphate (LP) response and causes root system changes. To understand the roles of auxin and gibberellic acid (GA) in the maize response to LP stress, inbred line Q319 was used to identify the changes in root morphology and the gene expression response to LP stress with or without exogenous auxin, GA or their inhibitors. The root morphology, IAA and GAs concentration and genes related to the LP response, cell elongation and division, auxin transport and signaling, and GA synthesis and signaling were analyzed. The LP-induced maize root morphological adaption was dependent on changes in the expression of related genes, like IPS1, pht1;1 LPR1b, KRPs, and EXPB1-4. The altered local auxin concentration and signaling were involved in promoting axial root elongation and reducing lateral root density and length under LP conditions, which were regulated by PID and PP2A activity and the auxin signaling pathway. The upregulation of the GA synthesis genes AN1, GA20ox1, and GA20ox2 and the downregulation of the GA inactive genes GA2ox1 and GA2ox2 were observed in maize roots subjected to LP stress, and the increased GA biosynthesis and signaling were involved in root growth. Both hormones participate in LP stress response and jointly regulated root modification and LP acclimation in maize.

Selenate Reduction and Selenium Enrichment of Tea by the Endophytic Herbaspirillum sp. Strain WT00C

Herbaspirillum sp. WT00C is a tea-plant-specific endophytic bacterium. A genomic survey revealed an intact pathway for selenocompound metabolism in the genome of this bacterium. When it was cultured with sodium selenate, Herbaspirillum sp. WT00C was able to turn the culture medium to red. Electron microscopy and energy-dispersive X-ray spectroscopy confirmed that Herbaspirillum sp. WT00C reduced selenite (Se⁶⁺) to elemental selenium (Se⁰), and selenium nanoparticles (SeNPs) were secreted outside bacterial cells and grew increasingly larger to form Se-nanospheres and finally crystallized to form selenoflowers. Biochemical assays showed that selenospheres contained proteins but not carbohydrates or lipids. The improvement of selenium enrichment of tea plants by Herbaspirillum sp. WT00C was also tested. After Herbaspirillum sp. WT00C was inoculated into tea seedlings via needle injection and soaking tea-cutting methods, this endophytic bacterium markedly enhanced selenium enrichment of tea. When the tea seedlings inoculated by soaking tea-cutting mode were cultivated in the selenium-containing soils, selenium contents of tea leaves in three experimental groups were more than twofold compared to those of control groups. Our study demonstrates that the endophytic bacterium Herbaspirillum sp. WT00C has the ability to reduce selenate and improve selenium enrichment of tea.

Evolution of Deeper Rooting 1-like homoeologs in wheat entails the C-terminus mutations as well as gain and loss of auxin response elements

Root growth angle (RGA) in response to gravity controlled by auxin is a pertinent target trait for obtainment of higher yield in cereals. But molecular basis of this root architecture trait remain obscure in wheat and barley. We selected four cultivars two each for wheat and barley to unveil the molecular genetic mechanism of Deeper Rooting 1-like gene which controls RGA in rice leading to higher yield under drought imposition. Morphological analyses revealed a deeper and vertically oriented root growth in “NARC 2009” variety of wheat than “Galaxy” and two other barley cultivars “Scarlet” and “ISR42-8”. Three new homoeologs designated as TaANDRO1-like, TaBNDRO1-like and TaDNDRO1-like corresponding to A, B and D genomes of wheat could be isolated from “NARC 2009”. Due to frameshift and intronization/exonization events the gene structures of these paralogs exhibit variations in size. DRO1-like genes with five distinct domains prevail in diverse plant phyla from mosses to angiosperms but in lower plants their differentiation from LAZY, NGR and TAC1 (root and shoot angle genes) is enigmatic. Instead of IGT as denominator motif of this family, a new C-terminus motif WxxTD in the V-domain is proposed as family specific motif. The EAR-like motif IVLEM at the C-terminus of the TaADRO1-like and TaDDRO1-like that diverged to KLHTLIPNK in TaBDRO1-like and HvDRO1-like is the hallmark of these proteins. Split-YFP and yeast two hybrid assays complemented the interaction of TaDRO1-like with TOPLESS—a repressor of auxin regulated root promoting genes in plants—through IVLEM/KLHTLIPNK motif. Quantitative RT-PCR revealed abundance of DRO1-like RNA in root tips and spikelets while transcript signals were barely detectable in shoot and leaf tissues. Interestingly, wheat exhibited stronger expression of TaBDRO1-like than barley (HvDRO1-like), but TaBDRO1-like was the least expressing among three paralogs. The underlying cause of this expression divergence seems to be the presence of AuxRE motif TGTCTC and core TGTC with a coupling AuxRE-like motif ATTTTCTT proximal to the transcriptional start site in TaBDRO1-like and HvDRO1-like promoters. This is evident from binding of ARF1 to TGTCTC and TGTC motifs of TaBDRO1-like as revealed by yeast one-hybrid assay. Thus, evolution of DRO1-like wheat homoeologs might incorporate the C-terminus mutations as well as gain and loss of AuxREs and other cis-regulatory elements during expression divergence. Since root architecture is an important target trait for wheat crop improvement, therefore DRO1-like genes have potential applications in plant breeding for enhancement of plant productivity by the use of modern genome editing approaches.