Polar Auxin Transport Determines Adventitious Root Emergence and Growth in Rice

Diverse geotropic responses in the orchid family

In epiphytes, aerial roots are important to combat water-deficient, nutrient-poor, and high-irradiance microhabitats. However, whether aerial roots can respond to gravity and whether auxin plays a role in regulating aerial root development remain open-ended questions. Here, we investigated the gravitropic response of the epiphytic orchid Phalaenopsis aphrodite. Our data showed that aerial roots of P. aphrodite failed to respond to gravity, and this was correlated with a lack of starch granules/statolith sedimentation in the roots and the absence of the auxin efflux carrier PIN2 gene. Using an established auxin reporter, we discovered that auxin maximum was absent in the quiescent center of aerial roots of P. aphrodite. Also, gravity failed to trigger auxin redistribution in the root caps. Hence, loss of gravity sensing and gravity-dependent auxin redistribution may be the genetic factors contributing to aerial root development. Moreover, the architectural and functional innovations that achieve fast gravitropism in the flowering plants appear to be lost in both terrestrial and epiphytic orchids, but are present in the early diverged orchid subfamilies. Taken together, our findings provide physiological and molecular evidence to support the notion that epiphytic orchids lack gravitropism and suggest diverse geotropic responses in the orchid family.

An atlas of Brachypodium distachyon lateral root development

The root system of plants is a vital part for successful development and adaptation to different soil types and environments. A major determinant of the shape of a plant root system is the formation of lateral roots, allowing for expansion of the root system. Arabidopsis thaliana, with its simple root anatomy, has been extensively studied to reveal the genetic program underlying root branching. However, to get a more general understanding of lateral root development, comparative studies in species with a more complex root anatomy are required. Here, by combining optimized clearing methods and histology, we describe an atlas of lateral root development in Brachypodium distachyon, a wild, temperate grass species. We show that lateral roots initiate from enlarged phloem pole pericycle cells and that the overlying endodermis reactivates its cell cycle and eventually forms the root cap. In addition, auxin signaling reported by the DR5 reporter was not detected in the phloem pole pericycle cells or young primordia. In contrast, auxin signaling was activated in the overlying cortical cell layers, including the exodermis. Thus, Brachypodium is a valuable model to investigate how signaling pathways and cellular responses have been repurposed to facilitate lateral root organogenesis.

Anatomical limitations in adventitious root formation revealed by magnetic resonance imaging, infrared spectroscopy, and histology of rose genotypes with contrasting rooting phenotypes

Adventitious root (AR) formation is one of the most important developmental processes in vegetative propagation. Although genotypic differences in rose rooting ability are well known, the causal factors are not well understood. The rooting of two contrasting genotypes, 'Herzogin Friederike' and 'Mariatheresia', was compared following a multiscale approach. Using magnetic resonance imaging, we non-invasively monitored the inner structure of stem cuttings during initiation and progression of AR formation for the first time. Spatially resolved Fourier-transform infrared spectroscopy characterized the chemical composition of the tissues involved in AR formation. The results were validated through light microscopy and complemented by immunolabelling. The outcome demonstrated similarity of both genotypes in root primordia formation, which did not result in root protrusion through the shoot cortex in the difficult-to-root genotype 'Mariatheresia'. The biochemical composition of the contrasting genotypes highlighted main differences in cell wall-associated components. Further spectroscopic analysis of 15 contrasting rose genotypes confirmed the biochemical differences between easy- and difficult-to-root groups. Collectively, our data indicate that it is not the lack of root primordia limiting AR formation in these rose genotypes, but the firmness of the outer stem tissue and/or cell wall modifications that pose a mechanical barrier and prevent root extension and protrusion.

The OsEIL1-OsWOX11 transcription factor module controls rice crown root development in response to soil compaction

Optimizing the root architecture of crops is an effective strategy for improving crop yields. Soil compaction is a serious global problem that limits crop productivity by restricting root growth, but the underlying molecular mechanisms are largely unclear. Here, we show that ethylene stimulates rice (Oryza sativa) crown root development in response to soil compaction. First, we demonstrate that compacted soil promotes ethylene production and the accumulation of ETHYLENE INSENSITIVE 3-LIKE 1 (OsEIL1) in rice roots, stimulating crown root primordia initiation and development, thereby increasing crown root number in lower stem nodes. Through transcriptome profiling and molecular analyses, we reveal that OsEIL1 directly activates the expression of WUSCHEL-RELATED HOMEOBOX 11 (OsWOX11), an activator of crown root emergence and growth, and that OsWOX11 mutations delay crown root development, thus impairing the plant's response to ethylene and soil compaction. Genetic analysis demonstrates that OsWOX11 functions downstream of OsEIL1. In summary, our results demonstrate that the OsEIL1-OsWOX11 module regulates ethylene action during crown root development in response to soil compaction, providing a strategy for the genetic modification of crop root architecture and grain agronomic traits.

RNA-seq-based comparative transcriptome analysis reveals the role of CsPrx73 in waterlogging-triggered adventitious root formation in cucumber

Abiotic stressors like waterlogging are detrimental to cucumber development and growth. However, comprehension of the highly complex molecular mechanism underlying waterlogging can provide an opportunity to enhance cucumber tolerance under waterlogging stress. We examined the hypocotyl and stage-specific transcriptomes of the waterlogging-tolerant YZ026A and the waterlogging-sensitive YZ106A, which had different adventitious rooting ability under waterlogging. YZ026A performed better under waterlogging stress by altering its antioxidative machinery and demonstrated a greater superoxide ion (O 2-) scavenging ability. KEGG pathway enrichment analysis showed that a high number of differentially expressed genes (DEGs) were enriched in phenylpropanoid biosynthesis. By pairwise comparison and weighted gene co-expression network analysis analysis, 2616 DEGs were obtained which were categorized into 11 gene co-expression modules. Amongst the 11 modules, black was identified as the common module and yielded a novel key regulatory gene, CsPrx73. Transgenic cucumber plants overexpressing CsPrx73 enhance adventitious root (AR) formation under waterlogging conditions and increase reactive oxygen species (ROS) scavenging. Silencing of CsPrx73 expression by virus-induced gene silencing adversely affects AR formation under the waterlogging condition. Our results also indicated that CsERF7-3, a waterlogging-responsive ERF transcription factor, can directly bind to the ATCTA-box motif in the CsPrx73 promoter to initiate its expression. Overexpression of CsERF7-3 enhanced CsPrx73 expression and AR formation. On the contrary, CsERF7-3-silenced plants decreased CsPrx73 expression and rooting ability. In conclusion , our study demonstrates a novel CsERF7-3-CsPrx73 module that allows cucumbers to adapt more efficiently to waterlogging stress by promoting AR production and ROS scavenging.

Ethylene Modulates Rice Root Plasticity under Abiotic Stresses

Plants live in constantly changing environments that are often unfavorable or stressful. Root development strongly affects plant growth and productivity, and the developmental plasticity of roots helps plants to survive under abiotic stress conditions. This review summarizes the progress being made in understanding the regulation of the phtyohormone ethylene in rice root development in response to abiotic stresses, highlighting the complexity associated with the integration of ethylene synthesis and signaling in root development under adverse environments. Understanding the molecular mechanisms of ethylene in regulating root architecture and response to environmental signals can contribute to the genetic improvement of crop root systems, enhancing their adaptation to stressful environmental conditions.

Novel Insights into Exogenous Phytohormones: Central Regulators in the Modulation of Physiological, Biochemical, and Molecular Responses in Rice under Metal(loid) Stress

Rice (Oryza sativa) is a research model for monocotyledonous plants. Rice is also one of the major staple foods and the primary crop for more than half of the world's population. Increasing industrial activities and the use of different fertilizers and pesticides containing heavy metals (HMs) contribute to the contamination of agriculture fields. HM contamination is among the leading causes that affect the health of rice plants by limiting their growth and causing plant death. Phytohormones have a crucial role in stress-coping mechanisms and in determining a range of plant development and growth aspects during heavy metal stress. This review summarizes the role of different exogenous applications of phytohormones including auxin, cytokinin, gibberellins, ethylene, abscisic acid, strigolactones, jasmonates, brassinosteroids, and salicylic acids in rice plants for mitigating heavy metal stress via manipulation of their stress-related physiological and biochemical processes, and alterations of signaling and biosynthesis of genes. Exogenous administration of phytohormones and regulation of endogenous levels by targeting their biosynthesis/signaling machineries is a potential strategy for protecting rice from HM stress. The current review primarily emphasizes the key mechanistic phytohormonal-mediated strategies for reducing the adverse effects of HM toxicity in rice. Herein, we have provided comprehensive evidence for the effective role of exogenous phytohormones in employing defense responses and tolerance in rice to the phytotoxic effects of HM toxicity along with endogenous hormonal crosstalk for modulation of subcellular mechanisms and modification of stress-related signaling pathways, and uptake and translocation of metals. Altogether, this information offers a systematic understanding of how phytohormones modulate a plant's tolerance to heavy metals and may assist in directing the development of new approaches to strengthen rice plant resistance to HM toxicity.

Arabidopsis root apical meristem survival during waterlogging is determined by phytoglobin through nitric oxide and auxin

MAIN CONCLUSION

Over-expression of phytoglobin mitigates the degradation of the root apical meristem (RAM) caused by waterlogging through changes in nitric oxide and auxin distribution at the root tip. Plant performance to waterlogging is ameliorated by the over-expression of the Arabidopsis Phytoglobin 1 (Pgb1) which also contributes to the maintenance of a functional RAM. Hypoxia induces accumulation of ROS and damage in roots of wild type plants; these events were preceded by the exhaustion of the RAM resulting from the loss of functionality of the WOX5-expressing quiescent cells (QCs). These phenotypic deviations were exacerbated by suppression of Pgb1 and attenuated when the same gene was up-regulated. Genetic and pharmacological studies demonstrated that degradation of the RAM in hypoxic roots is attributed to a reduction in the auxin maximum at the root tip, necessary for the specification of the QC. This reduction was primarily caused by alterations in PIN-mediated auxin flow but not auxin synthesis. The expression and localization patterns of several PINs, including PIN1, 2, 3 and 4, facilitating the basipetal translocation of auxin and its distribution at the root tip, were altered in hypoxic WT and Pgb1-suppressing roots but mostly unchanged in those over-expressing Pgb1. Disruption of PIN1 and PIN2 signal in hypoxic roots suppressing Pgb1 initiated in the transition zone at 12 h and was specifically associated to the absence of Pgb1 protein in the same region. Exogenous auxin restored a functional RAM, while inhibition of the directional auxin flow exacerbated the degradation of the RAM. The regulation of root behavior by Pgb1 was mediated by nitric oxide (NO) in a model consistent with the recognized function of Pgbs as NO scavengers. Collectively, this study contributes to our understanding of the role of Pgbs in preserving root meristem function and QC niche during conditions of stress, and suggests that the root transition zone is most vulnerable to hypoxia.

Genetic analysis of the rice jasmonate receptors reveals specialized functions for OsCOI2

COI1-mediated perception of jasmonate is critical for plant development and responses to environmental stresses. Monocots such as rice have two groups of COI genes due to gene duplication: OsCOI1a and OsCOI1b that are functionally equivalent to the dicotyledons COI1 and OsCOI2 whose function remains unclear. In order to assess the function of OsCOI2 and its functional redundancy with COI1 genes, we developed a series of rice mutants in the 3 genes OsCOI1a, OsCOI1b and OsCOI2 by CRISPR Cas9-mediated editing and characterized their phenotype and responses to jasmonate. Characterization of OsCOI2 uncovered its important roles in root, leaf and flower development. In particular, we show that crown root growth inhibition by jasmonate relies on OsCOI2 and not on OsCOI1a nor on OsCOI1b, revealing a major function for the non-canonical OsCOI2 in jasmonate-dependent control of rice root growth. Collectively, these results point to a specialized function of OsCOI2 in the regulation of plant development in rice and indicate that sub-functionalisation of jasmonate receptors has occurred in the monocot phylum.

Transcriptome analysis reveals that auxin promotes strigolactone-induced adventitious root growth in the hypocotyl of melon seedlings

Introduction

Strigolactone (SL) and auxin are two important phytohormones involved in plant root development, but whether they show synergistic or mutual promotion effects during adventitious root (AR) formation has not been adequately explored.

Methods

In this study, we investigated the mechanisms of GR24 (synthetic SL) and indole-3-acetic acid (IAA; a type of auxin) in the formation of ARs using melon as the study material.

Results

Morphological measurements showed that the AR number, length, superficial area, and volume under the GR24 treatment were 1.60-3.27, 1.58-3.99, 2.06-3.42, and 3.00-6.11 times greater than those of the control group, respectively, at 6-10 days; the GR24+IAA treatment further promoted AR formation in melon seedlings, and the AR number, length, superficial area, and volume under the GR24+IAA treatment were 1.44-1.51, 1.28-1.73, 1.19-1.83, and 1.31-1.87 times greater than those obtained with the GR24 treatment, respectively. Transcriptome analysis revealed 2,742, 3,352, and 2,321 differentially expressed genes (DEGs) identified from the GR24 vs. control, GR24+IAA vs. control, and GR24+IAA vs. GR24 comparisons, respectively. The GR24 treatment and GR24+IAA treatment affected auxin and SL synthesis as well as components of the phytohormone signal transduction pathway, such as auxin, brassinosteroid (BR), ethylene (ETH), cytokinin (CK), gibberellin (GA), and abscisic acid (ABA). The concentrations of auxin, GA, zeatin (ZT), and ABA were evaluated using high-performance liquid chromatography (HPLC). From 6 to 10 days, the auxin, GA, and ZT contents in the GR24 treatment group were increased by 11.48%-15.34%, 11.83%-19.50%, and 22.52%-66.17%, respectively, compared to the control group, and these features were increased by 22.00%-31.20%, 21.29%-25.75%, 51.76%-98.96%, respectively, in the GR24+IAA treatment group compared with the control group. Compared to that in the control, the ABA content decreased by 10.30%-11.83% in the GR24 treatment group and decreased by 18.78%-24.00% in the GR24+IAA treatment group at 6-10 days.

Discussion

Our study revealed an interaction between strigolactone and auxin in the induction of AR formation in melon seedlings by affecting the expression of genes related to plant hormone pathways and contents.

Mechanical Stimulation Decreases Auxin and Gibberellic Acid Synthesis but Does Not Affect Auxin Transport in Axillary Buds; It Also Stimulates Peroxidase Activity in Petunia × atkinsiana

Thigmomorphogenesis (or mechanical stimulation-MS) is a term created by Jaffe and means plant response to natural stimuli such as the blow of the wind, strong rain, or touch, resulting in a decrease in length and an increase of branching as well as an increase in the activity of axillary buds. MS is very well known in plant morphology, but physiological processes controlling plant growth are not well discovered yet. In the current study, we tried to find an answer to the question if MS truly may affect auxin synthesis or transport in the early stage of plant growth, and which physiological factors may be responsible for growth arrest in petunia. According to the results of current research, we noticed that MS affects plant growth but does not block auxin transport from the apical bud. MS arrests IAA and GA3 synthesis in MS-treated plants over the longer term. The main factor responsible for the thickening of cell walls and the same strengthening of vascular tissues and growth arrestment, in this case, is peroxidase (POX) activity, but special attention should be also paid to AGPs as signaling molecules which also are directly involved in growth regulation as well as in cell wall modifications.

Long Non-Coding RNA lncWOX11a Suppresses Adventitious Root Formation of Poplar by Regulating the Expression of PeWOX11a

Long non-coding RNAs (lncRNAs), a class of poorly conserved transcripts without protein-encoding ability, are widely involved in plant organogenesis and stress responses by mediating the transmission and expression of genetic information at the transcriptional, posttranscriptional, and epigenetic levels. Here, we cloned and characterized a novel lncRNA molecule through sequence alignment, Sanger sequencing, transient expression in protoplasts, and genetic transformation in poplar. lncWOX11a is a 215 bp transcript located on poplar chromosome 13, ~50 kbp upstream of PeWOX11a on the reverse strand, and the lncRNA may fold into a series of complex stem-loop structures. Despite the small open reading frame (sORF) of 51 bp within lncWOX11a, bioinformatics analysis and protoplast transfection revealed that lncWOX11a has no protein-coding ability. The overexpression of lncWOX11a led to a decrease in the quantity of adventitious roots on the cuttings of transgenic poplars. Further, cis-regulatory module prediction and CRISPR/Cas9 knockout experiments with poplar protoplasts demonstrated that lncWOX11a acts as a negative regulator of adventitious rooting by downregulating the WUSCHEL-related homeobox gene WOX11, which is supposed to activate adventitious root development in plants. Collectively, our findings imply that lncWOX11a is essential for modulating the formation and development of adventitious roots.

Genome-wide identification and characterization of PIN-FORMED (PIN) and PIN-LIKES (PILS) gene family reveals their role in adventitious root development in tea nodal cutting (Camellia Sinensis)

Auxin affects all aspects of plant growth and development, including morphogenesis and adaptive responses. Auxin transmembrane transport is promoted by PIN formation (PIN) and a structurally similar PIN-like (PILS) gene family, which jointly controls the directional transport of the auxin between plant cells, and the accumulation of intracellular auxin. At present, there is no study investigating the roles of CslPIN and CslPILS gene family in root development in the tea plant (Camellia sinensis). In this study, 8 CslPIN and 10 CslPILS genes were identified in the tea plant, and their evolutionary relationships, physical and chemical properties, conserved motifs, cis-acting elements, chromosome location, collinearity, and expression characteristics were analyzed. The mechanism of CslPIN and CslPILS in the formation of tea adventitious roots (ARs) was studied by the AR induction system. Through functional verification, the regulation of CslPIN3 gene on root growth and development of tea plant was studied by over-expression of CslPIN3 in Arabidopsis thaliana and in situ hybridization in Camellia sinensis. The results confirmed CslPIN3 was involved in the regulation of root growth and development as well as auxin accumulation. This study provides a better insight into the regulatory mechanism of CslPIN and CslPILS gene family on the formation of AR in tea plant.

Genetic and Hormonal Blueprint of Shoot-Borne Adventitious Root Development in Rice and Maize

The evolution of root architecture in plants was a prerequisite for the absorption of water and minerals from the soil, and thus a major determinant of terrestrial plant colonization. Cereals have a remarkably complex root system consisting of embryonic primary roots and post-embryonic lateral roots and shoot-borne adventitious roots. Among grass species, rice adventitious roots (also called crown roots) are developed from compressed nodes at the stem base, whereas in maize, besides crown roots, several aboveground brace roots are also formed, thus adventitious root types display species-specific diversity. Despite being the backbone for the adult root system in monocots, adventitious roots are the least studied of all the plant organs. In recent times, molecular genetics, genomics and proteomics-based approaches have been utilized to dissect the mechanism of post-embryonic meristem formation and tissue patterning. Adventitious root development is a cumulative effect of the actions and interactions of crucial genetic and hormonal regulators. In this review, we provide a comprehensive view of the key regulators involved during the different stages of adventitious root development in two important crop plants, rice and maize. We have reviewed the roles of major phytohormones, microRNAs and transcription factors and their crosstalk during adventitious root development in these cereal crops.

Characterization and expression profiling of PIN auxin efflux transporters reveal their role in developmental and abiotic stress conditions in rice

The auxin efflux transporter proteins called PINs ferry auxin from its source to sinks in particular directions depending on their polar localizations in the plasma membrane, thus facilitating the development of the entire plant architecture. The rice genome has 12 PIN genes distributed over eight chromosomes. To study their roles in plant development, abiotic stress responsiveness, and shaping an auxin-dependent root architecture, a genome-wide analysis was carried out. Based on phylogeny, cellular localization, and hydrophilic loop domain size, the PINs were categorized into canonical and noncanonical PINs. PINs were found expressed in all of the organs of plants that emphasized their indispensable role throughout the plant's life cycle. We discovered that PIN5C and PIN9 were upregulated during salt and drought stress. We also found that regardless of its cellular level, auxin functioned as a molecular switch to turn on auxin biosynthesis genes. On the contrary, although PIN expression was upregulated upon initial treatment with auxin, prolonged auxin treatment not only led to their downregulation but also led to the development of auxin-dependent altered root formation in rice. Our study paves the way for developing stress-tolerant rice and plants with a desirable root architecture by genetic engineering.

The Germin-like protein OsGER4 is involved in promoting crown root development under exogenous jasmonic acid treatment in rice

In rice (Oryza sativa L.), crown roots (CRs) have many important roles in processes such as root system expansion, water and mineral uptake, and adaptation to environmental stresses. Phytohormones such as auxin, cytokinin, and ethylene are known to control CR initiation and development in rice. However, the role of jasmonic acid (JA) in CR development remained elusive. Here, we report that JA promotes CR development by regulating OsGER4, a rice Germin-like protein. Root phenotyping analysis revealed that exogenous JA treatment induced an increase in CR number in a concentration-dependent manner. A subsequent genome-wide association study and gene expression analyses pinpointed a strong association between the Germin-like protein OsGER4 and the increase in CR number under exogenous JA treatment. The ProGER4::GUS reporter line showed that OsGER4 is a hormone-responsive gene involved in various stress responses, mainly confined to epidermal and vascular tissues during CR primordia development and to vascular bundles of mature crown and lateral roots. Notable changes in OsGER4 expression patterns caused by the polar auxin transport inhibitor NPA support its connection to auxin signaling. Phenotyping experiments with OsGER4 knockout mutants confirmed that this gene is required for CR development under exogenous JA treatment. Overall, our results provide important insights into JA-mediated regulation of CR development in rice.

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.

Transcriptomic profiles of poplar (Populus simonii × P. nigra) cuttings during adventitious root formation

The formation of adventitious roots (ARs) is vital for the vegetative propagation of poplars. However, the relevant mechanisms remain unclear. To reveal the underlying molecular mechanism, we used RNA-seq to investigate the transcriptional alterations of poplar cuttings soaked in water for 0, 2, 4, 6, 8, and 10 d; 3,798 genes were differentially expressed at all the time points, including 2,448 upregulated and 1,350 downregulated genes. Biological processes including “cell cycle,” “photosynthesis,” “regulation of hormone levels,” and “auxin transport” were enriched in the differentially expressed genes (DEGs). KEGG results showed that the common DEGs were most enriched in the pathway of “Carbon fixation in photosynthetic organisms” and “Starch and sucrose metabolism.” We further dissected 38 DEGs related to root and auxin, including two lateral root primordium 1 (LRP1), one root meristem growth factor (RGF9), one auxin-induced in the root (AIR12), three rooting-associated genes (AUR1 and AUR3), eight auxin transcription factors (ARFs and LBDs), 10 auxin respective genes (SAURs and GH3s), nine auxin transporters (PINs, ABCs, LAX2, and AUXs), and four auxin signal genes (IAAs and TIR1). We found that the rooting abilities of poplar cuttings with and without leaves are different. By applying different concentrations of IBA and sucrose to the top of cuttings without leaves, we found that 0.2 mg/ml IBA and 2 mg/ml sucrose had the best effect on promoting AR formation. The transcriptome results indicated photosynthesis may influence AR formation in poplar cuttings with leaves and revealed a potential regulatory mechanism of leafy cuttage from poplar cuttings. In addition, we provided a new perspective to resolve rooting difficulties in recalcitrant species.

Root plasticity under abiotic stress

Abiotic stresses increasingly threaten existing ecological and agricultural systems across the globe. Plant roots perceive these stresses in the soil and adapt their architecture accordingly. This review provides insights into recent discoveries showing the importance of root system architecture (RSA) and plasticity for the survival and development of plants under heat, cold, drought, salt, and flooding stress. In addition, we review the molecular regulation and hormonal pathways involved in controlling RSA plasticity, main root growth, branching and lateral root growth, root hair development, and formation of adventitious roots. Several stresses affect root anatomy by causing aerenchyma formation, lignin and suberin deposition, and Casparian strip modulation. Roots can also actively grow toward favorable soil conditions and avoid environments detrimental to their development. Recent advances in understanding the cellular mechanisms behind these different root tropisms are discussed. Understanding root plasticity will be instrumental for the development of crops that are resilient in the face of abiotic stress.

Genome-wide association study uncovers major genetic loci associated with seed flooding tolerance in soybean

BACKGROUND

Seed flooding stress is one of the threatening environmental stressors that adversely limits soybean at the germination stage across the globe. The knowledge on the genetic basis underlying seed-flooding tolerance is limited. Therefore, we performed a genome-wide association study (GWAS) using 34,718 single nucleotide polymorphism (SNPs) in a panel of 243 worldwide soybean collections to identify genetic loci linked to soybean seed flooding tolerance at the germination stage.

RESULTS

In the present study, GWAS was performed with two contrasting models, Mixed Linear Model (MLM) and Multi-Locus Random-SNP-Effect Mixed Linear Model (mrMLM) to identify significant SNPs associated with electrical conductivity (EC), germination rate (GR), shoot length (ShL), and root length (RL) traits at germination stage in soybean. With MLM, a total of 20, 40, 4, and 9 SNPs associated with EC, GR, ShL and RL, respectively, whereas in the same order mrMLM detected 27, 17, 13, and 18 SNPs. Among these SNPs, two major SNPs, Gm_08_11971416, and Gm_08_46239716 were found to be consistently connected with seed-flooding tolerance related traits, namely EC and GR across two environments. We also detected two SNPs, Gm_05_1000479 and Gm_01_53535790 linked to ShL and RL, respectively. Based on Gene Ontology enrichment analysis, gene functional annotations, and protein-protein interaction network analysis, we predicted eight candidate genes and three hub genes within the regions of the four SNPs with Cis-elements in promoter regions which may be involved in seed-flooding tolerance in soybeans and these warrant further screening and functional validation.

CONCLUSIONS

Our findings demonstrate that GWAS based on high-density SNP markers is an efficient approach to dissect the genetic basis of complex traits and identify candidate genes in soybean. The trait associated SNPs could be used for genetic improvement in soybean breeding programs. The candidate genes could help researchers better understand the molecular mechanisms underlying seed-flooding stress tolerance in soybean.

Permissive action of H2O2 mediated ClUGT75 expression for auxin glycosylation and Al3+- tolerance in watermelon

Although Al³⁺-toxicity is one of the limiting factors for crop production in acidic soils, little is known about the Al³⁺-tolerance mechanism in watermelon, a fairly acid-tolerant crop. This work aimed to identify the interaction between the H₂O₂ scavenging pathway and auxin glycosylation relevant to watermelon Al³⁺-tolerance. By analyzing expressions of hormone-related ClUGTs and antioxidant enzyme genes in Al³⁺-tolerant (ZJ) and Al³⁺-sensitive (NBT) cultivars, we identified ClUGT75s (B1, B2, and D1) and ClSOD1-2-ClCAT as crucial components associated with Al³⁺-tolerance. Al³⁺-stress significantly increased H₂O₂ content by 92.7% in NBT and 42.3% in ZJ, accompanied by less Al³⁺-, auxin (IAA and IBA), and MDA contents in ZJ than NBT. These findings coincided with significant ClSOD1-2 expression and stable dismutation activity in NBT than ZJ. Hence, higher H₂O₂ content in the root apex of NBT than ZJ correlated with a significant increase in auxin content and ClSOD1-2 up-regulation. Moreover, Al³⁺-activated ClUGT75D1 and ClUGT75B2 in ZJ coincided with no considerable change in IBA content, suggesting that glycosylation-mediated changes in IBA content might be relevant to Al³⁺-tolerance in watermelon. Furthermore, exogenous H₂O₂ and IBA indicated ClUGT75D1 modulating IBA is likely dependent on H₂O₂ background. We hypothesize that a higher H₂O₂ level in NBT represses ClUGT75, resulting in increased auxin than those in ZJ roots. Thus, excess in both H₂O₂ and auxin aggravated the inhibition of root elongation under Al³⁺-stress. Our findings provide insights on the permissive action of H₂O₂ in the mediation of auxin glycosylation by ClUGT75 in root apex for Al³⁺-tolerance in watermelon.

Plant programmed cell death meets auxin signalling

Both auxin signalling and programmed cell death (PCD) are essential components of a normally functioning plant. Auxin underpins plant growth and development, as well as regulating plant defences against environmental stresses. PCD, a genetically controlled pathway for selective elimination of redundant, damaged or infected cells, is also a key element of many developmental processes and stress response mechanisms in plants. An increasing body of evidence suggests that auxin signalling and PCD regulation are often connected. While generally auxin appears to suppress cell death, it has also been shown to promote PCD events, most likely via stimulation of ethylene biosynthesis. Intriguingly, certain cells undergoing PCD have also been suggested to control the distribution of auxin in plant tissues, by either releasing a burst of auxin or creating an anatomical barrier to auxin transport and distribution. These recent findings indicate novel roles of localized PCD events in the context of plant development such as control of root architecture, or tissue regeneration following injury, and suggest exciting possibilities for incorporation of this knowledge into crop improvement strategies.

Opportunities for Improving Waterlogging Tolerance in Cereal Crops-Physiological Traits and Genetic Mechanisms

Waterlogging occurs when soil is saturated with water, leading to anaerobic conditions in the root zone of plants. Climate change is increasing the frequency of waterlogging events, resulting in considerable crop losses. Plants respond to waterlogging stress by adventitious root growth, aerenchyma formation, energy metabolism, and phytohormone signalling. Genotypes differ in biomass reduction, photosynthesis rate, adventitious roots development, and aerenchyma formation in response to waterlogging. We reviewed the detrimental effects of waterlogging on physiological and genetic mechanisms in four major cereal crops (rice, maize, wheat, and barley). The review covers current knowledge on waterlogging tolerance mechanism, genes, and quantitative trait loci (QTL) associated with waterlogging tolerance-related traits, the conventional and modern breeding methods used in developing waterlogging tolerant germplasm. Lastly, we describe candidate genes controlling waterlogging tolerance identified in model plants Arabidopsis and rice to identify homologous genes in the less waterlogging-tolerant maize, wheat, and barley.

Transformation of Jatropha curcas L. for production of larger seeds and increased amount of biodiesel

The development of green energy is important to mitigate global warming. Jatropha (Jatropha curcas L.) is a promising candidate for the production of alternative biofuel, which could reduce the burden on the Earth's resources. Jatropha seeds contain a large quantity of lipids that can be used to produce biofuel, and the rest of the plant has many other uses. Currently, techniques for plant genetic transformation are extensively employed to study, create, and improve the specific characteristics of the target plant. Successful transformation involves the alteration of plants and their genetic materials. The aim of this study was to generate Jatropha plants that can support biofuel production by increasing their seed size using genes found via the rice FOX-hunting system. The present study improved previous protocols, enabling the production of transgenic Jatropha in two steps: the first step involved using auxins and dark incubation to promote root formation in excised shoots and the second step involved delaying the timing of antibiotic selection in the cultivation medium. Transgenic plants were subjected to PCR analysis; the transferred gene expression was confirmed via RT-PCR and the ploidy level was investigated. The results suggest that the genes associated with larger seed size in Arabidopsis thaliana, which were found using the rice FOX-hunting system, produce larger seeds in Jatropha.

New insight into the rapid growth of the Mikania micrantha stem based on DIA proteomic and RNA-Seq analysis

Mikania micrantha is one of the world's most invasive plants, which causes severe damage to natural ecosystems and agroforestry systems due to its rapid stem growth. This work investigated the proteomic and transcriptomic profiles of M. micrantha in different stem tissues (pre-internode, post-internode, and internode), as well as in adventitious roots and primary roots with the final goal of elucidating differentially expressed genes and proteins responsible for the rapid growth of stem. The objective was approached by using DIA-based proteomic and RNA-Seq technologies. More than seven giga-transcriptome clean reads were sequenced, and 5196 protein species were identified. Differentially expressed genes identified in all stem tissues were significantly enriched in photosynthesis and carbon fixation, suggesting that the stem possesses a strong photosynthetic capacity in order to maintain the energy supply for this species. Analysis of differentially expressed proteins showed that proteins related to photosystem I/II and the cytochrome b6/f complex, such as D1, D2, and cp43, were also highly accumulated in the adventitious roots, corroborating the transcriptome analysis results. These results provided basic proteomic and transcriptional expression information about the M. micrantha stem and adventitious root, thereby improving our understanding of the molecular mechanism underlying rapid growth in this species. SIGNIFICANCE: This is the first study to investigate the proteomic and transcriptomic profiles of Mikania micrantha, a highly invasive plant, in different stem tissues (pre-internode, post-internode, and internode), as well as in adventitious and primary roots, using the latest DIA-based (data-independent acquisition mode) proteomic and RNA-Seq technologies. A comprehensive study was carried out, and differentially expressed genes and differentially expressed proteins identified in the pre-internode, post-internode, and internode tissues were significantly enriched during photosynthesis and carbon fixation, suggesting that the M. micrantha stem possesses a strong photosynthetic capacity that allows the plant to maintain a high energy supply. Enriched plant hormone signal transduction pathway analysis revealed an interaction between auxin and other phytohormones involved in adventitious root development. The study provided basic data on the molecular mechanism of M. micrantha vegetative propagation and the rapid growth of its stem. The novel scientific content of this study successfully builds upon the limited information currently available on the subject, therefore warranting publication.

Regulation of root adaptive anatomical and morphological traits during low soil oxygen

Flooding causes oxygen deprivation in soils. Plants adapt to low soil oxygen availability by changes in root morphology, anatomy, and architecture to maintain root system functioning. Essential traits include aerenchyma formation, a barrier to radial oxygen loss, and outgrowth of adventitious roots into the soil or the floodwater. We highlight recent findings of mechanisms of constitutive aerenchyma formation and of changes in root architecture. Moreover, we use modelling of internal aeration to demonstrate the beneficial effect of increasing cortex-to-stele ratio on sustaining root growth in waterlogged soils. We know the genes for some of the beneficial traits, and the next step is to manipulate these genes in breeding in order to enhance the flood tolerance of our crops.

MERISTEM ACTIVITYLESS (MAL) is involved in root development through maintenance of meristem size in rice

Rice MERISTEM ACTIVITYLESS (MAL), a RING-H2 finger domain (RFD)-containing gene, regulates meristem cell viability after the initiation of root primordia mediated by cytokinin signaling. Genes in the RING-H2 finger domain (RFD) family play various roles during plant development and in biotic/abiotic stress responses. Rice gene MERISTEM ACTIVITYLESS (MAL), being contained in the RING-H2 finger domain (RFD), is characterized by a transmembrane domain at the N-terminal and a C3H2C3 zinc finger domain at the C-terminal. To elucidate the physiological and molecular functions of MAL, we generated MAL knockdown transgenic plants by RNA interference. MAL RNA-interfered (MRi) transgenic plants exhibited a phenotype with shorter crown root length and lower crown root number, accompanied by a lower cell division rate. The low division rate was observed in the root meristem exactly where MAL was expressed. Furthermore, transcriptome data revealed that cell wall macromolecule metabolism-related genes and redox-related genes were enriched in MAL RNAi lines. Most of these differentially expressed genes (DEGs) were induced by exogenous cytokinin. Hence, we conclude that MAL, as a novel regulatory factor, plays a major role in maintaining cell viability in the meristem after the initiation of root primordial formation, mediated by cytokinin signaling and reactive oxygen species (ROS).

Gravistimulation effects on Oryza sativa amino acid profile, growth pattern and expression of OsPIN genes

Gravity is an important ecological factor regulating plant growth and developmental processes. Here we used various molecular and biochemical approaches to investigate artificial and normal gravistimulation's effect on the early growth stages of rice (Oryza sativa L.) by changing the orientations of Petri dishes. Rate of amino acid formation, root and shoot growth, and OsPIN expression was significantly higher under gravistimulation compared with the control. Clinostat rotation positively affected plant growth and amino acid profile. However, under normal gravity, vertical-oriented seedlings showed high amino acid levels compared with clinostat, 90°-rotated, and control seedlings. Similarly, seedling growth significantly increased with 90°-rotated and vertical orientations. Artificial gravity and exogenous indole-3-acetic acid induced OsPIN1 expression in the roots, root shoot junction, and shoots of clinorotated seedlings. Phenyl acetic acid induced OsPIN1 expression in the roots and root shoot junction of clinorotated seedlings but not in the shoot. The current study suggests that OsPIN1 is differentially regulated and that it might be involved in the regulation of plant growth. Conversely, OsPIN2 and OsPIN3a are gravity sensors and highly induced in the roots and root shoot junctions of vertical and 90°-rotated seedlings and play an important role in stress conditions. Thus, on exposure to gravity, hormones, and UV-C radiation, these genes are highly regulated by jasmonic acid, 6-benzylaminopurine and gibberellic acid.

Sugar enhances waterlogging-induced adventitious root formation in cucumber by promoting auxin transport and signalling

Waterlogging is a severe environmental stress that causes severe crop productivity losses. Cucumber (Cucumis sativus L.) survives waterlogging by producing adventitious roots (ARs) that enhance gas exchange. Little is known about the role of light and sugars in the waterlogging-induced production of ARs. The role of these factors in AR production was therefore studied in cucumber seedlings grown in the absence or presence of waterlogging and different light conditions. The effect of photosynthesis was studied by removing the shoots of the seedlings and replacing them with exogenous applications of sucrose or stachyose. Shoot removal inhibited AR emergence and elongation. However, the exogenous application of sugars fully restored AR emergence and partially restored root elongation. The exogenous application of a synthetic auxin restored AR emergence but not AR elongation. Transcriptome profiling analysis was used to determine the effects of light on gene expression in the hypocotyls under these conditions. The levels of transcripts encoding proteins involved in auxin transport and signalling were higher in the light and following the exogenous application of sucrose and stachyose. These results show that the waterlogging-induced emergence of ARs is regulated by the interaction between sugars and auxin, whereas AR elongation depends only on sugars alone.

Mechanisms of Waterlogging Tolerance in Plants: Research Progress and Prospects

Waterlogging is one of the main abiotic stresses suffered by plants. Inhibition of aerobic respiration during waterlogging limits energy metabolism and restricts growth and a wide range of developmental processes, from seed germination to vegetative growth and further reproductive growth. Plants respond to waterlogging stress by regulating their morphological structure, energy metabolism, endogenous hormone biosynthesis, and signaling processes. In this updated review, we systematically summarize the changes in morphological structure, photosynthesis, respiration, reactive oxygen species damage, plant hormone synthesis, and signaling cascades after plants were subjected to waterlogging stress. Finally, we propose future challenges and research directions in this field.

What Makes Adventitious Roots?

The spermatophyte root system is composed of a primary root that develops from an embryonically formed root meristem, and of different post-embryonic root types: lateral and adventitious roots. Adventitious roots, arising from the stem of the plants, are the main component of the mature root system of many plants. Their development can also be induced in response to adverse environmental conditions or stresses. Here, in this review, we report on the morphological and functional diversity of adventitious roots and their origin. The hormonal and molecular regulation of the constitutive and inducible adventitious root initiation and development is discussed. Recent data confirmed the crucial role of the auxin/cytokinin balance in adventitious rooting. Nevertheless, other hormones must be considered. At the genetic level, adventitious root formation integrates the transduction of external signals, as well as a core auxin-regulated developmental pathway that is shared with lateral root formation. The knowledge acquired from adventitious root development opens new perspectives to improve micropropagation by cutting in recalcitrant species, root system architecture of crops such as cereals, and to understand how plants adapted during evolution to the terrestrial environment by producing different post-embryonic root types.