Gibberellins regulate lateral root formation in Populus through interactions with auxin and other hormones

Study on adventitious root induction and endogenous hormone dynamics during cutting propagation of Distylium chinense

Distylium chinense has strong ecological adaptability and high ornamental value, which should have broad application prospects in urban landscaping. However, its low cutting rooting rate and slow rooting speed, as well as limited varietal numbers, have hindered its promotion and application in landscape. This study aims to reveal the development characteristics of adventitious roots (AR) and the regulation mechanism of endogenous hormones during the cutting propagation. Through cutting propagation and paraffin section technology, combined with immunohistochemical localization and hormone quantitative analysis, the morphogenesis of cuttings and the dynamic changes of endogenous hormones were comprehensively analyzed. The study found that the development of AR experienced three stages: induction period, expression period and elongation period, and the root primordium originated from vascular cambium, phloem, cortex and callus. Indoleacetic acid (IAA) and abscisic acid (ABA) signals accumulated in different tissues with the development of AR. IAA content showed a trend of ' decrease-increase ', zeatin riboside (ZR) and gibberellin (GA3) content showed a trend of ' decrease-increase-decrease ', while ABA content showed a trend of ' increase-decrease-increase ' in the treatment group, which was compared with the ' decrease-increase ' trend of the control group. These results not only indicate that the development process of AR is closely related to the temporal and spatial changes of endogenous hormones, but also provide a new theoretical basis for the cultivation of new varieties and industrial production of D. chinense.

Cell wall dynamic changes and signaling during plant lateral root development

Lateral roots (LRs), are an important component of plant roots, playing a crucial role in anchoring the plant in the soil and facilitating the uptake of water and nutrients. As post-embryonic organs, LRs originate from the pericycle cells of the primary root, and their formation is characterized by precise regulation of cell division and complex intercellular interactions, both of which are closely tied to cell wall regulation. Considering the rapid advances in molecular techniques over the past three decades, we reframe the understanding of the dynamic change in cell wall during LR development by summarizing the factors that precipitate these changes and their effects, as well as the regulated signals involved. Additionally, we discuss current challenges in this field and propose potential solutions.

Genome-Wide Characterization of Gibberellin Oxidase Genes (GbGAoxs) and Illustration of Their Molecular Responses to Exogenous GA3 in Gossypium barbadense

As key enzymes in the gibberellin (GA) biosynthesis pathway, GAoxs function as regulators of bioactive GA levels and plant architecture, yet little is understood about GAoxs in Gossypium. In this study, 78 GAox genes identified in four cotton species were divided into three subgroups: GA2ox, GA3ox, and GA20ox. Syntenic relationships of GAoxs in Gossypium suggested that divergencies in gene function may be attributed to whole-genome duplication during evolution. Cis-acting element analysis suggested that the GbGAox genes might participate in plant growth, development, and hormone responses. Moreover, transcriptome analysis was performed to characterize the molecular response of the exogenous GA3 application. It was found that DEGs (differentially expressed genes) are widely involved in cell division and cell wall modification, in which the most XTH (xyloglucan endotransglucosylase/hydrolase) and GAox genes responded actively to the exogenous GA3 treatment. Some transcription factors and protein kinases cooperated with those GbGAoxs in response to GA3. These findings underlie the biological function of GAox genes and their responses to GA3 in regulating plant growth in Gossypium barbadense.

Mechanisms of Cannabis Growth Promotion by Bacillus velezensis S141

Cannabis sativa L. has a variety of uses, including fiber production, food, oil, and medicine. In response to environmental concerns regarding chemical fertilizers, Bacillus velezensis S141 was examined as a plant-growth-promoting bacterium (PGPB) for cannabis. This study evaluated the effects of S141 on cannabis growth and utilized transcriptomic analysis to identify the responsive pathways. Inoculation with S141 significantly increased growth in laboratory and field environments, with most of the bacteria residing in the leaves, followed by the stems and roots, as determined by quantitative polymerase chain reaction (qPCR). Transcriptomic analysis revealed 976 differentially expressed genes. Upregulated genes were associated with metabolism, cellular processes, and catalytic activities, especially in the biosynthesis of phenylpropanoid, plant-pathogen interactions, and hormone signaling pathways. S141 mutants deficient in the production of auxin and cytokinin displayed reduced growth enhancement, which affirmed the roles of these hormones in cannabis development. These findings emphasize the potential of S141 as a sustainable growth promoter for cannabis and provide insights into the underlying pathways it influences.

Comprehensive characterization of gibberellin oxidase gene family in Brassica napus reveals BnGA2ox15 involved in hormone signaling and response to drought stress

Brassica napus is a well-known allopolyploid oil crop with high commercial potential. Gibberellin oxidase (GAox) is an essential enzyme that activates gibberellins, which regulate plant growth, and development, and have a significant impact on plant responses to abiotic stress. However, the comprehensive understanding of GAox genes and their evolution in Brassica plants remains elusive. Using advanced bioinformatics tools, this study identified 125 candidate GAox genes from the whole genomes of three key Brassica species. This study also investigated sequence characteristics, conserved motifs, exon/intron structures, cis-acting elements, syntenic analysis, duplication events and expression patterns. Subcellular localization analysis showed that the BnGA2ox14 and BnGA2ox15 proteins are located in the nucleus, whereas BnGA2ox26 is specifically localized to the chloroplast. Yeast one-hybrid and dual-luciferase assays demonstrated that MYELOCYTOMATOSIS 4 (BnMYC4) and ABA-INDUCIBLE BHLH-TYPE TRANSCRIPTION FACTOR (BnAIB) bind to the BnGA2ox15 promoter and activate its transcription. Molecular docking analysis further elucidated their interaction structures and identified potential binding sites. Roots transformations show that overexpression of BnGA2ox15 increased sensitivity to PEG-6000 treatment in rapeseed. In brief, this study reveals that BnGA2ox15 is a downstream target in JA and ABA signaling pathways, functioning as a negative regulator in response to drought stress.

An F-box Kelch repeat protein, PmFBK2, from Persicaria minor interacts with GID1b to modulate gibberellin signalling

The F-box protein (FBP) family plays diverse functions in the plant kingdom, with the function of many members still unrevealed. In this study, a specific FBP called PmFBK2, containing Kelch repeats from Persicaria minor, was functionally investigated. Employing the yeast two-hybrid (Y2H) assay, PmFBK2 was found to interact with Skp1-like proteins from P. minor, suggesting its potential to form an E3 ubiquitin ligase, known as the SCF complex. Y2H and co-immunoprecipitation tests revealed that PmFBK2 interacts with full-length PmGID1b. The interaction marks the first documented binding between these two protein types, which have never been reported in other plants before, and they exhibited a negative effect on gibberellin (GA) signal transduction. The overexpression of PmFBK2 in the kmd3 mutant, a homolog from Arabidopsis, demonstrated the ability of PmFBK2 to restore the function of the mutated KMD3 gene. The function restoration was supported by morphophysiological and gene expression analyses, which exhibited patterns similar to the wild type (WT) compared to the kmd3 mutant. Interestingly, the overexpression of PmFBK2 or PmGID1b in Arabidopsis had opposite effects on rosette diameter, seed weight, and plant height. This study provides new insights into the complex GA signalling. It highlights the crucial roles of the interaction between FBP and the GA receptor (GID1b) in regulating GA responses. These findings have implications for developing strategies to enhance plant growth and yield by modulating GA signalling in crops.

Genome-Wide Analysis of the Gibberellin-Oxidases Family Members in Four Prunus Species and a Functional Analysis of PmGA2ox8 in Plant Height

Gibberellins (GAs), enzymes that play a significant role in plant growth and development, and their levels in plants could be regulated by gibberellin-oxidases (GAoxs). As important fruit trees and ornamental plants, the study of the mechanism of plant architecture formation of the Prunus genus is crucial. Here, 85 GAox genes were identified from P. mume, P. armeniaca, P. salicina, and P. persica, and they were classified into six subgroups. Conserved motif and gene structure analysis showed that GAoxs were conserved in the four Prunus species. Collinearity analysis revealed two fragment replication events of PmGAoxs in the P. mume genome. Promoter cis-elements analysis revealed 24 PmGAoxs contained hormone-responsive elements and development regulatory elements. The expression profile indicated that PmGAoxs have tissue expression specificity, and GA levels during the dormancy stage of flower buds were controlled by certain PmGAoxs. After being treated with IAA or GA3, the transcription level of PmGA2ox8 in stems was significantly increased and showed a differential expression level between upright and weeping stems. GUS activity driven by PmGA2ox8 promoter was detected in roots, stems, leaves, and flower organs of Arabidopsis. PmGA2ox8 overexpression in Arabidopsis leads to dwarfing phenotype, increased number of rosette leaves but decreased leaf area, and delayed flowering. Our results showed that GAoxs were conserved in Prunus species, and PmGA2ox8 played an essential role in regulating plant height.

Valorization of treated swine wastewater and generated biomass by microalgae: Their effects and salt tolerance mechanisms on wheat seedling growth

The extensive use of mineral fertilizers has a negative impact on the environment, whereas wastewater and microalgal biomass can provide crops with nutrients such as nitrogen, phosphorus, and potassium, and have the potential to be used as a source of fertilizers in circular agriculture. In this study, a step-by-step resource utilization study of algae-containing wastewater generated from microalgae treatment of swine wastewater was carried out. When wheat seedlings were cultivated in the effluent after microalgae separation, the root fresh weight, seedling fresh weight, and total seedling length were increased by 3.44%, 14.45%, and 13.64%, respectively, compared with that of the algae-containing wastewater, and there was no significant difference in seedling fresh weight, total seedling length, maximum quantum yields of PSII photochemistry (Fv/Fm), and performance index (PIABS) from that of the Hogland solution group, which has the potential to be an alternative liquid fertilizer. Under salt stress, microalgae extract increased the contents of GA3, IAA, ABA, and SA in wheat seedlings, antioxidant enzymes maintained high activity, and the PIABS value increased. Low-dose microalgae extract (1 mL/L) increased the root fresh weight, seedling fresh weight, longest seedling length, and total seedling length by 30.73%, 31.28%, 16.43%, and 28.85%, respectively. Algae extract can act as a plant biostimulant to regulate phytohormone levels to attenuate the damage of salt stress and promote growth.

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

BACKGROUND

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

RESULTS

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

CONCLUSIONS

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

Selenite reduced cadmium uptake, interfered signal transduction of endogenous phytohormones, and stimulated secretion of tartaric acid based on a combined analysis of non-invasive micro-test technique, transcriptome and metabolome

Selenium (Se) can reduce uptake and translocation of cadmium (Cd) in plants via plenty of ways, including regulation of root morphology. However, the underlying mechanisms on how Se will regulate root morphology under metal(loid) stresses are not fully illustrated. To fill up this knowledge gap, we investigated the effects of 0.5 mg L-1 selenite (Se(IV)) on root exudates, root morphology, root endogenous hormones, and Cd uptake efficiency of rice under the 1 mg L-1 Cd stress condition. The results showed that Se(IV) significantly reduced shoot and root Cd concentrations, and decreased Cd uptake efficiency via root hairs determined by a non-invasive micro-test (NMT) technology. When compared to the 1 mg L-1 Cd (Cd1) treatment, addition of 0.5 mg L-1 Se(IV) (1) significantly reduced root surface area and tip numbers, and non-significantly reduced root length, but significantly enhanced root diameter and root volume; (2) significantly enhanced concentrations of tartaric acid in the root exudate solution, root auxin (IAA) and root jasmonic acid (JA) via a UHPLC or a HPLC analysis; (3) significantly up-regulated metabolites correlated with synthesis of IAA, JA, gibberellin (GA), and salicylic acid, such as GA53, M-SA, (+/-)7-epi-JA, and derivatives of tryptophan and indole in the metabolome analysis. However, results of transcriptome analysis showed that (1) no upregulated differentially expressed genes (DEGs) were enriched in IAA synthesis; (2) some upregulated DEGs were found to be enriched in JA and GA53 synthesis pathways. In summary, although Se(IV) stimulated the synthesis of IAA, JA, and GA53, it significantly inhibited root growth mainly by 1) affecting signal transduction of IAA and GA; 2) altering IAA polar transport and homeostasis; and 3) regulating DEGs including SAUR32, SAUR36, SAUR76, OsSub33, OsEXPA8, OsEXPA18, and Os6bglu24.

Characterization of Almond Scion/Rootstock Communication in Cultivar and Rootstock Tissues through an RNA-Seq Approach

The rootstock genotype plays a crucial role in determining various aspects of scion development, including the scion three-dimensional structure, or tree architecture. Consequently, rootstock choice is a pivotal factor in the establishment of new almond (Prunus amygdalus (L.) Batsch, syn P. dulcis (Mill.)) intensive planting systems, demanding cultivars that can adapt to distinct requirements of vigor and shape. Nevertheless, considering the capacity of the rootstock genotype to influence scion development, it is likely that the scion genotype reciprocally affects rootstock performance. In the context of this study, we conducted a transcriptomic analysis of the scion/rootstock interaction in young almond trees, with a specific focus on elucidating the scion impact on the rootstock molecular response. Two commercial almond cultivars were grafted onto two hybrid rootstocks, thereby generating four distinct combinations. Through RNA-Seq analysis, we discerned that indeed, the scion genotype exerts an influence on the rootstock expression profile. This influence manifests through the modulation of genes associated with hormonal regulation, cell division, root development, and light signaling. This intricate interplay between scion and rootstock communication plays a pivotal role in the development of both scion and rootstock, underscoring the critical importance of a correct choice when establishing new almond orchards.

Ethylene response factor ERF022 is involved in regulating Arabidopsis root growth

Ethylene response factors (ERFs) are involved in the regulation of plant development processes and stress responses. In this study, we provide evidence for the role of ERF022, a member of the ERF transcription factor group III, in regulating Arabidopsis root growth. We found that ERF022-loss-of-function mutants exhibited increased primary root length and lateral root numbers, and also morphological growth advantages compared to wild-type. Further studies showed that mutants had enhanced cell size in length in the root elongation zones. These results were accompanied by significant increase in the expression of cell elongation and cell wall expansion related genes SAUR10, GASA14, LRX2, XTH19 in mutants. Moreover, ERF022-mediated root growth was associated with the enhanced endogenous auxin and gibberellins levels. Our results suggest that loss-of-function of ERF022 up-regulated the expression of cell elongation and cell wall related genes through auxin and gibberellins signal in the regulation of root growth. Unexpectedly, ERF022 overexpression lines also showed longer primary roots and more lateral roots compared to wild-type, and had longer root apical meristematic zone with increased cell numbers. Overexpression of ERF022 significantly up-regulated cell proliferation, organ growth and auxin biosynthesis genes EXO, HB2, GALK2, LBD26, YUC5, which contribute to enhanced root growth. Altogether, our results provide genetic evidence that ERF022 plays an important role in regulating root growth in Arabidopsis thaliana.

Application of an Improved 2-Dimensional High-Throughput Soybean Root Phenotyping Platform to Identify Novel Genetic Variants Regulating Root Architecture Traits

Nutrient-efficient root system architecture (RSA) is becoming an important breeding objective for generating crop varieties with improved nutrient and water acquisition efficiency. Genetic variants shaping soybean RSA is key in improving nutrient and water acquisition. Here, we report on the use of an improved 2-dimensional high-throughput root phenotyping platform that minimizes background noise by imaging pouch-grown root systems submerged in water. We also developed a background image cleaning Python pipeline that computationally removes images of small pieces of debris and filter paper fibers, which can be erroneously quantified as root tips. This platform was used to phenotype root traits in 286 soybean lines genotyped with 5.4 million single-nucleotide polymorphisms. There was a substantially higher correlation in manually counted number of root tips with computationally quantified root tips (95% correlation), when the background was cleaned of nonroot materials compared to root images without the background corrected (79%). Improvements in our RSA phenotyping pipeline significantly reduced overestimation of the root traits influenced by the number of root tips. Genome-wide association studies conducted on the root phenotypic data and quantitative gene expression analysis of candidate genes resulted in the identification of 3 putative positive regulators of root system depth, total root length and surface area, and root system volume and surface area of thicker roots (DOF1-like zinc finger transcription factor, protein of unknown function, and C2H2 zinc finger protein). We also identified a putative negative regulator (gibberellin 20 oxidase 3) of the total number of lateral roots.

GA20ox Family Genes Mediate Gibberellin and Auxin Crosstalk in Moso bamboo (Phyllostachys edulis)

Moso bamboo (Phyllostachys edulis) is one of the fastest growing plants. Gibberellin (GA) is a key phytohormone regulating growth, but there are few studies on the growth of Moso bamboo regulated by GA. The gibberellin 20 oxidase (GA20ox) gene family was targeted in this study. Chromosomal distribution and collinearity analysis identified 10 GA20ox genes evenly distributed on chromosomes, and the family genes were relatively conservative in evolution. The genetic relationship of GA20ox genes had been confirmed to be closest in different genera of plants in a phylogenetic and selective pressure analysis between Moso bamboo and rice. About 1/3 GA20ox genes experienced positive selective pressure with segmental duplication being the main driver of gene family expansion. Analysis of expression patterns revealed that only six PheGA20ox genes were expressed in different organs of shoot development and flowers, that there was redundancy in gene function. Underground organs were not the main site of GA synthesis in Moso bamboo, and floral organs are involved in the GA biosynthesis process. The auxin signaling factor PheARF47 was located upstream of PheGA20ox3 and PheGA20ox6 genes, where PheARF47 regulated PheGA20ox3 through cis-P box elements and cis-AuxRR elements, based on the result that promoter analysis combined with yeast one-hybrid and dual luciferase detection analysis identified. Overall, we identified the evolutionary pattern of PheGA20ox genes in Moso bamboo and the possible major synthesis sites of GA, screened for key genes in the crosstalk between auxin and GA, and laid the foundation for further exploration of the synergistic regulation of growth by GA and auxin in Moso bamboo.

Transcriptome-Based Construction of the Gibberellin Metabolism and Signaling Pathways in Eucalyptus grandis × E. urophylla, and Functional Characterization of GA20ox and GA2ox in Regulating Plant Development and Abiotic Stress Adaptations

Gibberellins (GAs) are the key regulators controlling plant growth, wood production and the stress responses in perennial woody plants. The role of GA in regulating the above-mentioned processes in Eucalyptus remain largely unclear. There is still a lack of systematic identification and functional characterization of GA-related genes in Eucalyptus. In this study, a total of 59,948 expressed genes were identified from the major vegetative tissues of the E. grandis × E. urophylla using transcriptome sequencing. Then, the key gene families in each step of GA biosynthesis, degradation and signaling were investigated and compared with those of Arabidopsis, rice, and Populus. The expression profile generated using Real-time quantitative PCR showed that most of these genes exhibited diverse expression patterns in different vegetative organs and in response to abiotic stresses. Furthermore, we selectively overexpressed EguGA20ox1, EguGA20ox2 and EguGA2ox1 in both Arabidopsis and Eucalyptus via Agrobacterium tumefaciens or A. rhizogenes-mediated transformation. Though both Arabidopsis EguGA20ox1- and EguGA20ox2-overexpressing (OE) lines exhibited better vegetative growth performance, they were more sensitive to abiotic stress, unlike EguGA2ox1-OE plants, which exhibited enhanced stress resistance. Moreover, overexpression of EguGA20ox in Eucalyptus roots caused significantly accelerated hairy root initiation and elongation and improved root xylem differentiation. Our study provided a comprehensive and systematic study of the genes of the GA metabolism and signaling and identified the role of GA20ox and GA2ox in regulating plant growth, stress tolerance, and xylem development in Eucalyptus; this could benefit molecular breeding for obtaining high-yield and stress-resistant Eucalyptus cultivars.

Novel insights into maize (Zea mays) development and organogenesis for agricultural optimization

In maize, intrinsic hormone activities and sap fluxes facilitate organogenesis patterning and plant holistic development; these hormone movements should be a primary focus of developmental biology and agricultural optimization strategies. Maize (Zea mays) is an important crop plant with distinctive life history characteristics and structural features. Genetic studies have extended our knowledge of maize developmental processes, genetics, and molecular ecophysiology. In this review, the classical life cycle and life history strategies of maize are analyzed to identify spatiotemporal organogenesis properties and develop a definitive understanding of maize development. The actions of genes and hormones involved in maize organogenesis and sex determination, along with potential molecular mechanisms, are investigated, with findings suggesting central roles of auxin and cytokinins in regulating maize holistic development. Furthermore, investigation of morphological and structural characteristics of maize, particularly node ubiquity and the alternate attachment pattern of lateral organs, yields a novel regulatory model suggesting that maize organ initiation and subsequent development are derived from the stimulation and interaction of auxin and cytokinin fluxes. Propositions that hormone activities and sap flow pathways control organogenesis are thoroughly explored, and initiation and development processes of distinctive maize organs are discussed. Analysis of physiological factors driving hormone and sap movement implicates cues of whole-plant activity for hormone and sap fluxes to stimulate maize inflorescence initiation and organ identity determination. The physiological origins and biogenetic mechanisms underlying maize floral sex determination occurring at the tassel and ear spikelet are thoroughly investigated. The comprehensive outline of maize development and morphogenetic physiology developed in this review will enable farmers to optimize field management and will provide a reference for de novo crop domestication and germplasm improvement using genome editing biotechnologies, promoting agricultural optimization.

A petunia transcription factor, PhOBF1, regulates flower senescence by modulating gibberellin biosynthesis

Flower senescence is commonly enhanced by the endogenous hormone ethylene and suppressed by the gibberellins (GAs) in plants. However, the detailed mechanisms for the antagonism of these hormones during flower senescence remain elusive. In this study, we characterized one up-regulated gene PhOBF1, belonging to the basic leucine zipper transcription factor family, in senescing petals of petunia (Petunia hybrida). Exogenous treatments with ethylene and GA3 provoked a dramatic increase in PhOBF1 transcripts. Compared with wild-type plants, PhOBF1-RNAi transgenic petunia plants exhibited shortened flower longevity, while overexpression of PhOBF1 resulted in delayed flower senescence. Transcript abundances of two senescence-related genes PhSAG12 and PhSAG29 were higher in PhOBF1-silenced plants but lower in PhOBF1-overexpressing plants. Silencing and overexpression of PhOBF1 affected expression levels of a few genes involved in the GA biosynthesis and signaling pathways, as well as accumulation levels of bioactive GAs GA1 and GA3. Application of GA3 restored the accelerated petal senescence to normal levels in PhOBF1-RNAi transgenic petunia lines, and reduced ethylene release and transcription of three ethylene biosynthetic genes PhACO1, PhACS1, and PhACS2. Moreover, PhOBF1 was observed to specifically bind to the PhGA20ox3 promoter containing a G-box motif. Transient silencing of PhGA20ox3 in petunia plants through tobacco rattle virus-based virus-induced gene silencing method led to accelerated corolla senescence. Our results suggest that PhOBF1 functions as a negative regulator of ethylene-mediated flower senescence by modulating the GA production.

Effects of arbuscular mycorrhizal fungus inoculation on the growth and nitrogen metabolism of Catalpa bungei C.A.Mey. under different nitrogen levels

Evidence suggests that arbuscular mycorrhizal fungi (AMF) may promote the growth of woody plants. However, the effects of AMF on nitrogen (N) metabolism in plants, especially trees, and its regulatory mechanism are rarely reported. Here, the effects of AMF inoculation on the growth and N nutrition status of Catalpa bungei under different N levels were reported. Three N levels (low, medium, high) and two mycorrhizal inoculation treatments (inoculation with Rhizophagus intraradices or not) were used with factorial design. The results showed that medium N could significantly improve the physiological metabolism and growth of C. bungei seedlings. However, when N was excessive, growth was significantly inhibited whether inoculated AMF or not. Compared with non-inoculated treatments, AMF inoculation could promote the absorption of N and P, improve photosynthesis under low to medium N levels, thus promoting the growth of seedlings. AMF changed the biomass allocation in seedlings by reducing the stem mass ratio and root/shoot ratio, and increasing the leaf mass ratio. At medium N levels, compared with non-inoculated treatment, AMF inoculation could significantly promote root growth by changing root hormone levels and improving root architecture and root activity. Under N addition, AMF inoculation could improve the absorption and assimilation of N by regulating the expression of key enzyme genes of N metabolism and nitrate transporter genes (NRT2.4, NRT2.5, NRT2.7) in roots, and enhancing the activities of the key enzyme of N metabolism. This study may provide a reference for the application of AMF in the cultivation and afforestation technology of C. bungei in Northwest China.

Transcriptomic and Metabolomic Analysis of Soybean Nodule Number Improvements with the Use of Water-Soluble Humic Materials

Water-soluble humic materials (WSHMs) can enhance the nodule numbers of soybean plants. In this study, targeted metabolomics and transcriptomics were used to understand this mechanism. Results showed that 500 mg/L WSHM increased the adsorption and colonization of rhizobia in soybean roots. High-performance liquid chromatography and targeted metabolomics showed that WSHMs could regulate the content and distribution of endogenous hormones of soybean plants at the initial stage of soybean nodulation. Transcriptomic analysis showed a total of 2406 differentially expressed genes (DEGs) by the 25th day, accounting for 4.89% of total annotation genes (49159). These DEGs were found to contribute primarily to the MAPK signaling pathway, glycolysis/gluconeogenesis, and plant hormone signal transduction according to the -log 10 (Padjust) value in the KEGG pathway. Subsequently, DEGs related to these hormones were selected for verification using quantity-PCR. The WSHM increased the number of nodules by regulating the expression of endogenous hormones in soybean plants.

Plant nitrogen availability and crosstalk with phytohormones signallings and their biotechnology breeding application in crops

Nitrogen (N), one of the most important nutrients, limits plant growth and crop yields in sustainable agriculture system, in which phytohormones are known to play essential roles in N availability. Hence, it is not surprising that massive studies about the crosstalk between N and phytohormones have been constantly emerging. In this review, with the intellectual landscape of N and phytohormones crosstalk provided by the bibliometric analysis, we trace the research story of best-known crosstalk between N and various phytohormones over the last 20 years. Then, we discuss how N regulates various phytohormones biosynthesis and transport in plants. In reverse, we also summarize how phytohormones signallings modulate root system architecture (RSA) in response to N availability. Besides, we expand to outline how phytohormones signallings regulate uptake, transport, and assimilation of N in plants. Further, we conclude advanced biotechnology strategies, explain their application, and provide potential phytohormones-regulated N use efficiency (NUE) targets in crops. Collectively, this review provides not only a better understanding on the recent progress of crosstalk between N and phytohormones, but also targeted strategies for improvement of NUE to increase crop yields in future biotechnology breeding of crops.

Network of the transcriptome and metabolomics reveals a novel regulation of drought resistance during germination in wheat

BACKGROUND AND AIMS

The North China Plain, the highest winter-wheat-producing region of China, is seriously threatened by drought. Traditional irrigation wastes a significant amount of water during the sowing season. Therefore, it is necessary to study the drought resistance of wheat during germination to maintain agricultural ecological security. From several main cultivars in the North China Plain, we screened the drought-resistant cultivar JM47 and drought-sensitive cultivar AK58 during germination using the polyethylene glycol (PEG) drought simulation method. An integrated analysis of the transcriptome and metabolomics was performed to understand the regulatory networks related to drought resistance in wheat germination and verify key regulatory genes.

METHODS

Transcriptional and metabolic changes were investigated using statistical analyses and gene-metabolite correlation networks. Transcript and metabolite profiles were obtained through high-throughput RNA-sequencing data analysis and ultra-performance liquid chromatography quadrupole time-of-flight tandem mass spectrometry, respectively.

KEY RESULTS

A total of 8083 and 2911 differentially expressed genes (DEGs) and 173 and 148 differential metabolites were identified in AK58 and JM47, respectively, under drought stress. According to the integrated analysis results, mammalian target of rapamycin (mTOR) signalling was prominently enriched in JM47. A decrease in α-linolenic acid content was consistent with the performance of DEGs involved in jasmonic acid biosynthesis in the two cultivars under drought stress. Abscisic acid (ABA) content decreased more in JM47 than in AK58, and linoleic acid content decreased in AK58 but increased in JM47. α-Tocotrienol was upregulated and strongly correlated with α-linolenic acid metabolism.

CONCLUSIONS

The DEGs that participated in the mTOR and α-linolenic acid metabolism pathways were considered candidate DEGs related to drought resistance and the key metabolites α-tocotrienol, linoleic acid and l-leucine, which could trigger a comprehensive and systemic effect on drought resistance during germination by activating mTOR-ABA signalling and the interaction of various hormones.

Transcriptomic analysis reveals the contribution of QMrl-7B to wheat root growth and development

Roots are the major organs for water and nutrient acquisition and substantially affect plant growth, development and reproduction. Improvements to root system architecture are highly important for the increased yield potential of bread wheat. QMrl-7B, a major stable quantitative trait locus (QTL) that controls maximum root length (MRL), essentially contributes to an improved root system in wheat. To further analyze the biological functions of QMrl-7B in root development, two sets of Triticum aestivum near-isogenic lines (NILs), one with superior QMrl-7B alleles from cultivar Kenong 9204 (KN9204) named NIL^KN9204 and another with inferior QMrl-7B alleles from cultivar Jing 411 (J411) named NIL^J411, were subjected to transcriptomic analysis. Among all the mapped genes analyzed, 4871 genes were identified as being differentially expressed between the pairwise NILs under different nitrogen (N) conditions, with 3543 genes expressed under normal-nitrogen (NN) condition and 2689 genes expressed under low-nitrogen (LN) condition. These genes encode proteins that mainly include N O 3 - transporters, phytohormone signaling components and transcription factors (TFs), indicating the presence of a complex regulatory network involved in root determination. In addition, among the 13524 LN-induced differentially expressed genes (DEGs) detected in this study, 4308 and 2463 were specifically expressed in the NIL^KN9204 and NIL^J411, respectively. These DEGs reflect different responses of the two sets of NILs to varying N supplies, which likely involve LN-induced root growth. These results explain the better-developed root system and increased root vitality conferred by the superior alleles of QMrl-7B and provide a deeper understanding of the genetic underpinnings of root traits, pointing to a valuable locus suitable for future breeding efforts for sustainable agriculture.

Plant Development and Crop Yield: The Role of Gibberellins

Gibberellins have been classically related to a few key developmental processes, thus being essential for the accurate unfolding of plant genetic programs. After more than a century of research, over one hundred different gibberellins have been described. There is a continuously increasing interest in gibberellins research because of their relevant role in the so-called "Green Revolution", as well as their current and possible applications in crop improvement. The functions attributed to gibberellins have been traditionally restricted to the regulation of plant stature, seed germination, and flowering. Nonetheless, research in the last years has shown that these functions extend to many other relevant processes. In this review, the current knowledge on gibberellins homeostasis and mode of action is briefly outlined, while specific attention is focused on the many different responses in which gibberellins take part. Thus, those genes and proteins identified as being involved in the regulation of gibberellin responses in model and non-model species are highlighted. The present review aims to provide a comprehensive picture of the state-of-the-art perception of gibberellins molecular biology and its effects on plant development. This picture might be helpful to enhance our current understanding of gibberellins biology and provide the know-how for the development of more accurate research and breeding programs.

Understanding the Role of PIN Auxin Carrier Genes under Biotic and Abiotic Stresses in Olea europaea L

The PIN-FORMED (PIN) proteins represent the most important polar auxin transporters in plants. Here, we characterized the PIN gene family in two olive genotypes, the Olea europaea subsp. europaea var. sylvestris and the var. europaea (cv. ‘Farga’). Twelve and 17 PIN genes were identified for vars. sylvestris and europaea, respectively, being distributed across 6 subfamilies. Genes encoding canonical OePINs consist of six exons, while genes encoding non-canonical OePINs are composed of five exons, with implications at protein specificities and functionality. A copia-LTR retrotransposon located in intron 4 of OePIN2b of var. europaea and the exaptation of partial sequences of that element as exons of the OePIN2b of var. sylvestris reveals such kind of event as a driving force in the olive PIN evolution. RNA-seq data showed that members from the subfamilies 1, 2, and 3 responded to abiotic and biotic stress factors. Co-expression of OePINs with genes involved in stress signaling and oxidative stress homeostasis were identified. This study highlights the importance of PIN genes on stress responses, contributing for a holistic understanding of the role of auxins in plants.

Molecular basis of differential adventitious rooting competence in poplar genotypes

Recalcitrant adventitious root (AR) development is a major hurdle in propagating commercially important woody plants. Although significant progress has been made to identify genes involved in subsequent steps of AR development, the molecular basis of differences in apparent recalcitrance to form AR between easy-to-root and difficult-to-root genotypes remains unknown. To address this, we generated cambium tissue-specific transcriptomic data from stem cuttings of hybrid aspen, T89 (difficult-to-root) and hybrid poplar OP42 (easy-to-root), and used transgenic approaches to verify the role of several transcription factors in the control of adventitious rooting. Increased peroxidase activity was positively correlated with better rooting. We found differentially expressed genes encoding reactive oxygen species scavenging proteins to be enriched in OP42 compared with T89. A greater number of differentially expressed transcription factors in cambium cells of OP42 compared with T89 was revealed by a more intense transcriptional reprograming in the former. PtMYC2, a potential negative regulator, was less expressed in OP42 compared with T89. Using transgenic approaches, we demonstrated that PttARF17.1 and PttMYC2.1 negatively regulate adventitious rooting. Our results provide insights into the molecular basis of genotypic differences in AR and implicate differential expression of the master regulator MYC2 as a critical player in this process.

Genome-Wide Identification and Evolution Analysis of the Gibberellin Oxidase Gene Family in Six Gramineae Crops

The plant hormones gibberellins (GAs) regulate plant growth and development and are closely related to the yield of cash crops. The GA oxidases (GAoxs), including the GA2ox, GA3ox, and GA20ox subfamilies, play pivotal roles in GAs' biosynthesis and metabolism, but their classification and evolutionary pattern in Gramineae crops remain unclear. We thus conducted a comparative genomic study of GAox genes in six Gramineae representative crops, namely, Setaria italica (Si), Zea mays (Zm), Sorghum bicolor (Sb), Hordeum vulgare (Hv), Brachypodium distachyon (Bd), and Oryza sativa (Os). A total of 105 GAox genes were identified in these six crop genomes, belonging to the C19-GA2ox, C20-GA2ox, GA3ox, and GA20ox subfamilies. Based on orthogroup (OG) analysis, GAox genes were divided into nine OGs and the number of GAox genes in each of the OGs was similar among all tested crops, which indicated that GAox genes may have completed their family differentiations before the species differentiations of the tested species. The motif composition of GAox proteins showed that motifs 1, 2, 4, and 5, forming the 2OG-FeII_Oxy domain, were conserved in all identified GAox protein sequences, while motifs 11, 14, and 15 existed specifically in the GA20ox, C19-GA2ox, and C20-GA2ox protein sequences. Subsequently, the results of gene duplication events suggested that GAox genes mainly expanded in the form of WGD/SD and underwent purification selection and that maize had more GAox genes than other species due to its recent duplication events. The cis-acting elements analysis indicated that GAox genes may respond to growth and development, stress, hormones, and light signals. Moreover, the expression profiles of rice and maize showed that GAox genes were predominantly expressed in the panicles of the above two plants and the expression of several GAox genes was significantly induced by salt or cold stresses. In conclusion, our results provided further insight into GAox genes' evolutionary differences among six representative Gramineae and highlighted GAox genes that may play a role in abiotic stress.

Remediation for trace metals in polluted soils by turfgrass assisted with chemical reagents

Trace metal pollution in soils is one of the universal environmental problems in the world. Phytoremediation is a green, safe, ecological, and economic method to achieve continuous reduction of soil pollutants. Turfgrass is a plant with great landscape value and has considerable biomass when used for remediation of trace metal contaminated soil. However, its remediation ability needs to be improved in future application. The combined application of turfgrass, citric acid (CA) and auxin (gibberellin, GA₃) were applied in the phytoremediation of an artificial nutritive soil derived from sludge, and a field scale orthogonal experiment (L₉) was conducted to understand the interaction effect and obtain the optimum phytoremediation. Experimental results showed that the types and cultural patterns of turfgrass mainly determined plant height, root length and trace metal concentration in turfgrass, however CA treatment was prone to increase the aboveground biomass and the concentrations of most trace metals in turfgrasses, especially the concentration of Ni in turfgrass. GA₃ spraying significantly increased the concentration of Cd in turfgrass. The culture patterns of turfgrass played 42.4% influence on acid-extractable Cd, while CA applying had 53.8% influence on the acid-extractable Ni. The annual phytoextraction amount of trace metals based on five mowing a year were proposed to assess the remediation ability of treatments, which of the combination treatment (T3, intercropping Zoysia matrella and Lolium perenne, and applying 400 mg kg^-1 CA and 30 mg kg^-1 GA₃) were 1.6-2.1 times higher CK group. This research provides technical reference for intercropping turfgrass for remediation of trace metals in sludge-derived nutritive soil.

Gibberellins regulate lateral root development that is associated with auxin and cell wall metabolisms in cucumber

Cucumber is an economically important crop cultivated worldwide. Gibberellins (GAs) play important roles in the development of lateral roots (LRs), which are critical for plant stress tolerance and productivity. Therefore, it is of great importance for cucumber production to study the role of GAs in LR development. Here, the results showed that GAs regulated cucumber LR development in a concentration-dependent manner. Treatment with 1, 10, 50 and 100 μM GA₃ significantly increased secondary root length, tertiary root number and length. Of these, 50 μM GA₃ treatment had strong effects on increasing root dry weight and the root/shoot dry weight ratio. Pairwise comparisons identified 417 down-regulated genes enriched for GA metabolism-related processes and 447 up-regulated genes enriched for cell wall metabolism-related processes in GA₃-treated roots. A total of 3523 non-redundant DEGs were identified in our RNA-Seq data through pairwise comparisons and linear factorial modeling. Of these, most of the genes involved in auxin and cell wall metabolisms were up-regulated in GA₃-treated roots. Our findings not only shed light on LR regulation mediated by GA but also offer an important resource for functional studies of candidate genes putatively involved in the regulation of LR development in cucumber and other crops.

Salicylic Acid in Root Growth and Development

In plants, salicylic acid (SA) is a hormone that mediates a plant’s defense against pathogens. SA also takes an active role in a plant’s response to various abiotic stresses, including chilling, drought, salinity, and heavy metals. In addition, in recent years, numerous studies have confirmed the important role of SA in plant morphogenesis. In this review, we summarize data on changes in root morphology following SA treatments under both normal and stress conditions. Finally, we provide evidence for the role of SA in maintaining the balance between stress responses and morphogenesis in plant development, and also for the presence of SA crosstalk with other plant hormones during this process.

The molecular events underpinning cultivar differences in melatonin counteracting salt damage in Phaseolus vulgaris

Melatonin (N -acetyl-5-methoxytryptamine) plays important roles in multiple stress responses, especially under salt stress. However, cultivar differences in melatonin mediated salt stress tolerance are unclear. Phaseolus vulgaris L. (common bean) cultivars Jiyin 1 (JY, salt-tolerant) and Xuliyabai (XL, salt-sensitive) were used in this study. Exogenous melatonin significantly improved root growth under salt stress in JY, but had little effect on XL. Physiology analysis showed significant differences in activities of antioxidant enzymes (superoxide, SOD; and catalase, CAT) and malondialdehyde content between JY and XL. Meanwhile, the change of ABA content in JY and XL root was opposite in salt plus melatonin treatment. Comparative root transcriptomes of JY and XL revealed 3505 and 668 differentially expressed genes (DEGs) regulated by salt stress and melatonin. The most enriched melatonin-responsive genes under salt stress are mainly involved in regulation of transcription, oxidation-reduction process, transcription factor activity, oxidoreductase activity. In addition, melatonin induced more obvious changes of DEGs in JY than that in XL under salt condition. Melatonin also significantly induced 41 DEGs only in JY, including signal transduction genes, transcription factors, ubiquitin protein ligases, ion homeostasis and osmotic adjustment genes etc. This study uncovered the molecular mechanism of cultivar difference of melatonin response under salt stress in common bean.

Gibberellin in tomato: metabolism, signaling and role in drought responses

The growth-promoting hormone gibberellin (GA) regulates numerous developmental processes throughout the plant life cycle. It also affects plant response to biotic and abiotic stresses. GA metabolism and signaling in tomato (Solanum lycopersicum) have been studied in the last three decades and major components of the pathways were characterized. These include major biosynthesis and catabolism enzymes and signaling components, such as the three GA receptors GIBBERELLIN INSENSITIVE DWARF 1 (GID1) and DELLA protein PROCERA (PRO), the central response suppressor. The role of these components in tomato plant development and response to the environment have been investigated. Cultivated tomato, similar to many other crop plants, are susceptible to water deficiency. Numerous studies on tomato response to drought have been conducted, including the possible role of GA in tomato drought resistance. Most studies showed that reduced levels or activity of GA improves drought tolerance and drought avoidance. This review aims to provide an overview on GA biosynthesis and signaling in tomato, how drought affects these pathways and how changes in GA activity affect tomato plant response to water deficiency. It also presents the potential of using the GA pathway to generate drought-tolerant tomato plants with improved performance under both irrigation and water-limited conditions.

GhWRKY21 regulates ABA-mediated drought tolerance by fine-tuning the expression of GhHAB in cotton

KEY MESSAGE

We report that GhWRKY21, a WRKY transcription factor, plays essential roles in regulating the intensity of the drought-induced ABA signalling pathway by facilitating the expression of GhHAB in cotton (Gossypium hirsutum). Abscisic acid (ABA) is one of the most important plant hormones in response to abiotic stress. However, activation of the ABA signalling pathway often leads to growth inhibition. The mechanisms that regulate the intensity of ABA signals are poorly understood. Here, we isolated and analysed the cotton group IId WRKY transcription factor (TF) gene GhWRKY21. Functional analysis indicated that GhWRKY21 plays a negative role in the drought response of cotton. Silencing of GhWRKY21 in cotton dramatically increased drought tolerance, whereas ectopic GhWRKY21 overexpression in Nicotiana benthamiana decreased drought tolerance. Furthermore, the GhWRKY21-mediated drought tolerance was ABA dependent. To clarify the mechanism underlying the GhWRKY21-mediated regulation of drought tolerance, 17 clade-A-type type 2C protein phosphatase (PP2C) genes, which are negative regulators of ABA signalling, were identified in cotton. Notably, GhWRKY21 interacted specifically with the W-box element within the promoter of GhHAB and regulated its expression. Silencing of GhHAB in cotton yielded a phenotype similar to that of GhWRKY21-silenced cotton. These results suggest that GhWRKY21 regulates the intensity of ABA signals by facilitating the expression of GhHAB. In summary, these findings dramatically improve our understanding of the function of WRKY TFs and provide insights into the mechanism of ABA-mediated drought tolerance.

The role of AcPGIP in the kiwifruit (Actinidia chinensis) response to Botrytis cinerea

Kiwifruit (Actinidia chinensis) is rich in nutritional and medicinal value. However, the organism responsible for grey mould, Botrytis cinerea, causes great economic losses and food safety problems to the kiwifruit industry. Understanding the molecular mechanism underlying postharvest kiwifruit responses to B. cinerea is important for preventing grey mould decay and enhancing resistance breeding. Kiwifruit cv. 'Hongyang' was used as experimental material. The AcPGIP gene was cloned and virus-induced gene silencing (VIGS) was used to explore the function of the polygalacturonase inhibiting protein (PGIP) gene in kiwifruit resistance to B. cinerea. Virus-induced silencing of AcPGIP resulted in enhanced susceptibility of kiwifruit to B. cinerea. Antioxidant enzymes, secondary metabolites and endogenous hormones were analysed to investigate kiwifruit responses to B. cinerea infection. Kiwifruit effectively activated antioxidant enzymes and secondary metabolite production in response to B. cinerea, which significantly increased Indole-3-acetic acid (IAA), gibberellin 3 (GA3) and abscisic acid (ABA) content relative to those in uninfected fruit. Silencing of AcPGIP enabled kiwifruit to quickly activate hormone-signaling pathways through an alternative mechanism to trigger defence responses against B. cinerea infection. These results expand our understanding of the regulatory mechanism for disease resistance in kiwifruit; further, they provide gene-resource reserves for molecular breeding of kiwifruit for disease resistance.

Gibberellic acid application on biomass, oxidative stress response, and photosynthesis in spinach (Spinacia oleracea L.) seedlings under copper stress

The mechanism of Cu tolerance in plants and its control measures are of considerable significance for the remediation of Cu-contaminated soils. Gibberellic acid (GA₃) is involved in plant growth and development and in the response to heavy metal stress. In the present study, changes in the biomass, oxidative stress response responses, and photosynthesis of spinach seedlings were examined under Cu stress with exogenous GA₃ applied at concentrations of 0, 3, 5, 10, 20, 40, 60, or 80 mg L^-1. Under Cu stress, the plant Cu concentration and oxidative damage were greater, photosynthetic parameters and biomass declined, and antioxidant enzyme activities and the proline concentration increased. However, spinach growth did not terminate, indicating that spinach seedlings had strong Cu tolerance. When low concentrations of GA₃ (3-5 mg L^-1) were added to Cu-stressed spinach seedlings, the damage caused by Cu stress to spinach seedlings was reduced, and the Cu tolerance of spinach seedlings was enhanced, which mainly manifested as reduced oxidation damage, an increased proline concentration, elevated antioxidant enzyme activities, decreased Cu concentration in leaves, and increased Cu concentration in roots, increased photosynthetic parameters, and an increased in the total biomass. In contrast, additions of GA₃ at concentrations higher than 40 mg L^-1 intensified oxidative damage and decreased the activities of antioxidant enzymes, photosynthetic parameters, and biomass. Additionally, the Cu concentration increased in leaves and decreased Cu concentration in roots, indicating that high concentrations of GA₃ aggravated stress damage and severely influenced physiological functions in spinach seedlings. In summary, the application of 3-5 mg L^-1 GA₃ to spinach seedlings in Cu-contaminated soil can be used to reduce Cu toxicity to plants and increase Cu tolerance.

A high concentration of abscisic acid inhibits hypocotyl phototropism in Gossypium arboreum by reducing accumulation and asymmetric distribution of auxin

Hypocotyl phototropism is mediated by the phototropins and plays a critical role in seedling morphogenesis by optimizing growth orientation. However, the mechanisms by which phototropism influences morphogenesis require additional study, especially for polyploid crops such as cotton. Here, we found that hypocotyl phototropism was weaker in Gossypium arboreum than in G. raimondii (two diploid cotton species), and LC-MS analysis indicated that G. arboreum hypocotyls had a higher content of abscisic acid (ABA) and a lower content of indole-3-acetic acid (IAA) and bioactive gibberellins (GAs). Consistently, the expression of ABA2, AAO3, and GA2OX1 was higher in G. arboreum than in G. raimondii, and that of GA3OX was lower; these changes promoted ABA synthesis and the transformation of active GA to inactive GA. Higher concentrations of ABA inhibited the asymmetric distribution of IAA across the hypocotyl and blocked the phototropic curvature of G. raimondii. Application of IAA or GA3 to the shaded and illuminated sides of the hypocotyl enhanced and inhibited phototropic curvature, respectively, in G. arboreum. The application of IAA, but not GA, to one side of the hypocotyl caused hypocotyl curvature in the dark. These results indicate that the asymmetric distribution of IAA promotes phototropic growth, and the weakened phototropic curvature of G. arboreum may be attributed to its higher ABA concentrations that inhibit the action of auxin, which is regulated by GA signaling.

Transcriptomic Analysis of Radish (Raphanus sativus L.) Spontaneous Tumor

Spontaneous tumors can develop in different organs of various plant species without any pathogen infection and, as a rule, appear in plants with a certain genotype: Mutants, interspecific hybrids, etc. In particular, among the inbred lines of radish (Raphanus sativus L.), lines that form spontaneous tumors on the taproot during the flowering period were obtained many years ago. In this work, we analyzed the differential gene expression in the spontaneous tumors of radish versus the lateral roots using the RNA-seq method. Data were obtained indicating the increased expression of genes associated with cell division and growth (especially genes that regulate G2-M transition and cytokinesis) in the spontaneous tumor. Among genes downregulated in the tumor tissue, genes participating in the response to stress and wounding, mainly involved in the biosynthesis of jasmonic acid and glucosinolates, were enriched. Our data will help elucidate the mechanisms of spontaneous tumor development in higher plants.

Loss of COMT activity reduces lateral root formation and alters the response to water limitation in sorghum brown midrib (bmr) 12 mutant

Lignin is a key target for modifying lignocellulosic biomass for efficient biofuel production. Brown midrib 12 (bmr12) encodes the sorghum caffeic acid O-methyltransferase (COMT) and is one of the key enzymes in monolignol biosynthesis. Loss of function mutations in COMT reduces syringyl (S) lignin subunits and improves biofuel conversion rate. Although lignin plays an important role in maintaining cell wall integrity of xylem vessels, physiological and molecular consequences due to loss of COMT on root growth and adaptation to water deficit remain unexplored. We addressed this gap by evaluating the root morphology, anatomy and transcriptome of bmr12 mutant. The mutant had reduced lateral root density (LRD) and altered root anatomy and response to water limitation. The wild-type exhibits similar phenotypes under water stress, suggesting that bmr12 may be in a water deficit responsive state even in well-watered conditions. bmr12 had increased transcript abundance of genes involved in (a)biotic stress response, gibberellic acid (GA) biosynthesis and signaling. We show that bmr12 is more sensitive to exogenous GA application and present evidence for the role of GA in regulating reduced LRD in bmr12. These findings elucidate the phenotypic and molecular consequences of COMT deficiency under optimal and water stress environments in grasses.

Genome-wide analysis of UGDH genes in Populus trichocarpa and responsiveness to nitrogen treatment

Plant UDP-glucose 6-dehydrogenase (UGDH) is an important enzyme for the formation of hemicellulose and pectin. Previous studies on UGDH have primarily focused on the biosynthesis of cell wall polysaccharides, while few studies have focused on their regulation by exogenous nitrogen. In the present study, four genes encoding PtUGDH proteins were analyzed by bioinformatics methods. And, the expression profiles of PtUGDH genes under different nitrogen treatments were evaluated with qRT-PCR. The results showed that PtUGDHs have conserved NAD coenzyme binding motif GAGYVGG and the catalytic motif GFGGSCFQKDIL. According to the phylogenetic analysis, PtUGDHs were divided into two subgroups. PtUGDH3 and PtUGDH4 were closely related to AtUGDH1 (important for normal development of Arabidopsis cell wall structure). Chromosomal distribution and genome synteny analysis revealed four segmental-duplicated gene pairs on chr4, 8, 10 and 17. Tissue-specific data from PlantGenIE showed that PtUGDH3 and PtUGDH4 were highly expressed in stems. The qRT-PCR detection showed that the expression of PtUGDH3 in the lower stem and PtUGDH2 of upper leaves were significantly increased induced by low ammonium or nitrate condition. This comprehensive analysis of the UGDH family in poplar provides new insights into their regulation by nitrogen, and would increase our understanding of the roles of UGDHs in hemicellulose and pectin biosynthesis in the cell wall and during poplar development.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-021-02697-9.

EARLY BUD-BREAK 1 and EARLY BUD-BREAK 3 control resumption of poplar growth after winter dormancy

Bud-break is an economically and environmentally important process in trees and shrubs from boreal and temperate latitudes, but its molecular mechanisms are poorly understood. Here, we show that two previously reported transcription factors, EARLY BUD BREAK 1 (EBB1) and SHORT VEGETATIVE PHASE-Like (SVL) directly interact to control bud-break. EBB1 is a positive regulator of bud-break, whereas SVL is a negative regulator of bud-break. EBB1 directly and negatively regulates SVL expression. We further report the identification and characterization of the EBB3 gene. EBB3 is a temperature-responsive, epigenetically-regulated, positive regulator of bud-break that provides a direct link to activation of the cell cycle during bud-break. EBB3 is an AP2/ERF transcription factor that positively and directly regulates CYCLIND3.1 gene. Our results reveal the architecture of a putative regulatory module that links temperature-mediated control of bud-break with activation of cell cycle.

Adventitious Rooting in Populus Species: Update and Perspectives

Populus spp. are among the most economically important species worldwide. These trees are used not only for wood and fiber production, but also in the rehabilitation of degraded lands. Since they are clonally propagated, the ability of stem cuttings to form adventitious roots is a critical point for plant establishment and survival in the field, and consequently for the forest industry. Adventitious rooting in different Populus clones has been an agronomic trait targeted in breeding programs for many years, and many factors have been identified that affect this quantitative trait. A huge variation in the rooting capacity has been observed among the species in the Populus genus, and the responses to some of the factors affecting this trait have been shown to be genotype-dependent. This review analyses similarities and differences between results obtained from studies examining the role of internal and external factors affecting rooting of Populus species cuttings. Since rooting is the most important requirement for stand establishment in clonally propagated species, understanding the physiological and genetic mechanisms that promote this trait is essential for successful commercial deployment.

Investigation of the role of AcTPR2 in kiwifruit and its response to Botrytis cinerea infection

BACKGROUND

Elucidation of the regulatory mechanism of kiwifruit response to gray mold disease caused by Botrytis cinerea can provide the basis for its molecular breeding to impart resistance against this disease. In this study, 'Hongyang' kiwifruit served as the experimental material; the TOPLESS/TOPLESS-RELATED (TPL/TPR) co-repressor gene AcTPR2 was cloned into a pTRV2 vector (AcTPR2-TRV) and the virus-induced gene silencing technique was used to establish the functions of the AcTPR2 gene in kiwifruit resistance to Botrytis cinerea.

RESULTS

Virus-induced silencing of AcTPR2 enhanced the susceptibility of kiwifruit to Botrytis cinerea. Defensive enzymes such as superoxide dismutase (SOD), peroxidase (POD), catalase (CAT), and phenylalanine ammonia-lyase (PAL) and endogenous phytohormones such as indole acetic acid (IAA), gibberellin (GA3), abscisic acid (ABA), and salicylic acid (SA) were detected. Kiwifruit activated these enzymes and endogenous phytohormones in response to pathogen-induced stress and injury. The expression levels of the IAA signaling genes-AcNIT, AcARF1, and AcARF2-were higher in the AcTPR2-TRV treatment group than in the control. The IAA levels were higher and the rot phenotype was more severe in AcTPR2-TRV kiwifruits than that in the control. These results suggested that AcTPR2 downregulation promotes expression of IAA and IAA signaling genes and accelerates postharvest kiwifruit senescence. Further, Botrytis cinerea dramatically upregulated AcTPR2, indicating that AcTPR2 augments kiwifruit defense against pathogens by downregulating the IAA and IAA signaling genes.

CONCLUSIONS

The results of the present study could help clarify the regulatory mechanisms of disease resistance in kiwifruit and furnish genetic resources for molecular breeding of kiwifruit disease resistance.

Exogenous 6-benzyladenine application affects root morphology by altering hormone status and gene expression of developing lateral roots in Malus hupehensis

Malus hupehensis is an extensively used apple rootstock in China. In the current study, M. hupehensis seedlings were treated with exogenous 2.2 µm 6-benzyladenine (6-BA) so as to investigate the mechanism by which 6-BA affects lateral root development. The results indicate that 6-BA treatment promotes elongation and thickening of both root and shoot in M. hupehensis, but reduces the number of lateral roots, as well as reducing the auxin level after 6-BA treatment. Moreover, MhAHK4, MhRR1 and MhRR2 were also significantly up-regulated in response to 6-BA treatment. Expression levels of auxin synthesis- and transport-related genes, such as MhYUCCA6, MhYUCCA10, MhPIN1 and MhPIN2, were down-regulated, which corresponds with lower auxin levels in the 6-BA-treated seedlings. A negative regulator of auxin, MhIAA3, was induced by 6-BA treatment, leading to reduced expression of MhARF7 and MhARF19 in 6-BA-treated seedlings. As a result, expression of MhWOX11, MhWOX5, MhLBD16 and MhLBD29 was blocked, which in turn inhibited lateral root initiation. In addition, a lower auxin level decreased expression of MhRR7 and MhRR15, which repressed expression of key transcription factors associated with root development, thus inhibiting lateral root development. In contrast, 6-BA treatment promoted secondary growth (thickening) of the root by inducing expression of MhCYCD3;1 and MhCYCD3;2. Collectively, the changes in hormone levels and gene expression resulted in a reduced number of lateral roots and thicker roots in 6-BA-treated plants.

Identifying key regulatory genes of maize root growth and development by RNA sequencing

Root system architecture (RSA), the spatio-temporal configuration of roots, plays vital roles in maize (Zea mays L.) development and productivity. We sequenced the maize root transcriptome of four key growth and development stages: the 6th leaf stage, the 12th leaf stage, the tasseling stage and the milk-ripe stage. Differentially expressed genes (DEGs) were detected. 81 DEGs involved in plant hormone signal transduction pathway and 26 transcription factor (TF) genes were screened. These DEGs and TFs were predicted to be potential candidate genes during maize root growth and development. Several of these genes are homologous to well-known genes regulating root architecture or development in Arabidopsis or rice, such as, Zm00001d005892 (AtERF109), Zm00001d027925 (AtERF73/HRE1), Zm00001d047017 (AtMYC2, OsMYC2), Zm00001d039245 (AtWRKY6). Identification of these key genes will provide a further understanding of the molecular mechanisms responsible for maize root growth and development, it will be beneficial to increase maize production and improve stress resistance by altering RSA traits in modern breeding.

The bZIP53-IAA4 module inhibits adventitious root development in Populus

Adventitious roots (ARs) are important for some plants that depend on clonal propagation. In this study, we demonstrate that a salt-responsive gene module is involved in the negative regulation of AR development in poplar. In this module, the expression of bZIP53 is induced by salt stress and it encodes a transcription factor with transactivation activity. Overexpression or induced expression of bZIP53 in poplar lines resulted in inhibition of AR growth, while heterologous overexpression of bZIP53 in Arabidopsis resulted in a similar phenotype. Results from RNA-seq and RT-qPCR assays predicted IAA4-1 and IAA4-2 to be downstream genes that were regulated by bZIP53. Further investigation of protein-DNA interactions using yeast one-hybrid, electrophoretic mobility shift, dual luciferase reporter, and GUS co-expression assays also showed that IAA4-1/2 were the genes that were directly regulated by bZIP53. Induced-expression IAA4-1/2 transgenic poplar lines also showed inhibited AR growth. In addition, both poplar bZIP53 and IAA4-1/2 showed a response to salt stress. On the basis of these results, we conclude that the bZIP53-IAA4 module is involved in the negative regulation of AR development in poplar.

A novel insight into nitrogen and auxin signaling in lateral root formation in tea plant [Camellia sinensis (L.) O. Kuntze]

BACKGROUND

Tea plant (Camellia sinensis) is one of the most popular non-alcoholic beverages worldwide. In tea, lateral roots (LRs) are the main organ responsible for the absorption of moisture and mineral nutrients from the soil. Lateral roots formation and development are regulated by the nitrogen and auxin signaling pathways. In order to understand the role of auxin and nitrogen signaling in LRs formation and development, transcriptome analysis was employed to investigate the differentially expressed genes involved in lateral roots of tea plants treated with indole-3-butyric acid (IBA), N-1-naphthylphthalamic acid (NPA), low and high concentrations of nitrogen.

RESULTS

A total of 296 common differentially expressed genes were identified and annotated to four signaling pathways, including nitrogen metabolism, plant hormone signal transduction, glutathione metabolism and transcription factors. RNA-sequencing results revealed that majority of differentially expressed genes play important roles in nitrogen metabolism and hormonal signal transduction. Low nitrogen condition induced the biosynthesis of auxin and accumulation of transcripts, thereby, regulating lateral roots formation. Furthermore, metabolism of cytokinin and ethylene biosynthesis were also involved in lateral roots development. Transcription factors like MYB genes also contributed to lateral roots formation of tea plants through secondary cell wall biosynthesis. Reversed phase ultra performance liquid chromatography (RP-UPLC) results showed that the auxin concentration increased with the decreased nitrogen level in lateral roots. Thus, tea plant lateral roots formation could be induced by low nitrogen concentration via auxin biosynthesis and accumulation.

CONCLUSION

This study provided insights into the mechanisms associated with nitrogen and auxin signaling pathways in LRs formation and provides information on the efficient utilization of nitrogen in tea plant at the genetic level.

Same same, but different: growth responses of primary and lateral roots

The root system architecture describes the shape and spatial arrangement of roots within the soil. Its spatial distribution depends on growth and branching rates as well as directional organ growth. The embryonic primary root gives rise to lateral (secondary) roots, and the ratio of both root types changes over the life span of a plant. Most studies have focused on the growth of primary roots and the development of lateral root primordia. Comparably less is known about the growth regulation of secondary root organs. Here, we review similarities and differences between primary and lateral root organ growth, and emphasize particularly how external stimuli and internal signals differentially integrate root system growth.

Functional genomics by integrated analysis of transcriptome of sweet potato (Ipomoea batatas (L.) Lam.) during root formation

BACKGROUND

Sweet potato is easily propagated by cuttings. But the molecular biological mechanism of adventitious root formation are not yet clear.

OBJECTIVE

To understand the molecular mechanisms of adventitious root formation from stem cuttings in sweet potato.

METHODS

RNA-seq analysis was performed using un-rooted stem (0 day) and rooted stem (3 days). Gene Ontology (GO) enrichment analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, comparison with Arabidopsis transcription factors (TFs) of DEGs were conducted to investigate the characteristics of genes and TFs involved in root formation. In addition, qRT-PCR analysis using roots at 0, 3, 6, 9, and 12 days after planting was performed to confirm RNA-seq reliability and related genes expression.

RESULTS

42,459 representative transcripts and 2092 DEGs were obtained through the RNA-seq analysis. The DEGs indicated the GO terms related to the single-organism metabolic process and cell periphery, and involved in the biosynthesis of secondary metabolites, and phenylpropanoid biosynthesis in KEGG pathways. The comparison with Arabidopsis thaliana TF database showed that 3 TFs (WRKY, NAC, bHLH) involved in root formation of sweet potato. qRT-PCR analysis, which was conducted to confirm the reliability of RNA-seq analysis, indicated that some metabolisms including oxidative stress and wounding, transport, hormone may be involved in adventitious root formation.

CONCLUSIONS

The detected genes related to secondary metabolism, some hormone (auxin, gibberellin), transports, etc. and 3 TFs (WRKY, NAC, bHLH) may have functions in adventitious roots formation. This results provide valuable resources for future research on the adventitious root formation of sweet potato.

Gibberellin repression of axillary bud formation in Arabidopsis by modulation of DELLA-SPL9 complex activity

The formation of lateral branches has an important and fundamental contribution to the remarkable developmental plasticity of plants, which allows plants to alter their architecture to adapt to the challenging environment conditions. The Gibberellin (GA) phytohormones have been known to regulate the outgrowth of axillary meristems (AMs), but the specific molecular mechanisms remain unclear. Here we show that DELLA proteins regulate axillary bud formation by interacting and regulating the DNA-binding ability of SQUAMOSA-PROMOTER BINDING PROTEIN LIKE 9 (SPL9), a microRNA156-targeted squamosa promoter binding protein-like transcription factor. SPL9 participates in the initial regulation of axillary buds by repressing the expression of LATERAL SUPPRESSOR (LAS), a key regulator in the initiation of AMs, and LAS contributes to the specific expression pattern of the GA deactivation enzyme GA2ox4, which is specifically expressed in the axils of leaves to form a low-GA cell niche in this anatomical region. Nevertheless, increasing GA levels in leaf axils by ectopically expressing the GA-biosynthesis enzyme GA20ox2 significantly impaired axillary meristem initiation. Our study demonstrates that DELLA-SPL9-LAS-GA2ox4 defines a core feedback regulatory module that spatially pattern GA content in the leaf axil and precisely control the axillary bud formation in different spatial and temporal.

An ectomycorrhizal fungus alters sensitivity to jasmonate, salicylate, gibberellin, and ethylene in host roots

The phytohormones jasmonate, gibberellin, salicylate, and ethylene regulate an interconnected reprogramming network integrating root development with plant responses against microbes. The establishment of mutualistic ectomycorrhizal symbiosis requires the suppression of plant defense responses against fungi as well as the modification of root architecture and cortical cell wall properties. Here, we investigated the contribution of phytohormones and their crosstalk to the ontogenesis of ectomycorrhizae (ECM) between grey poplar (Populus tremula x alba) roots and the fungus Laccaria bicolor. To obtain the hormonal blueprint of developing ECM, we quantified the concentrations of jasmonates, gibberellins, and salicylate via liquid chromatography-tandem mass spectrometry. Subsequently, we assessed root architecture, mycorrhizal morphology, and gene expression levels (RNA sequencing) in phytohormone-treated poplar lateral roots in the presence or absence of L. bicolor. Salicylic acid accumulated in mid-stage ECM. Exogenous phytohormone treatment affected the fungal colonization rate and/or frequency of Hartig net formation. Colonized lateral roots displayed diminished responsiveness to jasmonate but regulated some genes, implicated in defense and cell wall remodelling, that were specifically differentially expressed after jasmonate treatment. Responses to salicylate, gibberellin, and ethylene were enhanced in ECM. The dynamics of phytohormone accumulation and response suggest that jasmonate, gibberellin, salicylate, and ethylene signalling play multifaceted roles in poplar L. bicolor ectomycorrhizal development.

SlCAND1, encoding cullin-associated Nedd8-dissociated protein 1, regulates plant height, flowering time, seed germination, and root architecture in tomato

Silencing of SlCAND1 expression resulted in dwarfish, loss of apical dominance, early flowering, suppression of seed germination, and abnormal root architecture in tomato Cullin-RING E3 ligases (CRLs)-dependent ubiquitin proteasome system mediates degradation of numerous proteins that controls a wide range of developmental and physiological processes in eukaryotes. Cullin-associated Nedd8-dissociated protein 1 (CAND1) acts as an exchange factor allowing substrate recognition part exchange and plays a vital role in reactivating CRLs. The present study reports on the identification of SlCAND1, the only one CAND gene in tomato. SlCAND1 expression is ubiquitous and positively regulated by multiple plant hormones. Silencing of SlCAND1 expression using RNAi strategy resulted in a pleiotropic and gibberellin/auxin-associated phenotypes, including dwarf plant with reduced internode length, loss of apical dominance, early flowering, low seed germination percentage, delayed seed germination speed, short primary root, and increased lateral root proliferation and elongation. Moreover, application of exogenous GA₃ or IAA could partly rescue some SlCAND1-silenced phenotypes, and the expression levels of gibberellin/auxin-related genes were altered in SlCAND1-RNAi lines. These facts revealed that SlCAND1 is required for gibberellin/auxin-associated regulatory network in tomato. Although SlCAND1 is crucial for multiple developmental processes during vegetative growth stage, SlCAND1-RNAi lines didn't exhibit visible effect on fruit development and ripening. Meanwhile, we discussed that multiple physiological functions of SlCAND1 in tomato are different to previous report of its ortholog in Arabidopsis. Our study adds a new perspective on the functional roles of CAND1 in plants, and strongly supports the hypothesis that CAND1 and its regulated ubiquitin proteasome system are pivotal for plant vegetative growth but possibly have different roles in diverse plant species.