Exogenous gibberellin altered morphology, anatomic and transcriptional regulatory networks of hormones in carrot root and shoot

The Application of Paclobutrazol to GA3-Treated Seed Tuber Potato Fields Does Not Shorten the Growth Cycle or Mitigate Tuber Elongation

Potato seed tubers are a valuable product in potato agriculture. Over the years, studies have been conducted to increase the fraction of mid-size tubers, which are used as a planting material, within the general pool of tuber sizes. Gibberellic acid has been a central component of such studies and has successfully increased the seed-size pool. However, in many cases, misshapen tubers were formed, and the practice has not become widespread. The use of the gibberellic acid inhibitor paclobutrazol has been examined for its ability to increase seed tuber number and tuber growth and to overcome the heat inhibition of tuberization in warm climates. Paclobutrazol has been shown to increase tuber yield and growth rate. In this study, we aimed to test whether the combination of gibberellic acid and paclobutrazol can increase the seed tuber pool, reduce the number of misshapen tubers, and shorten the growth cycle, thus avoiding end-of-season elevated heat conditions and reducing agricultural inputs. Our findings suggest that gibberellic acid on its own can lead to an increase in the number of seed tubers at earlier stages of growth; however, the sequential addition of paclobutrazol was not able to drive even earlier growth or lower the number of misshapen tubers.

Crape myrtle LiGAoxs displaying activities of gibberellin oxidases respond to branching architecture

In the realm of ornamental horticulture, crape myrtle (Lagerstroemia indica) stands out for its aesthetic appeal, attributed largely to its vibrant flowers and distinctive branching architecture. This study embarked on a comprehensive exploration of the gibberellin oxidase (GAox) gene family in crape myrtle, illuminating its pivotal role in regulating GA levels, a key determinant of plant developmental processes. We identified and characterized 36 LiGAox genes, subdivided into GA2ox, GA3ox, GA20ox, and GAox-like subgroups, through genomic analyses. These genes' evolutionary trajectories were delineated, revealing significant gene expansions attributed to segmental duplication events. Functional analyses highlighted the divergent expression patterns of LiGAox genes across different crape myrtle varieties, associating them with variations in flower color and branching architecture. Enzymatic activity assays on selected LiGA2ox enzymes exhibited pronounced GA2 oxidase activity, suggesting a potential regulatory role in GA biosynthesis. Our findings offered a novel insight into the molecular underpinnings of GA-mediated growth and development in L. indica, providing a foundational framework for future genetic enhancements aimed at optimizing ornamental traits.

Plant communication with rhizosphere microbes can be revealed by understanding microbial functional gene composition

Understanding rhizosphere microbial ecology is necessary to reveal the interplay between plants and associated microbial communities. The significance of rhizosphere-microbial interactions in plant growth promotion, mediated by several key processes such as auxin synthesis, enhanced nutrient uptake, stress alleviation, disease resistance, etc., is unquestionable and well reported in numerous literature. Moreover, rhizosphere research has witnessed tremendous progress due to the integration of the metagenomics approach and further shift in our viewpoint from taxonomic to functional diversity over the past decades. The microbial functional genes corresponding to the beneficial functions provide a solid foundation for the successful establishment of positive plant-microbe interactions. The microbial functional gene composition in the rhizosphere can be regulated by several factors, e.g., the nutritional requirements of plants, soil chemistry, soil nutrient status, pathogen attack, abiotic stresses, etc. Knowing the pattern of functional gene composition in the rhizosphere can shed light on the dynamics of rhizosphere microbial ecology and the strength of cooperation between plants and associated microbes. This knowledge is crucial to realizing how microbial functions respond to unprecedented challenges which are obvious in the Anthropocene. Unraveling how microbes-mediated beneficial functions will change under the influence of several challenges, requires knowledge of the pattern and composition of functional genes corresponding to beneficial functions such as biogeochemical functions (nutrient cycle), plant growth promotion, stress mitigation, etc. Here, we focus on the molecular traits of plant growth-promoting functions delivered by a set of microbial functional genes that can be useful to the emerging field of rhizosphere functional ecology.

Integrated Methylome and Transcriptome Analysis between Wizened and Normal Flower Buds in Pyrus pyrifolia Cultivar 'Sucui 1'

Here, cytosine methylation in the whole genome of pear flower buds was mapped at a single-base resolution. There was 19.4% methylation across all sequenced C sites in the Pyrus pyrifolia cultivar 'Sucui 1' flower bud genome. Meantime, the CG, CHG, and CHH sequence contexts (where H = A, T or C) exhibited 47.4%, 33.3%, and 11.9% methylation, respectively. Methylation in different gene regions was revealed through combining methylome and transcriptome analysis, which presented various transcription trends. Genes with methylated promoters exhibited lower expression levels than genes with non-methylated promoters, while body-methylated genes displayed an obvious negative correlation with their transcription levels. The methylation profiles of auxin- and cytokinin-related genes were estimated. And some of them proved to be hypomethylated, with increased transcription levels, in wizened buds. More specifically, the expression of the genes PRXP73, CYP749A22, and CYP82A3 was upregulated as a result of methylation changes in their promoters. Finally, auxin and cytokinin concentrations were higher in wizened flower buds than in normal buds. The exogenous application of paclobutrazol (PP333) in the field influenced the DNA methylation status of some genes and changed their expression level, reducing the proportion of wizened flower buds in a concentration-dependent manner. Overall, our results demonstrated the relationship between DNA methylation and gene expression in wizened flower buds of P. pyrifolia cultivar 'Sucui 1', which was associated with changes in auxin and cytokinin concentrations.

Characterization, expression pattern, and function analysis of gibberellin oxidases in Salix matsudana

Gibberellin oxidases (GAoxs) identified from many species play indispensable roles in GA biosynthesis and GA signal transduction. However, there has been limited research conducted on the GAox family of Salix matsudana, a tetraploid ornamental tree species. Here, 54 GAox genes were identified from S. matsudana and renamed as SmGA20ox1-22, SmGA2ox1-24, SmGA3ox1-6, and SmGAox-like1/2. Gene structure and conserved motif analysis showed that SmGA3ox members possess the 1 intron and other SmGAoxs contain 2-3 introns, and motif 1/2/7 universally present in all SmGAoxs. A total of 69 gene pairs were identified from SmGAox family members, and the Ka/Ks values indicated the SmGAoxs experience the purifying selection. The intra species collinearity analysis implied S. matsudana, S. purpurea, and Populus trichocarpa have the close genetic relationship. The GO analysis suggested SmGAoxs are dominantly involved in GA metabolic process, ion binding, and oxidoreductase activity. RNA-sequencing demonstrated that some SmGAoxs may play an essential role in salt and submergence stresses. In addition, the SmGA20ox13/21 displayed the dominant vitality of GA20 oxidase, but the SmGA20ox13/21 still possessed low activities of GA2 and GA3 oxidases. This study can contribute to reveal the regulatory mechanism of salt and submergence tolerance in willow.

Transcriptional alterations of peanut root during interaction with growth-promoting Tsukamurella tyrosinosolvens strain P9

The plant growth-promoting rhizobacterium Tsukamurella tyrosinosolvens P9 can improve peanut growth. In this study, a co-culture system of strain P9 and peanut was established to analyze the transcriptome of peanut roots interacting with P9 for 24 and 72 h. During the early stage of co-culturing, genes related to mitogen-activated protein kinase (MAPK) and Ca2+ signal transduction, ethylene synthesis, and cell wall pectin degradation were induced, and the up-regulation of phenylpropanoid derivative, flavonoid, and isoflavone synthesis enhanced the defense response of peanut. The enhanced expression of genes associated with photosynthesis and carbon fixation, circadian rhythm regulation, indoleacetic acid (IAA) synthesis, and cytokinin decomposition promoted root growth and development. At the late stage of co-culturing, ethylene synthesis was reduced, whereas Ca2+ signal transduction, isoquinoline alkaloid synthesis, and ascorbate and aldarate metabolism were up-regulated, thereby maintaining root ROS homeostasis. Sugar decomposition and oxidative phosphorylation and nitrogen and fatty acid metabolism were induced, and peanut growth was significantly promoted. Finally, the gene expression of seedlings inoculated with strain P9 exhibited temporal differences. The results of our study, which explored transcriptional alterations of peanut root during interacting with P9, provide a basis for elucidating the growth-promoting mechanism of this bacterial strain in peanut.

Interkingdom Hormonal Regulations between Plants and Animals Provide New Insight into Food Safety

Food safety has become an attractive topic among consumers. Raw material production for food is also a focus of social attention. As hormones are widely used in agriculture and human disease control, consumers' concerns about the safety of hormone agents have never disappeared. The present review focuses on the interkingdom regulations of exogenous animal hormones in plants and phytohormones in animals, including physiology and stress resistance. We summarize these interactions to give the public, researchers, and policymakers some guidance and suggestions. Accumulated evidence demonstrates comprehensive hormonal regulation across plants and animals. Animal hormones, interacting with phytohormones, help regulate plant development and enhance environmental resistance. Correspondingly, phytohormones may also cause damage to the reproductive and urinary systems of animals. Notably, the disease-resistant role of phytohormones is revealed against neurodegenerative diseases, cardiovascular disease, cancer, and diabetes. These resistances derive from the control for abnormal cell cycle, energy balance, and activity of enzymes. Further exploration of these cross-kingdom mechanisms would surely be of greater benefit to human health and agriculture development.

The Complex Interplay between Arbuscular Mycorrhizal Fungi and Strigolactone: Mechanisms, Sinergies, Applications and Future Directions

Plants, the cornerstone of life on Earth, are constantly struggling with a number of challenges arising from both biotic and abiotic stressors. To overcome these adverse factors, plants have evolved complex defense mechanisms involving both a number of cell signaling pathways and a complex network of interactions with microorganisms. Among these interactions, the relationship between symbiotic arbuscular mycorrhizal fungi (AMF) and strigolactones (SLs) stands as an important interplay that has a significant impact on increased resistance to environmental stresses and improved nutrient uptake and the subsequent enhanced plant growth. AMF establishes mutualistic partnerships with plants by colonizing root systems, and offers a range of benefits, such as increased nutrient absorption, improved water uptake and increased resistance to both biotic and abiotic stresses. SLs play a fundamental role in shaping root architecture, promoting the growth of lateral roots and regulating plant defense responses. AMF can promote the production and release of SLs by plants, which in turn promote symbiotic interactions due to their role as signaling molecules with the ability to attract beneficial microbes. The complete knowledge of this synergy has the potential to develop applications to optimize agricultural practices, improve nutrient use efficiency and ultimately increase crop yields. This review explores the roles played by AMF and SLs in plant development and stress tolerance, highlighting their individual contributions and the synergistic nature of their interaction.

Comparative transcriptome profiling reveals the multiple levels of crosstalk in phytohormone networks in Brassica napus

Plant hormones are the intrinsic factors that control plant development. The integration of different phytohormone pathways in a complex network of synergistic, antagonistic and additive interactions has been elucidated in model plants. However, the systemic level of transcriptional responses to hormone crosstalk in Brassica napus is largely unknown. Here, we present an in-depth temporal-resolution study of the transcriptomes of the seven hormones in B. napus seedlings. Differentially expressed gene analysis revealed few common target genes that co-regulated (up- and down-regulated) by seven hormones; instead, different hormones appear to regulate distinct members of protein families. We then constructed the regulatory networks between the seven hormones side by side, which allowed us to identify key genes and transcription factors that regulate the hormone crosstalk in B. napus. Using this dataset, we uncovered a novel crosstalk between gibberellin and cytokinin in which cytokinin homeostasis was mediated by RGA-related CKXs expression. Moreover, the modulation of gibberellin metabolism by the identified key transcription factors was confirmed in B. napus. Furthermore, all data were available online from http://yanglab.hzau.edu.cn/BnTIR/hormone. Our study reveals an integrated hormone crosstalk network in Brassica napus, which also provides a versatile resource for future hormone studies in plant species.

Combining Metabolomics and Transcriptomics to Reveal the Regulatory Mechanism of Taproot Enlargement in Panax ginseng

Ginseng is regarded as the “king of herbs” in China, with its roots and rhizomes used as medicine, and it has a high medicinal value. In order to meet the market demand, the artificial cultivation of ginseng emerged, but different growth environments significantly affect the root morphology of garden ginseng. In this study, we used ginseng cultivated in deforested land (CF-CG) and ginseng cultivated in farmland (F-CG) as experimental materials. These two phenotypes were explored at the transcriptomic and metabolomic levels so as to understand the regulatory mechanism of taproot enlargement in garden ginseng. The results show that, compared with those of F-CG, the thickness of the main roots in CF-CG was increased by 70.5%, and the fresh weight of the taproots was increased by 305.4%. Sucrose, fructose and ginsenoside were significantly accumulated in CF-CG. During the enlargement of the taproots of CF-CG, genes related to starch and sucrose metabolism were significantly up-regulated, while genes related to lignin biosynthesis were significantly down-regulated. Auxin, gibberellin and abscisic acid synergistically regulated the enlargement of the taproots of the garden ginseng. In addition, as a sugar signaling molecule, T6P might act on the auxin synthesis gene ALDH2 to promote the synthesis of auxin and, thus, participate in the growth and development of garden ginseng roots. In summary, our study is conducive to clarifying the molecular regulation mechanism of taproot enlargement in garden ginseng, and it provides new insights for the further exploration of the morphogenesis of ginseng roots.

Paclobutrazol Promotes Root Development of Difficult-to-Root Plants by Coordinating Auxin and Abscisic Acid Signaling Pathways in Phoebe bournei

Phoebe bournei is a rare and endangered plant endemic to China with higher-value uses in essential oil and structural wood production. Its seedlings are prone to death because of its undeveloped system. Paclobutrazol (PBZ) can improve root growth and development in certain plants, but its concentration effect and molecular mechanism remain unclear. Here, we studied the physiological and molecular mechanisms by which PBZ regulates root growth under different treatments. We found that, with moderate concentration treatment (MT), PBZ significantly increased the total root length (69.90%), root surface area (56.35%), and lateral root number (47.17%). IAA content was the highest at MT and was 3.83, 1.86, and 2.47 times greater than the control, low, and high-concentration treatments. In comparison, ABA content was the lowest and reduced by 63.89%, 30.84%, and 44.79%, respectively. The number of upregulated differentially expressed genes (DEGs) induced at MT was more than that of down-regulated DEGs, which enriched 8022 DEGs in response to PBZ treatments. WGCNA showed that PBZ-responsive genes were significantly correlated with plant hormone content and involved in plant hormone signal transduction and MAPK signal pathway-plant pathways, which controls root growth. The hub genes are observably associated with auxin, abscisic acid syntheses, and signaling pathways, such as PINs, ABCBs, TARs, ARFs, LBDs, and PYLs. We constructed a model which showed PBZ treatments mediated the antagonism interaction of IAA and ABA to regulate the root growth in P. bournei. Our result provides new insights and molecular strategies for solving rare plants' root growth problems.

Effects of low temperature on flowering and the expression of related genes in Loropetalum chinense var. rubrum

INTRODUCTION

Loropetalum chinense var. rubrum blooms 2-3 times a year, among which the autumn flowering period has great potential for exploitation, but the number of flowers in the autumn flowering period is much smaller than that in the spring flowering period.

METHODS

Using 'Hei Zhenzhu' and 'Xiangnong Xiangyun' as experimental materials, the winter growth environment of L. chinense var. rubrum in Changsha, Hunan Province was simulated by setting a low temperature of 6-10°C in an artificial climate chamber to investigate the effect of winter low temperature on the flowering traits and related gene expression of L. chinense var. rubrum.

RESULTS

The results showed that after 45 days of low temperature culture and a subsequent period of 25°C greenhouse culture, flower buds and flowers started to appear on days 24 and 33 of 25°C greenhouse culture for 'Hei Zhenzhu', and flower buds and flowers started to appear on days 21 and 33 of 25°C greenhouse culture for 'Xiangnong Xiangyun'. The absolute growth rate of buds showed a 'Up-Down' pattern during the 7-28 days of low temperature culture; the chlorophyll fluorescence decay rate (Rfd) of both materials showed a 'Down-Up-Down' pattern during this period. The non-photochemical quenching coefficient (NPQ) showed the same trend as Rfd, and the photochemical quenching coefficient (QP) fluctuated above and below 0.05. The expression of AP1 and FT similar genes of L. chinense var. rubrum gradually increased after the beginning of low temperature culture, reaching the highest expression on day 14 and day 28, respectively, and the expression of both in the experimental group was higher than that in the control group. The expressions of FLC, SVP and TFL1 similar genes all decreased gradually with low temperature culture, among which the expressions of FLC similar genes and TFL1 similar genes in the experimental group were extremely significantly lower than those in the control group; in the experimental group, the expressions of GA3 similar genes were all extremely significantly higher than those in the control group, and the expressions all increased with the increase of low temperature culture time.

DISCUSSION

We found that the high expression of gibberellin genes may play an important role in the process of low temperature promotion of L. chinense var. rubrum flowering, and in the future, it may be possible to regulate L. chinense var. rubrum flowering by simply spraying exogenous gibberellin instead of the promotion effect of low temperature.

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.

Physiological and Transcriptomic Responses of Growth in Neolamarckia cadamba Stimulated by Exogenous Gibberellins

(1) The phytohormones gibberellins (GAs) play a crucial role in plant growth and development, such as seed germination, flowering, fruiting, and stem elongation. Although many biological roles of GAs have been studied intensively, the molecular mechanisms of GAs in woody plants are still unclear. (2) In this study, we investigated the effects of exogenous application of GAs on Neolamarckia cadamba. (3) The height and biomass of N. cadamba increased after 7 days of GA treatment, especially on the second internode. Transcriptome analysis showed that although the majority of genes involved in the GA signaling pathway were up-regulated, the expression of GA20 oxidase (GA20ox) and GA3 oxidase (GA3ox) was down-regulated in the 3 days GA-treated group compared to the CK group. The expression of the cell elongation-related basic helix-loop-helix genes bHLH74 and bHLH49 was up-regulated in the GA-treated group compared with the CK group. Transcriptional expression levels of transcription factors involved in hormone signaling were changed, mainly including bHLH, ethylene response factor (ERF), and WRKY families. In addition, the transcriptional expression level of the key enzymes engaged in the phenylalanine pathway was downregulated after GA treatment. (4) In brief, our findings reveal the physiological and molecular mechanisms of exogenous GA treatment stimulation in N. cadamba.

Plant growth-promoting bacteria in phytoremediation of metal-polluted soils: Current knowledge and future directions

Soil metal contamination is a major concern due to the ever-rising number of areas afflicted worldwide and the detrimental effects of metals to the environment and human health. Due to their non-biodegradability and toxicity, it is paramount to prevent further metal contamination and remediate the thousands of contaminated sites across the planet. Yet, conventional reclamation based on physical and chemical methods is often expensive, impractical, and triggers secondary pollution issues. Hence, microbe-aided phytoremediation has been gaining significant traction due to its environment-friendly character, cost-effectiveness, and the breakthroughs achieved during the past few decades. Microorganisms are an essential part of natural ecosystems and play a crucial role in their restoration. Indeed, plant-microbe associations in metal-polluted soils are pivotal for plants to tolerate metal toxicity and thrive in these harsh environments. Therefore, improving the understanding of this intricate relationship is invaluable for boosting phytoremediation. In this review, we focus on the potential of plant growth promoting bacteria (PGPB) for enhancing phytoremediation of metal-polluted soils. We discuss the mechanisms employed by microbes to promote plant growth and assist the removal or immobilization of metals in soil, thereby enhancing phytoextraction and phytostabilization, respectively. Microbe-mediated metal removal and detoxification through processes entailing adsorption, chelation, transformation, and precipitation, to list but a few, are also critically examined. Moreover, this work covers the direct and indirect mechanisms used by PGPB to facilitate plant acquisition of nutrients like nitrogen and phosphorus, supply and regulate phytohormones, and exert control over antagonistic microorganisms. Lastly, we provide an outlook on the future directions of microbe-aided phytoremediation and phytomining. Clearly, to fully validate and comprehend the potential of PGPB-aided phytoremediation, a considerable shift from bench-scale to field research is necessary. What's more, it is envisaged that recent advancements in genetic engineering may soon help furthering the efficiency of microbe-assisted phytoremediation.

Gibberellin-regulated proteins: Emergent allergens

About 10 years ago, a protein family was shown for the first time to contain allergenic members, gibberellin-regulated protein (GRP). The first reported member was from peach, Pru p 7. One can hypothesize that it was not detected before because its physicochemical characteristics overlap with those of lipid transfer protein (LTP), a well-known allergen, or because the exposure to GRP increased due to an increase in the gibberellin phythormone level in plant food, either exogenous or endogenous. Like LTPs, GRPs are small cationic proteins with disulfide bridges, are resistant to heat and proteolytic cleavage, and are involved in the defense of the plant. Besides peach, GRP allergens have been described in Japanese apricot (Pru m 7), sweet cherry (Pru av 7), orange (Cit s 7), pomegranate (Pun g 7), bell pepper (Cap a 7), strawberry (Fra a GRP), and also in pollen with a restriction to Cupressaceae tree family (Cup s 7, Cry j 7, and Jun a 7). IgE cross-reactivities were described between GRPs, and the reported peach/cypress and citrus/cypress syndromes may therefore be explained because of these GRP cross-reactivities. GRPs are clinically relevant, and severe adverse reactions may sometimes occur in association with cofactors. More than 60% and up to 95% sequence identities are calculated between various allergenic GRPs, and three-dimensional models show a cleft in the molecule and predict at least three epitopic regions. The structure of the protein and its properties and the matrix effect in the original allergenic source should be unraveled to understand why, despite the ubiquity of the protein family in plants, only a few members are able to sensitize patients.

Primary Growth Effect of Salix viminalis L. CV. Inger and Tordis in Controlled Conditions by Exploring Optimum Cutting Lengths and Rhizogenesis Treatments

The major disadvantage of setting up a willow coppice is the low survival rate, which reduces economic efficiency and crop sustainability. The aim of this research was to test, under controlled conditions, the impact of water, gibberellic acid A3 (0.05%), and humic acid (0.2%) on the growth and development of two willow clones. Under humic acid treatment, 20 cm cuttings of the Tordis clone developed up to 15 roots, and 25 cm cuttings developed more than 23. In comparison, water stimulated more than 15 roots for both 20 and 25 cm cuttings. Gibberellins acted as an inhibitor, especially on the roots, and the cuttings dried out from the top to the middle, with weak development of shoots and callus formation. For both clones, the highest number of active buds was observed on 20 and 25 cm cuttings grown in water, with more than four for Inger and more than seven for Tordis. Root development of the Inger clone had a maximum of eight for 25 cm cuttings grown in water; it was three times lower in the same variant of Tordis and two times lower for the Tordis clone with humic acid treatment. In general, Inger cuttings of 15 and 25 cm highlighted a delayed root formation when humic acids and gibberellins were applied. In controlled condition experiments, the Tordis clone was more suitable owing to its higher development and increased growth stability.

Genome-wide analysis of the CAD gene family reveals two bona fide CAD genes in oil palm

Cinnamyl alcohol dehydrogenase (CAD) is the key enzyme for lignin biosynthesis in plants. In this study, genome-wide analysis was performed to identify CAD genes in oil palm (Elaeis guineensis). Phylogenetic analysis was then conducted to select the bona fide EgCADs. The bona fide EgCAD genes and their respective 5' flanking regions were cloned and analysed. Their expression profiles were evaluated in various organs using RT-PCR. Seven EgCAD genes (EgCAD1-7) were identified and divided into four phylogenetic groups. EgCAD1 and EgCAD2 display high sequence similarities with other bona fide CADs and possess all the signature motifs of the bona fide CAD. They also display similar 3D protein structures. Gene expression analysis showed that EgCAD1 was expressed most abundantly in the root tissues, while EgCAD2 was expressed constitutively in all the tissues studied. EgCAD1 possesses only one transcription start site, while EgCAD2 has five. Interestingly, a TC microsatellite was found in the 5' flanking region of EgCAD2. The 5' flanking regions of EgCAD1 and EgCAD2 contain lignin-associated regulatory elements i.e. AC-elements, and other defence-related motifs, including W-box, GT-1 motif and CGTCA-motif. Altogether, these results imply that EgCAD1 and EgCAD2 are bona fide CAD involved in lignin biosynthesis during the normal development of oil palm and in response to stresses. Our findings shed some light on the roles of the bona fide CAD genes in oil palm and pave the way for manipulating lignin content in oil palm through a genetic approach.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-022-03208-0.

Bacillus subtilis HG-15, a Halotolerant Rhizoplane Bacterium, Promotes Growth and Salinity Tolerance in Wheat (Triticum aestivum)

Certain plant growth-promoting bacteria (PGPB) reduce salt stress damage in plants. Bacillus subtilis HG-15 is a halotolerant bacterium (able to withstand NaCl concentrations as high as 30%) isolated from the wheat rhizoplane in the Yellow River delta. A qualitative and quantitative investigation of the plant growth-promoting characteristics of this strain confirmed nitrogen fixation, potassium dissolution, ammonia, plant hormone, ACC deaminase, and proline production abilities. B. subtilis HG-15 colonization of wheat roots, stems, and leaves was examined via scanning electron microscopy, rep-PCR, and double antibiotic screening. After inoculation with the B. subtilis HG-15 strain, the pH (1.08–2.69%), electrical conductivity (3.17–11.48%), and Na⁺ (12.98–15.55%) concentrations of rhizosphere soil significantly decreased (p < 0.05). Under no-salt stress (0.15% NaCl), low-salt stress (0.25% NaCl), and high-salt stress (0.35% NaCl) conditions, this strain also significantly increased (p < 0.05) the dry weight (17.76%, 24.46%, and 9.31%), fresh weight (12.80%, 20.48%, and 7.43%), plant height (7.79%, 5.86%, and 13.13%), and root length (10.28%, 17.87%, and 48.95%). Our results indicated that B. subtilis HG-15 can effectively improve the growth of wheat and elicit induced systemic tolerance in these plants, thus showing its potential as a microbial inoculant that can protect wheat under salt stress conditions.

Roles of Abscisic Acid and Gibberellins in Stem/Root Tuber Development

Root and tuber crops are of great importance. They not only contribute to feeding the population but also provide raw material for medicine and small-scale industries. The yield of the root and tuber crops is subject to the development of stem/root tubers, which involves the initiation, expansion, and maturation of storage organs. The formation of the storage organ is a highly intricate process, regulated by multiple phytohormones. Gibberellins (GAs) and abscisic acid (ABA), as antagonists, are essential regulators during stem/root tuber development. This review summarizes the current knowledge of the roles of GA and ABA during stem/root tuber development in various tuber crops.

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.

Detection of Chromosomal Segments Introgressed from Wild Species of Carrot into Cultivars: Quantitative Trait Loci Mapping for Morphological Features in Backcross Inbred Lines

Cultivated carrot is thought to have been domesticated from a wild species, and various phenotypes developed through human domestication and selection over the past several centuries. Little is known about the genomic contribution of wild species to the phenotypes of present-day cultivars, although several studies have focused on identifying genetic loci that contribute to the morphology of storage roots. A backcross inbred line (BIL) population derived from a cross between the wild species Daucus carota ssp. carota "Songzi" and the orange cultivar "Amsterdam forcing" was developed. The morphological features in the BIL population became more diverse after several generations of selfing BC₂F₁ plants. Only few lines retained features of wild parent. Genomic resequencing of the two parental lines and the BILs resulted in 3,223,651 single nucleotide polymorphisms (SNPs), and 13,445 bin markers were generated using a sliding window approach. We constructed a genetic map with 2027 bins containing 154,776 SNPs; the total genetic distance was 1436.43 cM and the average interval between the bins was 0.71 cm. Five stable QTLs related to root length, root shoulder width, dry material content of root, and ratio of root shoulder width to root middle width were consistently detected on chromosome 2 in both years and explained 23.4-66.9% of the phenotypic variance. The effects of introgressed genomic segments from the wild species on the storage root are reported and will enable the identification of functional genes that control root morphological traits in carrot.

Irradiance-regulated biomass allocation in Raphanus sativus plants depends on gibberellin biosynthesis

Gibberellin has been proposed to increase leaf elongation in radish (Raphanus sativus L.) plants, which is associated with decreased tuber growth. Since light intensity can control growth through interaction with gibberellin, investigation of the effect of gibberellin levels on the growth of radish plants would be a step forward towards unraveling factors that underlie biomass accumulation and allocation in response to irradiance levels. Here, we report that the gibberellin biosynthesis inhibitor paclobutrazol (PAC) decreased petiole elongation, but not lamina growth of radish plants grown under full sunlight. However, shading promoted an increase in shoot elongation, while in plants treated with PAC the petiole and leaf lamina fail to elongate. Plants treated with PAC allocated proportionally more biomass to their tubers and less to shoot compared to control under shade. Moreover, PAC decreased the abundance of transcripts encoding cell wall expansion proteins in leaf lamina and petiole of plants grown under shade, which was positively correlated with sugar consumption by the tuber, thereby increasing the mass fraction and concentrations of minerals for tuber. Thus, allocation of biomass during the growth of radish plants and nutritional quality of tubers depend on gibberellin and light intensity.

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.

Study on the Regulatory Effects of GA3 on Soybean Internode Elongation

Excessive plant height is an important factor that can lead to lodging, which is closely related to soybean yield. Gibberellins are widely used as plant growth regulators in agricultural production. Gibberellic acid (GA₃), one of the most effective active gibberellins, has been used to regulate plant height and increase yields. The mechanism through which GA₃ regulates internode elongation has been extensively investigated. In 2019 and 2020, we applied GA₃ to the stems, leaves, and roots of two soybean cultivars, Heinong 48 (a high-stalk cultivar) and Henong 60 (a dwarf cultivar), and GA₃ was also applied to plants whose apical meristem was removed or to girded plants to compare the internode length and stem GA₃ content of soybean plants under different treatments. These results suggested that the application of GA₃ to the stems, leaves, and roots of soybean increased the internode length and GA₃ content in the stems. Application of GA₃ decreased the proportion of the pith in the soybean stems and primary xylem while increasing the proportion of secondary xylem. The apical meristem is an important site of GA₃ synthesis in soybean stems and is involved in the regulation of stem elongation. GA₃ was shown to be transported acropetally through the xylem and laterally between the xylem and phloem in soybean stems. We conclude that the GA₃ level in stems is an important factor affecting internode elongation.

Gibberellin Signaling Promotes the Secondary Growth of Storage Roots in Panax ginseng

Gibberellins (GAs) are an important group of phytohormones associated with diverse growth and developmental processes, including cell elongation, seed germination, and secondary growth. Recent genomic and genetic analyses have advanced our knowledge of GA signaling pathways and related genes in model plant species. However, functional genomics analyses of GA signaling pathways in Panax ginseng, a perennial herb, have rarely been carried out, despite its well-known economical and medicinal importance. Here, we conducted functional characterization of GA receptors and investigated their physiological roles in the secondary growth of P. ginseng storage roots. We found that the physiological and genetic functions of P. ginseng gibberellin-insensitive dwarf1s (PgGID1s) have been evolutionarily conserved. Additionally, the essential domains and residues in the primary protein structure for interaction with active GAs and DELLA proteins are well-conserved. Overexpression of PgGID1s in Arabidopsis completely restored the GA deficient phenotype of the Arabidopsis gid1a gid1c (atgid1a/c) double mutant. Exogenous GA treatment greatly enhanced the secondary growth of tap roots; however, paclobutrazol (PCZ), a GA biosynthetic inhibitor, reduced root growth in P. ginseng. Transcriptome profiling of P. ginseng roots revealed that GA-induced root secondary growth is closely associated with cell wall biogenesis, the cell cycle, the jasmonic acid (JA) response, and nitrate assimilation, suggesting that a transcriptional network regulate root secondary growth in P. ginseng. These results provide novel insights into the mechanism controlling secondary root growth in P. ginseng.

Gibberellin Oxidase Gene Family in L. chinense: Genome-Wide Identification and Gene Expression Analysis

GAox is a key enzyme for the transformation of gibberellins, and belongs to the 2-ketoglutarate dependent dioxygenase gene family (2ODD). However, a systematic analysis of GAox in the angiosperm L. chinense has not yet been reported. Here, we identified all LcGAox gene family members in L. chinense, which were classified into the three subgroups of GA20ox, C19GA2ox, and C20GA2ox. Comparison of the gene structure, conserve motifs, phylogenetic relationships, and syntenic relationships of gibberellin oxidase gene families in different species indicated that the gene functional differences may be due to the partial deletion of their domains during evolution. Furthermore, evidence for purifying selection was detected between orthologous GAox genes in rice, grape, Arabidopsis, and L. chinense. Analysis of the codon usage patterns showed that mutation pressure and natural selection might have induced codon usage bias in angiosperms; however, the LcGAox genes in mosses, lycophytes, and ambarella plants exhibited no obvious codon usage preference. These results suggested that the gibberellin oxidase genes were more primitive. The gene expression pattern was analyzed in different organs subjected to multiple abiotic stresses, including GA, abscisic acid (ABA), and chlormequat (CCC) treatment, by RNA-seq and qRT-PCR, and the stress- and phytohormone-responsive cis-elements were counted. The results showed that the synthesis and decomposition of GA were regulated by different LcGAox genes in the vegetative and reproductive organs of L. chinense, and only LcGA2ox1,4, and 7 responded to the NaCl, polyethylene glycol, 4 °C, GA, ABA, and CCC treatment in the roots, stems, and leaves of seedlings at different time periods, revealing the potential role of LcGAox in stress resistance.

Effect of elevated gibberellic acid application on growth and gene expression patterns in white spruce families from a tree improvement program in Alberta, Canada

Nine open-pollinated families of Picea glauca (Moench) Voss from the Region D1 Controlled Parentage Program (Alberta, Canada) were systematically chosen from fast, medium and slow-growth rankings based on breeding values for height from field progeny tests at age 30 years. Seeds from these families were sown and grown to age 3 years to analyze the performance and correlations of growth, physiological traits and expression of gibberellin-related genes, with and without elevated gibberellic acid 3 (GA3) application, under greenhouse conditions. We observed a significant interaction effect between families and growth groups subjected to 50 μg μl-1 of GA3 treatment, causing a decrease in apical internode length, diameter, volume and absolute transcript level for fast-growing families but an increase for families in the slow-growth group for the same traits. We also observed that in the apical internode, the gene PgGA20ox1 had significantly more relative expression under the elevated GA3 treatment than the control trees. In the stem, PgGA3ox1 showed a significantly higher relative expression under elevated GA3 treatment compared with control trees. Also, the slow-growth group showed more relative expression of PgGA20ox1 (in the apical internode) and PgGA3ox1 (in the stem) than the fast-growth group. The apical internode length and diameter significantly increased by 24% and 16%, respectively, with the hormone treatment in the slow growing group. In general, the PgGID1 and PgDELLA1 genes were upregulated and downregulated respectively, in spruce shoots under the GA3 treatment, meaning a positive feedback regulation by those genes were influencing PgGA20ox1 and PgGA3ox1 expression in that tissue type. Moreover, there was a significant correlation between absolute transcript levels of PgGA20ox1 in the apical internode and apical internode length, and absolute transcript levels of PgGA3ox1 in the stem and the diameter, in the fast-growth group families. This study shows that expression of GA genes is a limiting factor for growth in certain white spruce families with a complex feedback mechanism. Finally, absolute transcript levels of endogenous GA relative to growth parameters in juvenile seedlings could potentially be used to accelerate the early selection of families with inherently rapid apical and radial growth expansion.

Effects of auxin (indole-3-butyric acid) on growth characteristics, lignification, and expression profiles of genes involved in lignin biosynthesis in carrot taproot

Carrot is an important root vegetable crop abundant in bioactive compounds including carotenoids, vitamins, and dietary fibers. Carrot intake and its products are gradually growing owing to its high antioxidant activity. Auxins are a class of plant hormones that control many processes of plant growth and development. Yet, the effects of exogenous application of auxin on lignin biosynthesis and gene expression profiles of lignin-related genes in carrot taproot are still unclear. In order to investigate the effect of exogenous indole-3-butyric acid (IBA) on lignin-related gene profiles, lignin accumulation, anatomical structures and morphological characteristics in carrot taproots, carrots were treated with different concentrations of IBA (0, 50, 100, and 150 µM). The results showed that IBA application significantly improved the growth parameters of carrot. The 100 or 150 µM IBA treatment increased the number and area of xylem vessels, whereas transcript levels of lignin-related genes were restricted, resulting in a decline in lignin content in carrot taproots. The results indicate that taproot development and lignin accumulation may be influenced by the auxin levels within carrot plants.

Specific response mechanism to autotoxicity in melon (Cucumis melo L.) root revealed by physiological analyses combined with transcriptome profiling

Melon is of great value in food, medicine and industry. In recent years, the continuous cropping obstacles of melon is increasingly prominent, which seriously affects the cultivation. Autotoxicity is the key factor for the obstacles. Root is the first line against autotoxicity and main organs for autotoxins secretion. Some physiological responses and differentially expressed genes (DEGs) related to autotoxicity are only limited to root system. Considering the lack of relevant research, physiological researches combined with transcriptome sequencing of melon seedling after autotoxicity stress mediated by root exudates (RE) was performed to help characterize the response mechanism to autotoxicity in melon roots. The results showed that autotoxicity inhibited root morphogenesis of melon seedlings, induced the excessive accumulation of reactive oxygen species (ROS) and lipid peroxidation in roots, and activated most antioxidant enzymes. Compared with the control group, the osmoregulation substance content was always at a high level. DEGs response to autotoxicity in roots were distinguished from that in leaves. Functional annotation of these DEGs suggested that autotoxicity affected biological regulation in a negative manner. DEGs were mainly involved in the synthesis of antioxidants, DNA damage and metabolism, and stress response. These setbacks were associated with the deterioration of root morphogenesis, generation of dwarf and slender roots, and ultimately leading to plant death. The results may provide important information for revealing the response mechanism of root to autotoxicity, and provide theoretical basis for solving the continuous cropping obstacles in melon.

Mechanistic Insights of the Interaction of Plant Growth-Promoting Rhizobacteria (PGPR) With Plant Roots Toward Enhancing Plant Productivity by Alleviating Salinity Stress

Agriculture plays an important role in a country's economy. The sector is challenged by many stresses, which led to huge loss in plant productivity worldwide. The ever-increasing population, rapid urbanization with shrinking agricultural lands, dramatic change in climatic conditions, and extensive use of agrochemicals in agricultural practices that caused environmental disturbances confront mankind of escalating problems of food security and sustainability in agriculture. Escalating environmental problems and global hunger have led to the development and adoption of genetic engineering and other conventional plant breeding approaches in developing stress-tolerant varieties of crops. However, these approaches have drawn flaws in their adoption as the process of generating tolerant varieties takes months to years in bringing the technology from the lab to the field. Under such scenario, sustainable and climate-smart agricultural practices that avail bacterial usage open the avenues in fulfilling the incessant demand for food for the global population. Ensuring stability on economic fronts, bacteria minimizes plant salt uptake by trapping ions in their exopolysaccharide matrix besides checking the expression of Na+/H+ and high-affinity potassium transporters. Herein we describe information on salinity stress and its effect on plant health as well as strategies adopted by plant growth-promoting rhizobacteria (PGPR) in helping plants to overcome salinity stress and in mitigating loss in overall plant productivity. It is believed that acquisition of advanced knowledge of plant-beneficial PGPR will help in devising strategies for sustainable, environment-friendly, and climate-smart agricultural technologies for adoption in agriculture to overcome the constrained environmental conditions.

Differences in xylem development between Dutch and Japanese tomato (Solanum lycopersicum) correlate with cytokinin levels in hypocotyls

BACKGROUND AND AIMS

Dutch tomato cultivars tend to have a greater yield than Japanese cultivars even if they are grown under the same conditions. Factors contributing to the increased yield of the Dutch cultivars were a greater light use efficiency and greater leaf photosynthetic rate. On the other hand, the relationship between tomato yields and anatomical traits is still unclear. The aim of this study is to identify the anatomical traits related to the difference in yield between Dutch and Japanese cultivars.

METHODS

Anatomical properties were compared during different growth stages of Dutch and Japanese tomatoes. Hormone profiles and related gene expression in hypocotyls of Dutch and Japanese cultivars were compared in the hypocotyls of 3- and 4-week-old plants.

KEY RESULTS

Dutch cultivars have a more developed secondary xylem than Japanese cultivars, which would allow for greater transport of water, mineral nutrients and phytohormones to the shoots. The areas and ratios of the xylem in the hypocotyls of 3- to 6-week-old plants were larger in the Dutch cultivars. In reciprocal grafts of the Japanese and Dutch cultivars, xylem development at the scion and rootstock depended on the scion cultivar, suggesting that some factors in the scion are responsible for the difference in xylem development. The cytokinin content, especially the level of N6-(Δ 2-isopentenyl) adenine (iP)-type cytokinin, was higher in the Dutch cultivars. This result was supported by the greater expression of Sl-IPT3 (a cytokinin biosynthesis gene) and Sl-RR16/17 (a cytokinin-responsive gene) in the Dutch cultivars.

CONCLUSIONS

These results suggest that iP-type cytokinins, which are locally synthesized in the hypocotyl, contribute to xylem development. The greater xylem development in Dutch cultivars might contribute to the high yield of the tomato.

Effects of Enterobacter cloacae HG-1 on the Nitrogen-Fixing Community Structure of Wheat Rhizosphere Soil and on Salt Tolerance

The present study investigated the physiological and biochemical characteristics of Enterobacter cloacae HG-1 isolated from saline-alkali soil. We further studied the effect of this strain on the salt tolerance of wheat and on the community structure of nitrogen-fixing bacteria in rhizosphere soil. We determined that the investigated strain had high nitrogen fixation activity and produced iron carriers, 1-aminocyclopropane-1-carboxylic acid deaminase, and plant hormones. The metabolites of this strain contained 2,3-butanediol, [R-(R*, R*)], 2-heptanone, and other growth-promoting and antibacterial substances. The strain was also highly salt-tolerant (10% NaCl). After the inoculation of wheat with the HG-1 strain, we recorded increases in root length, plant height, fresh weight, and dry weight of 19.15%, 18.83%, 16.67%, and 17.96%, respectively, compared with uninoculated plants (P < 0.05). Compared with the leaves of uninoculated plants, the proline concentration in the leaves of inoculated plants increased by 12.43% (P < 0.05), the malondialdehyde level decreased by 27.26% (P < 0.05), K+ increased by 20.69%, Ca2+ increased by 57.53% and Na+ decreased by 31.43% (all P<0.05). Furthermore, we detected that inoculation with the HG-1 strain did not affect the species composition of nitrogen-fixing bacteria in wheat rhizosphere soil at the phylum level. However, the average relative abundance of Proteobacteria was significantly increased, whereas the abundance of Verrucomiorobia was significantly decreased compared with uninoculated plants. At the genus level, we detected 32 genera in control samples and 27 genera in inoculated samples, and the species diversity and relative abundance of samples inoculated with the HG-1 strain decreased compared with uninoculated plants. Inoculated samples had lower abundances of Azospirillum, Rhodomicrobium, and Anabaena. Our study demonstrated that the inoculation of wheat with E. cloacae HG-1 could promote the growth of wheat under salt stress and increase salt stress tolerance. The results of this study investigating the interaction among soil, plants, and microorganisms supplement agricultural microbial databases and could provide a reference for the development of microbial-based saline soil improvement programs.

Genome-wide identification, characterization and expression profiling of gibberellin metabolism genes in jute

BACKGROUND

Gibberellin (GA) is one of the most essential phytohormones that modulate plant growth and development. Jute (Corchorus sp.) is the second most important source of bast fiber. Our result has shown that exogenous GA can positively regulate jute height and related characteristics which mean increasing endogenous GA production will help to get a jute variety with improved characteristics. However, genes involved in jute GA biosynthesis have not been analyzed precisely.

RESULTS

Genome-wide analysis identified twenty-two candidate genes involved in jute GA biosynthesis pathway. Among them, four genes- CoCPS, CoKS, CoKO and CoKAO work in early steps. Seven CoGA20oxs, three CoGA3oxs, and eight GA2oxs genes work in the later steps. These genes were characterized through phylogenetic, motif, gene structure, and promoter region analysis along with chromosomal localization. Spatial gene expression analysis revealed that 11 GA oxidases were actively related to jute GA production and four of them were marked as key regulators based on their expression level. All the biosynthesis genes both early and later steps showed tissue specificity. GA oxidase genes were under feedback regulation whereas early steps genes were not subject to such regulation.

CONCLUSION

Enriched knowledge about jute GA biosynthesis pathway and genes will help to increase endogenous GA production in jute by changing the expression level of key regulator genes. CoGA20ox7, CoGA3ox2, CoGA2ox3, and CoGA2ox5 may be the most important genes for GA production.

Gene Regulatory Network Guided Investigations and Engineering of Storage Root Development in Root Crops

The plasticity of plant development relies on its ability to balance growth and stress resistance. To do this, plants have established highly coordinated gene regulatory networks (GRNs) of the transcription factors and signaling components involved in developmental processes and stress responses. In root crops, yields of storage roots are mainly determined by secondary growth driven by the vascular cambium. In relation to this, a dynamic yet intricate GRN should operate in the vascular cambium, in coordination with environmental changes. Despite the significance of root crops as food sources, GRNs wired to mediate secondary growth in the storage root have just begun to emerge, specifically with the study of the radish. Gene expression data available with regard to other important root crops are not detailed enough for us directly to infer underlying molecular mechanisms. Thus, in this review, we provide a general overview of the regulatory programs governing the development and functions of the vascular cambium in model systems, and the role of the vascular cambium on the growth and yield potential of the storage roots in root crops. We then undertake a reanalysis of recent gene expression data generated for major root crops and discuss common GRNs involved in the vascular cambium-driven secondary growth in storage roots using the wealth of information available in Arabidopsis. Finally, we propose future engineering schemes for improving root crop yields by modifying potential key nodes in GRNs.

Mechanism of Allium Crops Bulb Enlargement in Response to Photoperiod: A Review

The photoperiod marks a varied set of behaviors in plants, including bulbing. Bulbing is controlled by inner signals, which can be stimulated or subdued by the ecological environment. It had been broadly stated that phytohormones control the plant development, and they are considered to play a significant part in the bulb formation. The past decade has witnessed significant progress in understanding and advancement about the photoperiodic initiation of bulbing in plants. A noticeable query is to what degree the mechanisms discovered in bulb crops are also shared by other species and what other qualities are also dependent on photoperiod. The FLOWERING LOCUS T (FT) protein has a role in flowering; however, the FT genes were afterward reported to play further functions in other biological developments (e.g., bulbing). This is predominantly applicable in photoperiodic regulation, where the FT genes seem to have experienced significant development at the practical level and play a novel part in the switch of bulb formation in Alliums. The neofunctionalization of FT homologs in the photoperiodic environments detects these proteins as a new class of primary signaling mechanisms that control the growth and organogenesis in these agronomic-related species. In the present review, we report the underlying mechanisms regulating the photoperiodic-mediated bulb enlargement in Allium species. Therefore, the present review aims to systematically review the published literature on the bulbing mechanism of Allium crops in response to photoperiod. We also provide evidence showing that the bulbing transitions are controlled by phytohormones signaling and FT-like paralogues that respond to independent environmental cues (photoperiod), and we also show that an autorelay mechanism involving FT modulates the expression of the bulbing-control gene. Although a large number of studies have been conducted, several limitations and research gaps have been identified that need to be addressed in future studies.

Understanding the molecular mechanisms for the enhanced phytoremediation of heavy metals through plant growth promoting rhizobacteria: A review

Rapid industrialization, modern agricultural practices and other anthropogenic activities add a significant quantity of toxic heavy metals into the environment, which induces severe toxic effects on all form of living organisms, alter the soil properties and its biological activity. Remediation of heavy metal contaminated sites has become an urgent necessity. Among the existing strategies, phytoremediation is an eco-friendly and much convincing tool for the remediation of heavy metals. However, the applicability of phytoremediation in contaminated sites is restricted by two prime factors such as i) slow growth rate at higher metal contaminated sites and ii) metal bioavailability. This circumstance could be minimized and accelerate the phytoremediation efficiency by incorporating the potential plant growth promoting rhizobacterial (PGPR) as a combined approach. PGPR inoculation might improve the plant growth through the production of plant growth promoting substances and improve the heavy metal remediation efficiency by the secretion of chelating agents, acidification and redox changes. Moreover, rhizobacterial inoculation consolidates the metal tolerance and uptake by regulating the expression of various metal transporters, tolerant and metal chelator genes. However, the exact underlying molecular mechanism of PGPR mediated plant growth promotion and phytoremediation of heavy metals is poorly understood. Thus, the present review provides clear information about the molecular mechanisms excreted by PGPR strains in plant growth promotion and phytoremediation of heavy metals.

Effect of Partial Excision of Early Taproots on Growth and Components of Hydroponic Carrots

Hydroponics provides a stable root environment that can be easily controlled. In this paper, we investigated the effect of partial excision of early taproots of hydroponic carrots on their growth and components. Carrot taproots were excised after 30 days from sowing at 5 cm, 10 cm, and 15 cm from the stem base (C5, C10, and C15) and compared with nonexcised control plants. Time-course measurements revealed the taproot lengths of C10 and C15 plants gradually decreased. After 28 days of treatment, C5 taproot tips showed the most rounded shape among root-excised plants. Control plants possessed long taproots that were not enlarged at the site more than 15 cm from the stem base. Taproot fresh weight was lower in C5 plants and higher in C15 plants compared with controls. Although taproot sugar concentrations did not differ between treatments, total phenol concentration was higher in C5 taproots. These data suggest that partial removal of early taproots can regulate the shape and ingredients of hydroponic carrots.

Elevated gibberellin altered morphology, anatomical structure, and transcriptional regulatory networks of hormones in celery leaves

Gibberellins (GAs), as one of the important hormones in regulating the growth and development of higher plants, can significantly promote cell elongation and expansion. Celery is a widely grown leafy vegetable crop with rich nutritional value. However, the effect of gibberellins on celery leaves is unclear. In this paper, the celery variety "Jinnan Shiqin" plants were treated with gibberellic acid (GA₃) and paclobutrazol (PBZ, a gibberellin inhibitor). Our results showed that GA₃ treatment promoted the growth of celery leaves and caused lignification of celery leaf tissue. In addition, the transcript levels of genes associated with gibberellins, auxin, cytokinins, ethylene, jasmonic acid, abscisic acid, and brassinolide were altered in response to increased or decreased exogenous gibberellins or inhibitor. GA₃ may regulate celery growth by interacting with other hormones through crosstalk mechanisms. This study provided a reference for further study of the regulation mechanism of gibberellins metabolism, and exerted effects on understanding the role of gibberellins in the growth and development of celery.

Selection of appropriate reference genes for RT-qPCR analysis under abiotic stress and hormone treatment in celery

Celery is one of the most important vegetable crop and its yield and quality is influenced by many environmental factors. Researches on gene expression not only help to unravel the molecular regulatory mechanism but also identify the key genes in the biological response. RT-qPCR is a commonly used technology to quantify the gene expression. Selecting an appropriate reference gene is an effective approach to improve the accuracy of RT-qPCR assay. To our knowledge, the evaluation of reference genes under different treatments in celery has not been reported yet. In this study, the expression stabilities of eight candidate reference genes (ACTIN, eIF-4α , GAPDH, TBP, TUB-A, UBC, TUB-B, and EF-1α ) under abiotic stresses (heat, cold, drought, and salt) and hormone treatments (SA, MeJA, GA, and ABA) were detected. The expression stabilities of candidate genes were compared and ranked by geNorm, NormFinder, BestKeeper, ΔCt, and RefFinder programs. The results calculated by different programs were not completely consistent. Considering the comprehensive analysis results, ACTIN was the most stable reference gene and TUB-B showed the worst expression stabilities under the selected abiotic stress and hormone treatments in celery. The reliability of reference genes was further confirmed by the normalization of CAT1 gene under drought stress. This study presented evidences and basis to select the appropriate reference genes under different treatments in celery.

Advances in research on the carrot, an important root vegetable in the Apiaceae family

Carrots (Daucus carota L.), among the most important root vegetables in the Apiaceae family, are cultivated worldwide. The storage root is widely utilized due to its richness in carotenoids, anthocyanins, dietary fiber, vitamins and other nutrients. Carrot extracts, which serve as sources of antioxidants, have important functions in preventing many diseases. The biosynthesis, metabolism, and medicinal properties of carotenoids in carrots have been widely studied. Research on hormone regulation in the growth and development of carrots has also been widely performed. Recently, with the development of high-throughput sequencing technology, many efficient tools have been adopted in carrot research. A large amount of sequence data has been produced and applied to improve carrot breeding. A genome editing system based on CRISPR/Cas9 was also constructed for carrot research. In this review, we will briefly summarize the origins, genetic breeding, resistance breeding, genome editing, omics research, hormone regulation, and nutritional composition of carrots. Perspectives about future research work on carrots are also briefly provided.

Biostimulatory activities of Ascophyllum nodosum extract in tomato and sweet pepper crops in a tropical environment

This study evaluated the effectiveness of a commercially available Ascophyllum nodosum alkaline extract as a plant growth stimulant and defense elicitor against foliar diseases of tomato and sweet pepper caused by Xanthomonas campestris pv. vesicatoria and Alternaria solani in a tropical environment. Foliar applications of 0.5% A. nodosum extract (AN) at 10-day intervals resulted in significant (P < 0.05) increase in plant growth parameters, including plant height (40%), leaf number (50%), plant dry biomass (52%), root length (59%) and chlorophyll content (20%) compared to control. Treated plants also had a significantly higher number of flower clusters, flower numbers, fruits per cluster and total harvested fruit yield. The Ascophyllum extract significantly (P < 0.05) reduced disease incidence by the pathogens in both crops under greenhouse and field conditions. The combinatory treatment of seaweed extract and a minimum dose of contact fungicide in field trials, recorded the overall lowest disease levels (60% reduction) and highest yield (57% increase). Investigations into the mechanisms of disease suppression revealed the effects of the extract in inducing the activities of defense-related enzymes including phenylalanine ammonia lyase, peroxidase, polyphenol oxidase, chitinase and β-1,3-glucanase, as well as the levels of total phenolic compounds. The effect on SA, JA and ET-mediated signalling defense pathways was examined by quantifying expression levels of marker genes including PR1-a, PinII and ETR-1, for the above pathways respectively. Both crop plants treated with A. nodosum extract had significantly higher expression levels of the PinII and ETR-1 marker genes than controls. This was coupled with a marked increase in gene transcripts involved in auxin (IAA), gibberellin (Ga2Ox) and cytokinin (IPT) biosynthesis, which provides possible evidence for induced growth in plants treated with AN extract. Cross-talks between growth and defense responses as a result of seaweed extract application could evidently implicate the benefits of seaweed extract usage in sustainable crop production.

Transcriptome Profiling of the Elongating Internode of Cotton (Gossypium hirsutum L.) Seedlings in Response to Mepiquat Chloride

The plant growth retardant mepiquat chloride (MC) has been extensively used to produce compact plant canopies and increase yield in cotton (Gossypium hirsutum L.). Previous studies showed that MC reduced plant height and internode length by inhibiting GA biosynthesis and cell elongation. However, whether there are other molecular mechanisms underlying MC-induced growth retardation has remained largely unknown. In the present study, we conducted histological, transcriptomic, and phytohormone analyses of the second elongating internodes of cotton seedlings treated with MC. Histological analysis revealed that the MC shortened the internodes through suppressing both cell division and cell elongation. Consistent with the observed phenotype, many genes related to cell growth were significantly downregulated by MC. Transcriptome profiling showed that the expression of genes related not only to GA, but also to auxin, brassinosteroid (BR), and ethylene metabolism and signaling was remarkably suppressed, whereas that of genes related to cytokinin (CK) and abscisic acid (ABA) metabolism was induced by MC. Consistent with the expression pattern, significant decrease of endogenous GA, auxin, and BR content, but an increase in CK content was observed after MC treatment. Most of these hormone related genes displayed opposite regulation pattern by exogenous GA₃ treatment compared to MC; simultaneous application of MC and GA₃ could alleviate the genes expression changes induced by MC treatment, indicating MC does not directly affect other plant hormones, but through the inhibition of the GA biosynthesis. In addition, the expression of genes related to secondary metabolism and many transcription factors (TFs) were differentially regulated by MC. In summary, we confirmed the important role of GA in MC-induced growth inhibition of cotton, and further found that other hormones were also involved in this process in a GA-dependent manner. This study provides novel insights into the molecular mechanism underlying the MC-mediated inhibition of internode elongation in cotton seedlings.

Gibberellin Promotes Sweetpotato Root Vascular Lignification and Reduces Storage-Root Formation

Sweetpotato yield depends on a change in the developmental fate of adventitious roots into storage-roots. The mechanisms underlying this developmental switch are still unclear. We examined the hypothesis claiming that regulation of root lignification determines storage-root formation. We show that application of the plant hormone gibberellin increased stem elongation and root gibberellin levels, while having inhibitory effects on root system parameters, decreasing lateral root number and length, and significantly reducing storage-root number and diameter. Furthermore, gibberellin enhanced root xylem development, caused increased lignin deposition, and, at the same time, decreased root starch accumulation. In accordance with these developmental effects, gibberellin application upregulated expression levels of sweetpotato orthologues of Arabidopsis vascular development regulators (IbNA075, IbVND7, and IbSND2) and of lignin biosynthesis genes (IbPAL, IbC4H, Ib4CL, IbCCoAOMT, and IbCAD), while downregulating starch biosynthesis genes (IbAGPase and IbGBSS) in the roots. Interestingly, gibberellin downregulated root expression levels of orthologues of the Arabidopsis BREVIPEDICELLUS transcription factor (IbKN2 and IbKN3), regulator of meristem maintenance. The results substantiate our hypothesis and mark gibberellin as an important player in regulation of sweetpotato root development, suggesting that increased fiber formation and lignification inhibit storage-root formation and yield. Taken together, our findings provide insight into the mechanisms underlying sweetpotato storage-root formation and provide a valuable database of genes for further research.

Plant Vascular Tissues-Connecting Tissue Comes in All Shapes

For centuries, humans have grown and used structures based on vascular tissues in plants. One could imagine that life would have developed differently without wood as a resource for building material, paper, heating energy, or fuel and without edible tubers as a food source. In this review, we will summarise the status of research on Arabidopsis thaliana vascular development and subsequently focus on how this knowledge has been applied and expanded in research on the wood of trees and storage organs of crop plants. We will conclude with an outlook on interesting open questions and exciting new research opportunities in this growing and important field.

Comprehensive Analysis of Cucumber Gibberellin Oxidase Family Genes and Functional Characterization of CsGA20ox1 in Root Development in Arabidopsis

Cucumber (Cucumis sativus L.) is an important vegetable crop worldwide and gibberellins (GAs) play important roles in the regulation of cucumber developmental and growth processes. GA oxidases (GAoxs), which are encoded by different gene subfamilies, are particularly important in regulating bioactive GA levels by catalyzing the later steps in the biosynthetic pathway. Although GAoxs are critical enzymes in GA synthesis pathway, little is known about GAox genes in cucumber, in particular about their evolutionary relationships, expression profiles and biological function. In this study, we identified 17 GAox genes in cucumber genome and classified them into five subfamilies based on a phylogenetic tree, gene structures, and conserved motifs. Synteny analysis indicated that the tandem duplication or segmental duplication events played a minor role in the expansion of cucumber GA2ox, GA3ox and GA7ox gene families. Comparative syntenic analysis combined with phylogenetic analysis provided deep insight into the phylogenetic relationships of CsGAox genes and suggested that protein homology CsGAox are closer to AtGAox than OsGAox. In addition, candidate transcription factors BBR/BPC (BARLEY B RECOMBINANT/BASIC PENTACYSTEINE) and GRAS (GIBBERELLIC ACID-INSENSITIVE, REPRESSOR of GAI, and SCARECROW) which may directly bind promoters of CsGAox genes were predicted. Expression profiles derived from transcriptome data indicated that some CsGAox genes, especially CsGA20ox1, are highly expressed in seedling roots and were down-regulated under GA₃ treatment. Ectopic over-expression of CsGA20ox1 in Arabidopsis significantly increased primary root length and lateral root number. Taken together, comprehensive analysis of CsGAoxs would provide a basis for understanding the evolution and function of the CsGAox family.

Exogenous GA3 application altered morphology, anatomic and transcriptional regulatory networks of hormones in Eucalyptus grandis

Gibberellins (GAs) play a key role in plant growth and development including cell elongation, cell expansion, and xylem differentiation. Eucalyptus are the world's most widely planted hardwood trees providing fiber and energy. However, the roles of GAs in Eucalyptus remain unclear and their effects on xylem development remain to be determined. In this study, E. grandis plants were treated with 0.10 mg L^-1 GA₃ and/or paclobutrazol (PAC, a GA inhibitor). The growth of shoot and root were recorded, transverse sections of roots and stems were stained using toluidine blue, and expression levels of genes related to hormone response and secondary cell wall biosynthesis were analyzed by quantitative real-time PCR. The results showed that GA₃ dramatically promoted the length of shoot and root, but decreased the diameter of root and stem. Exogenous GA₃ application also significantly promoted xylem development in both stem and root. Expression analysis revealed that exogenous GA₃ application altered the transcript levels of genes related to the GA biosynthetic pathway and GA signaling, as well as genes related to auxin, cytokinin, and secondary cell wall. These findings suggest that GAs may interact with other hormones (such as auxin and cytokinin) to regulate the expression of secondary cell wall biosynthesis genes and trigger xylogenesis in Eucalyptus plants.

Transcriptome characterization of moso bamboo (Phyllostachys edulis) seedlings in response to exogenous gibberellin applications

BACKGROUND

Moso bamboo (Phyllostachys edulis) is a well-known bamboo species of high economic value in the textile industry due to its rapid growth. Phytohormones, which are master regulators of growth and development, serve as important endogenous signals. However, the mechanisms through which phytohormones regulate growth in moso bamboo remain unknown to date.

RESULTS

Here, we reported that exogenous gibberellins (GA) applications resulted in a significantly increased internode length and lignin condensation. Transcriptome sequencing revealed that photosynthesis-related genes were enriched in the GA-repressed gene class, which was consistent with the decrease in leaf chlorophyll concentrations and the lower rate of photosynthesis following GA treatment. Exogenous GA applications on seedlings are relatively easy to perform, thus we used 4-week-old whole seedlings of bamboo for GA- treatment followed by high throughput sequencing. In this study, we identified 932 cis-nature antisense transcripts (cis-NATs), and 22,196 alternative splicing (AS) events in total. Among them, 42 cis-nature antisense transcripts (cis-NATs) and 442 AS events were differentially expressed upon exposure to exogenous GA3, suggesting that post-transcriptional regulation might be also involved in the GA3 response. Targets of differential expression of cis-NATs included genes involved in hormone receptor, photosynthesis and cell wall biogenesis. For example, LAC4 and its corresponding cis-NATs were GA3-induced, and may be involved in the accumulation of lignin, thus affecting cell wall composition.

CONCLUSIONS

This study provides novel insights illustrating how GA alters post-transcriptional regulation and will shed light on the underlying mechanism of growth modulated by GA in moso bamboo.