Identification and overexpression of gibberellin 2-oxidase (GA2ox) in switchgrass (Panicum virgatum L.) for improved plant architecture and reduced biomass recalcitrance

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.

The apple MdGA2ox7 modulates the balance between growth and stress tolerance in an anthocyanin-dependent manner

Apple (Malus domestica Borkh.) is a widely cultivated fruit crop worldwide but often suffers from abiotic stresses such as salt and cold. Gibberellic acid (GA) plays a pivotal in controlling plant development, environmental adaptability, and secondary metabolism. The GA2-oxidase (GA2ox) is responsible for the deactivation of bioactive GA. In this study, seventeen GA2-oxidase genes were identified in the apple genome, and these members could be clustered into four clades based on phylogenetic relationships and conserved domain structures. MdGA2ox7 exhibited robust expression across various tissues, responded to cold and salt treatments, and was triggered in apple fruit peels via light-induced anthocyanin accumulation. Subcellular localization prediction and experiments confirmed that MdGA2ox7 was located in the cytoplasm. Overexpression of MdGA2ox7 in Arabidopsis caused a lower level of active GA and led to GA-deficient phenotypes, such as dwarfism and delayed flowering. MdGA2ox7 alleviated cold and salt stress damage in both Arabidopsis and apple in concert with melatonin (MT). Additionally, MdGA2ox7 enhanced anthocyanin biosynthesis in apple calli and activated genes involved in anthocyanin synthesis. These findings provide new insights into the functions of apple GA2ox in regulating development, stress tolerance, and secondary metabolism.

Physiological and transcriptome analysis of changes in endogenous hormone and sugar content during the formation of tender asparagus stems

Asparagus is a nutritionally dense stem vegetable whose growth and development are correlated with its quality and yield. To investigate the dynamic changes and underlying mechanisms during the elongation and growth process of asparagus stems, we documented the growth pattern of asparagus and selected stem segments from four consecutive elongation stages using physiological and transcriptome analyses. Notably, the growth rate of asparagus accelerated at a length of 25 cm. A significant decrease in the concentration of sucrose, fructose, glucose, and additional sugars was observed in the elongation region of tender stems. Conversely, the levels of auxin and gibberellins(GAs) were elevated along with increased activity of enzymes involved in sucrose degradation. A significant positive correlation existed between auxin, GAs, and enzymes involved in sucrose degradation. The ABA content gradually increased with stem elongation. The tissue section showed that cell elongation is an inherent manifestation of stem elongation. The differential genes screened by transcriptome analysis were enriched in pathways such as starch and sucrose metabolism, phytohormone synthesis metabolism, and signal transduction. The expression levels of genes such as ARF, GA20ox, NCED, PIF4, and otherswere upregulated during stem elongation, while DAO, GA2ox, and other genes were downregulated. The gene expression level was consistent with changes in hormone content and influenced the cell length elongation. Additionally, the expression results of RT-qPCR were consistent with RNA-seq. The observed variations in gene expression levels, endogenous hormones and sugar changes during the elongation and growth of asparagus tender stems offer valuable insights for future investigations into the molecular mechanisms of asparagus stem growth and development and provide a theoretical foundation for cultivation and production practices.

Endogenous Hormone Levels and Transcriptomic Analysis Reveal the Mechanisms of Bulbil Initiation in Pinellia ternata

Pinellia ternata is a medicinal plant that has important pharmacological value, and the bulbils serve as the primary reproductive organ; however, the mechanisms underlying bulbil initiation remain unclear. Here, we characterized bulbil development via histological, transcriptomic, and targeted metabolomic analyses to unearth the intricate relationship between hormones, genes, and bulbil development. The results show that the bulbils initiate growth from the leaf axillary meristem (AM). In this stage, jasmonic acid (JA), abscisic acid (ABA), isopentenyl adenosine (IPA), and salicylic acid (SA) were highly enriched, while indole-3-acetic acid (IAA), zeatin, methyl jasmonate (MeJA), and 5-dexoxystrigol (5-DS) were notably decreased. Through OPLS-DA analysis, SA has emerged as the most crucial factor in initiating and positively regulating bulbil formation. Furthermore, a strong association between IPA and SA was observed during bulbil initiation. The transcriptional changes in IPT (Isopentenyltransferase), CRE1 (Cytokinin Response 1), A-ARR (Type-A Arabidopsis Response Regulator), B-ARR (Type-B Arabidopsis Response Regulator), AUX1 (Auxin Resistant 1), ARF (Auxin Response Factor), AUX/IAA (Auxin/Indole-3-acetic acid), GH3 (Gretchen Hagen 3), SAUR (Small Auxin Up RNA), GA2ox (Gibberellin 2-oxidase), GA20ox (Gibberellin 20-oxidase), AOS (Allene oxide synthase), AOC (Allene oxide cyclase), OPR (Oxophytodienoate Reductase), JMT (JA carboxy l Methyltransferase), COI1 (Coronatine Insensitive 1), JAZ (Jasmonate ZIM-domain), MYC2 (Myelocytomatosis 2), D27 (DWARF27), SMAX (Suppressor of MAX2), PAL (Phenylalanine Ammonia-Lyase), ICS (Isochorismate Synthase), NPR1 (Non-expressor of Pathogenesis-related Genes1), TGA (TGACG Sequence-specific Binding), PR-1 (Pathogenesis-related), MCSU (Molybdenium Cofactor Sulfurase), PP2C (Protein Phosphatase 2C), and SnRK (Sucrose Non-fermenting-related Protein Kinase 2) were highly correlated with hormone concentrations, indicating that bulbil initiation is coordinately controlled by multiple phytohormones. Notably, eight TFs (transcription factors) that regulate AM initiation have been identified as pivotal regulators of bulbil formation. Among these, WUS (WUSCHEL), CLV (CLAVATA), ATH1 (Arabidopsis Thaliana Homeobox Gene 1), and RAX (Regulator of Axillary meristems) have been observed to exhibit elevated expression levels. Conversely, LEAFY demonstrated contrasting expression patterns. The intricate expression profiles of these TFs are closely associated with the upregulated expression of KNOX(KNOTTED-like homeobox), suggesting a intricate regulatory network underlying the complex process of bulbil initiation. This study offers a profound understanding of the bulbil initiation process and could potentially aid in refining molecular breeding techniques specific to P. ternata.

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.

Bulbil initiation: a comprehensive review on resources, development, and utilisation, with emphasis on molecular mechanisms, advanced technologies, and future prospects

Bulbil is an important asexual reproductive structure of bulbil plants. It mainly grows in leaf axils, leaf forks, tubers and the upper and near ground ends of flower stems of plants. They play a significant role in the reproduction of numerous herbaceous plant species by serving as agents of plant propagation, energy reserves, and survival mechanisms in adverse environmental conditions. Despite extensive research on bulbil-plants regarding their resources, development mechanisms, and utilisation, a comprehensive review of bulbil is lacking, hindering progress in exploiting bulbil resources. This paper provides a systematic overview of bulbil research, including bulbil-plant resources, identification of development stages and maturity of bulbils, cellular and molecular mechanisms of bulbil development, factors influencing bulbil development, gene research related to bulbil development, multi-bulbil phenomenon and its significance, medicinal value of bulbils, breeding value of bulbils, and the application of plant tissue culture technology in bulbil production. The application value of the Temporary Immersion Bioreactor System (TIBS) and Terahertz (THz) in bulbil breeding is also discussed, offering a comprehensive blueprint for further bulbil resource development. Additionally, additive, seven areas that require attention are proposed: (1) Utilization of modern network technologies, such as plant recognition apps or websites, to collect and identify bulbous plant resources efficiently and extensively; (2) Further research on cell and tissue structures that influence bulb cell development; (3) Investigation of the network regulatory relationship between genes, proteins, metabolites, and epigenetics in bulbil development; (4) Exploration of the potential utilization value of multiple sprouts, including medicinal, ecological, and horticultural applications; (5) Innovation and optimization of the plant tissue culture system for bulbils; (6) Comprehensive application research of TIBS for large-scale expansion of bulbil production; (7) To find out the common share genetics between bulbils and flowers.

Genome-wide identification of GA2ox genes family and analysis of PbrGA2ox1-mediated enhanced chlorophyll accumulation by promoting chloroplast development in pear

BACKGROUND

Chlorophyll (Chl) is an agronomic trait associated with photosynthesis and yield. Gibberellin 2-oxidases (GA2oxs) have previously been shown to be involved in Chl accumulation. However, whether and how the PbrGA2ox proteins (PbrGA2oxs) mediate Chl accumulation in pear (Pyrus spp.) is scarce.

RESULTS

Here, we aimed to elucidate the role of the pear GA2ox gene family in Chl accumulation and the related underlying mechanisms. We isolated 13 PbrGA2ox genes (PbrGA2oxs) from the pear database and identified PbrGA2ox1 as a potential regulator of Chl accumulation. We found that transiently overexpressing PbrGA2ox1 in chlorotic pear leaves led to Chl accumulation, and PbrGA2ox1 silencing in normal pear leaves led to Chl degradation, as evident by the regreening and chlorosis phenomenon, respectively. Meanwhile, PbrGA2ox1-overexpressing (OE) tobacco plants discernably exhibited Chl built-up, as evidenced by significantly higher Pn and Fv/Fm. In addition, RNA sequencing (RNA-seq), physiological and biochemical investigations revealed an increase in abscisic acid (ABA), methyl jasmonate (MeJA), and salicylic acid (SA) concentrations and signaling pathways; a marked elevation in reducing and soluble sugar contents; and a marginal decline in the starch and sucrose levels in OE plants. Interestingly, PbrGA2ox1 overexpression did not prominently affect Chl synthesis. However, it indeed facilitated chloroplast development by increasing chloroplast number per cell and compacting the thylakoid granum stacks. These findings might jointly contribute to Chl accumulation in OE plants.

CONCLUSION

Overall, our results suggested that GA2oxs accelerate Chl accumulation by stimulating chloroplast development and proved the potential of PbrGA2ox1 as a candidate gene for genetically breeding biofortified pear plants with a higher yield.

Preliminary Study on the Formation Mechanism of Malformed Sweet Cherry (Prunus avium L.) Fruits in Southern China Using Transcriptome and Metabolome Data

Gibberellin (GA) is an important plant hormone that is involved in various physiological processes during plant development. Sweet cherries planted in southern China have always encountered difficulty in bearing fruit. In recent years, gibberellin has successfully solved this problem, but there has also been an increase in malformed fruits. This study mainly explores the mechanism of malformed fruit formation in sweet cherries. By analyzing the synthesis pathway of gibberellin using metabolomics and transcriptomics, the relationship between gibberellin and the formation mechanism of deformed fruit was preliminarily determined. The results showed that the content of GA3 in malformed fruits was significantly higher than in normal fruits. The differentially expressed genes in the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway were mainly enriched in pathways such as "plant hormone signal transduction", "diterpenoid biosynthesis", and "carotenoid biosynthesis". Using Quantitative Real-Time Reverse Transcription PCR (qRT-PCR) analysis, the gibberellin hydrolase gene GA2ox and gibberellin synthase genes GA20ox and GA3ox were found to be significantly up-regulated. Therefore, we speculate that the formation of malformed fruits in sweet cherries may be related to the accumulation of GA3. This lays the foundation for further research on the mechanism of malformed sweet cherry fruits.

Transcriptome Profiling Provides Insights into the Early Development of Tiller Buds in High- and Low-Tillering Orchardgrass Genotypes

Orchardgrass (Dactylis glomerata L.) is among the most economically important perennial cool-season grasses, and is considered an excellent hay, pasture, and silage crop in temperate regions worldwide. Tillering is a vital feature that dominates orchardgrass regeneration and biomass yield. However, transcriptional dynamics underlying early-stage bud development in high- and low-tillering orchardgrass genotypes are unclear. Thus, this study assessed the photosynthetic parameters, the partially essential intermediate biomolecular substances, and the transcriptome to elaborate the early-stage profiles of tiller development. Photosynthetic efficiency and morphological development significantly differed between high- (AKZ-NRGR667) and low-tillering genotypes (D20170203) at the early stage after tiller formation. The 206.41 Gb of high-quality reads revealed stage-specific differentially expressed genes (DEGs), demonstrating that signal transduction and energy-related metabolism pathways, especially photosynthetic-related processes, influence tiller induction and development. Moreover, weighted correlation network analysis (WGCNA) and functional enrichment identified distinctively co-expressed gene clusters and four main regulatory pathways, including chlorophyll, lutein, nitrogen, and gibberellic acid (GA) metabolism pathways. Therefore, photosynthesis, carbohydrate synthesis, nitrogen efficient utilization, and phytohormone signaling pathways are closely and intrinsically linked at the transcriptional level. These findings enhance our understanding of tillering in orchardgrass and perennial grasses, providing a new breeding strategy for improving forage biomass yield.

Identification of GA2ox Family Genes and Expression Analysis under Gibberellin Treatment in Pineapple (Ananas comosus (L.) Merr.)

Gibberellin (GAs) plays an important regulatory role in the development and growth of pineapple (Ananas comosus (L.) Merr.). Bioinformatics was used to confirm the differential expression of GA2 gibberellin oxidase gene AcGA2oxs in the pineapple genome, which laid the foundation for exploring its role in pineapple. In this study, 42 GA2ox genes (AcGA2oxs) were identified in the pineapple genome, named from AcGA2ox1 to AcGA2ox42, and divided into four groups according to phylogenetic analysis. We also analyzed the gene structure, conserved motifs and chromosome localization of AcGA2oxs. AcGA2oxs within the same group had similar gene structure and motifs composition. Collinear analysis and cis-element analysis provided the basis for understanding the evolution and function of GA2ox genes in pineapple. In addition, we selected different tissue parts to analyze the expression profile of AcGA2oxs, and the results show that 41 genes were expressed, except for AcGA2ox18. AcGA2ox18 may not be expressed in these sites or may be pseudogenes. qRT-PCR (real-time fluorescence quantitative PCR) was used to detect the relative expression levels of the GA2ox gene family under different concentrations of GA3 treatment, and it was found that AcGA2ox gene expression was upregulated in different degrees under GA3 treatment. These results provide useful information for further study on the evolution and function of the GA2ox family in pineapple.

Integrated morphological, metabolome, and transcriptome analyses revealed the mechanism of exogenous gibberellin promoting petiole elongation in Oenanthe javanica

Oenanthe javanica (Blume) DC. is a popular vegetable with unique flavor and its leaf is the main product organ. Gibberellin (GA) is an important plant hormone that plays vital roles in regulating the growth of plants. In this study, the plants of water dropwort were treated with different concentrations of GA₃. The plant height of water dropwort was significantly increased after GA₃ treatment. Anatomical structure analysis indicated that the cell length of water dropwort was elongated under exogenous application of GA₃. The metabolome analysis showed flavonoids were the most abundant metabolites and the biosynthesis of secondary metabolites were also regulated by GA₃. The exogenous application of GA₃ altered the gene expressions of plant hormone signal transduction (GID and DELLA) and metabolites biosynthesis pathways to regulate the growth of water dropwort. The GA contents were modulated by up-regulating the expression of GA metabolism gene GA2ox. The differentially expressed genes related to cell wall formation were significantly enriched. A total of 22 cellulose synthase involved in cellulose biosynthesis were identified from the genome of water dropwort. Our results indicated that GA treatment promoted the cell elongation by inducing the expression of cellulose synthase and cell wall formation in water dropwort. These results revealed the molecular mechanism of GA-mediated cell elongation, which will provide valuable reference for using GA to regulate the growth of water dropwort.

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.

Physiological analysis reveals the mechanism of accelerated growth recovery for rice seedlings by nitrogen application after low temperature stress

Low temperature and overcast rain are harmful to directly seeding early rice, it can hinder rice growth and lower rice biomass during the seedling stage, which in turn lowers rice yield. Farmers usually use N to help rice recuperate after stress and minimize losses. However, the effect of N application on the growth recovery for rice seedlings after such low temperature stress and its associated physiological changes remain unclearly. Two temperature settings and four post-stress N application levels were used in a bucket experiment to compare B116 (strong growth recovery after stress) with B144 (weak growth recovery). The results showed that the stress (average daily temperature at 12°C for 4 days) inhibited the growth of rice seedlings. Compared to the zero N group, the N application group's seedling height, fresh weight and dry weight significantly increased after 12 days. In particular, the increases in all three growth indicators were relatively higher than that of N application at normal temperature, indicating the importance of N application to rice seedlings after low temperature stress. The antioxidant enzyme activity of rice seedlings increased significantly after N application, which reduced the damaging effect of ROS (reactive oxygen species) to rice seedlings. At the same time, the soluble protein content of seedlings showed a slow decrease, while the H₂O₂ and MDA (malondialdehyde) content decreased significantly. Nitrogen could also promote nitrogen uptake and utilization by increasing the expression of genes related to NH 4 + and NO 3 - uptake and transport, as well as improving the activity of NR (nitrate reductase) and GS (glutamine synthetase) in rice. N could affect GA₃ (gibberellin A3) and ABA (abscisic acid) levels by regulating the anabolism of GA₃ and ABA. The N application group maintained high ABA levels as well as low GA₃ levels from day 0 to day 6, and high GA₃ levels as well as low ABA levels from day 6 to day 12. The two rice varieties showed obvious characteristics of accelerated growth recovery and positive physiological changes by nitrogen application after stress, while B116 generally showed more obvious growth recovery and stronger growth-related physiological reaction than that of B144. The N application of 40 kg hm^-2 was more conducive to the rapid recovery of rice growth after stress. The above results indicated that appropriate N application promoted rice seedling growth recovery after low temperature stress mainly by increasing the activities of antioxidant enzymes and nitrogen metabolizing enzymes as well as regulating the levels of GA₃ and ABA. The results of this study will provide a reference for the regulation of N on the recovery of rice seedling growth after low temperature and weak light stress.

Agronomic Trait Analysis and Genetic Mapping of a New Wheat Semidwarf Gene Rht-SN33d

Plant height is a key agronomic trait that is closely to the plant morphology and lodging resistance in wheat. However, at present, the few dwarf genes widely used in wheat breeding have narrowed wheat genetic diversity. In this study, we selected a semi-dwarf wheat mutant dwarf33 that exhibits decreased plant height with little serious negative impact on other agronomic traits. Genetic analysis and mutant gene mapping indicated that dwarf33 contains a new recessive semi-dwarf gene Rht-SN33d, which was mapped into ~1.3 Mb interval on the 3DL chromosome. The gibberellin metabolism-related gene TraesCS3D02G542800, which encodes gibberellin 2-beta-dioxygenase, is considered a potential candidate gene of Rht-SN33d. Rht-SN33d reduced plant height by approximately 22.4% in mutant dwarf33. Further study revealed that shorter stem cell length may be the main factor causing plant height decrease. In addition, the coleoptile length of dwarf33 was just 9.3% shorter than that of wild-type Shaannong33. These results will help to expand our understanding of new mechanisms of wheat height regulation, and obtain new germplasm for wheat improvement.

Identification of two tandem genes associated with primary rosette branching in flowering Chinese cabbage

Branching is an important agronomic trait determining plant architecture and yield; however, the molecular mechanisms underlying branching in the stalk vegetable, flowering Chinese cabbage, remain unclear. The present study identified two tandem genes responsible for primary rosette branching in flowering Chinese cabbage by GradedPool-Seq (GPS) combined with Kompetitive Allele Specific PCR (KASP) genotyping. A 900 kb candidate region was mapped in the 28.0-28.9 Mb interval of chromosome A07 through whole-genome sequencing of three graded-pool samples from the F₂ population derived by crossing the branching and non-branching lines. KASP genotyping narrowed the candidate region to 24.6 kb. Two tandem genes, BraA07g041560.3C and BraA07g041570.3C, homologous to AT1G78440 encoding GA2ox1 oxidase, were identified as the candidate genes. The BraA07g041560.3C sequence was identical between the branching and non-branching lines, but BraA07g041570.3C had a synonymous single nucleotide polymorphic (SNP) mutation in the first exon (290^th bp, A to G). In addition, an ERE cis-regulatory element was absent in the promoter of BraA07g041560.3C, and an MYB cis-regulatory element in the promoter of BraA07g041570.3C in the branching line. Gibberellic acid (GA₃) treatment decreased the primary rosette branch number in the branching line, indicating the significant role of GA in regulating branching in flowering Chinese cabbage. These results provide valuable information for revealing the regulatory mechanisms of branching and contributing to the breeding programs of developing high-yielding species in flowering Chinese cabbage.

Modifications of Phytohormone Metabolism Aimed at Stimulation of Plant Growth, Improving Their Productivity and Tolerance to Abiotic and Biotic Stress Factors

Due to the growing human population, the increase in crop yield is an important challenge for modern agriculture. As abiotic and biotic stresses cause severe losses in agriculture, it is also crucial to obtain varieties that are more tolerant to these factors. In the past, traditional breeding methods were used to obtain new varieties displaying demanded traits. Nowadays, genetic engineering is another available tool. An important direction of the research on genetically modified plants concerns the modification of phytohormone metabolism. This review summarizes the state-of-the-art research concerning the modulation of phytohormone content aimed at the stimulation of plant growth and the improvement of stress tolerance. It aims to provide a useful basis for developing new strategies for crop yield improvement by genetic engineering of phytohormone metabolism.

Biomolecular Strategies for Vascular Bundle Development to Improve Crop Yield

The need to produce crops with higher yields is critical due to a growing global population, depletion of agricultural land, and severe climate change. Compared with the "source" and "sink" transport systems that have been studied a lot, the development and utilization of vascular bundles (conducting vessels in plants) are increasingly important. Due to the complexity of the vascular system, its structure, and its delicate and deep position in the plant body, the current research on model plants remains basic knowledge and has not been repeated for crops and applied to field production. In this review, we aim to summarize the current knowledge regarding biomolecular strategies of vascular bundles in transport systems (source-flow-sink), allocation, helping crop architecture establishment, and influence of the external environment. It is expected to help understand how to use sophisticated and advancing genetic engineering technology to improve the vascular system of crops to increase yield.

Physiological and Transcriptomic Analyses Reveal the Mechanisms of Compensatory Growth Ability for Early Rice after Low Temperature and Weak Light Stress

“Late spring coldness” (T) is a frequent meteorological disaster in the spring in southern China, often causing severe yield losses of direct-seeded early rice. In this study, we investigated the mechanisms underlying the differences in the compensatory growth ability of different rice genotypes by focusing on agronomic traits, physiological indicators, and transcriptome. The results showed that there were significant differences in the compensatory growth recovery ability of different genotypes after a combination of four days of low temperature and weak light stress. Only the strong compensatory growth genotype B116 was able to grow rapidly and reduce soluble protein and H2O2 concentrations rapidly after stress. By analyzing enzyme activity as well as endogenous hormone concentration, we found that the high superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) activities and high levels of abscisic acid (ABA) could reduce the damage of B116 during stress. Meanwhile, higher glutamine synthetase (GS) and nitrate reductase (NR) activity and higher levels of gibberellin A3(GA3), indoleacetic acid (IAA), and zeatin nucleoside (ZR) could enable B116 to grow rapidly after stress. The identified differentially expressed genes (DEGs) indicated that there were large differences in POD-related genes and gibberellin metabolism between B116 and B144 after stress; RT-PCR quantification also showed a trend consistent with RNA-seq, which may be an important reason for the differences in compensatory growth ability.

PavGA2ox-2L inhibits the plant growth and development interacting with PavDWARF in sweet cherry (Prunus avium L.)

Dwarf dense planting is helpful to improve the yield and quality of sweet cherry, which has enormous market demand. GA2oxs (GA oxidases) affect plant height, dormancy release, flower development, and seed germination by participating in the metabolic regulation and signal transduction of GA (Gibberellin). However, the research on GA2ox in sweet cherry is little and worthy of further investigation. Therefore, we identified the PavGA2ox-2L gene from sweet cherry, close to PynGA2ox-2 from Prunus yedoensis var. Nudiflora. The phylogenetic analysis indicated conserved functions with these evolutionarily closer GA2ox subfamily genes. Subcellular localization forecast analysis indicated that PavGA2ox-2L was localized in the nucleus or cytoplasm. The expression levels of PavGA2ox-2L were higher in winter, indicating that PavGA2ox-2L promoted maintained flower bud dormancy. The expression levels of PavGA2ox-2L were significantly increased after GA₄₊₇ treatment while decreased after GR24 (a synthetic analog of SLs (Strigolactones)) or TIS108 (a triazole-type SL-biosynthesis inhibitor) treatments. Over-expression of PavGA2ox-2L resulted in decreased plant height, delayed flowering time, and low seed germination rate in Arabidopsis thaliana. Furthermore, the interaction between PavGA2ox-2L and PavDWARF was verified by Y2H and BiFC assays. In the current investigation, PavGA2ox-2L functions as a GA metabolic gene that promotes dwarf dense planting, delays flowering time, and inhibits seed germination. In addition, it also participates in regulating plant growth and development through the interaction with the critical negative regulator PavDWARF of Gibberellin. These results will help us better explore the molecular mechanism of GA2ox-mediated dwarf and late-maturing varieties for fruit trees.

Transcriptome analysis provides new ideas for studying the regulation of glucose-induced lignin biosynthesis in pear calli

BACKGROUND

Glucose can be involved in metabolic activities as a structural substance or signaling molecule and plays an important regulatory role in fruit development. Glucose metabolism is closely related to the phenylpropanoid pathway, but the specific role of glucose in regulating lignin biosynthesis in pear fruit is still unclear. The transcriptome of pear calli generated from fruit and treated with glucose was analyzed to investigate the role of glucose in lignin biosynthesis.

RESULTS

The treatment of exogenous glucose significantly enhanced the accumulation of lignin in pear calli. A total of 6566 differentially expressed genes were obtained by transcriptome sequencing. Glycolysis was found to be the pathway with significant changes. Many differentially expressed genes were enriched in secondary metabolic pathways, especially the phenylpropanoid pathway. Expression of structural genes (PbPAL, PbHCT, PbCOMT, PbPRX) in lignin biosynthesis was up-regulated after glucose treatment. In addition, glucose might regulate lignin biosynthesis through interactions with ABA, GA, and SA signaling. Several candidate MYB transcription factors involved in glucose-induced lignin biosynthesis have also been revealed. The qRT-PCR analyses showed that the expression pattern of PbPFP at early developmental stage in 'Dangshansuli' fruits was consistent with the trend of lignin content. Transient expression of PbPFP resulted in a significant increase of lignin content in 'Dangshansuli' fruits at 35 days after full bloom (DAB) and tobacco leaves, indicating that PbPFP (Pbr015118.1) might be associated with the enhancement of lignin biosynthesis in response to glucose treatment.

CONCLUSIONS

PbPFP plays a positive role in regulating lignin biosynthesis in response to glucose treatment. This study may reveal the regulatory pathway related to lignin accumulation in pear calli induced by glucose.

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.

Identification and Characterization of Key Genes Responsible for Weedy and Cultivar Growth Types in Soybean

In cultivated plants, shoot morphology is an important factor that influences crop economic value. However, the effects of gene expression patterns on shoot morphology are not clearly understood. In this study, the molecular mechanism behind shoot morphology (including leaf, stem, and node) was analyzed using RNA sequencing to compare weedy (creeper) and cultivar (stand) growth types obtained in F7 derived from a cross of wild and cultivated soybeans. A total of 12,513 (in leaves), 14,255 (in stems), and 11,850 (in nodes) differentially expressed genes were identified among weedy and cultivar soybeans. Comparative transcriptome and expression analyses revealed 22 phytohormone-responsive genes. We found that GIBBERELLIN 2-OXIDASE 8 (GA2ox), SPINDLY (SPY), FERONIA (FER), AUXIN RESPONSE FACTOR 8 (ARF8), CYTOKININ DEHYDROGENASE-1 (CKX1), and ARABIDOPSIS HISTIDINE KINASE-3 (AHK3), which are crucial phytohormone response genes, were mainly regulated in the shoot of weedy and cultivar types. These results indicate that interactions between phytohormone signaling genes regulate shoot morphology in weedy and cultivar growth type plants. Our study provides insights that are useful for breeding and improving crops to generate high-yield soybean varieties.

Morphological Characterization and Transcriptome Analysis of New Dwarf and Narrow-Leaf (dnl2) Mutant in Maize

Lodging is the primary factor limiting high yield under a high plant density. However, an optimal plant height and leaf shape can effectively decrease the lodging risk. Here we studied an ethyl methanesulfonate (EMS)-induced dwarf and a narrow-leaf mutant, dnl2. Gene mapping indicated that the mutant was controlled by a gene located on chromosome nine. Phenotypic and cytological observations revealed that dnl2 showed inhibited cell growth, altered vascular bundle patterning, and disrupted secondary cell wall structure when compared with the wild-type, which could be the direct cause of the dwarf and narrow-leaf phenotype. The phytohormone levels, especially auxin and gibberellin, were significantly decreased in dnl2 compared to the wild-type plants. Transcriptome profiling of the internodes of the dnl2 mutant and wild-type revealed a large number of differentially expressed genes enriched in the cell wall biosynthesis, remodeling, and hormone biosynthesis and signaling pathways. Therefore, we suggest that crosstalk between hormones (the altered vascular bundle and secondary cell wall structure) may contribute to the dwarf and narrow-leaf phenotype by influencing cell growth. These results provide a foundation for DNL2 gene cloning and further elucidation of the molecular mechanism of the regulation of plant height and leaf shape in maize.

Overexpression of PvWOX3a in switchgrass promotes stem development and increases plant height

Switchgrass (Panicum virgatum L.) is an important perennial, noninvasive, tall ornamental grass that adds color and texture to gardens and landscapes. Moreover, switchgrass has been considered a forage and bioenergy crop because of its vigorous growth, low-input requirements, and broad geography. Here, we identified PvWOX3a from switchgrass, which encodes a WUSCHEL-related homeobox transcription factor. Transgenic overexpression of PvWOX3a in switchgrass increased stem length, internode diameter, and leaf blade length and width, all of which contributed to a 95% average increase in dry weight biomass compared with control plants. Yeast one-hybrid and transient dual-luciferase assays showed that PvWOX3a can repress the expression of gibberellin 2-oxidase and cytokinin oxidase/dehydrogenase through apparently direct interaction with their promoter sequences. These results suggested that overexpression of PvWOX3a could increase gibberellin and cytokinin levels in transgenic switchgrass plants, which promotes cell division, elongation, and vascular bundle development. We also overexpressed PvWOX3a in a transgenic miR156-overexpressing switchgrass line that characteristically exhibited more tillers, thinner internodes, and narrower leaf blades. Double transgenic switchgrass plants displayed significant increases in internode length and diameter, leaf blade width, and plant height but retained a tiller number comparable to that of plants expressing miR156 alone. Ultimately, the double transgenic switchgrass plants produced 174% more dry-weight biomass and 162% more solubilized sugars on average than control plants. These findings indicated that PvWOX3a is a viable potential genetic target for engineering improved shoot architecture and biomass yield of horticulture, fodder, and biofuel crops.

Serendipita Fungi Modulate the Switchgrass Root Transcriptome to Circumvent Host Defenses and Establish a Symbiotic Relationship

The fungal family Serendipitaceae encompasses root-associated lineages with endophytic, ericoid, orchid, and ectomycorrhizal lifestyles. Switchgrass is an important bioenergy crop for cellulosic ethanol production owing to high biomass production on marginal soils otherwise unfit for food crop cultivation. The aim of this study was to investigate the host plant responses to Serendipita spp. colonization by characterizing the switchgrass root transcriptome during different stages of symbiosis in vitro. For this, we included a native switchgrass strain, Serendipita bescii, and a related strain, S. vermifera, isolated from Australian orchids. Serendipita colonization progresses from thin hyphae that grow between root cells to, finally, the production of large, bulbous hyphae that fill root cells during the later stages of colonization. We report that switchgrass seems to perceive both fungi prior to physical contact, leading to the activation of chemical and structural defense responses and putative host disease resistance genes. Subsequently, the host defense system appears to be quenched and carbohydrate metabolism adjusted, potentially to accommodate the fungal symbiont. In addition, prior to contact, switchgrass exhibited significant increases in root hair density and root surface area. Furthermore, genes involved in phytohormone metabolism such as gibberellin, jasmonic acid, and salicylic acid were activated during different stages of colonization. Both fungal strains induced plant gene expression in a similar manner, indicating a conserved plant response to members of this fungal order. Understanding plant responsiveness to Serendipita spp. will inform our efforts to integrate them into forages and row crops for optimal plant-microbe functioning, thus facilitating low-input, sustainable agricultural practices.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Response of Lignin Metabolism to Light Quality in Wheat Population

The low red/far-red (R/FR) light proportion at the base of the high-density wheat population leads to poor stem quality and increases lodging risk. We used Shannong 23 and Shannong 16 as the test materials. By setting three-light quality treatments: normal light (CK), red light (RL), and far-red light (FRL), we irradiated the base internodes of the stem with RL and FRL for 7h. Our results showed that RL irradiation enhanced stem quality, as revealed by increased breaking strength, stem diameter, wall thickness and, dry weight per unit length, and the total amount of lignin and related gene expression increased, at the same time. The composition of lignin subunits was related to the lodging resistance of wheat. The proportion of S+G subunits and H subunits played a key role in wheat lodging resistance. RL could increase the content of S subunits and G subunits and the proportion of S+G subunits, reduce the proportion of H subunits. We described here, to the best of our knowledge, the systematic study of the mechanism involved in the regulation of stem breaking strength by light quality, particularly the effect of light quality on lignin biosynthesis and its relationship with lodging resistance in wheat.

MiR396-GRF module associates with switchgrass biomass yield and feedstock quality

Improving plant biomass yield and/or feedstock quality for highly efficient lignocellulose conversion has been the main research focus in genetic modification of switchgrass (Panicum virgatum L.), a dedicated model plant for biofuel production. Here, we proved that overexpression of miR396 (OE-miR396) leads to reduced plant height and lignin content mainly by reducing G-lignin monomer content. We identified nineteen PvGRFs in switchgrass and proved thirteen of them were cleaved by miR396. MiR396-targeted PvGRF1, PvGRF9 and PvGRF3 showed significantly higher expression in stem. By separately overexpressing rPvGRF1, 3 and 9, in which synonymous mutations abolished the miR396 target sites, and suppression of PvGRF1/3/9 activity via PvGRF1/3/9-SRDX overexpression in switchgrass, we confirmed PvGRF1 and PvGRF9 played positive roles in improving plant height and G-lignin content. Overexpression of PvGRF9 was sufficient to complement the defective phenotype of OE-miR396 plants. MiR396-PvGRF9 modulates these traits partly by interfering GA and auxin biosynthesis and signalling transduction and cell wall lignin, glucose and xylan biosynthesis pathways. Moreover, by enzymatic hydrolysis analyses, we found that overexpression of rPvGRF9 significantly enhanced per plant sugar yield. Our results suggest that PvGRF9 can be utilized as a candidate molecular tool in modifying plant biomass yield and feedstock quality.

Tuber and Tuberous Root Development

Root and tuber crops have been an important part of human nutrition since the early days of humanity, providing us with essential carbohydrates, proteins, and vitamins. Today, they are especially important in tropical and subtropical regions of the world, where they help to feed an ever-growing population. Early induction and storage organ size are important agricultural traits, as they determine yield over time. During potato tuberization, environmental and metabolic status are sensed, ensuring proper timing of tuberization mediated by phloem-mobile signals. Coordinated cellular restructuring and expansion growth, as well as controlled storage metabolism in the tuber, are executed. This review summarizes our current understanding of potato tuber development and highlights similarities and differences to important tuberous root crop species like sweetpotato and cassava. Finally, we point out knowledge gaps that need to be filled before a complete picture of storage organ development can emerge.

Functional Analysis of the Gibberellin 2-oxidase Gene Family in Peach

Peach (Prunus persica L. Batsch) trees grow vigorously and are subject to intense pruning during orchard cultivation. Reducing the levels of endogenous gibberellins (GAs) represents an effective method for controlling branch growth. Gibberellin 2-oxidases (GA2oxs) deactivate bioactive GAs, but little is known about the GA2ox gene family in peach. In this study, we identified seven PpGA2ox genes in the peach genome, which were clustered into three subgroups: C₁₉-GA2ox-I, C₁₉-GA2ox-II, and C₂₀-GA2ox-I. Overexpressing representative genes from the three subgroups, PpGA2ox-1, PpGA2ox-5, and PpGA2ox-2, in tobacco resulted in dwarf plants with shorter stems and smaller leaves than the wild type. An analysis of the GA metabolic profiles of the transgenic plants showed that PpGA2ox-5 (a member of subgroup C₁₉-GA2ox-II) is simultaneously active against both C₁₉-GAs and C₂₀-GAs,which implied that C₁₉-GA2ox-II enzymes represent intermediates of C₁₉-GA2oxs and C₂₀-GA2oxs. Exogenous GA₃ treatment of shoot tips activated the expression of all seven PpGA2ox genes, with different response times: the C ₁₉-GA2ox genes were transcriptionally activated more rapidly than the C₂₀-GA2ox genes. GA metabolic profile analysis suggested that C₂₀-GA2ox depletes GA levels more broadly than C₁₉-GA2ox. These results suggest that the PpGA2ox gene family is responsible for fine-tuning endogenous GA levels in peach. Our findings provide a theoretical basis for appropriately controlling the vigorous growth of peach trees.

Crosstalk between auxin and gibberellin during stalk elongation in flowering Chinese cabbage

Plant growth and development are tightly regulated by phytohormones. However, little is known about the interaction between auxin and gibberellin acid (GA) during flower stalk elongation and how it is directly related to organ formation. Therefore, the effects of indole acetic acid (IAA) and GA₃ treatments and their interaction on flower stalk elongation in flowering Chinese cabbage were investigated. The growth of flowering Chinese cabbage is regulated by IAA and GA_3, and the opposite results were observed after treatments with uniconazole (GA synthesis inhibitor) and N-1-naphthylphthalamic acid (NPA) (auxin transport inhibitor). Anatomical analysis of the pith region in stalks revealed that IAA promoted expansion via signal transduction and transport pathways. GA₃ regulated the elongation of flower stalks by controlling GA synthesis and partially controlling the IAA signaling pathway. GA₃ also had a stronger effect on stalk elongation than IAA. The results of qRT-PCR and histological analysis revealed that GA₃ and IAA induced the expansion of cell walls by activating the expression of genes encoding cell wall structural proteins such as Expansin (EXP). These findings provide new insights into the mechanism of stalk formation regulated by the combination of IAA and GA₃.

Plant buffering against the high-light stress-induced accumulation of CsGA2ox8 transcripts via alternative splicing to finely tune gibberellin levels and maintain hypocotyl elongation

In plants, alternative splicing (AS) is markedly induced in response to environmental stresses, but it is unclear why plants generate multiple transcripts under stress conditions. In this study, RNA-seq was performed to identify AS events in cucumber seedlings grown under different light intensities. We identified a novel transcript of the gibberellin (GA)-deactivating enzyme Gibberellin 2-beta-dioxygenase 8 (CsGA2ox8). Compared with canonical CsGA2ox8.1, the CsGA2ox8.2 isoform presented intron retention between the second and third exons. Functional analysis proved that the transcript of CsGA2ox8.1 but not CsGA2ox8.2 played a role in the deactivation of bioactive GAs. Moreover, expression analysis demonstrated that both transcripts were upregulated by increased light intensity, but the expression level of CsGA2ox8.1 increased slowly when the light intensity was >400 µmol·m^-2·s^-1 PPFD (photosynthetic photon flux density), while the CsGA2ox8.2 transcript levels increased rapidly when the light intensity was >200 µmol·m^-2·s^-1 PPFD. Our findings provide evidence that plants might finely tune their GA levels by buffering against the normal transcripts of CsGA2ox8 through AS.

Overexpression Levels of LbDREB6 Differentially Affect Growth, Drought, and Disease Tolerance in Poplar

The application of drought stress-regulating transcription factors (TFs) offers a credible way to improve drought tolerance in plants. However, many drought resistant TFs always showed unintended adverse effects on plant growth or other traits. Few studies have been conducted in trees to evaluate and overcome the pleiotropic effects of drought tolerance TFs. Here, we report the dose-dependent effect of the Limonium bicolor LbDREB6 gene on its overexpression in Populus ussurensis. High- and moderate-level overexpression of LbDREB6 significantly increased drought tolerance in a dose-dependent manner. However, the OE18 plants showed stunted growth under normal conditions, but they were also more sensitive to Marssonina brunnea infection than wild type (WT) and OE14 plants. While, OE14 showed normal growth, the pathogen tolerance of them was not significantly different from WT. Many stress-responsive genes were up-regulated in OE18 and OE14 compared to WT, especially for OE18 plants. Meanwhile, more pathogen tolerance related genes were down-regulated in OE18 compared to OE14 and WT plants. We achieved improved drought tolerance by adjusting the increased levels of exogenous DREB genes to avoid the occurrence of growth reduction and reduced disease tolerance.

Serendipita bescii promotes winter wheat growth and modulates the host root transcriptome under phosphorus and nitrogen starvation

Serendipita vermifera ssp. bescii, hereafter referred to as S. bescii, is a root‐associated fungus that promotes plant growth in both its native switchgrass host and a variety of monocots and dicots. Winter wheat (Triticum aestivum L.), a dual‐purpose crop, used for both forage and grain production, significantly contributes to the agricultural economies of the Southern Great Plains, USA. In this study, we investigated the influence of S. bescii on growth and transcriptome regulation of nitrogen (N) and phosphorus (P) metabolism in winter wheat. Serendipita bescii significantly improved lateral root growth and forage biomass under a limited N or P regime. Further, S. bescii activated sets of host genes regulating N and P starvation responses. These genes include, root‐specific auxin transport, strigolactone and gibberellin biosynthesis, degradation of phospholipids and biosynthesis of glycerolipid, downregulation of ammonium transport and nitrate assimilation, restriction of protein degradation by autophagy and subsequent N remobilization. All these genes are hypothesized to regulate acquisition, assimilation and remobilization of N and P. Based on transcriptional level gene regulation and physiological responses to N or P limitation, we suggest S. bescii plays a critical role in modulating stress imposed by limitation of these two critical nutrients in winter wheat.

Transcriptome Profiles Reveal the Growth-Promoting Mechanisms of Paenibacillus polymyxa YC0136 on Tobacco (Nicotiana tabacum L.)

Paenibacillus polymyxa is an important member of the plant growth-promoting rhizobacteria. P. polymyxa YC0136 inoculation had beneficial effect on growth promotion and biological control of tobacco (Nicotiana tabacum L.) under field conditions. This study aimed to reveal the growth-promoting mechanisms of strain YC0136. In growth-promotion assays, tobacco plant height was increased by 8.42% and 8.25% at 60 and 90 days, respectively, after inoculation with strain YC0136. Strain YC0136 also promoted the accumulation of tobacco biomass in varying degrees. Following inoculation with strain YC0136, 3,525 and 4,368 tobacco genes were up-regulated and down-regulated, respectively. Strain YC0136 induced the expression of plant hormone-related genes in tobacco, including auxin, cytokinin, and gibberellin, as well as transcription factors related to stress resistance such as WRKY and MYB. In addition, strain YC0136 induced the up-regulation of genes in the phenylpropanoid biosynthesis pathway by 1.51-4.59 times. Interaction with tobacco also induced gene expression changes in strain YC0136, with 286 and 223 genes up-regulated and down-regulated, respectively. Tobacco interaction induced up-regulation of the ilvB gene related to auxin biosynthesis in strain YC0136 by 1.72 times and induced expression of some nutrient transport genes. This study contributes to our understanding of the growth-promoting mechanisms of strain YC0136 on tobacco and provides a theoretical basis for the application of P. polymyxa YC0136 as a biological fertilizer.

A mutation in the intron splice acceptor site of a GA3ox gene confers dwarf architecture in watermelon (Citrullus lanatus L.)

Dwarf architecture is an important trait associated with plant yield, lodging resistance and labor cost. Here, we aimed to identify a gene causing dwarfism in watermelon. The ‘w106’ (dwarf) and ‘Charleston Gray’ (vine) were used as parents to construct F₁ and F₂ progeny. Dwarf architecture of ‘w106’ was mainly caused by longitudinal cell length reduction and was controlled by a single recessive gene. Whole-genome sequencing of two parents and two bulk DNAs of F₂ population localized this gene to a 2.63-Mb region on chromosome 9; this was further narrowed to a 541-kb region. Within this region, Cla015407, encoding a gibberellin 3β-hydroxylase (GA3ox), was the candidate gene. Cla015407 had a SNP mutation (G → A) in the splice acceptor site of the intron, leading to altered splicing event and generating two splicing isoforms in dwarf plants. One splicing isoform retained the intron sequences, while the other had a 13-bp deletion in the second exon of GA3ox transcript, both resulting in truncated proteins and loss of the functional Fe2OG dioxygenase domain in dwarf plants. RNA-Seq analysis indicated that expression of Cla015407 and other GA biosynthetic and metabolic genes were mostly up-regulated in the shoots of dwarf plants compared with vine plants in F₂ population. Measurement of endogenous GA levels indicated that bioactive GA₄ was significantly decreased in the shoots of dwarf plants. Moreover, the dwarf phenotype can be rescued by exogenous applications of GA₃ or GA₄₊₇, with the latter having a more distinct effect than the former. Subcellular localization analyses of GA3ox proteins from two parents revealed their subcellular targeting in nucleus and cytosol. Here, a GA3ox gene controlling dwarf architecture was identified, and loss function of GA3ox leads to GA₄ reduction and dwarfism phenotype in watermelon.

Comparative transcriptome analyses reveal different mechanism of high- and low-tillering genotypes controlling tiller growth in orchardgrass (Dactylis glomerata L.)

BACKGROUND

Tillering is an important agronomic trait underlying the yields and reproduction of orchardgrass (Dactylis glomerata), an important perennial forage grass. Although some genes affecting tiller initiation have been identified, the tillering regulatory network is still largely unknown, especially in perennial forage grasses. Thus, unraveling the regulatory mechanisms of tillering in orchardgrass could be helpful in developing selective strategies for high-yield perennial grasses. In this study, we generated high-throughput RNA-sequencing data from multiple tissues of tillering stage plants to identify differentially expressed genes (DEGs) between high- and low-tillering orchardgrass genotypes. Gene Ontology and pathway enrichment analyses connecting the DEGs to tillering number diversity were conducted.

RESULTS

In the present study, approximately 26,282 DEGs were identified between two orchardgrass genotypes, AKZ-NRGR667 (a high-tillering genotype) and D20170203 (a low-tillering genotype), which significantly differed in tiller number. Pathway enrichment analysis indicated that DEGs related to the biosynthesis of three classes of phytohormones, i.e., strigolactones (SLs), abscisic acid (ABA), and gibberellic acid (GA), as well as nitrogen metabolism dominated such differences between the high- and low-tillering genotypes. We also confirmed that under phosphorus deficiency, the expression level of the major SL biosynthesis genes encoding DWARF27 (D27), 9-cis-beta-carotene 9',10'-cleaving dioxygenase (CCD7), carlactone synthase (CCD8), and more axillary branching1 (MAX1) proteins in the high-tillering orchardgrass genotype increased more slowly relative to the low-tillering genotype.

CONCLUSIONS

Here, we used transcriptomic data to study the tillering mechanism of perennial forage grasses. We demonstrated that differential expression patterns of genes involved in SL, ABA, and GA biosynthesis may differentiate high- and low-tillering orchardgrass genotypes at the tillering stage. Furthermore, the core SL biosynthesis-associated genes in high-tillering orchardgrass were more insensitive than the low-tillering genotype to phosphorus deficiency which can lead to increases in SL biosynthesis, raising the possibility that there may be distinct SL biosynthesis way in tillering regulation in orchardgrass. Our research has revealed some candidate genes involved in the regulation of tillering in perennial grasses that is available for establishment of new breeding resources for high-yield perennial grasses and will serve as a new resource for future studies into molecular mechanism of tillering regulation in orchardgrass.

Cloning and Functional Analysis of Dwarf Gene Mini Plant 1 (MNP1) in Medicago truncatula

Plant height is a vital agronomic trait that greatly determines crop yields because of the close relationship between plant height and lodging resistance. Legumes play a unique role in the worldwide agriculture; however, little attention has been given to the molecular basis of their height. Here, we characterized the first dwarf mutant mini plant 1 (mnp1) of the model legume plant Medicago truncatula. Our study found that both cell length and the cell number of internodes were reduced in a mnp1 mutant. Using the forward genetic screening and subsequent whole-genome resequencing approach, we cloned the MNP1 gene and found that it encodes a putative copalyl diphosphate synthase (CPS) implicated in the first step of gibberellin (GA) biosynthesis. MNP1 was highly homologous to Pisum sativum LS. The subcellular localization showed that MNP1 was located in the chloroplast. Further analysis indicated that GA3 could significantly restore the plant height of mnp1-1, and expression of MNP1 in a cps1 mutant of Arabidopsis partially rescued its mini-plant phenotype, indicating the conservation function of MNP1 in GA biosynthesis. Our results provide valuable information for understanding the genetic regulation of plant height in M. truncatula.

Heterologous expression of a chimeric gene, OsDST-SRDX, enhanced salt tolerance of transgenic switchgrass (Panicum virgatum L.)

Overexpression of OsDST-SRDX chimeric gene in switchgrass promotes plant growth and improves the salt tolerance of transgenic switchgrass by improving its antioxidative ability. Switchgrass (Panicum virgatum L.) is a forage and model feedstock plant. To avoid competing with crops in arable land utilization, improving salt tolerance of switchgrass is required to use marginal saline land for switchgrass production. To improve salt tolerance of switchgrass, a chimeric DROUGHT AND SALT TOLERANCE (DST) gene OsDST-SRDX was constructed using the Chimeric REpressor gene-Silencing Technology (CRES-T), and introduced into switchgrass genome by Agrobacterium-mediated transformation. Compared to wild-type (WT) plants, OsDST-SRDX transgenic (TG) switchgrass plants showed wider leaves and thicker stems. They performed better under salt stress, had higher relative leaf water content, lower electrolyte leakage and lower malondialdehyde (MDA) content, and accumulated less Na⁺ and more K⁺ than WT controls. The transgenic plants had also higher activities of antioxidant enzymes associated with suppressed expressing of genes in H₂O₂ homeostasis, including glutathione S-transferase (GST2, GST6), cytochrome P450, peroxidase 24 precursor, and induced expressing of CAT and SOD under salt stress to eliminate excess H₂O₂. Our results indicate that overexpression of the chimeric gene OsDST-SRDX improves salt tolerance of switchgrass, a C₄ biofuel crop.

Changes in carbohydrate metabolism and endogenous hormone regulation during bulblet initiation and development in Lycoris radiata

BACKGROUND

Lycoris species have great ornamental and medicinal values; however, their low regeneration efficiency seriously restricts their commercial production. Understanding the mechanism of bulblet propagation in this genus, which has remained underexplored to date, could provide a theoretical basis for improving the reproductive efficiency. Therefore, we studied the bulblet initiation and developmental processes in Lycoris radiata.

RESULTS

We found that bulblets are formed on the junctions of the innermost layers of scales and the basal plate, and initially present as an axillary bud and gradually develop into a bulblet. We also determined the changes in carbohydrate and endogenous hormone contents during bulblet initiation and development, as well as the expression patterns of genes involved in carbohydrate metabolism and hormone biosynthesis and signaling through transcriptome analysis. Soluble sugars derived from starch degradation in the outer scales are transported to and promote bulblet initiation and development through starch synthesis in the inner scales. This process is mediated by several genes involved in carbohydrate metabolism, especially genes encoding ADP glucose pyrophosphorylase, a crucial starch synthesis enzyme. As for hormones, endogenous IAA, GA, and ABA content showed an increase and decrease during bulblet initiation and development, respectively, which were consistent with the expression patterns of genes involved in IAA, GA, and ABA synthesis and signal transduction. In addition, a decrease in ZR content may be down- and up-regulated by CK biosynthesis and degradation related genes, respectively, with increasing auxin content. Furthermore, expression levels of genes related to BR, JA, and SA biosynthesis were increased, while that of ethylene biosynthesis genes was decreased, which was also consistent with the expression patterns of their signal transduction genes.

CONCLUSIONS

The present study provides insights into the effect of carbohydrate metabolism and endogenous hormone regulation on control of L. radiata bulblet initiation and development. Based on the results, we propose several suggestions to improve L. radiata propagation efficiency in production, which will provide directions for future research.

Phalaenopsis orchid miniaturization by overexpression of OsGA2ox6, a rice GA2-oxidase gene

BACKGROUND

Phalaenopsis orchids are one of the most common potted orchids sold worldwide. Most Phalaenopsis cultivars have long inflorescences that cause shipping problems and increase handling costs. Miniaturization of Phalaenopsis orchids not only reduces overall production costs but also can expand the appeal of the orchids to a different group of consumers who prefer to keep flowers on desks or tabletops. Although some miniature Phalaenopsis plants can be obtained via hybridization or mutation, they are unpredictable and limited in variety. We therefore used the transgenic approach of overexpressing gibberellin 2-oxidase 6 (OsGA2ox6), a rice GA deactivation gene, to investigate its functional effect in miniaturizing Phalaenopsis and to create a stable miniaturization platform to facilitate a supply for the potential demands of the miniature flower market.

RESULTS

A commercial moth orchid, Phalaenopsis Sogo Yukidian 'SPM313', was transformed with the plasmid vector Ubi:OsGA2ox6 and successfully overexpressed the OsGA2ox6 gene in planta. The transgenic lines displayed darker-green, shorter, and wider leaves, thicker roots and much shorter flower spikes (10 cm vs 33 cm) than the nontransgenic line with a normal flower size and blooming ability and are therefore an ideal miniaturized form of Phalaenopsis orchids.

CONCLUSIONS

We demonstrated that the ectopic expression of OsGA2ox6 can miniaturize Phalaenopsis Sogo Yukidian 'SPM313' while preserving its blooming ability, providing an alternative, useful method for miniaturizing Phalaenopsis species. This miniaturization by a transgenic approach can be further expanded by using GA2ox genes from different plant species or different gene variants, thereby expanding the technical platform for miniaturizing Phalaenopsis species to meet the potential demands of the miniature Phalaenopsis flower market.

Transcriptome profiles reveal that gibberellin-related genes regulate weeping traits in crape myrtle

Plant architecture includes vital traits that influence and benefit crops, and economically important trees. Different plant architectures provide natural beauty. Weeping ornamental plants are aesthetically appealing to people. The regulatory mechanism controlling the weeping trait is poorly understood in crape myrtle. To investigate the weeping trait mechanism, transcriptional profiling of different organs in weeping and upright crape myrtle was performed based on phenotype. Phenotypic and histological analyses demonstrated that endodermal cells were absent, and that new shoot phenotypes could be rescued by the GA3 treatment of weeping plants. The transcriptional analysis and coexpression network analysis (WGCNA) of differentially expressed genes indicated that GA synthesis and signal transduction pathways play a role in weeping traits. When the expression level of a negative element of GA signaling, LfiGRAS1, was reduced by virus-induced gene silencing (VIGS), new branches grew in infected plants in a negatively geotropic manner. An integrated analysis implied that GA had a strong influence on weeping crape myrtle by interacting with other factors. This study helps to elucidate the mechanism governing the weeping trait and can improve the efficiency of breeding in Lagerstroemia.

Heteroexpression of Osa-miR319b improved switchgrass biomass yield and feedstock quality by repression of PvPCF5

BACKGROUND

Switchgrass (Panicum virgatum L.), a C₄ perennial grass, has been recognized as one of the most potentially important lignocellulose biofuel crops. MicroRNA319 (miR319) plays a key role in plant development, abiotic resistance, and cell wall biosynthesis by repressing expression of its target TCP genes. We hypothesized miR319-TCP pathway could play important roles in switchgrass feedstock characteristics for biofuel production, and produced switchgrass transgenic plants overexpressing miR319 (by ectopic expressing Osa-MIR319b gene), blocking miR319 (by overexpressing a target mimicry of miR319/MIM319) and repression of miR319 target gene PvPCF5. Plant phenotype, biomass yield, and feedstock quality of transgenic plants were analyzed.

RESULTS

Overexpression of miR319 in switchgrass promoted leaf elongation and expansion of transgenic plants, increased plant height, stem diameter, and resulted in a significant increase in plant biomass yield. Transgenic plants overexpressing of miR319 reduced lignin content, showed significantly higher enzymatic hydrolysis efficiency compared to the wild type plant. However, opposite results were observed in the MIM319 plants. Furthermore, suppression of miR319 target gene PvPCF5 activity also reduced lignin content, increased lignin monomer S/G ratio and the proportion of β-O-4 linkages, while significantly improving the sugar production per plant. Quantitative real-time (qRT-PCR) analysis indicated that expression of PvMYB58/63B and PvHCT with predicted TCP binding sites in their promoter regions was negatively regulated by miR319-PvPCF5 module.

CONCLUSIONS

MiR319-PvPCF5 module plays positive roles in regulating biomass yield and quality of switchgrass. It can be utilized as a candidate molecular tool in regulating biomass yield and feedstock quality. The finding could also be transferred to other grasses for forage quality improvement through genetic manipulation.

MiR319 mediated salt tolerance by ethylene

Salinity-induced accumulation of certain microRNAs accompanied by gaseous phytohormone ethylene production has been recognized as a mechanism of plant salt tolerance. MicroRNA319 (miR319) has been characterized as an important player in abiotic stress resistance in some C3 plants, such as Arabidopsis thaliana and rice. However, its role in the dedicated biomass plant switchgrass (Panicum virgatum L.), a C4 plant, has not been reported. Here, we show crosstalk between miR319 and ethylene (ET) for increasing salt tolerance. By overexpressing Osa-MIR319b and a target mimicry form of miR319 (MIM319), we showed that miR319 positively regulated ET synthesis and salt tolerance in switchgrass. By experimental treatments, we demonstrated that ET-mediated salt tolerance in switchgrass was dose-dependent, and miR319 regulated the switchgrass salt response by fine-tuning ET synthesis. Further experiments showed that the repression of a miR319 target, PvPCF5, in switchgrass also led to enhanced ethylene accumulation and salt tolerance in transgenic plants. Genome-wide transcriptome analysis demonstrated that overexpression of miR319 (OE-miR319) down-regulated the expression of key genes in the methionine (Met) cycle but promoted the expression of genes in ethylene synthesis. The results enrich our understanding of the synergistic effects of the miR319-PvPCF5 module and ethylene synthesis in the salt tolerance of switchgrass, a C4 bioenergy plant.

Genome-wide association analysis for maize stem Cell Wall-bound Hydroxycinnamates

BACKGROUND

The structural reinforcement of cell walls by hydroxycinnamates has a significant role in defense against pests and pathogens, but it also interferes with forage digestibility and biofuel production. Elucidation of maize genetic variations that contribute to variation for stem hydroxycinnamate content could simplify breeding for cell wall strengthening by using markers linked to the most favorable genetic variants in marker-assisted selection or genomic selection approaches​.

RESULTS

A genome-wide association study was conducted using a subset of 282 inbred lines from a maize diversity panel to identify single nucleotide polymorphisms (SNPs) associated with stem cell wall hydroxycinnamate content. A total of 5, 8, and 2 SNPs were identified as significantly associated to p-coumarate, ferulate, and total diferulate concentrations, respectively in the maize pith. Attending to particular diferulate isomers, 3, 6, 1 and 2 SNPs were related to 8-O-4 diferulate, 5-5 diferulate, 8-5 diferulate and 8-5 linear diferulate contents, respectively. This study has the advantage of being done with direct biochemical determinations instead of using estimates based on Near-infrared spectroscopy (NIRS) predictions. In addition, novel genomic regions involved in hydroxycinnamate content were found, such as those in bins 1.06 (for FA), 4.01 (for PCA and FA), 5.04 (for FA), 8.05 (for PCA), and 10.03 and 3.06 (for DFAT and some dimers).

CONCLUSIONS

The effect of individual SNPs significantly associated with stem hydroxycinnamate content was low, explaining a low percentage of total phenotypic variability (7 to 10%). Nevertheless, we spotlighted new genomic regions associated with the accumulation of cell-wall-bound hydroxycinnamic acids in the maize stem, and genes involved in cell wall modulation in response to biotic and abiotic stresses have been proposed as candidate genes for those quantitative trait loci (QTL). In addition, we cannot rule out that uncharacterized genes linked to significant SNPs could be implicated in dimer formation and arobinoxylan feruloylation because genes involved in those processes have been poorly characterized. Overall, genomic selection considering markers distributed throughout the whole genome seems to be a more appropriate breeding strategy than marker-assisted selection focused in markers linked to QTL.

Genome-Wide Identification and Expression Analysis of GA2ox, GA3ox, and GA20ox Are Related to Gibberellin Oxidase Genes in Grape (Vitis Vinifera L.)

Gibberellin (GAs) plays the important role in the regulation of grape developmental and growth processes. The bioinformatics analysis confirmed the differential expression of GA2, GA3, and GA20 gibberellin oxidase genes (VvGA2oxs, VvGA3oxs, and VvGA20oxs) in the grape genome, and laid a theoretical basis for exploring its role in grape. Based on the Arabidopsis GA2oxs, GA3oxs, and GA20oxs genes already reported, the VvGA2oxs, VvGA3oxs, and VvGA20oxs genes in the grape genome were identified using the BLAST software in the grape genome database. Bioinformatics analysis was performed using software such as DNAMAN v.5.0, Clustalx, MapGene2Chrom, MEME, GSDS v.2.0, ExPASy, DNAsp v.5.0, and MEGA v.7.0. Chip expression profiles were generated using grape Affymetrix GeneChip 16K and Grape eFP Browser gene chip data in PLEXdb. The expression of VvGA2oxs, VvGA3oxs, and VvGA20oxs gene families in stress was examined by qRT-PCR (Quantitative real-time-PCR). There are 24 GAoxs genes identified with the grape genome that can be classified into seven subgroups based on a phylogenetic tree, gene structures, and conserved Motifs in our research. The gene family has higher codon preference, while selectivity is negative selection of codon bias and selective stress was analyzed. The expression profiles indicated that the most of VvGAox genes were highly expressed under different time lengths of ABA (Abscisic Acid) treatment, NaCl, PEG and 5 °C. Tissue expression analysis showed that the expression levels of VvGA2oxs and VvGA20oxs in different tissues at different developmental stages of grapes were relatively higher than that of VvGA3oxs. Last but not least, qRT-PCR (Real-time fluorescent quantitative PCR) was used to determine the relative expression of the GAoxs gene family under the treatment of GA3 (gibberellin 3) and uniconazole, which can find that some VvGA2oxs was upregulated under GA3 treatment. Simultaneously, some VvGA3oxs and VvGA20oxs were upregulated under uniconazole treatment. In a nutshell, the GA2ox gene mainly functions to inactivate biologically active GAs, while GA20ox mainly degrades C20 gibberellins, and GA3ox is mainly composed of biologically active GAs. The comprehensive analysis of the three classes of VvGAoxs would provide a basis for understanding the evolution and function of the VvGAox gene family in a grape plant.

A single nucleotide mutation in GID1c disrupts its interaction with DELLA1 and causes a GA-insensitive dwarf phenotype in peach

Plant stature is one important factor that affects the productivity of peach orchards. However, little is known about the molecular mechanism(s) underlying the dwarf phenotype of peach tree. Here, we report a dwarfing mechanism in the peach cv. FenHuaShouXingTao (FHSXT). The dwarf phenotype of 'FHSXT' was caused by shorter cell length compared to the standard cv. QiuMiHong (QMH). 'FHSXT' contained higher endogenous GA levels than did 'QMH' and did not response to exogenous GA treatment (internode elongation). These results indicated that 'FHSXT' is a GA-insensitive dwarf mutant. A dwarf phenotype-related single nucleotide mutation in the gibberellic acid receptor GID1 was identified in 'FHSXT' (GID1c^S191F ), which was also cosegregated with dwarf phenotype in 30 tested cultivars. GID1c^S191F was unable to interact with the growth-repressor DELLA1 even in the presence of GA. 'FHSXT' accumulated a higher level of DELLA1, the degradation of which is normally induced by its interaction with GID1. The DELLA1 protein level was almost undetectable in 'QMH', but not reduced in 'FHSXT' after GA₃ treatment. Our results suggested that a nonsynonymous single nucleotide mutation in GID1c disrupts its interaction with DELLA1 resulting in a GA-insensitive dwarf phenotype in peach.

Comparative transcriptome analysis provides key insights into seedling development in switchgrass (Panicum virgatum L.)

BACKGROUND

Switchgrass (Panicum virgatum L.), a warm-season perennial C4 plant, can be used as a forage plant, a soil and water conservation plant, a windbreak plant, and as a good source of biofuels and alternative energy with low planting costs. However, switchgrass exhibits low rates of seedling development compared to other crops, which means it is typically out-competed by weeds. There is a large variation in seedling development rates among different plantlets in switchgrass, which limits its usefulness for large-scale cultivation. Little is currently known about the molecular reasons for slow seedling growth.

RESULTS

Characterization of the seedling development process via growth indices indicated a relatively stagnant growth stage in switchgrass. A total of 678 differentially expressed genes (DEGs) were identified from the comparison of transcriptomes from slowly developed (sd) and rapidly developed (rd) switchgrass seedlings. Gene ontology and pathway enrichment analysis showed that DEGs were enriched in diterpenoid biosynthesis, thiamine metabolism, and circadian rhythm. Transcription factor enrichment and expression analyses showed MYB-related, bHLH and NAC family genes were essential for seedling growth. The transcriptome results were consistent with those of quantitative real-time polymerase chain reaction. Then, the expression profiles of maize and switchgrass were compared during seedling leaf development. A total of 128 DEGs that play key roles in seedling growth were aligned to maize genes. Transcriptional information and physiological indices suggested that several genes involved in the circadian rhythm, thiamine metabolism, energy metabolism, gibberellic acid biosynthesis, and signal transduction played important roles in seedling development.

CONCLUSIONS

The seedling development process of switchgrass was characterized, and the molecular differences between slowly developed and rapidly developed seedlings were discussed. This study provides new insights into the reasons for slow seedling development in switchgrass and will be useful for the genetic improvement of switchgrass and other crops.

Comprehensive expression analysis of Arabidopsis GA2-oxidase genes and their functional insights

Bioactive gibberellins (GAs) play multiple roles in plant development and stress responses. GA2-oxidases (GA2oxs) are a class of 2-oxoglutarate-dependent dioxygenases that regulate the deactivation of bioactive GAs. In this study, we investigated the phylogeny and domain structures of the seven GA2ox genes present in the Arabidopsis thaliana genome. Comprehensive expression analysis using translational reporter lines showed that the seven GA2ox genes are differentially expressed during Arabidopsis growth and development: GA2ox1 is specifically expressed in the hypocotyl and lateral root primordium; GA2ox2 is highly expressed in aboveground tissues; GA2ox3 is expressed in the chalazal endosperm of the early embryo sac and inflorescences; GA2ox4 is expressed in the shoot apical meristem and during lateral root initiation; GA2ox6 is expressed in the maturation zone, but not in the meristem or elongating zone of the root; GA2ox7 is constitutively expressed during almost all developmental stages; and GA2ox8 is exclusively expressed in stomatal cells. Overexpression of each of these GA2ox genes inhibited high temperature-induced hypocotyl elongation in both wild-type and elongated hypocotyl 5 plants, which have an elongated hypocotyl phenotype, suggesting that these genes negatively regulate hypocotyl elongation by reducing bioactive GA levels. This study provides a valuable resource for further elucidating the roles of GA2ox genes during different stages of development.

QTL architecture of vine growth habit and gibberellin oxidase gene diversity in wild soybean (Glycine soja)

Vine growth habit (VGH) is a beneficial phenotype in many wild plants, and is considered an important domesticated-related trait in soybean. However, its genetic basis remains largely unclear. Hence, in the present study we used an integrated strategy combining linkage mapping and population genome diversity analyses to reveal the genetics of VGH in soybean. In this regard, two recombinant inbred line (RIL) populations derived by crossing a common wild soybean genotype (PI342618B) with two cultivated lines viz., NN 86-4 and NN 493-1 were used to map quantitative trait loci (QTL) for VGH. Here, we identified seven and five QTLs at flowering stage (R1) and maturity stage (R8), respectively, and among them qVGH-18-1, qVGH-18-2, qVGH-19-3, qVGH-19-4 were identified as major loci (R2 > 10% and detection time ≥2). However, qVGH-18-2 was considered as a main QTL for VGH being consistently identified in both RIL populations as well as all growth stages and cropping years. Out of all the annotated genes within qVGH-18-2, Glyma18g06870 was identified as the candidate gene and named as VGH1, which was a gibberellin oxidase (GAox) belongs to 2-oxoglutarate-dependent dioxygenase (2- ODD). Interestingly, there was one member of 2-ODD/GAox in qVGH-18-1 and qVGH-19-4 named as VGH2 and VGH3, respectively. Moreover, from sequencing data analysis VGH1 and three other GAox genes were found significantly divergent between vine and erect soybean with FST value larger than 0.25. Hence, GAox was assumed to play a major role in governing inheritance of VGH in soybean. Therefore, elucidating the genetic mechanism of GAox is very useful for exploring VGH and other stem traits, as well as genetic improvement of plant type in soybean.