Gibberellin signaling: biosynthesis, catabolism, and response pathways

Rice transcription factor OsMADS57 regulates plant height by modulating gibberellin catabolism

BACKGROUND

The MADS-box transcription factors mainly function in floral organ organogenesis and identity specification. Few research on their roles in vegetative growth has been reported.

RESULTS

Here we investigated the functions of OsMADS57 in plant vegetative growth in rice (Oryza sativa). Knockdown of OsMADS57 reduced the plant height, internode elongation and panicle exsertion in rice plants. Further study showed that the cell length was remarkably reduced in the uppermost internode in OsMADS57 knockdown plants at maturity. Moreover, OsMADS57 knockdown plants were more sensitive to gibberellic acid (GA₃), and contained less bioactive GA₃ than wild-type plants, which implied that OsMADS57 is involved in gibberellin (GA) pathway. Expectedly, the transcript levels of OsGA2ox3, encoding GAs deactivated enzyme, were significantly enhanced in OsMADS57 knockdown plants. The level of EUI1 transcripts involved in GA deactivation was also increased in OsMADS57 knockdown plants. More importantly, dual-luciferase reporter assay and electrophoretic mobility shift assay showed that OsMADS57 directly regulates the transcription of OsGA2ox3 as well as EUI1 through binding to the CArG-box motifs in their promoter regions. In addition, OsMADS57 also modulated the expression of multiple genes involved in GA metabolism or GA signaling pathway, indicating the key and complex regulatory role of OsMADS57 in GA pathway in rice.

CONCLUSIONS

These results indicated that OsMADS57 acts as an important transcriptional regulator that regulates stem elongation and panicle exsertion in rice via GA-mediated regulatory pathway.

Comparative transcriptome analysis revealing the potential mechanism of seed germination stimulated by exogenous gibberellin in Fraxinus hupehensis

BACKGROUND

Fraxinus hupehensis is an endangered tree species that is endemic to in China; the species has very high commercial value because of its intricate shape and potential to improve and protect the environment. Its seeds show very low germination rates in natural conditions. Preliminary experiments indicated that gibberellin (GA₃) effectively stimulated the seed germination of F. hupehensis. However, little is known about the physiological and molecular mechanisms underlying the effect of GA₃ on F. hupehensis seed germination.

RESULTS

We compared dormant seeds (CK group) and germinated seeds after treatment with water (W group) and GA₃ (G group) in terms of seed vigor and several other physiological indicators related to germination, hormone content, and transcriptomics. Results showed that GA₃ treatment increases seed vigor, energy requirements, and trans-Zetain (ZT) and GA₃ contents but decreases sugar and abscisic acid (ABA) contents. A total of 116,932 unigenes were obtained from F. hupehensis transcriptome. RNA-seq analysis identified 31,856, 33,188 and 2056 differentially expressed genes (DEGs) between the W and CK groups, the G and CK groups, and the G and W groups, respectively. Up-regulation of eight selected DEGs of the glycolytic pathway accelerated the oxidative decomposition of sugar to release energy for germination. Up-regulated genes involved in ZT (two genes) and GA₃ (one gene) biosynthesis, ABA degradation pathway (one gene), and ABA signal transduction (two genes) may contribute to seed germination. Two down-regulated genes associated with GA₃ signal transduction were also observed in the G group. GA₃-regulated genes may alter hormone levels to facilitate germination. Candidate transcription factors played important roles in GA₃-promoted F. hupehensis seed germination, and Quantitative Real-time PCR (qRT-PCR) analysis verified the expression patterns of these genes.

CONCLUSION

Exogenous GA₃ increased the germination rate, vigor, and water absorption rate of F. hupehensis seeds. Our results provide novel insights into the transcriptional regulation mechanism of effect of exogenous GA₃ on F. hupehensis seed germination. The transcriptome data generated in this study may be used for further molecular research on this unique species.

Identification and Characterization of EI (Elongated Internode) Gene in Tomato (Solanum lycopersicum)

Internode length is an important agronomic trait affecting plant architecture and crop yield. However, few genes for internode elongation have been identified in tomato. In this study, we characterized an elongated internode inbred line P502, which is a natural mutant of the tomato cultivar 05T606. The mutant P502 exhibits longer internode and higher bioactive GA concentration compared with wild-type 05T606. Genetic analysis suggested that the elongated internode trait is controlled by quantitative trait loci (QTL). Then, we identified a major QTL on chromosome 2 based on molecular markers and bulked segregant analysis (BSA). The locus was designated as EI (Elongated Internode), which explained 73.6% genetic variance. The EI was further mapped to a 75.8-kb region containing 10 genes in the reference Heinz 1706 genome. One single nucleotide polymorphism (SNP) in the coding region of solyc02g080120.1 was identified, which encodes gibberellin 2-beta-dioxygenase 7 (SlGA2ox7). SlGA2ox7, orthologous to AtGA2ox7 and AtGA2ox8, is involved in the regulation of GA degradation. Overexpression of the wild EI gene in mutant P502 caused a dwarf phenotype with a shortened internode. The difference of EI expression levels was not significant in the P502 and wild-type, but the expression levels of GA biosynthetic genes including CPS, KO, KAO, GA20ox1, GA20ox2, GA20ox4, GA3ox1, GA2ox1, GA2ox2, GA2ox4, and GA2ox5, were upregulated in mutant P502. Our results may provide a better understanding of the genetics underlying the internode elongation and valuable information to improve plant architecture of the tomato.

Induction of desiccation tolerance in desiccation sensitive Citrus limon seeds

Many economically important perennial species bear recalcitrant seeds, including tea, coffee, cocoa, mango, citrus, rubber, oil palm and coconut. Orthodox seeds can be dried almost completely without losing viability, but so-called recalcitrant seeds have a very limited storage life and die upon drying below a higher critical moisture content than orthodox seeds. As a result, the development of long-term storage methods for recalcitrant seeds is compromised. Lowering this critical moisture content would be very valuable since dry seed storage is the safest, most convenient and cheapest method for conserving plant genetic resources. Therefore, we have attempted to induce desiccation tolerance (DT) in the desiccation sensitive seeds of Citrus limon. We show that DT can be induced by paclobutrazol (an inhibitor of gibberellin biosynthesis) and we studied its associated transcriptome to delineate the molecular mechanisms underlying this induction of DT. Paclobutrazol not only interfered with gibberellin related gene expression but also caused extensive changes in expression of genes involved in the biosynthesis and signaling of other hormones. Paclobutrazol induced a transcriptomic switch encompassing suppression of biotic- and induction of abiotic responses. We hypothesize that this is the main driver of the induction of DT by paclobutrazol in C. limon seeds.

Seed enhancing treatments: comparative analysis of germination characteristics of 23 key herbaceous species used in European restoration programmes

The response of seeds from 23 wild plant species to a range of seed enhancing treatments was studied. We tested the hypothesis that sensitivity of the 23 species to these compounds is related to their ecological niche. The three ecological niches considered were open land, open-pioneer and woodland. Hence, the germination of a species is likely adapted to different light conditions and other environmental signals related to the niche. As representatives of environmental signals, the effects of smoke-related compounds (karrikinolide, KAR₁ ), nitrate and plant growth regulator (gibberellic acid, GA₃ ) on germination were studied. Seeds were exposed to these additives in the imbibition medium; all described as germination cues. We also investigated the effect of light regimes and additives on germination parameters, which included final germination, germination rate and uniformity of germination. Seeds were placed to germinate under three light conditions: constant red light, constant darkness and 12 h white light photoperiod. We observed inhibition by KAR under light in some species, which may have ecological implications. The results showed that no single treatment increased the germination of all the tested species, rather a wide variation of responsiveness of the different species to the three compounds was found. Additionally, no interaction was found between responsiveness to compounds and ecological niche. However, species in the same ecological niche and dormancy class showed a similar responsiveness to light. Species that share a similar environment have similar light requirements for germination, while differences exist among species in their responsiveness to other germination cues.

Identification of cotton MOTHER OF FT AND TFL1 homologs, GhMFT1 and GhMFT2, involved in seed germination

Plant phosphatidylethanolamine-binding protein (PEBP) is comprised of three clades: FLOWERING LOCUS T (FT), TERMINAL FLOWER1 (TFL1) and MOTHER OF FT AND TFL1 (MFT). FT/TFL1-like clades regulate identities of the determinate and indeterminate meristems, and ultimately affect flowering time and plant architecture. MFT is generally considered to be the ancestor of FT/TFL1, but its function is not well understood. Here, two MFT homoeologous gene pairs in Gossypium hirsutum, GhMFT1-A/D and GhMFT2-A/D, were identified by genome-wide identification of MFT-like genes. Detailed expression analysis revealed that GhMFT1 and GhMFT2 homoeologous genes were predominately expressed in ovules, and their expression increased remarkably during ovule development but decreased quickly during seed germination. Expressions of GhMFT1 and GhMFT2 homoeologous genes in germinating seeds were upregulated in response to abscisic acid (ABA), and their expressions also responded to gibberellin (GA). In addition, ectopic overexpression of GhMFT1 and GhMFT2 in Arabidopsis inhibited seed germination at the early stage. Gene transcription analysis showed that ABA metabolism genes ABA-INSENSITIVE3 (ABI3) and ABI5, GA signal transduction pathway genes REPRESSOR OF ga1-3 (RGA) and RGA-LIKE2 (RGL2) were all upregulated in the 35S:GhMFT1 and 35S:GhMFT2 transgenic Arabidopsis seeds. GhMFT1 and GhMFT2 localize in the cytoplasm and nucleus, and both interact with a cotton bZIP transcription factor GhFD, suggesting that both of GhMFT1, 2 have similar intracellular regulation mechanisms. Taken together, the results suggest that GhMFT1 and GhMFT2 may act redundantly and differentially in the regulation of seed germination.

MtGA2ox10 encoding C20-GA2-oxidase regulates rhizobial infection and nodule development in Medicago truncatula

Gibberellin (GA) plays a controversial role in the legume-rhizobium symbiosis. Recent studies have shown that the GA level in legumes must be precisely controlled for successful rhizobial infection and nodule organogenesis. However, regulation of the GA level via catabolism in legume roots has not been reported to date. Here, we investigate a novel GA inactivating C20-GA2-oxidase gene MtGA2ox10 in Medicago truncatula. RNA sequencing analysis and quantitative polymerase chain reaction revealed that MtGA2ox10 was induced as early as 6 h post-inoculation (hpi) of rhizobia and reached peak transcript abundance at 12 hpi. Promoter::β-glucuronidase fusion showed that the promoter activity was localized in the root infection/differentiation zone during the early stage of rhizobial infection and in the vascular bundle of the mature nodule. The CRISPR/Cas9-mediated deletion mutation of MtGA2ox10 suppressed infection thread formation, which resulted in reduced development and retarded growth of nodules on the Agrobacterium rhizogenes-transformed roots. Over-expression of MtGA2ox10 in the stable transgenic plants caused dwarfism, which was rescued by GA₃ application, and increased infection thread formation but inhibition of nodule development. We conclude that MtGA2ox10 plays an important role in the rhizobial infection and the development of root nodules through fine catabolic tuning of GA in M. truncatula.

Identification and Expression Profiling of the Regulator of Chromosome Condensation 1 (RCC1) Gene Family in Gossypium Hirsutum L. under Abiotic Stress and Hormone Treatments

The regulator of chromosome condensation 1 (RCC1) is the nucleotide exchange factor for a GTPase called the Ras-related nuclear protein, and it is important for nucleo-plasmic transport, mitosis, nuclear membrane assembly, and control of chromatin agglutination during the S phase of mitosis in animals. In plants, RCC1 molecules act mainly as regulating factors for a series of downstream genes during biological processes such as the ultraviolet-B radiation (UV-B) response and cold tolerance. In this study, 56 genes were identified in upland cotton by searching the associated reference genomes. The genes were found to be unevenly distributed on 26 chromosomes, except A06, A12, D03, and D12. Phylogenetic analysis by maximum-likelihood revealed that the genes were divided into five subgroups. The RCC1 genes within the same group shared similar exon/intron patterns and conserved motifs in their encoded proteins. Most genes of the RCC1 family are expressed differently under various hormone treatments and are negatively controlled by salt stress. Gh_A05G3028 and Gh_D10G2310, which encode two proteins located in the nucleus, were strongly induced under salt treatment, while mutants of their homoeologous gene (UVR8) in Arabidopsis and VIGS (virus induced gene silencing) lines of the two genes above in G. hirsutum exhibited a salt-sensitive phenotype indicating their potential role in salt resistance in cotton. These results provide valuable reference data for further study of RCC1 genes in cotton.

Regulation of α-expansins genes in Arabidopsis thaliana seeds during post-osmopriming germination

Seed osmopriming is a pre-sowing treatment that involves limitation of the seed water imbibition, so that pre-germinative metabolic activities proceed without radicular protrusion. This technique is used for improving germination rate, uniformity of seedling growth and hastening the time to start germination. In Arabidopsis thaliana, seed germination has been associated with the induction of enzymes involved in cell wall modifications, such as expansins. The α-expansins (EXPAs) are involved in cell wall relaxation and extension during seed germination. We used online tools to identify AtEXPA genes with preferential expression during seed germination and RT-qPCR to study the expression of five EXPA genes at different germination stages of non-primed and osmoprimed seeds. In silico promoter analysis of these genes showed that motifs similar to cis-acting elements related to abiotic stress, light and phytohormone responses are the most overrepresented in promoters of these AtEXPA genes, showing that their expression is likely be regulated by intrinsic developmental and environmental signals during Arabidopsis seed germination. The osmopriming conditioning had a decreased time and mean to 50% germination without affecting the percentage of final seed germination. The dried PEG-treated seeds showed noticeable high mRNA levels earlier at the beginning of water imbibition (18 h), showing that transcripts of all five EXPA isoforms were significantly produced during the osmopriming process. The strong up-regulation of these AtEXPA genes, mainly AtEXPA2, were associated with the earlier germination of the osmoprimed seeds, which qualifies them to monitor osmopriming procedures and the advancement of germination.

Hormones and Heterosis in Hybrid Balsam Poplar (Populus balsamifera L.)

Balsam poplar (Populus balsamifera L.) is a transcontinental tree species in North America, making it an ideal species to study intra-specific hybrid vigour as a tool for increasing genetic gain in growth. We tested the hypothesis that intra-specific breeding of disparate populations of balsam poplar would lead to the expression of hybrid vigour and we determined the role of endogenous hormones linked to ecophysiological and growth performance. In September 2009, three field trials were established in Canada (two in Alberta (AB), i.e., Fields AB1 and AB2, and one in Quebec (QC), i.e., Field QC1) in conjunction with Alberta-Pacific Forest Industries Inc. and the Ministry of Forests, Wildlife and Parks, Quebec. Five male parents from each province as well as five female parents from QC and four female parents from AB were used for breeding intra-regional and inter-regional crosses. Based on a significant difference at year six for height and diameter, from the AB1 and AB2 field trials, the AB × QC cross-type was selected for further study. Cuttings from the AB × QC cross-type were grown in a randomized complete block design under near-optimal greenhouse conditions. Families were identified as slow- or fast-growing, and the relationship between hormone levels and growth performance of the genotypes within the families were examined. In late June, after 34 days of growth, internode tissue samples collected from each progeny were analyzed for gibberellic acids, indole-3-acetic acid, and abscisic acid content. Stem volume of two-month-old rooted cuttings, grown under optimal greenhouse conditions, was positively and significantly correlated with the photosynthetic rate, greenhouse growth, and stem volume of 8-year-old field-grown trees (Fields AB1 values: r = 0.629 and p = 0.012; AB2 values: r = 0.619 and p = 0.014, and QC1 values: r = 0.588 and p = 0.021, respectively). We determined that disparate and native populations of balsam poplar can be bred to produce superior progeny with enhanced stem growth traits.

The regulatory mechanism of chilling-induced dormancy transition from endo-dormancy to non-dormancy in Polygonatum kingianum Coll.et Hemsl rhizome bud

We identified three dormant stages of Polygonatum kingianum and changes that occurred during dormancy transition in the following aspects including cell wall and hormones, as well as interaction among them. Polygonatum kingianum Coll.et Hemsl (P. kingianum) is an important traditional Chinese medicine, but the mechanism of its rhizome bud dormancy has not yet been studied systematically. In this study, three dormancy phases were induced under controlled conditions, and changes occurring during the transition were examined, focusing on phytohormones and the cell wall. As revealed by HPLC-MS (High Performance Liquid Chromatography-Mass Spectrometry) analysis, the endo- to non-dormancy transition was association with a reduced abscisic acid (ABA)/gibberellin (GA₃) ratio, a decreased level of auxin (IAA) and an increased level of trans-zeatin (tZR). Transmission electron microscopy showed that plasmodesmata (PDs) and the cell wall of the bud underwent significant changes between endo- and eco-dormancy. A total of 95,462 differentially expressed genes (DEGs) were identified based on transcriptomics, and clustering and principal component analysis confirmed the different physiological statuses of the three types of bud samples. Changes in the abundance of transcripts associated with IAA, cytokinins (CTKs), GA, ABA, brassinolide (BR), jasmonic acid (JA), ethylene, salicylic acid (SA), PDs and cell wall-loosening factors were analysed during the bud dormancy transition in P. kingianum. Furthermore, nitrilase 4 (NIT4) and tryptophan synthase alpha chain (TSA1), which are related to IAA synthesis, were identified as hub genes of the co-expression network, and strong interactions between hormones and cell wall-related factors were observed. This research will provide a good model for chilling-treated rhizome bud dormancy in P. kingianum and cultivation of this plant.

MdBZR1 and MdBZR1-2like Transcription Factors Improves Salt Tolerance by Regulating Gibberellin Biosynthesis in Apple

Brassinosteroids (BRs) are a group of plant steroid hormones that play important roles in regulating plant development. In addition, BRs show considerable functional redundancy with other plant hormones such as gibberellins (GAs). BRASSINAZOLE RESISTANT1 (BZR1) and BRI1-EMS-SUPPRESSOR1 (BES1) transcription factors are negative feedback regulators of BR biosynthesis. This study provides evidence for the roles of MdBZR1 and MdBZR1-2like in promoting GA production. These results also show that BRs regulate GA biosynthesis to improve salt tolerance in apple calli. Moreover, this research proposes a regulatory model, in which MdBZR1 and MdBZR1-2like bind to the promoters of GA biosynthetic genes to regulate their expression in a BR-dependent manner. The expression of key GA biosynthetic genes, MdGA20ox1, MdGA20ox2, and MdGA3ox1 in yeast helps to maintain normal growth even under intense salt stress. In summary, this study underscores the roles of MdBZR1 and MdBZR1-2like in improving salt tolerance by regulating GA biosynthesis in apple calli.

Using CRISPR/Cas9 genome editing in tomato to create a gibberellin-responsive dominant dwarf DELLA allele

The tomato PROCERA gene encodes a DELLA protein, and loss-of-function mutations derepress growth. We used CRISPR/Cas9 and a single guide RNAs (sgRNA) to target mutations to the PROCERA DELLA domain, and recovered several loss-of-function mutations and a dominant dwarf mutation that carries a deletion of one amino acid in the DELLA domain. This is the first report of a dominant dwarf PROCERA allele. This allele retains partial responsiveness to exogenously applied gibberellin. Heterozygotes show an intermediate phenotype at the seedling stage, but adult heterozygotes are as dwarfed as homozygotes.

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.

Physical and thermodynamic characterization of the rice gibberellin receptor/gibberellin/DELLA protein complex

Gibberellins (GAs) are phytohormones that regulate various developmental processes in plants. The initial GA signalling events involve the binding of a GA to the soluble GA receptor protein GID1, followed by the binding of the complex to the negative transcriptional regulator of GA signaling, the DELLA protein. Although X-ray structures for certain Arabidopsis GID1/GA/DELLA protein complexes have previously been determined, examination of these complexes did not fully clarify how a DELLA protein recognizes and binds to a GID1/GA complex. Herein, we present a study aimed at physically defining, via a combination of gel chromatography, isothermal titration calorimetry (ITC), small-angle X-ray scattering experiments (SAXS), NMR spectroscopy and mutagenesis, how the rice DELLA protein (SLR1) binds to the rice GID1/GA complex. We have identified the shortest SLR1 sequence (M28-A112) that binds the rice GID/GA complex tightly. The binding constant for the ternary complex that includes SLR1(M28-A112) is 2.9 × 10⁷ M⁻¹; the binding is enthalpically driven and does not depend on the chemical nature of the bound GA. Furthermore, the results of SAXS, ITC, and gel filtration experiments indicate that when free in solution, SLR1(M28-A112) is a natively unfolded protein. The NMR experiments expand this observation to show that the unfolded mutant also contains a small amount of marginally stable secondary structure. Conversely, the protein has a highly ordered structure when bound one-to-one to GID1/GA.

Genetic dissection of the mechanism of flowering time based on an environmentally stable and specific QTL in Brassica napus

Flowering time is an important agronomic trait that is highly influenced by the environment. To elucidate the genetic mechanism of flowering time in rapeseed (Brassica napus L.), a genome-wide QTL analysis was performed in a doubled haploid population grown in winter, semi-winter and spring ecological conditions. Fifty-five consensus QTLs were identified after combining phenotype and genomic data, including 12 environment-stable QTLs and 43 environment-specific QTLs. Importantly, six major QTLs for flowering time were identified, of which two were considered environment-specific QTLs in spring ecological condition and four were considered environment-stable QTLs in winter and semi-winter ecological conditions. Through QTL comparison, 18 QTLs were colocalized with QTLs from six other published studies. Combining the candidate genes with their functional annotation, in 49 of 55 consensus QTLs, 151 candidate genes in B. napus corresponding to 95 homologous genes in Arabidopsis thaliana related to flowering were identified, including BnaC03g32910D (CO), BnaA02g12130D (FT) and BnaA03g13630D (FLC). Most of the candidate genes were involved in different flowering regulatory pathways. Based on re-sequencing and differences in sequence annotation between the two parents, we found that regions containing some candidate genes have numerous non-frameshift InDels and many non- synonymous mutations, which might directly lead to gene functional variation. Flowering time was negativly correlated with seed yield and thousand seed weight based on a QTL comparison of flowering time and seed yield traits, which has implications in breeding new early-maturing varieties of B. napus. Moreover, a putative flowering regulatory network was constructed, including the photoperiod, circadian clock, vernalization, autonomous and gibberellin pathways. Multiple copies of genes led to functional difference among the different copies of homologous genes, which also increased the complexity of the flowering regulatory networks. Taken together, the present results not only provide new insights into the genetic regulatory network underlying the control of flowering time but also improve our understanding of flowering time regulatory pathways in rapeseed.

Phytomelatonin: Recent advances and future prospects

Melatonin (MEL) has been revealed as a phylogenetically conserved molecule with a ubiquitous distribution from primitive photosynthetic bacteria to higher plants, including algae and fungi. Since MEL is implicated in numerous plant developmental processes and stress responses, the exploration of its functions in plant has become a rapidly progressing field with the new paradigm of involvement in plants growth and development. The pleiotropic involvement of MEL in regulating the transcripts of numerous genes confirms its vital involvement as a multi-regulatory molecule that architects many aspects of plant development. However, the cumulative research in plants is still preliminary and fragmentary in terms of its established functions compared to what is known about MEL physiology in animals. This supports the need for a comprehensive review that summarizes the new aspects pertaining to its functional role in photosynthesis, phytohormonal interactions under stress, cellular redox signaling, along with other regulatory roles in plant immunity, phytoremediation, and plant microbial interactions. The present review covers the latest advances on the mechanistic roles of phytomelatonin. While phytomelatonin is a sovereign plant growth regulator that can interact with the functions of other plant growth regulators or hormones, its qualifications as a complete phytohormone are still to be established. This review also showcases the yet to be identified potentials of phytomelatonin that will surely encourage the plant scientists to uncover new functional aspects of phytomelatonin in plant growth and development, subsequently improving its status as a potential new phytohormone.

OsWRKY28 Regulates Phosphate and Arsenate Accumulation, Root System Architecture and Fertility in Rice

WRKYs are transcriptional factors involved in stress tolerance and development of plants. In the present study, we characterized OsWRKY28, a group IIa WRKY gene, in rice, because its expression was found to be upregulated by arsenate exposure in previous transcriptomic studies. Subcellular localization using YFP-OsWRKY28 fusion protein showed that the protein was localized in the nuclei. Transgenic rice plants expressing pOsWRKY28::GUS suggested that the gene was expressed in various tissues in the whole plant, with a strong expression in the root tips, lateral roots and reproductive organs. The expression of OsWRKY28 was markedly induced by arsenate and other oxidative stresses. In a hydroponic experiment, loss-of-function mutation in OsWRKY28 resulted in lower accumulation of arsenate and phosphate concentration in the shoots. The mutants showed altered root system architecture, with fewer lateral roots and shorter total root length than wild-type plants. In a soil pot experiment, the mutants produced lower grain yield than wild-type because of reduced fertility and smaller effective tiller numbers. Transcriptomic profiling using RNA-seq showed altered expression in the mutant of genes involved in the biosynthesis of phytohormones, especially jasmonic acid (JA). Exogenous JA treatments mimicked the phenotypes of the oswrky28 mutants with inhibited root elongation and decreased arsenate/phosphate translocation. Our results suggested that OsWRKY28 affected arsenate/phosphate accumulation, root development at the seedling stage and fertility at the reproductive stage possibly by influencing homeostasis of JA or other phytohormones.

Germination constraints of dicarpic cypselae of Bidens pilosa L

Bidens pilosa L. is a heterocarpic weed species with two cypselae types that present morpho-physiological differences, being the peripheral type smaller and slower to germinate than the central one. We aimed to verify how the germination mechanism varied between types. We focused on two mechanisms: (1) pericarp constraints (physical and chemical) and (2) hormonal stimulation (Abcisic acid [ABA] and Gibberellin [GA]). Both cypselae types are physically constrained by the pericarp, for when it is excised both seed types increase their germination, but behavioral differences still remain. The pericarp of the peripheral type also has chemical inhibitors that effectively inhibited germination of the intact central cypsela. To test the hormonal effects, we focused on the ABA:GA control. Both cypselae responded to an exogenous ABA concentration gradient, however there is no variation between types on the sensitivity to it. Also, both cypselae types were indifferent to Fluridone (ABA inhibitor), which indicates that the dormancy is not maintained by de novo ABA synthesis. Cypselae types had different sensitivity to an exogenous GA3 gradient, the central type being more sensitive to the treatment than the peripheral one. But when the endogenous GA synthesis was blocked by Paclobutrazol, both types responded equally to same GA3 concentrations. This indicates that endogenous GA synthesis may be related to differences observed on germination of cypselae types. To conclude, seed types differ on their growth potential to overcome the pericarp resistance: while the inhibitor in the peripheral pericarp reduces growth potential, GA increases it.

Plant Stature Related receptor-like Kinanse2 (PSRK2) acts as a factor that determines stem elongation toward gibberellins response in rice

Gibberellins (GAs) are a family of plant hormones that are important to multiple aspects of plant growth and development, especially stem elongation. A PSRK2 was obtained through screening and identifying RLK dominant negative mutants. Phenotype of the loss-of-function mutants, psrk2-DN and psrk2-RNAi, showed that PSRK2 could influence the length of the uppermost and fourth internodes, indicating that PSRK2 might regulate cell division in the intercalary meristems and/or cell elongation in the internodes. Moreover, the expression pattern showed that PSRK2 was strongly expressed in the joined-nodes after the start-up of reproductive growth, but undetectable in leaves. PSRK2 expression was also found to be induced by GA₃, and PSRK2 was involved in GA signaling in cereal aleurone cells, and PSRK2 influence the relative length of the second leaf sheaths in seedling stage. These results indicate PSRK2 is a component of GA signaling pathway that controls stem elongation by negatively regulating GA responses. Abbreviations: Os: Oryza sativa; At: Arabidopsis thaliana; RNAi: RNA interfere; DN: Dominate Negative; SMART: Simple Modular Architecture Research Tool; Uni : Uniconazol; PSRK2: Plant Stature Related receptor-like Kinase 2; RLK: Receptor-like Kinase; GA: Gibberellin; IAA: indole-3-acetic acid; BL: Brassinosteroid.

Evolution and diversification of the plant gibberellin receptor GID1

The plant gibberellin receptor GID1 shows sequence similarity to carboxylesterase, suggesting that it is derived from an enzyme. However, how GID1 evolved and was modified is unclear. We identified two amino acids that are essential for GID1 activity, and we found that adjustment of these residues caused GID1 to recognize novel GAs carrying 13-OH as active GAs and to strictly refuse inactive GAs. Phylogenetic analysis of 169 GID1s revealed seven subtypes, and the B-type in core eudicots showed unique characteristics. In fact, certain B-type GID1s showed a higher nonsynonymous-to-synonymous divergence ratio in the region determining GA affinity. Such B-type GID1s with higher affinity were preferentially expressed in the roots in some core eudicot plants and conferred adaptive growth under stress.

The plant gibberellin (GA) receptor GID1 shows sequence similarity to carboxylesterase (CXE). Here, we report the molecular evolution of GID1 from establishment to functionally diverse forms in eudicots. By introducing 18 mutagenized rice GID1s into a rice gid1 null mutant, we identified the amino acids crucial for GID1 activity in planta. We focused on two amino acids facing the C2/C3 positions of ent-gibberellane, not shared by lycophytes and euphyllophytes, and found that adjustment of these residues resulted in increased GID1 affinity toward GA₄, new acceptance of GA₁ and GA₃ carrying C13-OH as bioactive ligands, and elimination of inactive GAs. These residues rendered the GA perception system more sophisticated. We conducted phylogenetic analysis of 169 GID1s from 66 plant species and found that, unlike other taxa, nearly all eudicots contain two types of GID1, named A- and B-type. Certain B-type GID1s showed a unique evolutionary characteristic of significantly higher nonsynonymous-to-synonymous divergence in the region determining GA₄ affinity. Furthermore, these B-type GID1s were preferentially expressed in the roots of Arabidopsis, soybean, and lettuce and might be involved in root elongation without shoot elongation for adaptive growth under low-temperature stress. Based on these observations, we discuss the establishment and adaption of GID1s during plant evolution.

GhWIP2, a WIP zinc finger protein, suppresses cell expansion in Gerbera hybrida by mediating crosstalk between gibberellin, abscisic acid, and auxin

Cell expansion is a key determinant for the final size and shape of plant organ, and is regulated by various phytohormones. Zinc finger proteins (ZFPs) consist of a superfamily involved in multiple aspects of organ morphogenesis. However, little is known about WIP-type ZFP function in phytohormone-mediated organ growth. Using reverse genetics, RNA-seq and phytohormone quantification, we elucidated the role of a new WIP-type ZFP from Gerbera hybrida, GhWIP2, in controlling organ growth via regulation of cell expansion. GhWIP2 localizes to the nucleus and acts as a transcriptional repressor. Constitutive overexpression of GhWIP2 (GhWIP2OE) in both Gerbera and Arabidopsis thaliana caused major developmental defects associated with cell expansion, including dwarfism, short petals, scapes, and petioles. Furthermore, GhWIP2OE plants were hypersensitive to GA, but not to ABA, and showed a reduction in endogenous GA and auxin, but not ABA concentrations. Consistent with these observations, RNA-seq analysis revealed that genes involved in GA and auxin signaling were down-regulated, while those involved in ABA signaling were up-regulated in GhWIP2OE plants. Our findings suggest that GhWIP2 acts as a transcriptional repressor, suppressing cell expansion during organ growth by modulating crosstalk between GA, ABA, and auxin.

Expansion and diversification of the gibberellin receptor GIBBERELLIN INSENSITIVE DWARF1 (GID1) family in land plants

Here we uncover the major evolutionary events shaping the evolution of the GID1 family of gibberellin receptors in land plants at the sequence, structure and gene expression levels. Gibberellic acid (gibberellin, GA) controls key developmental processes in the life cycle of land plants. By interacting with the GIBBERELLIN INSENSITIVE DWARF1 (GID1) receptor, GA regulates the expression of a wide range of genes through different pathways. Here we report the systematic identification and classification of GID1s in 54 plants genomes, encompassing from bryophytes and lycophytes, to several monocots and eudicots. We investigated the evolutionary relationship of GID1s using a comparative genomics framework and found strong support for a previously proposed phylogenetic classification of this family in land plants. We identified lineage-specific expansions of particular subfamilies (i.e. GID1ac and GID1b) in different eudicot lineages (e.g. GID1b in legumes). Further, we found both, shared and divergent structural features between GID1ac and GID1b subgroups in eudicots that provide mechanistic insights on their functions. Gene expression data from several species show that at least one GID1 gene is expressed in every sampled tissue, with a strong bias of GID1b expression towards underground tissues and dry legume seeds (which typically have low GA levels). Taken together, our results indicate that GID1ac retained canonical GA signaling roles, whereas GID1b specialized in conditions of low GA concentrations. We propose that this functional specialization occurred initially at the gene expression level and was later fine-tuned by mutations that conferred greater GA affinity to GID1b, including a Phe residue in the GA-binding pocket. Finally, we discuss the importance of our findings to understand the diversification of GA perception mechanisms in land plants.

Comparative genomics analysis reveals gene family expansion and changes of expression patterns associated with natural adaptations of flowering time and secondary metabolism in yellow Camellia

Yellow-flowering species are unique in the genus Camellia not only for their bright yellow pigments but also the health-improving substances in petals. However, little is known regarding the biosynthesis pathways of pigments and secondary metabolites. Here, we performed comparative genomics studies in two yellow-flowered species of the genus Camellia with distinctive flowering periods. We obtained 112,190 and 89,609 unigenes from Camellia nitidissima and Camellia chuongtsoensis, respectively, and identified 9547 gene family clusters shared with various plant species and 3414 single-copy gene families. Global gene expression analysis revealed six comparisons of differentially expressed gene sets in different developmental stages of floral bud. Through the identification of orthologous pairs, conserved and specific differentially expressed genes (DEGs) between species were compared. Functional enrichment analysis suggested that the gibberellin (GA) biosynthesis pathway might be related to the alteration of flowering responses. Furthermore, the expression patterns of secondary metabolism pathway genes were analyzed between yellow- and red-flowered Camellias. We showed that the key enzymes involved in glycosylation of flavonoids displayed differential expression patterns, indicating that the direct glycosylation of flavonols rather than anthocyanins was pivotal to coloration and health-improving metabolites in the yellow Camellia petals. Finally, the gene family analysis of UDP-glycosyltransferases revealed an expansion of group C members in C. nitidissima. Through comparative genomics analysis, we demonstrate that changes of gene expression and gene family members are critical to the variation of natural traits. This work provides valuable insights into the molecular regulation of trait adaptations of floral pigmentation and flowering timing.

Poplar MYB transcription factor PtrMYB012 and its Arabidopsis AtGAMYB orthologs are differentially repressed by the Arabidopsis miR159 family

A phenotype-based screening of the T1 transgenic Arabidopsis population transformed by overexpression constructs of the entire poplar MYB transcription factor family found that overexpression of a poplar MYB transcription factor, PtrMYB012, in Arabidopsis resulted in upwardly curled rosette leaves, dwarfism and male sterility. Sequence analysis identified that PtrMYB012 is homologous to the Arabidopsis GAMYB genes (e.g., AtMYB65 and AtMYB33). Gene expression analysis revealed that PtrMYB012 is specifically expressed in floral tissues, especially in male catkins, similar to AtMYB65. It was well known that Arabidopsis GAMYBs are negatively regulated by microRNA159 (miR159) during vegetative growth; thus, the typical phenotypes of upwardly curled leaves, dwarfism and male sterility were only shown in overexpression of GAMYBs with mutations in the miR159 target sequence. To confirm our phenotypic consequences, we independently re-produced transgenic Arabidopsis plants overexpressing PtrMYB012 without mutations in the miR159 target sequence. The resulting 35 S::PtrMYB012 Arabidopsis plants phenocopied the previous transgenic Arabidopsis plants, suggesting that PtrMYB012 is probably not a target of Arabidopsis miR159 despite containing the conserved miR159 target sequence. To gain further insight, we produced transgenic poplars overexpressing the intact PtrMYB012. As a result, no conspicuous phenotype was found in 35 S::PtrMYB012 poplar plants. These results suggest that PtrMYB012 transcripts are down-regulated by miR159 in poplar but not in Arabidopsis. Indeed, subsequent 5'-RACE analysis confirmed that PtrMYB012 transcripts are completely degraded in poplar, probably by miR159, but not in Arabidopsis. These results suggest that species-specific family members of miR159 are important for the regulation of normal growth and development in plants.

Identification of the dwarf gene GmDW1 in soybean (Glycine max L.) by combining mapping-by-sequencing and linkage analysis

KEY MESSAGE

GmDW1 encodes an ent-kaurene synthase (KS) acting at the early step of the biosynthesis pathway for gibberellins (GAs) and regulates the development of plant height in soybean. Plant height is an important component of plant architecture, and significantly affects crop breeding practices and yield. Here, we report the characterization of an EMS-induced dwarf mutant (dw) of the soybean cultivar Zhongpin 661 (ZDD23893). The dw mutant displayed reduced plant height and shortened internodes, both of which were mainly attributed to the longitudinally decreased cell length. The bioactive GA1 (gibberellin A1) and GA4 (gibberellin A4) were not detectable in the stem of dw, and the dwarf phenotype could be rescued by treatment with exogenous GA3. Genetic analysis showed that the dwarf trait of dw was controlled by a recessive nuclear gene. By combining linkage analysis and mapping-by-sequencing, we mapped the GmDW1 gene to an approximately 460-kb region on chromosome (Chr.) 8, containing 36 annotated genes in the reference Willliams 82 genome. Of these genes, we identified two nonsynonymous single nucleotide polymorphisms (SNPs) that are present in the encoding regions of Gmdw1 and Glyma.08G165100 in dw, respectively. However, only the SNP mutation (T>A) at nucleotide 1224 in Gmdw1 cosegregated with the dwarf phenotype. GmDW1 encodes an ent-kaurene synthase, and was expressed in various tissues including root, stem, and leaf. Further phenotypic analysis of the allelic variations in soybean accessions strongly indicated that GmDW1 is responsible for the dwarf phenotype in dw. Our results provide important information for improving our understanding of the genetics of soybean plant height and crop breeding.

Wheat miR9678 Affects Seed Germination by Generating Phased siRNAs and Modulating Abscisic Acid/Gibberellin Signaling

Seed germination is important for grain yield and quality and rapid, near-simultaneous germination helps in cultivation; however, cultivars that germinate too readily can undergo preharvest sprouting (PHS), which causes substantial losses in areas that tend to get rain around harvest time. Moreover, our knowledge of mechanisms regulating seed germination in wheat (Triticum aestivum) remains limited. In this study, we analyzed function of a wheat-specific microRNA 9678 (miR9678), which is specifically expressed in the scutellum of developing and germinating seeds. Overexpression of miR9678 delayed germination and improved resistance to PHS in wheat through reducing bioactive gibberellin (GA) levels; miR9678 silencing enhanced germination rates. We provide evidence that miR9678 targets a long noncoding RNA (WSGAR) and triggers the generation of phased small interfering RNAs that play a role in the delay of seed germination. Finally, we found that abscisic acid (ABA) signaling proteins bind the promoter of miR9678 precursor and activate its expression, indicating that miR9678 affects germination by modulating the GA/ABA signaling.

Gibberellin antagonizes jasmonate-induced defense against Meloidogyne graminicola in rice

Gibberellin (GA) regulates various plant growth and developmental processes, but its role in pathogen attack, and especially nematode-plant interactions, still remains to be elucidated. An in-depth characterization of the role of GA in nematode infection was conducted using mutant lines of rice, chemical inhibitors, and phytohormone measurements. Our results showed that GA influences rice-Meloidogyne graminicola interactions in a concentration-dependent manner. Foliar spray of plants with a low concentration of gibberellic acid enhanced nematode infection. Biosynthetic and signaling mutants confirmed the importance of gibberellin for rice susceptibility to M. graminicola infection. Our study also demonstrates that GA signaling suppresses jasmonate (JA)-mediated defense against M. graminicola, and likewise the JA-induced defense against M. graminicola requires SLENDER RICE1 (SLR1)-mediated repression of the GA pathway. In contrast to observations from other plant-pathogen interactions, GA plays a dominant role over JA in determining susceptibility to M. graminicola in rice. This GA-induced nematode susceptibility was largely independent of auxin biosynthesis, but relied on auxin transport. In conclusion, we showed that GA-JA antagonistic crosstalk is at the forefront of the interaction between rice and M. graminicola, and SLR1 plays a central role in the JA-mediated defense response in rice against this nematode.

Transcriptome profiling provides insights into dormancy release during cold storage of Lilium pumilum

Background

Bulbs of the ornamental flower Lilium pumilum enter a period of dormancy after flowering in spring, and require exposure to cold for a period of time in order to release dormancy. Previous studies focused mainly on anatomical, physiological and biochemical changes during dormancy release. There are no dormancy studies of the northern cold-hardy wild species of Lilium at the molecular level. This study observed bulb cell and starch granule ultrastructures during cold storage; and analysed the transcriptome using sequencing. The combination of morphological and transcriptomic methods provides valuable insights into dormancy release during cold storage of Lilium pumilum.

Results

Ultrastructural changes reflected dormancy release during cold storage of the bulbs. We compared gene expression levels among samples at 0 (S1 stage), 30 (S2 stage), 60 (S3 stage) and 90 (S4 stage) d of cold storage, with 0 d as the control. The data showed that some regulatory pathways such as carbohydrate metabolism and plant hormone signal transduction were activated to break dormancy. Some differentially expressed genes (DEGs) related to antioxidant activity, epigenetic modification and transcription factors were induced to respond to low temperature conditions. These genes constituted a complex regulatory mechanism of dormancy release.

Conclusions

Cytological data related to dormancy regulation was obtained through histomorphological observation; transcriptome sequencing provided comprehensive sequences and digital gene expression tag profiling (DGE) data, and bulb cell ultrastructural changes were closely related to DEGs. The novel Lilium pumilum genetic information from this study provides a reference for the regulation of dormancy by genetic engineering using molecular biology tools.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-4536-x) contains supplementary material, which is available to authorized users.

Analysis of Transcriptional Responses of the Inflorescence Meristems in Jatropha curcas Following Gibberellin Treatment

Jatropha curcas L. seeds an oilseed plant with great potential for biodiesel production. However, low seed yield, which was limited by its lower female flowers, was a major drawback for its utilization. Our previous study found that the flower number and female-to-male ratio were increased by gibberellin treatment. Here, we compared the transcriptomic profiles of inflorescence meristem at different time points after gibberellic acid A3 (GA₃) treatment. The present study showed that 951 differentially expressed genes were obtained in response to gibberellin treatment, compared with control samples. The 6-h time point was an important phase in the response to exogenous gibberellin. Furthermore, the plant endogenous gibberellin, auxin, ethylene, abscisic acid, and brassinolide-signaling transduction pathways were repressed, whereas the genes associated with cytokinin and jasmonic acid signaling were upregulated for 24-h time point following GA₃ treatment. In addition, the floral meristem determinacy genes (JcLFY, JcSOC1) and floral organ identity genes (JcAP3, JcPI, JcSEP1-3) were significantly upregulated, but their negative regulator (JcSVP) was downregulated after GA₃ treatment. Moreover, the effects of phytohormone, which was induced by exogenous plant growth regulator, mainly acted on the female floral differentiation process. To the best of our knowledge, this data is the first comprehensive analysis of the underlying transcriptional response mechanism of floral differentiation following GA₃ treatment in J. curcas, which helps in engineering high-yielding varieties of Jatropha.

Characterization of ent-kaurene synthase and kaurene oxidase involved in gibberellin biosynthesis from Scoparia dulcis

Gibberellins (GAs) are ubiquitous diterpenoids in higher plants, whereas some higher plants produce unique species-specific diterpenoids. In GA biosynthesis, ent-kaurene synthase (KS) and ent-kaurene oxidase (KO) are key players which catalyze early step(s) of the cyclization and oxidation reactions. We have studied the functional characterization of gene products of a KS (SdKS) and two KOs (SdKO1 and SdKO2) involved in GA biosynthesis in Scoparia dulcis. Using an in vivo heterologous expression system of Escherichia coli, we found that SdKS catalyzed a cyclization reaction from ent-CPP to ent-kaurene and that the SdKOs oxidized ent-kaurene to ent-kaurenoic acid after modification of the N-terminal region for adaptation to the E. coli expression system. The real-time PCR results showed that the SdKS, SdKO1 and SdKO2 genes were mainly expressed in the root and lateral root systems, which are elongating tissues. Based on these results, we suggest that these three genes may be responsible for the metabolism of GAs in S. dulcis.

Salinity Inhibits Rice Seed Germination by Reducing α-Amylase Activity via Decreased Bioactive Gibberellin Content

Seed germination plays important roles in the establishment of seedlings and their subsequent growth; however, seed germination is inhibited by salinity, and the inhibitory mechanism remains elusive. Our results indicate that NaCl treatment inhibits rice seed germination by decreasing the contents of bioactive gibberellins (GAs), such as GA₁ and GA_4, and that this inhibition can be rescued by exogenous bioactive GA application. To explore the mechanism of bioactive GA deficiency, the effect of NaCl on GA metabolic gene expression was investigated, revealing that expression of both GA biosynthetic genes and GA-inactivated genes was up-regulated by NaCl treatment. These results suggest that NaCl-induced bioactive GA deficiency is caused by up-regulated expression of GA-inactivated genes, and the up-regulated expression of GA biosynthetic genes might be a consequence of negative feedback regulation of the bioactive GA deficiency. Moreover, we provide evidence that NaCl-induced bioactive GA deficiency inhibits rice seed germination by decreasing α-amylase activity via down-regulation of α-amylase gene expression. Additionally, exogenous bioactive GA rescues NaCl-inhibited seed germination by enhancing α-amylase activity. Thus, NaCl treatment reduces bioactive GA content through promotion of bioactive GA inactivation, which in turn inhibits rice seed germination by decreasing α-amylase activity via down-regulation of α-amylase gene expression.

MLK1 and MLK2 Coordinate RGA and CCA1 Activity to Regulate Hypocotyl Elongation in Arabidopsis thaliana

Gibberellins (GAs) modulate diverse developmental processes throughout the plant life cycle. However, the interaction between GAs and the circadian rhythm remains unclear. Here, we report that MUT9p-LIKE KINASE1 (MLK1) and MLK2 mediate the interaction between GAs and the circadian clock to regulate hypocotyl elongation in Arabidopsis thaliana DELLA proteins function as master growth repressors that integrate phytohormone signaling and environmental pathways in plant development. MLK1 and MLK2 interact with the DELLA protein REPRESSOR OF ga1-3 (RGA). Loss of MLK1 and MLK2 function results in plants with short hypocotyls and hyposensitivity to GAs. MLK1/2 and RGA directly interact with CIRCADIAN CLOCK ASSOCIATED1 (CCA1), which targets the promoter of DWARF4 (DWF4) to regulate its roles in cell expansion. MLK1/2 antagonize the ability of RGA to bind CCA1, and these factors coordinately regulate the expression of DWF4 RGA suppressed the ability of CCA1 to activate expression from the DWF4 promoter, but MLK1/2 reversed this suppression. Genetically, MLK1/2 act in the same pathway as RGA and CCA1 in hypocotyl elongation. Together, our results provide insight into the mechanism by which MLK1 and MLK2 antagonize the function of RGA in hypocotyl elongation and suggest that MLK1/2 coordinately mediate the regulation of plant development by GAs and the circadian rhythm in Arabidopsis.

Suppression of SlMBP15 Inhibits Plant Vegetative Growth and Delays Fruit Ripening in Tomato

MADS-box genes have been demonstrated to participate in a number of processes in tomato development, especially fruit ripening. In this study, we reported a novel MADS-box gene, SlMBP15, which is implicated in fruit ripening. Based on statistical analysis, the ripening time of SlMBP15-silenced tomato was delayed by 2-4 days compared with that of the wild-type (WT). The accumulation of carotenoids and biosynthesis of ethylene in fruits were decreased in SlMBP15-silenced tomato. Genes related to carotenoid and ethylene biosynthesis were greatly repressed. SlMBP15 can interact with RIN, a MADS-box regulator affecting the carotenoid accumulation and ethylene biosynthesis in tomato. In addition, SlMBP15-silenced tomato produced dark green leaves, and its plant height was reduced. The gibberellin (GA) content of transgenic plants was lower than that of the WT and GA biosynthesis genes were repressed. These results demonstrated that SlMBP15 not only positively regulated tomato fruit ripening but also affected the morphogenesis of the vegetative organs.

The genetic and molecular basis of crop height based on a rice model

This review presents genetic and molecular basis of crop height using a rice crop model. Height is controlled by multiple genes with potential to be manipulated through breeding strategies to improve productivity. Height is an important factor affecting crop architecture, apical dominance, biomass, resistance to lodging, tolerance to crowding and mechanical harvesting. The impressive increase in wheat and rice yield during the 'green revolution' benefited from a combination of breeding for high-yielding dwarf varieties together with advances in agricultural mechanization, irrigation and agrochemical/fertilizer use. To maximize yield under irrigation and high fertilizer use, semi-dwarfing is optimal, whereas extreme dwarfing leads to decreased yield. Rice plant height is controlled by genes that lie in a complex regulatory network, mainly involved in the biosynthesis or signal transduction of phytohormones such as gibberellins, brassinosteroids and strigolactones. Additional dwarfing genes have been discovered that are involved in other pathways, some of which are uncharacterized. This review discusses our current understanding of the regulation of plant height using rice as a well-characterized model and highlights some of the most promising research that could lead to the development of new, high-yielding varieties. This knowledge underpins future work towards the genetic improvement of plant height in rice and other crops.

Increased Gibberellins and Light Levels Promotes Cell Wall Thickness and Enhance Lignin Deposition in Xylem Fibers

Light intensity and hormones (gibberellins; GAs) alter plant growth and development. A fine regulation triggered by light and GAs induces changes in stem cell walls (CW). Cross-talk between light-stimulated and GAs-induced processes as well as the phenolic compounds metabolism leads to modifications in lignin formation and deposition on cell walls. How these factors (light and GAs) promote changes in lignin content and composition. In addition, structural changes were evaluated in the stem anatomy of tobacco plants. GA₃ was sprayed onto the leaves and paclobutrazol (PAC), a GA biosynthesis inhibitor, via soil, at different irradiance levels. Fluorescence microscopy techniques were applied to detect lignin, and electron microscopy (SEM and TEM) was used to obtain details on cell wall structure. Furthermore, determination of total lignin and monomer contents were analyzed. Both light and GAs induces increased lignin content and CW thickening as well as greater number of fiber-like cells but not tracheary elements. The assays demonstrate that light exerts a role in lignification under GA₃ supplementation. In addition, the existence of an exclusive response mechanism to light was detected, that GAs are not able to replace.

Nitric oxide-mediated integrative alterations in plant metabolism to confer abiotic stress tolerance, NO crosstalk with phytohormones and NO-mediated post translational modifications in modulating diverse plant stress

Nitric oxide (NO) is a major signaling biomolecule associated with signal transduction in plants. The beneficial role of NO in plants, exposed to several abiotic stresses shifted our understanding as it being not only free radical, released from the toxic byproducts of oxidative metabolism but also helps in plant sustenance. An explosion of research in plant NO biology during the last two decades has revealed that NO is a key signal associated with plant growth, germination, photosynthesis, leaf senescence, pollen growth and reorientation. NO is beneficial as well as harmful to plants in a dose-dependent manner. Exogenous application of NO at lower concentrations promotes seed germination, hypocotyl elongation, pollen development, flowering and delays senescence but at higher concentrations it causes nitrosative damage to plants. However, this review concentrates on the beneficial impact of NO in lower concentrations in the plants and also highlights the NO crosstalk of NO with other plant hormones, such as auxins, gibberellins, abscisic acid, cytokinins, ethylene, salicylic acid and jasmonic acid, under diverse stresses. While concentrating on the multidimensional role of NO, an attempt has been made to cover the role of NO-mediated genes associated with plant developmental processes, metal uptake, and plant defense responses as well as stress-related genes. More recently, several NO-mediated post translational modifications, such as S-nitrosylation, N-end rule pathway operates under hypoxia and tyrosine nitration also occurs to modulate plant physiology.

Metabolome and transcriptome profiling reveal new insights into somatic embryo germination in Norway spruce (Picea abies)

Transcriptome, metabolome and histological profiling were performed on normal and aberrant somatic embryo germinants of Norway spruce (Picea abies L. Karst) providing a simplistic systems biology description of conifer germination. Aberrant germinants (AGs) formed periderm-like tissue at the apical pole and lacked shoot growth above the cotyledons. Transcriptome profiling (RNA-Sequencing) revealed a total of 370 differentially expressed genes at ≥1 or ≤-1 log2-fold change, where 92% were down-regulated in AGs compared with normal germinants (NGs). Genes associated with shoot apical meristem formation were down-regulated in AGs, or not differentially expressed between AGs and NGs. Genes involved in hormone signaling and transport were also down-regulated. Metabolite profiling by gas chromatography-mass spectrometry (MS) and liquid chromatography-MS revealed biochemical difference between AGs and NGs, notably increased levels of sugars including glucose in AGs. Genes involved in glucose signaling were down-regulated and genes involved in starch biosynthesis were up-regulated, suggesting involvement of sugar signaling during late embryo development and germination. The overall results provide new data enabling further studies to confirm potential markers for a normal germination process in conifers.

Phytohormones and Beneficial Microbes: Essential Components for Plants to Balance Stress and Fitness

Plants are subjected to various abiotic stresses, such as drought, extreme temperature, salinity, and heavy metals. Abiotic stresses have negative impact on the physiology and morphology of plants through defects in the genetic regulation of cellular pathways. Plants employ several tolerance mechanisms and pathways to avert the effects of stresses that are triggered whenever alterations in metabolism are encountered. Phytohormones are among the most important growth regulators; they are known for having a prominent impact on plant metabolism, and additionally, they play a vital role in the stimulation of plant defense response mechanisms against stresses. Exogenous phytohormone supplementation has been adopted to improve growth and metabolism under stress conditions. Recent investigations have shown that phytohormones produced by root-associated microbes may prove to be important metabolic engineering targets for inducing host tolerance to abiotic stresses. Phytohormone biosynthetic pathways have been identified using several genetic and biochemical methods, and numerous reviews are currently available on this topic. Here, we review current knowledge on the function of phytohormones involved in the improvement of abiotic stress tolerance and defense response in plants exposed to different stressors. We focus on recent successes in identifying the roles of microbial phytohormones that induce stress tolerance, especially in crop plants. In doing so, this review highlights important plant morpho-physiological traits that can be exploited to identify the positive effects of phytohormones on stress tolerance. This review will therefore be helpful to plant physiologists and agricultural microbiologists in designing strategies and tools for the development of broad spectrum microbial inoculants supporting sustainable crop production under hostile environments.

Genome-Wide Analysis of the Biosynthesis and Deactivation of Gibberellin-Dioxygenases Gene Family in Camellia sinensis (L.) O. Kuntze

Gibberellins (GAs), a class of diterpenoid phytohormones, play a key role in regulating diverse processes throughout the life cycle of plants. Bioactive GA levels are rapidly regulated by Gibberellin-dioxygenases (GAox), which are involved in the biosynthesis and deactivation of gibberellin. In this manuscript, a comprehensive genome-wide analysis was carried out to find all GAox in Camellia sinensis. For the first time in a tea plant, 14 CsGAox genes, containing two domains, DIOX_N (PF14226) and 2OG-FeII_Oxy, were identified (PF03171). These genes all belong to 2-oxoglutarate-dependent dioxygenases (2-ODD), including four CsGA20ox (EC: 1.14.11.12), three CsGA3ox (EC: 1.14.11.15), and seven CsGA2ox (EC: 1.14.11.13). According to the phylogenetic classification as in Arabidopsis, the CsGAox genes spanned five subgroups. Each CsGAox shows tissue-specific expression patterns, although these vary greatly. Some candidate genes, which may play an important role in response to external abiotic stresses, have been identified with regards to patterns, such as CsGA20ox2, CsGA3ox2, CsGA3ox3, CsGA2ox1, CsGA2ox2, and CsGA2ox4. The bioactive GA levels may be closely related to the GA20ox, GA3ox and GA2ox genes. In addition, the candidate genes could be used as marker genes for abiotic stress resistance breeding in tea plants.

Quantification of near-attomole gibberellins in floral organs dissected from a single Arabidopsis thaliana flower

There remains a methodological bottleneck in the quantification of ultra-trace plant hormones in very tiny plant organs at fresh weights below a milligram. The challenge becomes even more serious in the determination of endogenous gibberellins (GAs), which are a class of compounds that are difficult to separate and detect. Herein, a quantification method using ultra-high-performance liquid chromatography-tandem mass spectrometry was developed, combined with a derivatization technique in which GAs react with N-(3-dimethylaminopropyl)-N'-ethylcarbodiimide in ethanol. The method was validated as capable of determining GAs in floral organs (about 80-250 μg) - pistil, stamens, petals, sepals and receptacle - which were dissected from only one flower of Arabidopsis thaliana. Substantially different abundance patterns of GAs were measured from the floral organs at floral stages 13, 14 and 15 along the non-13-hydroxylation pathway and the early 13-hydroxylation pathway in plants. This allows sub-flower-level insights into how GAs affect floral development. The method exhibited excellent limit of detection and limit of quantification down to 5.41 and 18.0 attomole, respectively, and offered a fairly wide linear range from 0.01 to 25 femtomole with linear coefficients above 0.9961. The precision of the method was evaluated with relative standard deviations below 10.6% for intra-day and 11.4% for inter-day assays, and recoveries ranged from 64.0% to 107%.

Seed tolerance to deterioration in arabidopsis is affected by virus infection

Seed longevity is the period during which the plant seed is able to germinate. This property is strongly influenced by environment conditions experienced by seeds during their formation and storage. In the present study we have analyzed how the biotic stress derived from the infection of Cauliflower mosaic virus (CaMV), Turnip mosaic virus (TuMV), Cucumber mosaic virus (CMV) and Alfalfa mosaic virus (AMV) affects seed tolerance to deterioration measuring germination rates after an accelerated aging treatment. Arabidopsis wild type plants infected with AMV and CMV rendered seeds with improved tolerance to deterioration when compared to the non-inoculated plants. On the other hand, CaMV infection generated seeds more sensitive to deterioration. No seeds were obtained from TuMV infected plants. Similar pattern of viral effects was observed in the double mutant athb22 athb25, which is more sensitive to accelerated seed aging than wild type. However, we observed a significant reduction of the seed germination for CMV (65% vs 55%) and healthy (50% vs 30%) plants in these mutants. The seed quality differences were overcomed using the A. thaliana athb25-1D dominant mutant, which over accumulated gibberellic acid (GA), except for TuMV which generated some siliques with low seed tolerance to deterioration. For AMV and TuMV (in athb25-1D), the seed quality correlated with the accumulation of the messengers of the gibberellin 3-oxidase family, the mucilage of the seed and the GA1. For CMV and CaMV it was not a good correlation suggesting that other factors are affecting seed viability.

Gibberellic Acid Signaling Is Required to Induce Flowering of Chrysanthemums Grown under Both Short and Long Days

Flower bud formation and flowering in chrysanthemums occur under short day conditions (SD), but the molecular basis for the switch to reproductive growth is less well understood than in model plants. Here, a spontaneous mutant able to flower under long days is described. In an attempt to reveal the pathway(s) involved in the formation of flower buds under contrasting daylengths, transcriptome sequencing was carried out in plants grown both under SD and long day conditions (LD). A number of differentially transcribed genes involved in the various known flowering pathways were identified. Both circadian clock genes and Chrysanthemum FLOWERING LOCUS T Like3 (CmFTL3) were up-regulated under SD, thereby inducing floral bud formation and flowering. The gibberellin (GA) signaling pathway-related genes Gibberellin 20-oxidase (GA20ox) and Gibberellin receptor (GID1) were up-regulated in the mutant under LD, while the catabolic genes Gibberellin 2-oxidase (GA2ox) and GA-INSENSITIVE (GAI) were down-regulated, thereby inducing the transcription of SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1) and LEAFY (LFY). The GA content of the leaf was higher in the mutant than in the wild type (WT) under LD and SD, and the mutant has more branching than WT plants under LD or SD. When treated with GA, the mutant flowered earlier under both SD and LD relative to WT, but there was no detectable phenotype difference between the two lines. The indication was that the photoperiod pathway majorly regulates flower bud formation and flowering time in chrysanthemums under SD. The GA signaling pathway only plays a subsidiary role for flowering. However, the GA signaling pathway predominated for flowering under LD.

Rice black streaked dwarf virus P7-2 forms a SCF complex through binding to Oryza sativa SKP1-like proteins, and interacts with GID2 involved in the gibberellin pathway

As a core subunit of the SCF complex that promotes protein degradation through the 26S proteasome, S-phase kinase-associated protein 1 (SKP1) plays important roles in multiple cellular processes in eukaryotes, including gibberellin (GA), jasmonate, ethylene, auxin and light responses. P7-2 encoded by Rice black streaked dwarf virus (RBSDV), a devastating viral pathogen that causes severe symptoms in infected plants, interacts with SKP1 from different plants. However, whether RBSDV P7-2 forms a SCF complex and targets host proteins is poorly understood. In this study, we conducted yeast two-hybrid assays to further explore the interactions between P7-2 and 25 type I Oryza sativa SKP1-like (OSK) proteins, and found that P7-2 interacted with eight OSK members with different binding affinity. Co-immunoprecipitation assay further confirmed the interaction of P7-2 with OSK1, OSK5 and OSK20. It was also shown that P7-2, together with OSK1 and O. sativa Cullin-1, was able to form the SCF complex. Moreover, yeast two-hybrid assays revealed that P7-2 interacted with gibberellin insensitive dwarf2 (GID2) from rice and maize plants, which is essential for regulating the GA signaling pathway. It was further demonstrated that the N-terminal region of P7-2 was necessary for the interaction with GID2. Overall, these results indicated that P7-2 functioned as a component of the SCF complex in rice, and interaction of P7-2 with GID2 implied possible roles of the GA signaling pathway during RBSDV infection.

AaMYB1 and its orthologue AtMYB61 affect terpene metabolism and trichome development in Artemisia annua and Arabidopsis thaliana

The effective anti-malarial drug artemisinin (AN) isolated from Artemisia annua is relatively expensive due to the low AN content in the plant as AN is only synthesized within the glandular trichomes. Therefore, genetic engineering of A. annua is one of the most promising approaches for improving the yield of AN. In this work, the AaMYB1 transcription factor has been identified and characterized. When AaMYB1 is overexpressed in A. annua, either exclusively in trichomes or in the whole plant, essential AN biosynthetic genes are also overexpressed and consequently the amount of AN is significantly increased. Artemisia AaMYB1 constitutively overexpressing plants displayed a greater number of trichomes. In order to study the role of AaMYB1 on trichome development and other possibly connected biological processes, AaMYB1 was overexpressed in Arabidopsis thaliana. To support our findings in Arabidopsis thaliana, an AaMYB1 orthologue from this model plant, AtMYB61, was identified and atmyb61 mutants characterized. Both AaMYB1 and AtMYB61 affected trichome initiation, root development and stomatal aperture in A. thaliana. Molecular analyses indicated that two crucial trichome activator genes are misexpressed in atmyb61 mutant plants and in plants overexpressing AaMYB1. Furthermore, AaMYB1 and AtMYB61 are also essential for gibberellin (GA) biosynthesis and degradation in both species by positively affecting the expression of the enzymes that convert GA₉ into the bioactive GA₄ as well as the enzymes involved in the degradation of GA₄ . Overall, these results identify AaMYB1/AtMYB61 as a key component of the molecular network that connects important biosynthetic processes, and reveal its potential value for AN production through genetic engineering.

Arabidopsis thaliana RECEPTOR DEAD KINASE1 Functions as a Positive Regulator in Plant Responses to ABA

Abscisic acid (ABA) is a major phytohormone involved in important stress-related and developmental plant processes. Membrane-delimited ABA signal transduction plays an important role in early ABA signaling, but the molecular mechanisms connecting core signaling components to the plasma membrane remain unclear. Plants have evolved a large number of receptor-like kinases (RLKs) to modulate diverse biological processes by perceiving extracellular stimuli and activating downstream signaling responses. In this study, a putative leucine-rich repeat-RLK gene named RECEPTOR DEAD KINASE1 (AtRDK1) was identified and characterized in Arabidopsis thaliana. RDK1 promoter-GUS analysis revealed that RDK1 is expressed ubiquitously in the various tissues in Arabidopsis, and its expression is mainly induced by ABA. In the presence of ABA, RDK1-deficient rdk1-1 and rdk1-2 lines showed significant resistance in cotyledon greening and root growth, whereas RDK1-overexpressing lines showed enhanced sensitivity. Consistently, the expression of ABA-responsive genes was significantly downregulated in rdk1 mutant seedlings, which were also hypersensitive to drought stress with increased water loss. Interestingly, RDK1 was found to be an atypical kinase localized to the plasma membrane and did not require its kinase activity during ABA-mediated inhibition of seedling development. Accordingly, RDK1 interacted in the plasma membrane with type 2C protein phosphatase ABSCISIC ACID INSENSITIVE1 (ABI1); this interaction was further enhanced by exogenous application of ABA, suggesting that RDK1-mediated recruitment of ABI1 onto the plasma membrane is important for ABA signaling. Taken together, these results reveal an important role for RDK1 in plant responses to abiotic stress conditions in an ABA-dependent manner.