Inflorescence Stem Research Articles

Revealing biomass heterosis in the allodiploid xBrassicoraphanus, a hybrid between Brassica rapa and Raphanus sativus, through integrated transcriptome and metabolites analysis

BackgroundHeterosis is biologically important but the molecular basis of the phenomenon is poorly understood. We characterized intergeneric hybrids between B. rapa cv. Chiifu and R. sativus cv. WK10039 as an extreme example of heterosis. Taking advantage of clear heterosis phenotypes and the genetic distance between parents, we performed transcriptome and metabolite analysis to decipher the molecular basis of heterosis.ResultsThe heterosis was expressed as fresh weight in the field and as inflorescence stem length in the glass house. Flowering time, distributed as a normal segregating population, ranged from the early flowering of one parent to the late flowering of the other, in contrast to the homogeneous flowering time in a typical F1 population, indicating unstable allelic interactions. The transcriptome and metabolome both indicated that sugar metabolism was altered, suggesting that the change in metabolism was linked to the heterosis. Because alleles were not shared between the hybridized genomes, classic models only partly explain this heterosis, indicating that other mechanisms are involved.ConclusionThe differential expression of genes for primary and secondary metabolism, along with the altered metabolite profiles, suggests that heterosis could involve a change in balance between primary and secondary metabolism.

Stem phototropism toward blue and ultraviolet light.

Positive phototropism is the process through which plants orient their organs toward a directional light source. While the blue light receptors phototropins (phot) play a major role in phototropism toward blue (B) and ultraviolet (UV) radiation, recent research showed that the UVB light receptor UVR8 also triggers phototropism toward UVB. In addition, new details of the molecular mechanisms underlying the activity of these receptors and interaction with other environmental signals have emerged in the past years. In this review, we summarize the current knowledge about hypocotyledoneous and inflorescence stem growth reorientation toward B and UVB, with a focus on the molecular mechanisms.

DeepPod: a convolutional neural network based quantification of fruit number in Arabidopsis.

BackgroundHigh-throughput phenotyping based on non-destructive imaging has great potential in plant biology and breeding programs. However, efficient feature extraction and quantification from image data remains a bottleneck that needs to be addressed. Advances in sensor technology have led to the increasing use of imaging to monitor and measure a range of plants including the model Arabidopsis thaliana. These extensive datasets contain diverse trait information, but feature extraction is often still implemented using approaches requiring substantial manual input.ResultsThe computational detection and segmentation of individual fruits from images is a challenging task, for which we have developed DeepPod, a patch-based 2-phase deep learning framework. The associated manual annotation task is simple and cost-effective without the need for detailed segmentation or bounding boxes. Convolutional neural networks (CNNs) are used for classifying different parts of the plant inflorescence, including the tip, base, and body of the siliques and the stem inflorescence. In a post-processing step, different parts of the same silique are joined together for silique detection and localization, whilst taking into account possible overlapping among the siliques. The proposed framework is further validated on a separate test dataset of 2,408 images. Comparisons of the CNN-based prediction with manual counting (R2 = 0.90) showed the desired capability of methods for estimating silique number.ConclusionsThe DeepPod framework provides a rapid and accurate estimate of fruit number in a model system widely used by biologists to investigate many fundemental processes underlying growth and reproduction

Characteristics of Microsatellites Mined from Transcriptome Data and the Development of Novel Markers in Paeonia lactiflora.

The insufficient number of available simple sequence repeats (SSRs) inhibits genetic research on and molecular breeding of Paeonia lactiflora, a flowering crop with great economic value. The objective of this study was to develop SSRs for P. lactiflora with Illumina RNA sequencing and assess the role of SSRs in gene regulation. The results showed that dinucleotides with AG/CT repeats were the most abundant type of repeat motif in P. lactiflora and were preferentially distributed in untranslated regions. Significant differences in SSR size were observed among motif types and locations. A large number of unigenes containing SSRs participated in catalytic activity, metabolic processes and cellular processes, and 28.16% of all transcription factors and 21.74% of hub genes for inflorescence stem straightness were found to contain SSRs. Successful amplification was achieved with 89.05% of 960 pairs of SSR primers, 55.83% of which were polymorphic, and most of the 46 tested primers had a high level of transferability to the genus Paeonia. Principal component and cluster dendrogram analyses produced results consistent with known genealogical relationships. This study provides a set of SSRs with abundant information for future accession identification, marker-trait association and molecular assisted breeding in P. lactiflora.

Roles of Brassinosteroids in Plant Reproduction.

Brassinosteroids (BRs) are a group of steroid hormones, essentially important for plant development and growth. BR signaling functions to promote cell expansion and cell division, and plays a role in etiolation and reproduction. As the phytohormone originally identified in the pollen grains of Brassica napus, BR promotes the elongation of stigma. Recent studies have revealed that BR is also critical for floral transition, inflorescence stem architecture formation and other aspects of plant reproductive processes. In this review, we focus on the current understanding of BRs in plant reproduction, the spatial and temporal control of BR signaling, and the downstream molecular mechanisms in both the model plant Arabidopsis and crops. The crosstalk of BR with environmental factors and other hormones in reproduction will also be discussed.

Effects of Metaxenia on Stone Cell Formation in Pear (Pyrus bretschneideri) Based on Transcriptomic Analysis and Functional Characterization of the Lignin-Related Gene PbC4H2

The deposition of lignin in flesh parenchyma cells for pear stone cells, and excessive stone cells reduce the taste and quality of the fruit. The effect of metaxenia on the quality of fruit has been heavily studied, but the effect of metaxenia on stone cell formation has not been fully elucidated to date. This study used P. bretschneideri (Chinese white pear) cv. ‘Yali’ (high-stone cell content) and P. pyrifolia (Sand pear) cv. ‘Cuiguan’ (low-stone cell content) as pollination trees to pollinate P. bretschneideri cv. ‘Lianglizaosu’ separately to fill this gap in the literature. The results of quantitative determination, histochemical staining and electron microscopy indicated that the content of stone cells and lignin in YL fruit (‘Yali’ (pollen parent) × ‘Lianglizaosu’ (seed parent)) was significantly higher than that in CL fruit (‘Cuiguan’ (pollen parent) × ‘Lianglizaosu’ (seed parent)). The transcriptome sequencing results that were obtained from the three developmental stages of the two types of hybrid fruits indicated that a large number of differentially expressed genes (DEGs) related to auxin signal transduction (AUX/IAAs and ARFs), lignin biosynthesis, and lignin metabolism regulation (MYBs, LIMs, and KNOXs) between the CL and YL fruits at the early stage of fruit development. Therefore, metaxenia might change the signal transduction process of auxin in pear fruit, thereby regulating the expression of transcription factors (TFs) related to lignin metabolism, and ultimately affecting lignin deposition and stone cell development. In addition, we performed functional verification of a differentially expressed gene, PbC4H2 (cinnamate 4-hydroxylase). Heterologous expression of PbC4H2 in the c4h mutant not only restored its collapsed cell wall, but also significantly increased the lignin content in the inflorescence stem. The results of our research help to elucidate the metaxenia-mediated regulation of pear stone cell development and clarify the function of PbC4H2 in cell wall development and lignin synthesis, which establishes a foundation for subsequent molecular breeding.

Transcriptome and weighted correlation network analyses provide insights into inflorescence stem straightness in Paeonia lactiflora.

Lack of structural components results in inflorescence stem bending. Differentially expressed genes involved in lignin and hemicellulose biosynthesis are vital; genes involved in cellulose and glycan biosynthesis are also relevant. An erect inflorescence stem is essential for high-quality cut herbaceous peony flowers. To explore the factors underlying inflorescence stem bending, major cell walls contents were measured, and stem structure was observed in two herbaceous peony varieties with contrasting stem straightness traits ('Da Fugui', upright; 'Chui Touhong', bending). In addition, Illumina sequencing was performed and weighted correlation network analysis (WGCNA) was used to analyze the results. The results showed significant differences in lignin, hemicellulose and soluble sugar contents, sclerenchyma and xylem areas and thickening in cell walls in pith at stage S3, when bending begins. In addition, 44,182 significantly differentially expressed genes (DEGs) were found, and these DEGs were mainly enriched in 36 pathways. Among the DEGs, hub genes involved in lignin, cellulose, and xylan biosynthesis and transcription factors that regulated these process were identified by WGCNA. These results suggested that the contents of compounds that provided cell wall rigidity were vital factors affecting inflorescence stem straightness in herbaceous peony. Genes involved in or regulating the biosynthesis of these compounds are thus important; lignin and hemicellulose are of great interest, and cellulose and glycan should not be ignored. This paper lays a foundation for developing new herbaceous peony varieties suitable for cut flowers by molecular-assisted breeding.

The relationship between cuticular lipids and associated gene expression in above ground organs of Thellungiella salsugineum (Pall.) Al-Shehbaz & Warwick

The cuticle plays a critical role as barrier between plant and environment. Here, cuticular wax morphology, cuticular wax and cutin monomer composition, and expression of associated genes in five above ground organs were examined in model extremophyte Thellungiella salsugineum. Alkanes, ketones, and 2-alcohols were the predominant wax constitutes in rosette leaves, inflorescence stem leaves, stems, and siliques, whereas alkanes and acids were the predominant cuticular lipids in whole flowers. Unsubstituted acids were the most abundant cutin monomers in vegetative organs, especially C18:2 dioic acids, which reached the highest levels in stems. Hydroxy fatty acids were the predominant cutin monomers in flowers, especially 16−OH C16:0 and diOH C16:0. High-throughput RNA-Seq analysis using the Hiseq4000 platform was performed on these five above organs of T. salsugineum, and the differentially expressed lipid-associated genes and their associated metabolic pathways were identified. Expression of genes associated in previous reports to cuticle production, including those having roles in cuticle lipid biosynthesis, transport, and regulation were examined. The association of cuticle lipid composition and gene expression within different organs of T. salsugineum, and potential relationships between T. salsugineum’s extreme cuticle and its adaptation to extreme environments is discussed.

GTR-Mediated Radial Import Directs Accumulation of Defensive Glucosinolates to Sulfur-Rich Cells in the Phloem Cap of Arabidopsis Inflorescence Stem

In the phloem cap region of Arabidopsis plants, sulfur-rich cells (S-cells) accumulate >100 mM glucosinolates (GLS), but are biosynthetically inactive. The source and route of S-cell-bound GLS remain elusive. In this study, using single-cell sampling and scanning electron microscopy with energy-dispersive X-ray analysis we show that two GLS importers, NPF2.10/GTR1 and NPF2.11/GTR2, are critical for GLS accumulation in S-cells, although they are not localized in the S-cells. Comparison of GLS levels in S-cells in multiple combinations of homo- and heterografts of gtr1 gtr2, biosynthetic null mutant and wild-type plants indicate that S-cells accumulate GLS via symplasmic connections either directly from neighboring biosynthetic cells or indirectly to non-neighboring cells expressing GTR1/2. Distinct sources and transport routes exist for different types of GLS, and vary depending on the position of S-cells in the inflorescence stem. Based on these findings, we propose a model illustrating the GLS transport routes either directly from biosynthetic cells or via GTR-mediated import from apoplastic space radially into a symplasmic domain, wherein the S-cells are the ultimate sink. Similarly, we observed accumulation of the cyanogenic glucoside defensive compounds in high-turgor cells in the phloem cap of Lotus japonicus, suggesting that storage of defensive compounds in high-turgor cells may be a general mechanism for chemical protection of the phloem cap.

R2R3-MYB transcription factor MYB6 promotes anthocyanin and proanthocyanidin biosynthesis but inhibits secondary cell wall formation in Populus tomentosa.

The secondary cell wall is an important carbon sink in higher plants and its biosynthesis requires coordination of metabolic fluxes in the phenylpropanoid pathway. In Arabidopsis (Arabidopsis thaliana), MYB75 and the KNOX transcription factor KNAT7 form functional complexes to regulate secondary cell wall formation in the inflorescence stem. However, the molecular mechanism by which these transcription factors control different branches of the phenylpropanoid pathway remains poorly understood in woody species. We isolated an R2R3-MYB transcription factor MYB6 from Populus tomentosa and determined that it was expressed predominately in young leaves. Overexpression of MYB6 in transgenic poplar upregulated flavonoid biosynthetic gene expression, resulting in significantly increased accumulation of anthocyanin and proanthocyanidins. MYB6-overexpression plants showed reduced secondary cell wall deposition, accompanied by repressed expression of secondary cell wall biosynthetic genes. We further showed that MYB6 interacted physically with KNAT7 and formed functional complexes that acted to repress secondary cell wall development in poplar and Arabidopsis. The results provide an insight into the transcriptional mechanisms involved in the regulation of the metabolic fluxes between the flavonoid and lignin biosynthetic pathways in poplar.

Bolting, an Important Process in Plant Development, Two Types in Plants

Bolting refers to the rapid lengthening of the plant stem, and is due to the coordinated effects of developmental and environmental factors. The shoot apical meristem differentiates into the inflorescence meristem and eventually the floral meristem, which then develops into various floral organs during the bolting period. The timing of bolting is critical for plant propagation and reproductive success because it influences seed production, species survival, and crop yield. Therefore, analyses of the causes of bolting and how it occurs may enable researchers to regulate bolting. In this review, two different bolting phenotypes are described, namely inflorescence axis elongation and stem internode elongations. Various factors, such as light, temperature, and endogenous hormones, are integrated to mediate bolting. Moreover, the mechanism underlying bolting, including signal cascades and epigenetic inheritance, are discussed, and appropriate future research directions are proposed.

Bird pollination in an African Satyrium (Orchidaceae) confirmed by camera traps and selective exclusion experiments

Motion-activated cameras (“camera traps”) are useful for recording plant–animal interactions that are difficult to observe using conventional means. We used camera traps to document interactions between animal flower visitors and the orchid Satyrium neglectum subsp. woodii and used mesh exclosures which selectively exclude access of larger animals to flowers to test the importance of bird visits for pollination. Camera footage revealed that the orchid is visited by two sunbird species (amethyst and greater double-collared) which carry pollinaria on the upper mandible of their beaks. Plants which could only be accessed by bees and other small insects had few pollinaria removed and set very few fruits relative to plants which could also be accessed by larger animals such as sunbirds. The sturdy inflorescence stem, and thick fleshy perianth tissue, orange–red colour of the flowers, low scent production and large viscidia, are traits shared with other, distantly related bird-pollinated Satyrium species and can therefore be considered likely to play a functional role in bird pollination. We previously made anecdotal observations of sunbird visits to this orchid species in south-central Africa, and this study conducted in populations in South Africa confirms that sunbird pollination is consistent across the highly disjunct distribution of the taxon.

Characterization of an Arabidopsis thaliana DUF761-containing protein with a potential role in development and defense responses

The Arabidopsis thaliana genome contains many genes that encode proteins with a domain of unknown function (DUF). To improve our understanding of the functions of these DUF family members, a DUF761-containing gene at the At4g16790 locus was isolated and designated DUF761-1. Duf761-1 loss-of-function mutant did not significantly affect plant growth and development, whereas transgenic plants overexpressing DUF761-1 exhibited several unique phenotypes during vegetative and reproductive growth. DUF761-1 overexpression was associated with altered leaf and root morphology, inhibition of inflorescence stem elongation and thickening, defects in flower development, and reduced seed production compared to that of wild-type plants. Moreover, DUF761-1 overexpressing plants exhibited constitutively activated plant defense responses and displayed enhanced resistance to Pseudomonas syringae L. pv. tomato DC3000 during pathogen infection assays. Taken together, the combination of characterization of plant phenotypes, gene expression analysis and pathogen resistance assays in loss-of-function mutant and overexpression lines suggests that DUF761-1 may be involved in plant development and defense responses.

Characterization of a NAC transcription factor involved in the regulation of pomegranate seed hardness (Punica granatum L.)

The pomegranate, Punica granatum L., which has been cultivated since antiquity, is known to be a superfruit, possessing an array of functional anti-oxidants and various other health benefits. The hardness of pomegranate seeds is an important indicator of fruit quality, which in turn affects economic value and market demand. However, the molecular mechanism underlying pomegranate seed hardness remains to be fully understood. In this study, we found a positive correlation between seed hardness and lignin content in two pomegranate varieties: “Tunisia” and “Sanbai”. Specifically, genes associated with lignin biosynthesis were differentially expressed in soft-seed and hard-seed pomegranate varieties. Among these differential genes, we cloned and characterized the NAC transcription factor PgSND1-like. Sequence alignment found a single base replacement at the 166-bp position of CDS in the PgSND1-like gene from “Tunisia” and “Sanbai”. Both PgSND1-like (Sanbai) and PgSND1-like (Tunisia) proteins are localized in the cell nucleus and have a transcription activation domain in the C-terminus. Yeast two-hybrid analysis indicated that PgSND1-like protein interacts with itself to form a homodimer. Overexpression of PgSND1-like (Sanbai) in Arabidopsis showed a higher lignin content in inflorescence stem and mature seed compared with wild-type Arabidopsis. Accordingly, the expression levels of several lignin biosynthesis-associated genes were upregulated in stem cells and mature seeds of transgenic plants. However, PgSND1-like (Tunisia) transgenic Arabidopsis showed no phenotypic differences with wild-type Arabidopsis. Taken together, we suggest that PgSND1-like may regulate at least two different functions in two pomegranate varieties, promoting lignin biosynthesis and seed hardness of pomegranate.

EGTA reduces the inflorescence stem mechanical strength of herbaceous peony by modifying secondary wall biosynthesis

The mechanical strength of inflorescence stems is an important trait in cut flowers. Calcium ions (Ca2+) play a pivotal role in maintaining stem strength, but little is known about the underlying molecular mechanisms. In this study, we treated herbaceous peony (Paeonia lactiflora Pall.) with ethyl glycol tetraacetic acid (EGTA), an effective Ca2+ chelator, and used morphology indicators, spectroscopic analysis, histochemical staining, electron microscopy, and proteomic techniques to investigate the role of Ca2+ in inflorescence stem mechanical strength. The EGTA treatment reduced the mechanical strength of inflorescence stems, triggered the loss of Ca2+ from cell walls, and reduced lignin in thickened secondary walls in xylem cells as determined by spectroscopic analysis and histochemical staining. Electron microscopy showed that the EGTA treatment also resulted in significantly fewer xylem cell layers with thickened secondary walls as well as in reducing the thickness of these secondary walls. The proteomic analysis showed 1065 differentially expressed proteins (DEPs) at the full-flowering stage (S4). By overlapping the Kyoto encyclopedia of genes and genomes (KEGG) and gene ontology (GO) analysis results, we identified 43 DEPs involved in signal transduction, transport, energy metabolism, carbohydrate metabolism, and secondary metabolite biosynthesis. Using quantitative real-time polymerase chain reaction (qRT-PCR) analysis, we showed that EGTA treatment inhibited Ca2+ sensors and secondary wall biosynthesis-related genes. Our findings revealed that EGTA treatment reduced the inflorescence stem mechanical strength by reducing lignin deposition in xylem cells through altering the expression of genes involved in Ca2+ binding and secondary wall biosynthesis.

Integration of Transcriptome, Proteome, and Metabolome Provides Insights into How Calcium Enhances the Mechanical Strength of Herbaceous Peony Inflorescence Stems.

Weak stem mechanical strength severely restrains cut flowers quality and stem weakness can be alleviated by calcium (Ca) treatment, but the mechanisms underlying Ca-mediated enhancement of stem mechanical strength remain largely unknown. In this study, we performed a comparative transcriptomic, proteomic, and metabolomic analysis of herbaceous peony (Paeonia lactiflora Pall.) inflorescence stems treated with nanometer Ca carbonate (Nano-CaCO3). In total, 2643 differentially expressed genes (DEGs) and 892 differentially expressed proteins (DEPs) were detected between the Control and nano-CaCO3 treatment. Among the 892 DEPs, 152 were coregulated at both the proteomic and transcriptomic levels, and 24 DEPs related to the secondary cell wall were involved in signal transduction, energy metabolism, carbohydrate metabolism and lignin biosynthesis, most of which were upregulated after nano-CaCO3 treatment during the development of inflorescence stems. Among these four pathways, numerous differentially expressed metabolites (DEMs) related to lignin biosynthesis were identified. Furthermore, structural observations revealed the thickening of the sclerenchyma cell walls, and the main wall constitutive component lignin accumulated significantly in response to nano-CaCO3 treatment, thereby indicating that Ca can enhance the mechanical strength of the inflorescence stems by increasing the lignin accumulation. These results provided insights into how Ca treatment enhances the mechanical strength of inflorescence stems in P. lactiflora.

Ontogenetic Changes in Auxin Biosynthesis and Distribution Determine the Organogenic Activity of the Shoot Apical Meristem in pin1 Mutants.

In the shoot apical meristem (SAM) of Arabidopsis, PIN1-dependent polar auxin transport (PAT) regulates two crucial developmental processes: organogenesis and vascular system formation. However, the knockout mutation in the PIN1 gene does not fully inhibit these two processes. Therefore, we investigated a potential source of auxin for organogenesis and vascularization during inflorescence stem development. We analyzed auxin distribution in wild-type (WT) and pin1 mutant plants using a refined protocol of auxin immunolocalization; auxin activity, with the response reporter pDR5:GFP; and expression of auxin biosynthesis genes YUC1 and YUC4. Our results revealed that regardless of the functionality of PIN1-mediated PAT, auxin is present in the SAM and vascular strands. In WT plants, auxin always accumulates in all cells of the SAM, whereas in pin1 mutants, its localization within the SAM changes ontogenetically and is related to changes in the structure of the vascular system, organogenic activity of SAM, and expression levels of YUC1 and YUC4 genes. Our findings indicate that the presence of auxin in the meristem of pin1 mutants is an outcome of at least two PIN1-independent mechanisms: acropetal auxin transport from differentiated tissues with the use of vascular strands and auxin biosynthesis within the SAM.

Tensile Testing Assay for the Measurement of Tissue Stiffness in Arabidopsis Inflorescence Stem.

Lignocellulosic biomass is a versatile renewable resource for fuels, buildings, crafts, and biomaterials. Strategies of molecularly designing lignocellulose for industrial application has been developed by the discoveries of novel genes after the screenings of various mutants and transformed lines of Arabidopsis whose cell walls could be modified in the inflorescence stem, a model woody tissue. The mechanical properties are used as a quantitative index for the chemorehological behavior of the genetically modified cell wall in the tissue. This parameter can be measured with tensile or bending tests of tissue explants, the vibration analysis of tissue behavior or using atomic force microscopy to probe the tissue surface. Here, we describe in detail the procedure to determine the stiffness of methanol-fixed, rehydrated and pronase-treated inflorescence explants with a tensile testing machine based on classical methods for the determination of cell wall extensibility.

Effects of plant growth regulators on the in vitro flowering of carnation (Dianthus caryophyllus L.)

The flowering of terminal shoot of carnation has three stages: inflorescence, floral initiation and blooming. Respiration rate increased in the transition from the vegetative growth to the flowering and all the stages of flowering had high respiration rate. Auxin and gibberellin activities, the proportion of auxin to cytokinin increased, and the elongation of inflorescence stem began in the transition from the vegetative growth to floral initiation stage are involved. Auxin and cytokinin activity increased, the proportion of auxin to cytokinin and gibberellin activity decreased in the transition from the floral initiation to blooming stage. Most vegetative shoots became floral buds by two ways: one way induced by auxin with 0.25 mg/LIAA, and the other by cytokinin with 0.25 mg/L BA.

The papain-like cysteine protease CEP1 is involved in programmed cell death and secondary wall thickening during xylem development in Arabidopsis.

Both tracheary elements and fiber cells undergo programmed cell death (PCD) during xylem development. In this study we investigated the role of papain-like cysteine protease CEP1 in PCD in the xylem of Arabidopsis. CEP1 was located in the cell wall of xylem cells, and CEP1 expression levels in inflorescence stems increased during stem maturation. cep1 mutant plants exhibited delayed stem growth and reduced xylem cell number compared to wild-type plants. Transmission electron microscopy demonstrated that organelle degradation was delayed during PCD, and thicker secondary walls were present in fiber cells and tracheary elements of the cep1 mutant. Transcriptional analyses of the maturation stage of the inflorescence stem revealed that genes involved in the biosynthesis of secondary wall components, including cellulose, hemicellulose, and lignin, as well as wood-associated transcriptional factors, were up-regulated in the cep1 mutant. These results suggest that CEP1 is directly involved in the clearing of cellular content during PCD and regulates secondary wall thickening during xylem development.