How animals establish and pattern the primary body axis is one of the most fundamental problems in biology. Data from diverse deuterostomes (frog, fish, mouse, and amphioxus) and from planarians (protostomes) suggest that Wnt signaling through β-catenin controls posterior identity during body plan formation in most bilaterally symmetric animals. Wnt signaling also influences primary axis polarity of pre-bilaterian animals, indicating that an axial patterning role for Wnt signaling predates the evolution of bilaterally symmetric animals. The use of posterior Wnt signaling and anterior Wnt inhibition might be a unifying principle of body plan development in most animals.

Wnt Signaling and the Polarity of the Primary Body Axis

The primary issues regarding the lack of protocol reproducibility among laboratories are environmental factors. Light (quantity and particularly quality), is one of those main factors, and studies seldom present the spectral quality of the light sources used. With the advent of light-emitting diode (LED) technology, impressive progress has been made in environmental controls and morphogenetic responses, as directed by the light used in the culture shelves. A wide array of LED lights with different spectra are currently available and light is important in large-scale propagation, especially liquid bioreactor systems. LED technology continues to evolve rapidly and has created additional possibilities. This laboratory has dedicated extensive efforts to implement photoautotrophic propagation, and light is a key component of the system. This review presents relevant topics on the influence of light in various plant tissue culture-based techniques.

Light quality in plant tissue culture: does it matter?

Dormancy is an adaptive mechanism that allows temperate deciduous plants to survive unfavorable winter conditions. In the present work, we investigated the possible function of abscisic acid (ABA) on the endodormancy process in pear. The ABA content increased during pear flower bud endodormancy establishment and decreased towards endodormancy release. In total, 39 putative genes related to ABA metabolism and signal transductions were identified from pear genome. During the para- to endodormancy transition, PpNCED-2 and PpNCED-3 had high expression levels, while PpCYP707As expression levels were low. However, during endodormancy, the expression of PpCYP707A-3 sharply increased with increasing cold accumulation. At the same time, the ABA content of pear buds declined, and the percentage of bud breaks rapidly increased. On the other hand, the expression levels of PpPYLs, PpPP2Cs, PpSnRK2s, and PpABI4/ABI5s were also changed during the pear flower bud dormancy cycle. Furthermore, exogenous ABA application to para-dormant buds significantly reduced the bud breaks and accelerated the transition to endodormancy. During the whole treatment time, the expression level of PpPP2C-12 decreased to a greater extent in ABA-treated buds than in control. However, the expression levels of PpSnRK2-1, PpSnRK2-4, and PpABI5-1 were higher in ABA-treated buds. Our results indicated that PpCYP707A-3 and PpNCEDs play pivotal roles on the regulation of endodormancy release, while ABA signal transduction pathway also appears to be involved in the process. The present work provided the basic information about the function of ABA-related genes during pear flower bud dormancy process.

https://www.mdpi.com/1422-0067/19/1/310/pdf

Abscisic Acid (ABA ) Promotes the Induction and Maintenance of Pear (Pyrus pyrifolia White Pear Group) Flower Bud Endodormancy.

The molecular mechanism regulating dormancy release in grapevine buds is as yet unclear. It has been hypothesized that (i) abscisic acid (ABA) represses bud-meristem activity; (ii) perturbation of respiration induces an interplay between ethylene and ABA metabolism, which leads to removal of repression; and (iii) gibberellin (GA)-mediated growth is resumed. The first two hypothesis have been formally supported. The current study examines the third hypothesis regarding the potential involvement of GA in dormancy release. We found that during natural dormancy induction, levels of VvGA3ox, VvGA20ox, and VvGASA2 transcripts and of GA1 were decreased. However, during dormancy release, expression of these genes was enhanced, accompanied by decreased expression of the bud-expressed GA-deactivating VvGA2ox. Despite indications for its positive role during natural dormancy release, GA application had inhibitory effects on bud break. Hydrogen cyanamide up-regulated VvGA2ox and down-regulated VvGA3ox and VvGA20ox expression, reduced GA1 levels, and partially rescued the negative effect of GA. GA had an inhibitory effect only when applied simultaneously with bud-forcing initiation. Given these results, we hypothesize that during initial activation of the dormant bud meristem, the level of GA must be restricted, but after meristem activation an increase in its level serves to enhance primordia regrowth.

Distinct gibberellin functions during and after grapevine bud dormancy release.

Grapevine immune signaling network in response to drought stress as revealed by transcriptomic analysis.

Bud dormancy is an important biological phenomenon of perennial plants that enables them to survive under harsh environmental circumstances. Grape (Vitis vinifera) is one of the most grown fruit crop worldwide; however, underlying mechanisms involved in grape bud dormancy are not yet clear. This work was aimed to explore the underlying molecular mechanism regulating bud dormancy in grape. We have performed transcriptome and differential transcript expression analyses of “Shine Muscat” grape buds using the Illumina RNA-seq system. Comparisons of transcript expression levels among three stages of dormancy, paradormancy (PD) vs endodormancy (ED), summer buds (SB) vs ED and SB vs PD, resulted in the detection of 8949, 9780 and 3938 differentially expressed transcripts, respectively. Out of approximately 78 million high-quality generated reads, 6096 transcripts were differentially expressed (log2 ratio ≥ 1, FDR ≤ 0.001). Grape reference genome was used for alignment of sequence reads and to measure the expression level of transcripts. Furthermore, findings obtained were then compared using two different databases; Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG), to annotate the transcript descriptions and to assign a pathway to each transcript. KEGG analysis revealed that secondary metabolites biosynthesis and plant hormone signaling was found most enriched out of the 127 total pathways. In the comparisons of the PD vs ED and SB vs ED stages of grape buds, the gibberellin (GA) and abscisic acid (ABA) pathways were found to be the most enriched. The ABA and GA pathways were further analyzed to observe the expression pattern of differentially expressed transcripts. Transcripts related to the PP2C family (ABA pathway) were found to be up-regulated in the PD vs ED comparison and down-regulated in the SB vs ED and SB vs PD comparisons. GID1 family transcripts (GA pathway) were up-regulated while DELLA family transcripts were down-regulated during the three dormancy stages. Differentially expressed transcripts (DEGs) related to redox activity were abundant in the GO biological process category. RT-qPCR assay results for 12 selected transcripts validated the data obtained by RNA-seq. At this stage, taking into account the results obtained so far, it is possible to put forward a hypothesis for the molecular mechanism underlying grape bud dormancy, which may pave the way for ultimate improvements in the grape industry.

/pdf/comparative-rna-seq-based-transcriptomic-analysis-of-bud-2s98rjb4xz.pdf

Comparative RNA-seq based transcriptomic analysis of bud dormancy in grape

Using an RNA sequencing (RNA-seq) approach, we analyzed the differentially expressed genes (DEGs) and physiological behaviors of 'Manicure Finger' grape plantlets grown in vitro under white, blue, green and red light. A total of 670, 1601 and 746 DEGs were identified in plants exposed to blue, green and red light, respectively, compared to the control (white light). By comparing the gene expression patterns with the growth and physiological responses of the grape plantlets, we were able to link the responses of the plants to light of different spectral wavelengths and the expression of particular sets of genes. Exposure to red and green light primarily triggered responses associated with the shade-avoidance syndrome (SAS), such as enhanced elongation of stems, reduced investment in leaf growth and decreased chlorophyll levels accompanied by the expression of genes encoding histone H3, auxin repressed protein, xyloglucan endotransglycosylase/hydrolase, the ELIP protein and microtubule proteins. Furthermore, specific light treatments were associated with the expression of a large number of genes, including those involved in the glucan metabolic pathway and the starch and sucrose metabolic pathways; these genes were up/down-regulated in ways that may explain the increase in the starch, sucrose and total sugar contents in the plants. Moreover, the enhanced root growth and up-regulation of the expression of defense genes accompanied with SAS after exposure to red and green light may be related to the addition of 30 g/L sucrose to the culture medium of plantlets grown in vitro. In contrast, blue light induced the up-regulation of genes related to microtubules, serine carboxypeptidase, chlorophyll synthesis and sugar degradation and the down-regulation of auxin-repressed protein as well as a large number of resistance-related genes that may promote leaf growth, improve chlorophyll synthesis and chloroplast development, increase the ratio of chlorophyll a (chla)/chlorophyll b (chlb), and decrease the ratio of carbohydrates to proteins in plants. Although exposure to red and green light seems to impose “shade stress” on the plantlets, growth under blue light is comparable to growth observed under white or broad-spectrum light.

/pdf/an-rna-seq-analysis-of-grape-plantlets-grown-in-vitro-32bwimejgw.pdf

An RNA-Seq Analysis of Grape Plantlets Grown in vitro Reveals Different Responses to Blue, Green, Red LED Light, and White Fluorescent Light

Additional file 7: Table S7. of Comparative RNA-seq based transcriptomic analysis of bud dormancy in grape

RNA-seq based transcriptomic analysis of CPPU treated grape berries and emission of volatile compounds

To elucidate promoting and inhibiting effects of hydrogen cynamide (HC) and abscisic acid (ABA) on quiescence release of grape buds, physiological and molecular approaches were used to explore the mechanisms of quiescence based on metabolic and gene expression analysis. Physiological and molecular mechanisms involved in bud quiescence of grape were studied before and after application of HC, ABA and ABA-HC. The data showed that ABA inhibited quiescence release in grape buds and attenuated the effect of HC. Bud quiescence was promoted and regulated by HC and ABA pre-treatment on buds of grape cultivar “Shine Muscat” with 5% HC ,100 μM ABA and combination of ABA-HC(5% HC+100 μM ABA) during quiescence under forcing condition. Exogenous application of ABA enhanced the activities of ascorbate peroxidase (APX), peroxidase (POD) and superoxide dismutase (SOD) while activity of catalase (CAT) increased during initial period of forcing and then decreased. The concentration of plant growth hormones including gibberellins (GA) and indole acetic acid (IAA) increased by HC application but decreased the ABA contents under forcing condition. ABA increased the fructose content during quiescence under forcing condition while sucrose and total soluble sugars peaked in HC treated buds as compared to control. Genes related to ABA pathway, protein phosphatase 2C (PP2C family) were down regulated in the buds treated with HC, ABA and ABA-HC as compared to control while two genes related to GA pathway (GID1 family), out of which one gene showed down regulation during initial period of forcing while other gene was up regulated in response to HC and ABA-HC treatments as compared to control. Exogenous ABA application up regulated genes related to antioxidant enzymes as compared to control. The gene probable fructose-bisphosphate aldolase 1, chloroplastic-like, was up regulated in response to ABA treatment as compared to control. Analysis of metabolites and related gene expression pattern would provide a comprehensive view of quiescence after HC, ABA and ABA-HC treatments in grape buds which may helpful for ultimate improvement in table grape production.

/pdf/comparative-study-on-reagents-involved-in-grape-bud-break-17x2u1e09z.pdf

Jianmin Tao

Papers

Comparative RNA-seq based transcriptomic analysis of bud dormancy in grape

An RNA-Seq Analysis of Grape Plantlets Grown in vitro Reveals Different Responses to Blue, Green, Red LED Light, and White Fluorescent Light

Additional file 7: Table S7. of Comparative RNA-seq based transcriptomic analysis of bud dormancy in grape

RNA-seq based transcriptomic analysis of CPPU treated grape berries and emission of volatile compounds

Comparative Study on Reagents Involved in Grape Bud Break and Their Effects on Different Metabolites and Related Gene Expression during Winter.