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.

BackgroundBud 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.ResultsWe 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.ConclusionAt 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-016-0960-8) contains supplementary material, which is available to authorized users.

It is indispensable to comprehend the mechanism that regulates plant responses to drought conditions to intensify the water use efficiency of stone fruits. The physiological, biochemical and molecular responses of drought-treated peach leaves were investigated. Results revealed that drought-treated plants manifested a significant attenuation in water potential as compared to control plants. Furthermore, sorbitol and proline contents were accumulated contrary to glucose, fructose, and sucrose that were dwindled significantly throughout the drought period. Similarly, the activities of antioxidant enzymes and expression pattern of related genes were hoisted to counter the lipid peroxidation in drought-treated plants. Moreover, reduced stomatal conductance has repressed the photosynthesis process and linked genes during drought stress. The expression level of regulatory genes (dehydration-responsive element-bindings and WRKYs) exhibited up-regulation in the drought-treated group. Overall, this study asserts that 'Yoshihime' peach cultivar possesses unique physiological, biochemical, and molecular responses under different spells of drought stress.

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Terpenes and their derivatives are important biomarkers of grape quality as they contribute to the flavor and aroma of grapes. However, the molecular basis of terpene biosynthesis throughout the grapevine phenological developmental cycle remains elusive. Our current study investigates the free and bound terpene biosynthesis of berries at different phenological stages from preveraison to harvest. Detailed gene expression (transcriptomics) analysis, terpenoid volatile production by gas chromatography–mass spectrometry (GC–MS), and in planta transient expression were employed. Our results show that concentrations of most individual terpenes at different stages are distinctive and increase from preveraison to the veraison stage followed by a decrease from veraison to maturity. The combined transcriptomic analysis and terpene profiling revealed that 22 genes belonging to the MEP pathway and multiple classes of transcription factor family members including bHLH and several hormone biosynthesis- or signaling-related genes likely participate in the regulation of terpenoid biosynthesis according to their specific expression patterns in berries. Quantitative real-time polymerase chain expression analysis of 8 key differentially expressed genes in MEP pathways and further 12 randomly selected genes was performed during 8 sampling stages and validated the RNA-seq-derived expression profiles. To further confirm the function of a subset of the differentially expressed genes, we investigated the effects of combined overexpression of 1-deoxy-d-xylulose-5-phosphate synthase (VvDXS1-LOC100249323), 1-deoxy-d-xylulose-5-phosphate reductoisomerase (VvDXR-LOC100248516), and terpene synthase (VvTPS56-LOC100266449) on the production of terpenes by transient overexpression in Nicotiana benthamiana leaves. The overall developmental patterns of total terpenes and gene expression profiles will help guide the functional analyses of further candidate genes important for terpene biosynthesis of grape as well as identifying the master transcriptional and hormonal regulators of this pathway in the future.