RNA sequencing reveals high resolution expression change of major plant hormone pathway genes after young seedless grape berries treated with gibberellin

Non-climacteric fruit development and ripening regulation: 'the phytohormones show'

Fruit ripening involves numerous physiological, structural, and metabolic changes that result in the formation of edible fruits. This process is controlled at different molecular levels, with essential roles for phytohormones, transcription factors, and epigenetic modifications. Fleshy fruits are classified as either climacteric or non-climacteric species. Climacteric fruits are characterized by a burst in respiration and ethylene production at the onset of ripening, while regulation of non-climacteric fruit ripening has been commonly attributed to abscisic acid (ABA). However, there is controversy as to whether mechanisms regulating fruit ripening are shared between non-climacteric species, and to what extent other hormones contribute alongside ABA. In this review, we summarize classic and recent studies on the accumulation profile and role of ABA and other important hormones in the regulation of non-climacteric fruit development and ripening, as well as their crosstalk, paying special attention to the two main non-climacteric plant models, strawberry and grape. We highlight both the common and different roles of these regulators in these two crops, and discuss the importance of the transcriptional and environmental regulation of fruit ripening, as well as the need to optimize genetic transformation methodologies to facilitate gene functional analyses.

Interaction of VvDELLA2 and VvCEB1 Mediates Expression of Expansion-Related Gene during GA-Induced Enlargement of Grape Fruit

Exogenous gibberellin treatment can promote early growth of grape fruit, but the underlying regulatory mechanisms are not well understood. Here, we show that VvDELLA2 directly regulates the activity of the VvCEB1 transcription factor, a key regulator in the control of cell expansion in grape fruit. Our results show that VvCEB1 binds directly to the promoters of cell expansion-related genes in grape fruit and acts as a transcriptional activator, while VvDELLA2 blocks VvCEB1 function by binding to its activating structural domain. The exogenous gibberellin treatment relieved this inhibition by promoting the degradation of VvDELLA2 protein, thus, allowing VvCEB1 to transcriptionally activate the expression of cell expansion-related genes. In conclusion, we conclude that exogenous GA3 treatment regulates early fruit expansion by affecting the VvDELLA-VvCEB1 interaction in grape fruit development.

Regulatory of miRNAs in tri-lineage differentiation of C3H10T1/2

MicroRNAs (miRNAs) are non-coding single-stranded RNA molecules encoded by endogenous genes, which play a vital role in cell generation, metabolism, apoptosis and stem cell differentiation. C3H10T1/2, a mesenchymal cell extracted from mouse embryos, is capable of osteogenic differentiation, adipogenic differentiation and chondrogenic differentiation. Extensive studies have shown that not only miRNAs can directly trigger targeted genes to regulate the tri-lineage differentiation of C3H10T1/2, but it also can indirectly regulate the differentiation by triggering different signaling pathways or various downstream molecules. This paper aims to clarify the regulatory roles of different miRNAs on C3H10T1/2 differentiation, and discussing their balance effect among osteogenic differentiation, adipogenic differentiation and chondrogenic differentiation of C3H10T1/2. We also review the biogenesis of miRNAs, Wnt signaling pathways, MAPK signaling pathways and BMP signaling pathways and provide some specific examples of how these signaling pathways act on C3H10T1/2 tri-lineage differentiation. On this basis, we hope that a deeper understanding of the differentiation and regulation mechanism of miRNAs in C3H10T1/2 can provide a promising therapeutic method for the clinical treatment of bone defects, osteoporosis, osteoarthritis and other diseases.

Genome-Wide Analysis of Anthocyanin Biosynthesis Regulatory WD40 Gene FcTTG1 and Related Family in Ficus carica L

WD40 proteins serve as crucial regulators in a broad spectrum of plant developmental and physiological processes, including anthocyanin biosynthesis. However, in fig (Ficus carica L.), neither the WD40 family nor any member involved in anthocyanin biosynthesis has been elucidated. In the present study, 204 WD40 genes were identified from the fig genome and phylogenetically classified into 5 clusters and 12 subfamilies. Bioinformatics analysis prediction localized 109, 69, and 26 FcWD40 proteins to the cytoplasm, nucleus and other cellular compartments, respectively. RNA-seq data mining revealed 127 FcWD40s expressed at FPKM > 10 in fig fruit. Most of these genes demonstrated higher expression in the early stages of fruit development. FcWD40-97 was recruited according to three criteria: high expression in fig fruit, predicted nuclear localization, and closest clustering with TTG1s identified in other plants. FcWD40-97, encoding 339 amino acids including 5 WD-repeat motifs, showed 88.01 and 87.94% amino acid sequence similarity to apple and peach TTG1, respectively. The gene is located on fig chromosome 4, and is composed of 1 intron and 2 exons. Promoter analysis revealed multiple light-responsive elements, one salicylic acid-responsive element, three methyl jasmonate-responsive elements, and one MYB-binding site involved in flavonoid biosynthesis gene regulation. FcWD40-97 was in the FPKM > 100 expression level group in fig fruit, and higher expression was consistently found in the peel compared to the flesh at the same development stages. Expression level did not change significantly under light deprivation, whereas in leaves and roots, its expression was relatively low. Transient expression verified FcWD40-97's localization to the nucleus. Yeast two-hybrid (Y2H) and biomolecular fluorescence complementation (BiFC) assays revealed that FcWD40-97 interacts with FcMYB114, FcMYB123, and FcbHLH42 proteins in vitro and in vivo, showing that FcWD40-97 functions as a member of the MYB-bHLH-WD40 (MBW) complex in anthocyanin-biosynthesis regulation in fig. We therefore renamed FcWD40-97 as FcTTG1. Our results provide the first systematic analysis of the FcWD40 family and identification of FcTTG1 in fig pigmentation.

Transcriptome and proteome analysis of ultrasound pretreated peanut sprouts

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It was first time to combined transcriptomic and proteome analyses to investigate the ultrasound pretreated peanut sprouts.

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A total of 1104 DEGs and 399 DEPs between ultrasound pretreated and nontreated peanut sprouts.

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Ultrasound upregulated three key genes that could have increased the content of resveratrol via phenylpropanoid biosynthesis.

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The genes and proteins related to phenylpropanoid biosynthesis, flavonoids biosynthesis, and lipid metabolism.

Combined transcriptomic and proteome analyses were carried out to investigate the influence of ultrasound pretreatment on peanut sprouts. In total, 1104 differentially expressed genes (upregulated:538, downregulated:521) and 399 differentially accumulated proteins (upregulated: 197, downregulated: 202) were identified between ultrasound pretreated and nontreated peanut sprouts. These genes and proteins were related to a series of crucial biomolecular processes, including the metabolism of carbohydrates, terpenoids, and polyketides. The most enriched pathways were further analyzed in each category. Importantly, ultrasound upregulated three key genes namely the arahy. Tifrunner. gnm1.ann1.DXZI51, arahy.Tifrunner.gnm1.ann1.VGN2GE, and arahy.Tifrunner.gnm1.ann1.Y23DM6 that could have increased the content of resveratrol via phenylpropanoid biosynthesis. Furthermore, this study shows that B3, MYB transcription factor-like families play a significant role in response to ultrasound treatment. Overall, this study provides useful transcriptomics and proteomics information highlighting the molecular mechanisms that influence nutritional differences in peanut sprouts.

Comparative Transcriptome and Proteome Analysis Provides New Insights Into the Mechanism of Protein Synthesis in Kenaf (Hibiscus cannabinus L.) Leaves

Given the rising domestic demand and increasing global prices of corn and soybean, China is looking for alternatives for these imports to produce animal fodder. Kenaf (Hibiscus cannabinus L.) has great potential as a new forage source, due to abundant proteins, phenols and flavonoids in its leaves. However, few studies have evaluated the mechanism of protein synthesis in kenaf leaves. In the current work, compared with kenaf material "L332," the percentage of crude protein content in leaves of material "Q303" increased by 6.13%; combined with transcriptome and proteome data, the kenaf samples were systematically studied to obtain mRNA-protein correlation. Then, the genes/proteins related to protein synthesis in the kenaf leaves were obtained. Moreover, this work detected mRNA expression of 20 differentially expressed genes (DEGs). Meanwhile, 20 differentially expressed proteins (DEPs) related to protein synthesis were performed parallel reaction monitoring. Fructose-1,6-bisphosphatase (FBP), nitrite reductase (NirA), prolyl tRNA synthase (PARS) and glycine dehydrogenase (GLDC) presented increased mRNA and protein levels within kenaf leaves with high protein content. Based on the obtained findings, FBP, NirA, PARS, and GLDC genes may exert a vital function in the protein synthesis of kenaf leaves. The results provide a new idea for further studying the potential genes affecting the quality trait of protein content in kenaf leaves and provide gene resources and a theoretical foundation for further cultivating high protein kenaf varieties.

Transcriptome Profiles of Leaves and Roots of Goldenrain Tree (Koelreuteria paniculata Laxm.) in Response to Cadmium Stress

Cadmium (Cd) pollution is a widespread environmental problem. In this study, we explored the transcriptome and biochemical responses of goldenrain tree (Koelreuteria paniculata Laxm.) leaves and roots to Cd stress. Leaf and root growth decreased substantially under Cd stress (50 mg/L CdCl2), but leaf and root antioxidant mechanisms were significantly activated. In RNA-seq analysis, roots treated with 25 mg/L CdCl2 featured enriched GO terms in cellular components related to intracellular ribonucleoprotein complex, ribonucleoprotein complex, and macromolecular complex. In leaves under Cd stress, most differentially expressed genes were enriched in the cellular component terms intrinsic component of membrane and membrane part. Weighted gene co-expression network analysis and analysis of module-trait relations revealed candidate genes associated with superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) activities and malondialdehyde (MDA). Ten transcription factors responded to Cd stress expression, including those in C2H2, MYB, WRKY, and bZIP families. Transcriptomic analysis of goldenrain tree revealed that Cd stress rapidly induced the intracellular ribonucleoprotein complex in the roots and the intrinsic component of membrane in the leaves. The results also indicate directions for further analyses of molecular mechanisms of Cd tolerance and accumulation in goldenrain tree.

RNAseq reveals different transcriptomic responses to GA3 in early and midseason varieties before ripening initiation in sweet cherry fruits

Gibberellin (GA) negatively affects color evolution and other ripening-related processes in non-climacteric fruits. The bioactive GA, gibberellic acid (GA₃), is commonly applied at the light green-to-straw yellow transition to increase firmness and delay ripening in sweet cherry (Prunus avium L.), though causing different effects depending on the variety. Recently, we reported that GA₃ delayed the IAD parameter (a ripening index) in a mid-season variety, whereas GA₃ did not delay IAD but reduced it at ripeness in an early-season variety. To further explore this contrasting behavior between varieties, we analyzed the transcriptomic responses to GA₃ applied on two sweet cherry varieties with different maturity time phenotypes. At harvest, GA₃ produced fruits with less color in both varieties. Similar to our previous report, GA₃ delayed fruit color initiation and IAD only in the mid-season variety and reduced IAD at harvest only in the early-season variety. RNA-seq analysis of control- and GA₃-treated fruits revealed that ripening-related categories were overrepresented in the early-season variety, including 'photosynthesis' and 'auxin response'. GA₃ also changed the expression of carotenoid and abscisic acid (ABA) biosynthetic genes in this variety. In contrast, overrepresented categories in the mid-season variety were mainly related to metabolic processes. In this variety, some PP2Cs putative genes were positively regulated by GA₃, which are negative regulators of ABA responses, and MYB44-like genes (putative repressors of PP2Cs expression) were downregulated. These results show that GA₃ differentially modulates the transcriptome at the onset of ripening in a variety-dependent manner and suggest that GA₃ impairs ripening through the modification of ripening associated gene expression only in the early-season variety; whereas in the mid-season variety, control of the ripening timing may occur through the PP2C gene expression regulation. This work contributes to the understanding of the role of GA in non-climacteric fruit ripening.

Liquid Chromatographic Quadrupole Time-of-Flight Mass Spectrometric Untargeted Profiling of (Poly)phenolic Compounds in Rubus idaeus L. and Rubus occidentalis L. Fruits and Their Comparative Evaluation

This study provided a detailed profiling of the antioxidant and bioactive compounds occurring in three varieties of Rubus idaeus L. fruits (“Fall Gold”, “Glen Ample” and “Tulameen”) compared to Rubus occidentalis L. black raspberry (“Jewel” cultivar), adopting a comprehensive untargeted metabolomics approach developed with UHPLC analysis coupled with quadrupole/time-of-flight high resolution mass spectrometry, using the SWATH^® acquisition protocol. The feature selection and annotation workflow, applied to the analysis of raspberry extracts in both polarities, allowed identifying 68 bioactive compounds mainly belonging to the classes of (poly)phenolic compounds. Interestingly, some of these identifications (e.g., ferulic acid glycosides and the ellagitannin-like nobotanin/malabathrin) represent the first report in raspberry fruits. Principal component analysis made possible highlighting the features more related to the expression of a genotype effect within the R. idaeus species or between the two raspberry species herein investigated. Overall, flavanols were the most discriminating features for the Fall Gold variety, whereas ellagitannins and flavonol glycosides represent more distinctive metabolic traits in Glen Ample and Tulameen fruits. Moreover, R. occidentalis Jewel variety was strongly characterized by the occurrence of anthocyanins, such as cyanidin, pelargonidin and delphinidin glycosides.

Ethephon induces coordinated ripening acceleration and divergent coloration responses in fig (Ficus carica L.) flowers and receptacles

The regulatory landscape of ethephon-accelerated fig ripening is revealed; flowers and receptacles exhibit opposite responses in anthocyanin accumulation; PG, PL and EXP are suggested key genes in fig softening. Ethephon is used to accelerate fig-fruit ripening for improvement of harvesting efficiency, but the underlying molecular mechanism is still unclear. To elucidate the detailed biological mechanism of ethylene-accelerated fig ripening, fruit in phase II (the lag phase on the double sigmoid growth curve) were treated with ethephon, and reached commercial ripeness 6 days earlier than the nontreated controls. Transcriptomes of flowers and the surrounding receptacles-which together make up the pseudocarp in fig fruit-were analyzed. There were 5189, 5818 and 2563 differentially expressed genes (DEGs) 2, 4 and 6 days after treatment (DAT) in treated compared to control fruit, screened by p-adjust < 0.05 and |log2(fold change) |≥ 2. The DEGs were significantly enriched in plant hormone metabolism and signal transduction, cell-wall modification, sugar accumulation and anthocyanin accumulation pathways. DEGs in the first three pathway categories demonstrated an overall similar expression change in flowers and receptacles, whereas DEGs in anthocyanin pigmentation revealed divergent transcript abundance. Specifically, in both flowers and receptacles, ethephon significantly upregulated 1-aminocyclopropane-1-carboxylate oxidase and downregulated most of the ethylene-response factor genes; polygalacturonase, pectate lyase and expansin were mainly upregulated; two acid beta-fructofuranosidases were upregulated. However, structural genes in the anthocyanin-synthesis pathway were mainly downregulated in female flowers 2 and 4 DAT, whereas they were upregulated in the receptacles. Our study reveals the regulatory landscape of the two tissues of fig fruit in ethylene-induced ripening; the differentially expressed pathways and genes provide valuable resources for the mining of target genes for crucial biological and commercial trait improvement.

Papain-Like Cysteine Protease Gene Family in Fig (Ficus carica L.): Genome-Wide Analysis and Expression Patterns

The papain-like cysteine proteases (PLCPs) are the most abundant family of cysteine proteases in plants, with essential roles in biotic/abiotic stress responses, growth and senescence. Papain, bromelain and ficin are widely used in food, medicine and other industries. In this study, 31 PLCP genes (FcPCLPs) were identified in the fig (Ficus carica L.) genome by HMM search and manual screening, and assigned to one of nine subfamilies based on gene structure and conserved motifs. SAG12 and RD21 were the largest subfamilies with 10 and 7 members, respectively. The FcPCLPs ranged from 1,128 to 5,075 bp in length, containing 1-10 introns, and the coding sequence ranged from 624 to 1,518 bp, encoding 207-505 amino acids. Subcellular localization analysis indicated that 24, 2, and 5 PLCP proteins were targeted to the lysosome/vacuole, cytoplasm and extracellular matrix, respectively. Promoter (2,000 bp upstream) analysis of FcPLCPs revealed a high number of plant hormone and low temperature response elements. RNA-seq revealed differential expression of 17 FcPLCPs in the inflorescence and receptacle, and RD21 subfamily members were the major PLCPs expressed in the fruit; 16 and 5 FcPLCPs responded significantly to ethylene and light, respectively. Proteome analyses revealed 18 and 5 PLCPs in the fruit cell soluble proteome and fruit latex, respectively. Ficins were the major PLCP in fig fruit, with decreased abundance in inflorescences, but increased abundance in receptacles of commercial-ripe fruit. FcRD21B/C and FcALP1 were aligned as the genes encoding the main ficin isoforms. Our study provides valuable multi-omics information on the FcPLCP family and lays the foundation for further functional studies.

Genome-wide identification and characterization of gibberellin metabolic and signal transduction (GA MST) pathway mediating seed and berry development (SBD) in grape (Vitis vinifera L.)

BACKGROUND

Grape is highly sensitive to gibberellin (GA), which is crucial during seed and berry development (SBD) either by itself or by interacting with other hormones, such as auxin, Abscisic acid (ABA), and Cytokinin (CK). However, no systematic analysis of GA metabolic and signal transduction (MST) pathway has been undertaken in grapevine.

RESULTS

In this study, total endogenous GA3 content significantly decreased during SBD, and a total of 48 known genes in GA metabolic (GAM; 31) and signal transduction (ST; 17) pathways were identified in this process. In the GAM pathway, out of 31 genes, VvGA20ox1-1, VvGA3ox4-1, and VvGA2ox1-1 may be the major factors interacting at the green-berry stage (GBS) accompanied with higher accumulation rate. GA biosynthesis was greater than GA inactivation at GBS, confirming the importance of seeds in GA synthesis. The visible correlation between endogenous GA3 content and gene expression profiles suggested that the transcriptional regulation of GA biosynthesis pathway genes was a key mechanism of GA accumulation at the stone-hardening stage (SHS). Interestingly, we observed a negative feedback regulation between VvGA3oxs-VvGAI1-4, VvGA2oxs-VvGAI1-4, and VvGID1B-VvGAI1-4 in maintaining the balance of GA3 content in berries. Moreover, 11 miRNAs may be involved in the modulation of GA MST pathway by mediating their target genes, such as VvGA3ox, VvGID1B, and VvGAMYB. Many genes in auxin, ABA, and CK MST pathways were further identified and found to have a special pattern in the berry, and the crosstalk between GA and these hormones may modulate the complex process during SBD through the interaction gene network of the multihormone pathway. Lastly, based on the expression characterization of multihormone MST pathway genes, a proposed model of the GA-mediated multihormone regulatory network during SBD was proposed.

CONCLUSIONS

Our results provided novel insights into GA-mediated regulatory networks during SBD in grape. The complexity of GA-mediated multihormone ST in SBD was also elucidated, thereby providing valuable information for future functional characterizations of specific genes in grape.

Transcriptomic study of pedicels from GA3-treated table grape genotypes with different susceptibility to berry drop reveals responses elicited in cell wall yield, primary growth and phenylpropanoids synthesis

BACKGROUND

Gibberellins (GA₃) are the most sprayed growth regulator for table grape production worldwide, increasing berry size of seedless varieties through pericarp cell expansion. However, these treatments also exacerbate berry drop, which has a detrimental effect on the postharvest quality of commercialized clusters. Several studies have suggested that pedicel stiffening caused by GA₃ would have a role in this disorder. Nevertheless, transcriptional and phenotypic information regarding pedicel responses to GA₃ is minimal.

RESULTS

Characterization of responses to GA₃ treatments using the lines L23 and Thompson Seedless showed that the former was up to six times more susceptible to berry drop than the latter. GA₃ also increased the diameter and dry matter percentage of the pedicel on both genotypes. Induction of lignin biosynthesis-related genes by GA₃ has been reported, so the quantity of this polymer was measured. The acetyl bromide method detected a decreased concentration of lignin 7 days after GA₃ treatment, due to a higher cell wall yield of the isolated fractions of GA₃-treated pedicel samples which caused a dilution effect. Thus, an initial enrichment of primary cell wall components in response to GA₃ was suggested, particularly in the L23 background. A transcriptomic profiling was performed to identify which genes were associated with these phenotypic changes. This analysis identified 1281 and 1787 genes differentially upregulated by GA₃ in L23 and cv. Thompson Seedless, respectively. Concomitantly, 1202 and 1317 downregulated genes were detected in L23 and cv. Thompson Seedless (FDR < 0.05). Gene ontology analysis of upregulated genes showed enrichment in pathways including phenylpropanoids, cell wall metabolism, xylem development, photosynthesis and the cell cycle at 7 days post GA₃ application. Twelve genes were characterized by qPCR and striking differences were observed between genotypes, mainly in genes related to cell wall synthesis.

CONCLUSIONS

High levels of berry drop are related to an early strong response of primary cell wall synthesis in the pedicel promoted by GA₃ treatment. Genetic backgrounds can produce similar phenotypic responses to GA₃, although there is considerable variation in the regulation of genes in terms of which are expressed, and the extent of transcript levels achieved within the same time frame.

The Molecular Regulation of Carbon Sink Strength in Grapevine (Vitis vinifera L.)

Sink organs, the net receivers of resources from source tissues, provide food and energy for humans. Crops yield and quality are improved by increased sink strength and source activity, which are affected by many factors, including sugars and hormones. With the growing global population, it is necessary to increase photosynthesis into crop biomass and yield on a per plant basis by enhancing sink strength. Sugar translocation and accumulation are the major determinants of sink strength, so understanding molecular mechanisms and sugar allocation regulation are conducive to develop biotechnology to enhance sink strength. Grapevine (Vitis vinifera L.) is an excellent model to study the sink strength mechanism and regulation for perennial fruit crops, which export sucrose from leaves and accumulates high concentrations of hexoses in the vacuoles of fruit mesocarp cells. Here recent advances of this topic in grape are updated and discussed, including the molecular biology of sink strength, including sugar transportation and accumulation, the genes involved in sugar mobilization and their regulation of sugar and other regulators, and the effects of hormones on sink size and sink activity. Finally, a molecular basis model of the regulation of sugar accumulation in the grape is proposed.

Identification and characterization of cherry (Cerasus pseudocerasus G. Don) genes responding to parthenocarpy induced by GA3 through transcriptome analysis

Background

Fruit set after successful pollination is key for the production of sweet cherries, and a low fruit-setting rate is the main problem in production of this crop. As gibberellin treatment can directly induce parthenogenesis and satisfy the hormone requirement during fruit growth and development, such treatment is an important strategy for improving the fruit-setting rate of sweet cherries. Previous studies have mainly focused on physiological aspects, such as fruit quality, fruit size, and anatomical structure, whereas the molecular mechanism remains clear.

Results

In this study, we analyzed the transcriptome of ‘Meizao’ sweet cherry fruit treated with gibberellin during the anthesis and hard-core periods to identify genes associated with parthenocarpic fruit set. A total of 25,341 genes were identified at the anthesis and hard-core stages, 765 (681 upregulated, 84 downregulated) and 186 (141 upregulated, 45 downregulated) of which were significant differentially expressed genes (DEGs) at the anthesis and the hard-core stages after gibberellin 3 (GA3) treatment, respectively. Based on DEGs between the control and GA3 treatments, the GA3 response mainly involves parthenocarpic fruit set and cell division. Exogenous gibberellin stimulated sweet cherry fruit parthenocarpy and enlargement, as verified by qRT-PCR results of related genes as well as the parthenocarpic fruit set and fruit size. Based on our research and previous studies in Arabidopsis thaliana, we identified key genes associated with parthenocarpic fruit set and cell division. Interestingly, we observed patterns among sweet cherry fruit setting-related DEGs, especially those associated with hormone balance, cytoskeleton formation and cell wall modification.

Conclusions

Overall, the result provides a possible molecular mechanism regulating parthenocarpic fruit set that will be important for basic research and industrial development of sweet cherries.

Electronic supplementary material

The online version of this article (10.1186/s12863-019-0746-8) contains supplementary material, which is available to authorized users.

Maize transcriptomic repertoires respond to gibberellin stimulation

Phytohormone gibberellin (GA) serves as hub modulator of diverse biological events. Understanding the transcriptomic features of GA-mediated processes has scientific significance. The transcriptomic landscapes of cereal crops upon GA stimulation remains largely unknown. Herein, to reveal the transcriptomic changes in cereal crop maize under GA treatment, we first selected normal height and GA-sensitive maize dwarf plants from advanced backcross population for GA treatment. RNA-seq analysis discovered multiple protein-coding transcripts that were differentially expressed in GA-treated samples compared to distilled water-treated ones. Some differentially expressed transcripts, namely GA-responsive transcripts in this study, encoded the components of GA pathway, including CPS, KS, and KO enzymes for GA biosynthesis, GA2ox enzymes for GA degradation, DELLA repressors and GID1 receptor for GA signaling. A total of 214 shared GA-responsive transcripts were identified both in GA₃-treated normal height and GA-sensitive dwarf samples. Shared GA-responsive transcripts were involved in GA signaling, auxin biosynthesis, ethylene response, the composition and structure of cell wall, chlorophyll biogenesis, and sugar homeostasis. In addition, the convergence and divergence in expression of shared GA-responsive transcripts were observed in GA₃-treated normal height and GA-sensitive dwarf plants. Interaction network modeling indicated that some shared GA-responsive transcripts tended to be co-regulated, which increases the complexity of GA-triggered regulation at transcriptomic layer. Results presented here will extend our knowledge of GA-mediated regulatory cascade, and enhance our ability to apply hormone GA knowledge in agricultural practice.

Gibberellin causes wide transcriptional modifications in the early stage of grape cluster development

Yaghooti grape of Sistan is seedless, early ripening but has compact clusters. To study gibberellin effect on cluster compactness of Yaghooti grape, it has been studied transcriptomic changes in three developmental stages (cluster formation, berry formation and final size of cluster). We found out that 5409 of 22,756 genes in cluster tissue showed significant changes under gibberellin. Finally, it was showed that 2855, 2862 and 497 genes have critically important role on above developmental stages, respectively. GO enrichment analysis showed that gibberellin enhances biochemical pathways activity. Moreover, genes involved in ribosomal structure and photosynthesis rate in cluster tissue were up- and down- regulated, respectively. In addition, we observed location of metabolomic activities was transferred from nucleus to cytoplasm and from cytoplasm to cell wall and intercellular spaces during cluster development; but there is not such situation in gibberellin treated samples.

Differential color development and response to light deprivation of fig (Ficus carica L.) syconia peel and female flower tissues: transcriptome elucidation

BACKGROUND

Color directly affects fruit quality and consumer preference. In fig syconia, the female flower tissue is contained in a receptacle. Anthocyanin pigmentation of this tissue and the peel differs temporally and spatially. A transcriptome study was carried out to elucidate key genes and transcription factors regulating differences in fig coloring.

RESULTS

Anthocyanins in the female flower tissue were identified mainly as pelargonidin-3-glucoside and cyanidin-3-rutinoside; in the peel, the major anthocyanins were cyanidin 3-O-glucoside and cyanidin-3-rutinoside. Anthocyanin content was significantly higher in the female flower tissue vs. peel before fig ripening, whereas at ripening, the anthocyanin content in the peel was 5.39 times higher than that in the female flower tissue. Light-deprivation treatment strongly inhibited peel, but not female flower tissue, anthocyanin pigmentation. RNA-Seq revealed 522 differentially expressed genes (recruited with criteria log₂ ≥ 2 and P < 0.05) at fig ripening, with 50 upregulated and 472 downregulated genes in the female flower tissue. Light deprivation upregulated 1180 and downregulated 856 genes in the peel, and upregulated 909 and downregulated 817 genes in the female flower tissue. KEGG enrichment revealed significantly changed expression in the phenylpropanoid-biosynthesis and flavonoid-biosynthesis pathways in the peel, but not in the female flower tissue, with significant repression of FcCHS, FcCHI, FcF3H, FcF3'H, FcDFR and FcUFGT transcripts. Light deprivation led to differential expression of 71 and 80 transcription factor genes in the peel and female flower tissue, respectively. Yeast one-hybrid screen revealed that FcHY5 and FcMYB114 bind the promoter regions of FcCHS and FcDFR, respectively in the flavonoid-biosynthesis pathway.

CONCLUSIONS

Phenylpropanoid- and flavonoid-biosynthesis pathways were differentially expressed spatially and temporally in the peel and female flower tissue of fig syconia; pathway expression in the peel was strongly regulated by light signal. Differentially expressed transcription factors were recruited as candidates to screen important expression regulators in the light-dependent and light-independent anthocyanin-synthesis pathway. Our study lays the groundwork for further elucidation of crucial players in fig pigmentation.

Comparative transcript profiling reveals the mechanism of female sterility associated with seedless Ponkan mandarin (Citrus reticulata Blanco)

Seedlessness is a highly desirable trait in citrus varieties. Sterility is the key determination for seedlessness formation. However, the molecular basis for female sterility in seedless mandarin remains unclear. Thus, a seedless Ponkan mandarin (Citrus reticulata Blanco 'Lipeng No.2'), considered the bud mutation of normal seedy Ponkan, was collected to identify candidate genes involved in seedless variation. Suppression subtractive hybridization (SSH) screened 1091 uniESTs related to seedy and seedless Ponkan (727 singlets and 364 contigs), which mainly governed catalytic activity, transferase activity, and oxygen binding. By using RNA-Seq technology, 106 differentially expressed genes (DEGs) were captured, of which 74 were up-regulated and 32 were down-regulated. Gene Ontology and pathway analysis showed that six DEGs were enriched in the biosynthesis of secondary metabolite, whereas five DEGs were enriched in the signaling of plant hormones. The combined results of SSH and RNA-Seq indicated the importance of amino acid metabolism in seedless Ponkan. Our findings revealed that the mechanism of seedless Ponkan generation may be related to gene regulation, signal cascade, and hormone levels. This study provided a solid foundation for functional gene identification in seedless Ponkan and a good reference for relevant research on molecular mechanisms of female sterility in Ponkan mandarin.

Transcriptome analysis unravels spatiotemporal modulation of phytohormone-pathway expression underlying gibberellin-induced parthenocarpic fruit set in San Pedro-type fig (Ficus carica L.)

BACKGROUND

Gibberellin (GA) treatments can induce parthenocarpy in the main crop of San Pedro-type figs, the native non-parthenocarpic fruit, however, the underlying mechanism is still largely unclear.

RESULTS

In our study, GA3 was applied to San Pedro-type fig main crop at anthesis. Sharply increased GA3 content was detected in both female flowers and receptacle, along with significantly decreased indole-3-acetic acid (IAA), zeatin and abscisic acid (ABA) levels in female flowers, and increased zeatin peak intensity and earlier ABA peak in receptacles. Transcriptome comparison between control and treatment groups identified more differentially expressed genes (DEGs) in receptacles than in female flowers 2 and 4 days after treatment (DAT); 10 DAT, the number of DEGs became similar in the two tissues. Synchronized changing trends of phytohormone-associated DEGs were observed in female flowers and receptacles with fruit development. Modulation of ethylene and GA signaling and auxin metabolism by exogenous GA3 occurred mainly 2 DAT, whereas changes in auxin, cytokinin and ABA signaling occurred mainly 10 DAT. Auxin-, ethylene- and ABA-metabolism and response pathways were largely regulated in the two tissues, mostly 2 and 10 DAT. The major components altering fig phytohormone metabolic and response patterns included downregulated GA2ox, BAS1, NCED and ACO, and upregulated ABA 8'-h and AUX/IAA.

CONCLUSIONS

Thus GA-induced parthenocarpy in fig is co-modulated by the female flowers and receptacle, and repression of ABA and ethylene biosynthesis and GA catabolism might be the main forces deflecting abscission and producing fig parthenocarpy.

Unraveling the transcriptional complexity of compactness in sistan grape cluster

Yaghooti grape of Sistan is the earliest ripening grape in Iran, harvested every May annually. It is adapted to dry conditions in Sistan region and its water requirement is less than the other grape cultivars. The transcriptional complexity of this grape was studied in three stages of cluster development. Totally, 24121 genes were expressed in different cluster development steps (step 1: cluster formation, step 2: berry formation, step 3: final size of cluster) of which 3040 genes in the first stage, 2381 genes in the second stage and 2400 genes in the third stage showed a significant increase in expression. GO analysis showed that when the clusters are ripening, the activity of the nucleus, cytoplasmic, cytosol, membrane and chloroplast genes in the cluster architecture cells decreases. In contrast, the activity of the endoplasmic reticulum, vacuole and extracellular region genes enhances. When Yaghooti grape is growing and developing, some of metabolic pathways were activated in the response to biotic and abiotic stresses. Gene co-expression network reconstruction showed that AGAMOUS is a key gene in compactness of Sistan grape cluster, because it influences on expression of GA gene which leads to increase cluster length and berries size.

GA3 application in grapes (Vitis vinifera L.) modulates different sets of genes at cluster emergence, full bloom, and berry stage as revealed by RNA sequence-based transcriptome analysis

In grapes (Vitis vinifera L.), exogenous gibberellic acid (GA₃) is applied at different stages of bunch development to achieve desirable bunch shape and berry size in seedless grapes used for table purpose. RNA sequence-based transcriptome analysis was used to understand the mechanism of GA₃ action at cluster emergence, full bloom, and berry stage in table grape variety Thompson Seedless. At cluster emergence, rachis samples were collected at 6 and 24 h after application of GA₃, whereas flower clusters and berry samples were collected at 6, 24, and 48 h after application at full bloom and 3-4 mm berry stages. Seven hundred thirty-three genes were differentially expressed in GA₃-treated samples. At rachis and flower cluster stage respectively, 126 and 264 genes were found to be significantly differentially expressed within 6 h of GA₃ application. The number of DEG reduced considerably at 24 h. However, at berry stage, major changes occurred even at 24 h and a number of DEGs at 6 and 24 h were 174 and 191, respectively. As compared to upregulated genes, larger numbers of genes were downregulated. Stage-specific response to the GA₃ application was observed as evident from the unique set of DEGs at each stage and only a few common genes among three stages. Among the DEGs, 67 were transcription factors. Functional categorization and enrichment analysis revealed that several transcripts involved in sucrose and hexose metabolism, hormone and secondary metabolism, and abiotic and biotic stimuli were enriched in response to application of GA₃. A high correlation was recorded for real-time PCR and transcriptome data for selected DEGs, thus indicating the robustness of transcriptome data obtained in this study for understanding the GA₃ response at different stages of berry development in grape. Chromosomal localization of DEGs and identification of polymorphic microsatellite markers in selected genes have potential for their use in breeding for varieties with improved bunch architecture.

Developmental, chemical and transcriptional characteristics of artificially pollinated and hormone-induced parthenocarpic fruits of Siraitia grosvenorii

Unpollinated ovaries of Siraitia grosvenorii grew parthenocarpically in response to the application of GA₃ and CPPU.

Regulation of Fig (Ficus carica L.) Fruit Color: Metabolomic and Transcriptomic Analyses of the Flavonoid Biosynthetic Pathway

Combined metabolomic and transcriptomic analyses were carried out with fig cultivar Green Peel and its color mutant "Purple Peel." Five and twenty-two metabolites were identified as having significantly different contents between fruit peels of the two cultivars at young and mature stages, respectively. Cyanidin O-malonylhexoside demonstrated a 3,992-fold increase in the mature purple peel, the first identification of a major cyanidin in fig fruit; cyanidin 3-O-glucoside, cyanidin O-malonylhexoside O-hexoside and cyanidin-3,5-O-diglucoside were upregulated 100-fold, revealing the anthocyanins underlying the purple mutation. Beyond the visible differences, there was very significant accumulation of the colorless flavonoids procyanidin B1, luteolin-3',7-di-O-glucoside, epicatechin and quercetin-3-O-rhamnoside in the mature "Purple Peel" compared to "Green Peel." At the young stage, only cyanidin O-malonylhexoside, cyanidin O-malonylhexoside O-hexoside and esculetin were upregulated a few fold in the mutant. Transcriptome analysis revealed a downregulated expression trend of genes encoding phenylpropanoid and flavonoid biosynthetic pathway enzyme in the young "Purple Peel" compared to the young "Green Peel," whereas significant and simultaneous upregulation was revealed in almost all of the flavonoid and anthocyanin pathway components and relevant transcription factors in the mature-stage mutant. The role of R2R3-MYB transcription factors in the color morph mutation and its possible relation to the activity of retrotransposons are discussed. Moreover, large-scale upregulation of small heat-shock protein genes was found in the mature mutant. This is the first work to reveal comprehensive metabolome and transcriptome network changes underlying a fig mutation in a single horticultural attribute, and its profound effects on fruit nutrition and quality.

Omics Approaches for Understanding Grapevine Berry Development: Regulatory Networks Associated with Endogenous Processes and Environmental Responses

Grapevine fruit development is a dynamic process that can be divided into three stages: formation (I), lag (II), and ripening (III), in which physiological and biochemical changes occur, leading to cell differentiation and accumulation of different solutes. These stages can be positively or negatively affected by multiple environmental factors. During the last decade, efforts have been made to understand berry development from a global perspective. Special attention has been paid to transcriptional and metabolic networks associated with the control of grape berry development, and how external factors affect the ripening process. In this review, we focus on the integration of global approaches, including proteomics, metabolomics, and especially transcriptomics, to understand grape berry development. Several aspects will be considered, including seed development and the production of seedless fruits; veraison, at which anthocyanin accumulation begins in the berry skin of colored varieties; and hormonal regulation of berry development and signaling throughout ripening, focusing on the transcriptional regulation of hormone receptors, protein kinases, and genes related to secondary messenger sensing. Finally, berry responses to different environmental factors, including abiotic (temperature, water-related stress and UV-B radiation) and biotic (fungi and viruses) stresses, and how they can significantly modify both, development and composition of vine fruit, will be discussed. Until now, advances have been made due to the application of Omics tools at different molecular levels. However, the potential of these technologies should not be limited to the study of single-level questions; instead, data obtained by these platforms should be integrated to unravel the molecular aspects of grapevine development. Therefore, the current challenge is the generation of new tools that integrate large-scale data to assess new questions in this field, and to support agronomical practices.

Transcriptome analyses of seed development in grape hybrids reveals a possible mechanism influencing seed size

Background

Seedlessness in grape (Vitis vinifera) is of considerable commercial importance for both the table grape and processing industries. Studies to date of grape seed development have been made certain progress, but many key genes have yet to be identified and characterized.

Results

In this study we analyzed the seed transcriptomes of progeny derived from the V. vinifera seeded maternal parent ‘Red Globe’ and the seedless paternal parent ‘Centennial seedless’ to identify genes associated with seedlessness. A total of 6,607 differentially expressed genes (DEGs) were identified and examined from multiple perspectives, including expression patterns, Gene Ontology (GO) annotations, pathway enrichment, inferred hormone influence and epigenetic regulation. The expression data of hormone-related genes and hormone level measurement reveals the differences during seed development between seedless and seeded progeny. Based on both our results and previous studies of A. thaliana seed development, we generated network maps of grape seed-related DEGs, with particular reference to hormone balance, seed coat and endosperm development, and seed identity complexes.

Conclusion

In summary, the major differences identified during seed development of seedless and seeded progeny were associated with hormone and epigenetic regulation, the development of the seed coat and endosperm, and the formation of seed identity complexes. Overall the data provides insights into the possible molecular mechanism controlling grape seed size, which is of great importance for both basic research and future translation applications in the grape industry.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-3193-1) contains supplementary material, which is available to authorized users.

Shared and divergent pathways for flower abscission are triggered by gibberellic acid and carbon starvation in seedless Vitis vinifera L

BACKGROUND

Abscission is a highly coordinated developmental process by which plants control vegetative and reproductive organs load. Aiming at get new insights on flower abscission regulation, changes in the global transcriptome, metabolome and physiology were analyzed in 'Thompson Seedless' grapevine (Vitis vinifera L.) inflorescences, using gibberellic acid (GAc) spraying and shading as abscission stimuli, applied at bloom.

RESULTS

Natural flower drop rates increased from 63.1% in non-treated vines to 83% and 99% in response to GAc and shade treatments, respectively. Both treatments had a broad effect on inflorescences metabolism. Specific impacts from shade included photosynthesis inhibition, associated nutritional stress, carbon/nitrogen imbalance and cell division repression, whereas GAc spraying induced energetic metabolism simultaneously with induction of nucleotide biosynthesis and carbon metabolism, therefore, disclosing alternative mechanisms to regulate abscission. Regarding secondary metabolism, changes in flavonoid metabolism were the most represented metabolic pathways in the samples collected following GAc treatment while phenylpropanoid and stilbenoid related pathways were predominantly affected in the inflorescences by the shade treatment. However, both GAc and shade treated inflorescences revealed also shared pathways, that involved the regulation of putrescine catabolism, the repression of gibberellin biosynthesis, the induction of auxin biosynthesis and the activation of ethylene signaling pathways and antioxidant mechanisms, although often the quantitative changes occurred on specific transcripts and metabolites of the pathways.

CONCLUSIONS

Globally, the results suggest that chemical and environmental cues induced contrasting effects on inflorescence metabolism, triggering flower abscission by different mechanisms and pinpointing the participation of novel abscission regulators. Grapevine showed to be considered a valid model to study molecular pathways of flower abscission competence acquisition, noticeably responding to independent stimuli.

Omics studies of citrus, grape and rosaceae fruit trees

Recent advance of bioinformatics and analytical apparatuses such as next generation DNA sequencer (NGS) and mass spectrometer (MS) has brought a big wave of comprehensive study to biology. Comprehensive study targeting all genes, transcripts (RNAs), proteins, metabolites, hormones, ions or phenotypes is called genomics, transcriptomics, proteomics, metabolomics, hormonomics, ionomics or phenomics, respectively. These omics are powerful approaches to identify key genes for important traits, to clarify events of physiological mechanisms and to reveal unknown metabolic pathways in crops. Recently, the use of omics approach has increased dramatically in fruit tree research. Although the most reported omics studies on fruit trees are transcriptomics, proteomics and metabolomics, and a few is reported on hormonomics and ionomics. In this article, we reviewed recent omics studies of major fruit trees, i.e. citrus, grapevine and rosaceae fruit trees. The effectiveness and prospects of omics in fruit tree research will as well be highlighted.

Complex Interplay of Hormonal Signals during Grape Berry Ripening

Grape and wine production and quality is extremely dependent on the fruit ripening process. Sensory and nutritional characteristics are important aspects for consumers and their development during fruit ripening involves complex hormonal control. In this review, we explored data already published on grape ripening and compared it with the hormonal regulation of ripening of other climacteric and non-climacteric fruits. The roles of abscisic acid, ethylene, and brassinosteroids as promoters of ripening are discussed, as well as the role of auxins, cytokinins, gibberellins, jasmonates, and polyamines as inhibitors of ripening. In particular, the recently described role of polyamine catabolism in grape ripening is discussed, together with its putative interaction with other hormones. Furthermore, other recent examples of cross-talk among the different hormones are presented, revealing a complex interplay of signals during grape development and ripening.