Transcriptional analysis of tendril and inflorescence development in grapevine (Vitis vinifera L.)

Regulatory frameworks involved in the floral induction, formation and developmental programming of woody horticultural plants: a case study on blueberries

Flowering represents a crucial stage in the life cycles of plants. Ensuring strong and consistent flowering is vital for maintaining crop production amidst the challenges presented by climate change. In this review, we summarized key recent efforts aimed at unraveling the complexities of plant flowering through genetic, genomic, physiological, and biochemical studies in woody species, with a special focus on the genetic control of floral initiation and activation in woody horticultural species. Key topics covered in the review include major flowering pathway genes in deciduous woody plants, regulation of the phase transition from juvenile to adult stage, the roles of CONSTANS (CO) and CO-like gene and FLOWERING LOCUS T genes in flower induction, the floral regulatory role of GA-DELLA pathway, and the multifunctional roles of MADS-box genes in flowering and dormancy release triggered by chilling. Based on our own research work in blueberries, we highlighted the central roles played by two key flowering pathway genes, FLOWERING LOCUS T and SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1, which regulate floral initiation and activation (dormancy release), respectively. Collectively, our survey shows both the conserved and diverse aspects of the flowering pathway in annual and woody plants, providing insights into the potential molecular mechanisms governing woody plants. This paves the way for enhancing the resilience and productivity of fruit-bearing crops in the face of changing climatic conditions, all through the perspective of genetic interventions.

Comparative transcriptomic analysis of transcription factors and hormones during flower bud differentiation in 'Red Globe' grape under red‒blue light

Grape is a globally significant fruit-bearing crop, and the grape flower bud differentiation essential to fruit production is closely related to light quality. To investigate the regulatory mechanism of grape flower bud differentiation under red‒blue light, the transcriptome and hormone content were determined at four stages of flower bud differentiation. The levels of indole-3-acetic acid (IAA) and abscisic acid (ABA) in grape flower buds at all stages of differentiation under red‒blue light were higher than those in the control. However, the levels of cytokinins (CKs) and gibberellic acid (giberellins, GAs) fluctuated continuously over the course of flower bud differentiation. Moreover, many differentially expressed genes were involved in auxin, CK, GA, and the ABA signal transduction pathways. There were significant differences in the AUX/IAA, SAUR, A-RR, and ABF gene expression levels between the red‒blue light treatment and the control buds, especially in regard to the ABF genes, the expression levels of which were completely different between the two groups. The expression of GBF4 and AI5L2 in the control was always low, while the expression under red‒blue light increased. AI5L7 and AI5L5 expression levels showed an upwards trend in the control plant buds and gradually decreased in red‒blue light treatment plant buds. Through weighted gene coexpression network analysis, we determined that the transcription factors WRK48 (WRKY family), EF110 (ERF family), ABR1, CAMTA3 (CAMTA family), and HSFA3 (HSF family) may be involved in the regulation of the GBF4 gene. This study lays a foundation for further analysis of grape flower bud differentiation regulation under red‒blue light.

Transcriptomic and metabolomic integration as a resource in grapevine to study fruit metabolite quality traits

Transcriptomics and metabolomics are methodologies being increasingly chosen to perform molecular studies in grapevine (Vitis vinifera L.), focusing either on plant and fruit development or on interaction with abiotic or biotic factors. Currently, the integration of these approaches has become of utmost relevance when studying key plant physiological and metabolic processes. The results from these analyses can undoubtedly be incorporated in breeding programs whereby genes associated with better fruit quality (e.g., those enhancing the accumulation of health-promoting compounds) or with stress resistance (e.g., those regulating beneficial responses to environmental transition) can be used as selection markers in crop improvement programs. Despite the vast amount of data being generated, integrative transcriptome/metabolome meta-analyses (i.e., the joint analysis of several studies) have not yet been fully accomplished in this species, mainly due to particular specificities of metabolomic studies, such as differences in data acquisition (i.e., different compounds being investigated), unappropriated and unstandardized metadata, or simply no deposition of data in public repositories. These meta-analyses require a high computational capacity for data mining a priori, but they also need appropriate tools to explore and visualize the integrated results. This perspective article explores the universe of omics studies conducted in V. vinifera, focusing on fruit-transcriptome and metabolome analyses as leading approaches to understand berry physiology, secondary metabolism, and quality. Moreover, we show how omics data can be integrated in a simple format and offered to the research community as a web resource, giving the chance to inspect potential gene-to-gene and gene-to-metabolite relationships that can later be tested in hypothesis-driven research. In the frame of the activities promoted by the COST Action CA17111 INTEGRAPE, we present the first grapevine transcriptomic and metabolomic integrated database (TransMetaDb) developed within the Vitis Visualization (VitViz) platform (https://tomsbiolab.com/vitviz). This tool also enables the user to conduct and explore meta-analyses utilizing different experiments, therefore hopefully motivating the community to generate Findable, Accessible, Interoperable and Reusable (F.A.I.R.) data to be included in the future.

Genetic variation and association analyses identify genes linked to fruit set-related traits in grapevine

Grapevine is one of the most valuable fruit crops in the world. Adverse environmental conditions reduce fruit quality and crop yield, so understanding the genetic and molecular mechanisms determining crop yield components is essential to optimize grape production. The analysis of a diverse collection of grapevine cultivars allowed us to evaluate the relationship between fruit set-related components of yield, including the incidence of reproductive disorders such as coulure and millerandage. The collection displayed a great phenotypic variation that we surveyed in a genetics association study using 15,309 single nucleotide polymorphisms (SNPs) detected in the sequence of 289 candidate genes scattered across the 19 grapevine linkage groups. After correcting statistical models for population structure and linkage disequilibrium effects, 164 SNPs from 34 of these genes were found to associate with fruit set-related traits, supporting a complex polygenic determinism. Many of them were found in the sequence of different putative MADS-box transcription factors, a gene family related with plant reproductive development control. In addition, we observed an additive effect of some of the associated SNPs on the phenotype, suggesting that advantageous alleles from different loci could be pyramided to generate superior cultivars with optimized fruit production.

Differential expression of transcription factor- and further growth-related genes correlates with contrasting cluster architecture in Vitis vinifera 'Pinot Noir' and Vitis spp. genotypes

Grapevine (Vitis vinifera L.) is an economically important crop that needs to comply with high quality standards for fruit, juice and wine production. Intense plant protection is required to avoid fungal damage. Grapevine cultivars with loose cluster architecture enable reducing protective treatments due to their enhanced resilience against fungal infections, such as Botrytis cinerea-induced gray mold. A recent study identified transcription factor gene VvGRF4 as determinant of pedicel length, an important component of cluster architecture, in samples of two loose and two compact quasi-isogenic 'Pinot Noir' clones. Here, we extended the analysis to 12 differently clustered 'Pinot Noir' clones from five diverse clonal selection programs. Differential gene expression of these clones was studied in three different locations over three seasons. Two phenotypically opposite clones were grown at all three locations and served for standardization. Data were correlated with the phenotypic variation of cluster architecture sub-traits. A set of 14 genes with consistent expression differences between loosely and compactly clustered clones-independent from season and location-was newly identified. These genes have annotations related to cellular growth, cell division and auxin metabolism and include two more transcription factor genes, PRE6 and SEP1-like. The differential expression of VvGRF4 in relation to loose clusters was exclusively found in 'Pinot Noir' clones. Gene expression studies were further broadened to phenotypically contrasting F1 individuals of an interspecific cross and OIV reference varieties of loose cluster architecture. This investigation confirmed PRE6 and six growth-related genes to show differential expression related to cluster architecture over genetically divergent backgrounds.

Characterization of FLOWERING LOCUS C Homologs in Apple as a Model for Fruit Trees

To elucidate the molecular mechanism of juvenility and annual flowering of fruit trees, FLOWERING LOCUS C (FLC), an integrator of flowering signals, was investigated in apple as a model. We performed sequence and expression analyses and transgenic experiments related to juvenility with annual flowering to characterize the apple FLC homologs MdFLC. The phylogenetic tree analysis, which included other MADS-box genes, showed that both MdFLC1 and MdFLC3 belong to the same FLC group. MdFLC1c from one of the MdFLC1 splice variants and MdFLC3 contain the four conserved motives of an MIKC-type MADS protein. The mRNA of variants MdFLC1a and MdFLC1b contain intron sequences, and their deduced amino acid sequences lack K- and C-domains. The expression levels of MdFLC1a, MdFLC1b, and MdFLC1c decreased during the flowering induction period in a seasonal expression pattern in the adult trees, whereas the expression level of MdFLC3 did not decrease during that period. This suggests that MdFLC1 is involved in flowering induction in the annual growth cycle of adult trees. In apple seedlings, because phase change can be observed in individuals, seedlings can be used for analysis of expression during phase transition. The expression levels of MdFLC1b, MdFLC1c, and MdFLC3 were high during the juvenile phase and low during the transitional and adult phases. Because the expression pattern of MdFLC3 suggests that it plays a specific role in juvenility, MdFLC3 was subjected to functional analysis by transformation of Arabidopsis. The results revealed the function of MdFLC3 as a floral repressor. In addition, MdFT had CArG box-like sequences, putative targets for the suppression of flowering by MdFLC binding, in the introns and promoter regions. These results indicate that apple homologs of FLC, which might play a role upstream of the flowering signals, could be involved in juvenility as well as in annual flowering. Apples with sufficient genome-related information are useful as a model for studying phenomena unique to woody plants such as juvenility and annual flowering.

VviUCC1 Nucleotide Diversity, Linkage Disequilibrium and Association with Rachis Architecture Traits in Grapevine

Cluster compactness is a trait with high agronomic relevance, affecting crop yield and grape composition. Rachis architecture is a major component of cluster compactness determinism, and is a target trait toward the breeding of grapevine varieties less susceptible to pests and diseases. Although its genetic basis is scarcely understood, a preliminary result indicated a possible involvement of the VviUCC1 gene. The aim of this study was to characterize the VviUCC1 gene in grapevine and to test the association between the natural variation observed for a series of rachis architecture traits and the polymorphisms detected in the VviUCC1 sequence. This gene encodes an uclacyanin plant-specific cell-wall protein involved in fiber formation and/or lignification processes. A high nucleotide diversity in the VviUCC1 gene promoter and coding regions was observed, but no critical effects were predicted in the protein domains, indicating a high level of conservation of its function in the cultivated grapevine. After correcting statistical models for genetic stratification and linkage disequilibrium effects, marker-trait association results revealed a series of single nucleotide polymorphisms (SNPs) significantly associated with cluster compactness and rachis traits variation. Two of them (Y-984 and K-88) affected two common cis-transcriptional regulatory elements, suggesting an effect on phenotype via gene expression regulation. This work reinforces the interest of further studies aiming to reveal the functional effect of the detected VviUCC1 variants on grapevine rachis architecture.

Quantitative Trait Locus Analysis of Leaf Morphology Indicates Conserved Shape Loci in Grapevine

Leaf shape in plants plays important roles in water use, canopy structure, and physiological tolerances to abiotic stresses; all important traits for the future development and sustainability of grapevine cultivation. Historically, researchers have used ampelography, the study of leaf shape in grapevines, to differentiate Vitis species and cultivars based on finite leaf attributes. However, ampelographic measurements have limitations and new methods for quantifying shape are now available. We paired an analysis of finite trait attributes with a 17-point landmark survey and generalized Procrustes analysis (GPA) to reconstruct grapevine leaves digitally from five interspecific hybrid mapping families. Using the reconstructed leaves, we performed three types of quantitative trait loci (QTL) analyses to determine the genetic architecture that defines leaf shape. In the first analysis, we compared several important ampelographic measurements as finite trait QTL. In the second and third analyses, we identified significant shape variation via principal components analysis (PCA) and using a multivariate least squares interval mapping (MLSIM) approach. In total, we identified 271 significant QTL across the three measures of leaf shape and identified specific QTL hotspots in the grape genome which appear to drive major aspects of grapevine leaf shape.

Sucrose transporters of resistant grapevine are involved in stress resistance

The whole promoter regions of SUTs in Vitis were firstly isolated. SUTs are involved in the adaptation to biotic and abiotic stresses. The vulnerability of Vitis vinifera to abiotic and biotic stresses limits its yields. In contrast, Vitis amurensis displays resistance to environmental stresses, such as microbial pathogens, low temperatures, and drought. Sucrose transporters (SUTs) are important regulators for plant growth and stress tolerance; however, the role that SUTs play in stress resistance in V. amurensis is not known. Using V. amurensis Ruper. 'Zuoshan-1' and V. vinifera 'Chardonnay', we found that SUC27 was highly expressed in several vegetative organs of Zuoshan-1, SUC12 was weakly expressed or absent in most organs in both the species, and the distribution of SUC11 in source and sink organs was highest in Zuoshan-1. A search for cis-regulatory elements in the promoter sequences of SUTs revealed that they were regulated by light, environmental stresses, physiological correlation, and hormones. The SUTs in Zuoshan-1 mostly show a higher and rapid response than in Chardonnay under the induction by Plasmopara viticola infection, cold, water deficit, and dark conditions. The induction of SUTs was associated with the upregulation of key genes involved in sucrose metabolism and the biosynthesis of plant hormones. These results indicate that stress resistance in Zuoshan-1 is governed by the differential distribution and induction of SUTs by various stimuli, and the subsequent promotion of sucrose metabolism and hormone synthesis.

TM8 represses developmental timing in Nicotiana benthamiana and has functionally diversified in angiosperms

BACKGROUND

MADS-box genes are key regulators of plant reproductive development and members of most lineages of this gene family have been extensively studied. However, the function and diversification of the ancient TM8 lineage remains elusive to date. The available data suggest a possible function in flower development in tomato and fast evolution through numerous gene loss events in flowering plants.

RESULTS

We show the broad conservation of TM8 within angiosperms and find that in contrast to other MADS-box gene lineages, no gene duplicates have been retained after major whole genome duplication events. Through knock-down of NbTM8 by virus induced gene silencing in Nicotiana benthamiana, we show that NbTM8 represses miR172 together with another MADS-box gene, SHORT VEGETATIVE PHASE (NbSVP). In the closely related species Petunia hybrida, PhTM8 is not expressed under the conditions we investigated and consistent with this, a knock-out mutant did not show a phenotype. Finally, we generated transgenic tomato plants in which TM8 was silenced or ectopically expressed, but these plants did not display a clear phenotype. Therefore, no clear function could be confirmed for Solanum lycopersium.

CONCLUSIONS

While the presence of TM8 is generally conserved, it remains difficult to propose a general function in angiosperms. Based on all the available data to date, supplemented with our own results, TM8 function seems to have diversified quickly throughout angiosperms and acts as repressor of miR172 in Nicotiana benthamiana, together with NbSVP.

The molecular control of tendril development in angiosperms

The climbing habit has evolved multiple times during the evolutionary history of angiosperms. Plants evolved various strategies for climbing, such as twining stems, tendrils and hooks. Tendrils are threadlike organs with the ability to twine around other structures through helical growth; they may be derived from a variety of structures, such as branches, leaflets and inflorescences. The genetic capacity to grow as a tendrilled climber existed in some of the earliest land plants; however, the underlying molecular basis of tendril development has been studied in only a few taxa. Here, we summarize what is known about the molecular basis of tendril development in model and candidate model species from key tendrilled families, that is, Fabaceae, Vitaceae, Cucurbitaceae, Passifloraceae and Bignoniaceae. Studies on tendril molecular genetics and development show the molecular basis of tendril formation and ontogenesis is diverse, even when tendrils have the same ontogenetic origin, for example leaflet-derived tendrils in Fabaceae and Bignoniaceae. Interestingly, all tendrils perform helical growth during contact-induced coiling, indicating that such ability is not correlated with their ontogenetic origin or phylogenetic history. Whether the same genetic networks are involved during helical growth in diverse tendrils still remains to be investigated.

Comparative transcriptomics reveals a reduction in carbon capture and flux between source and sink in cytokinin-treated inflorescences of Jatropha curcas L

The low seed yield of Jatropha curcas has been a stumbling block in realizing its full potential as an ideal bioenergy crop. Low female to male flower ratio is considered as a major limiting factor responsible for low seed yield in Jatropha. An exogenous cytokinin application was performed on floral meristems to increase the seed yield. This resulted in an increase of total flowers count with a higher female to male flower ratio. However, the seed biomass did not increase in the same proportion. The possible reason for this was hypothesized to be the lack of increased photosynthesis efficiency at source tissues which could fulfil the increased demand of photosynthates and primary metabolites in maturing seeds. After cytokinin application, possible molecular mechanisms underlying carbon capture and flux affected between the source and sink in developing flowers, fruits and seeds were investigated. Comparative transcriptome analysis was performed on inflorescence meristems (treated with cytokinin) and control (untreated inflorescence meristems) at time intervals of 15 and 30 days, respectively. KEGG-based functional annotation identified various metabolic pathways associated with carbon capture and flux. Pathways such as photosynthesis, carbon fixation, carbohydrate metabolism and nitrogen metabolism were upregulated after 15 days of cytokinin treatment; however, those were downregulated after 30 days. Five genes FBP, SBP, GS, GDH and AGPase showed significant increase in transcript abundance after 15 days of treatment but showed a significant decrease after 30 days. These genes, after functional validation, can be suitable targets in designing a suitable genetic intervention strategy to increase overall seed yield in Jatropha.

A transcriptome analysis of two grapevine populations segregating for tendril phyllotaxy

The shoot structure of cultivated grapevine Vitis vinifera L. typically exhibits a three-node modular repetitive pattern, two sequential leaf-opposed tendrils followed by a tendril-free node. In this study, we investigated the molecular basis of this pattern by characterizing differentially expressed genes in 10 bulk samples of young tendril tissue from two grapevine populations showing segregation of mutant or wild-type shoot/tendril phyllotaxy. One population was the selfed progeny and the other one, an outcrossed progeny of a Vitis hybrid, 'Roger's Red'. We analyzed 13 375 expressed genes and carried out in-depth analyses of 324 of them, which were differentially expressed with a minimum of 1.5-fold changes between the mutant and wild-type bulk samples in both selfed and cross populations. A significant portion of these genes were direct cis-binding targets of 14 transcription factor families that were themselves differentially expressed. Network-based dependency analysis further revealed that most of the significantly rewired connections among the 10 most connected hub genes involved at least one transcription factor. TCP3 and MYB12, which were known important for plant-form development, were among these transcription factors. More importantly, TCP3 and MYB12 were found in this study to be involved in regulating the lignin gene PRX52, which is important to plant-form development. A further support evidence for the roles of TCP3-MYB12-PRX52 in contributing to tendril phyllotaxy was the findings of two other lignin-related genes uniquely expressed in the mutant phyllotaxy background.

Comparative transcriptome analyses of flower development in four species of Achimenes (Gesneriaceae)

BACKGROUND

Flowers have an amazingly diverse display of colors and shapes, and these characteristics often vary significantly among closely related species. The evolution of diverse floral form can be thought of as an adaptive response to pollination and reproduction, but it can also be seen through the lens of morphological and developmental constraints. To explore these interactions, we use RNA-seq across species and development to investigate gene expression and sequence evolution as they relate to the evolution of the diverse flowers in a group of Neotropical plants native to Mexico-magic flowers (Achimenes, Gesneriaceae).

RESULTS

The assembled transcriptomes contain between 29,000 and 42,000 genes expressed during development. We combine sequence orthology and coexpression clustering with analyses of protein evolution to identify candidate genes for roles in floral form evolution. Over 25% of transcripts captured were distinctive to Achimenes and overrepresented by genes involved in transcription factor activity. Using a model-based clustering approach we find dynamic, temporal patterns of gene expression among species. Selection tests provide evidence of positive selection in several genes with roles in pigment production, flowering time, and morphology. Combining these approaches to explore genes related to flower color and flower shape, we find distinct patterns that correspond to transitions of floral form among Achimenes species.

CONCLUSIONS

The floral transcriptomes developed from four species of Achimenes provide insight into the mechanisms involved in the evolution of diverse floral form among closely related species with different pollinators. We identified several candidate genes that will serve as an important and useful resource for future research. High conservation of sequence structure, patterns of gene coexpression, and detection of positive selection acting on few genes suggests that large phenotypic differences in floral form may be caused by genetic differences in a small set of genes. Our characterized floral transcriptomes provided here should facilitate further analyses into the genomics of flower development and the mechanisms underlying the evolution of diverse flowers in Achimenes and other Neotropical Gesneriaceae.

Nataraja K. An Approach to Function Annotation for Proteins of Unknown Function (PUFs) in the Transcriptome of Indian Mulberry

The modern sequencing technologies are generating large volumes of information at the transcriptome and genome level. Translation of this information into a biological meaning is far behind the race due to which a significant portion of proteins discovered remain as proteins of unknown function (PUFs). Attempts to uncover the functional significance of PUFs are limited due to lack of easy and high throughput functional annotation tools. Here, we report an approach to assign putative functions to PUFs, identified in the transcriptome of mulberry, a perennial tree commonly cultivated as host of silkworm. We utilized the mulberry PUFs generated from leaf tissues exposed to drought stress at whole plant level. A sequence and structure based computational analysis predicted the probable function of the PUFs. For rapid and easy annotation of PUFs, we developed an automated pipeline by integrating diverse bioinformatics tools, designated as PUFs Annotation Server (PUFAS), which also provides a web service API (Application Programming Interface) for a large-scale analysis up to a genome. The expression analysis of three selected PUFs annotated by the pipeline revealed abiotic stress responsiveness of the genes, and hence their potential role in stress acclimation pathways. The automated pipeline developed here could be extended to assign functions to PUFs from any organism in general. PUFAS web server is available at http://caps.ncbs.res.in/pufas/ and the web service is accessible at http://capservices.ncbs.res.in/help/pufas.

Factors controlling inflorescence primordia formation of grapevine: their role in latent bud fruitfulness? A review

The grapevine (Vitis vinifera L.) is a widely cultivated species of major economic importance for wine production. The quality and quantity of grapes are criteria of prime importance to the wine industry, but they are highly variable from year to year. Unlike many perennial plants, cluster formation unfolds in two seasons: season 1 takes place in the bud until dormancy, and season 2 starts after budbreak in the following year. Season 1 corresponds to the initiation and differentiation of inflorescence primordia, controlled by many exogenous and endogenous factors, which explains up to 60% seasonal variation in yield. Season 2 consists of flowering and fruit development, which explains, respectively, 30% and 10% of seasonal variation in yield. It is therefore essential to understand the impact of these factors to better control the yield. This review aims to summarize past and present knowledge concerning the physiology of latent buds relating to their fruitfulness, and to assess the impact of environmental, hormonal, and regulation factors on the final yield. Avenues of further research to understand physiological, biochemical and molecular regulatory mechanisms of initiation and differentiation of clusters will be then proposed.

Association analysis of grapevine bunch traits using a comprehensive approach

KEY MESSAGE

A set of SNP markers associated to bunch compactness and related traits were identified in grapevine.

ABSTRACT

Bunch compactness plays an important role in the sanitary status and perceived quality of table and wine grapes, being influenced by cultural practices and by environmental and genetic factors, which are mostly unknown. In this work, we took advantage of genetic, genomic and bioinformatic advances to analyze part of its molecular basis through a combination of transcriptomic and association analyses. Results from different transcriptomic comparisons between loose and compact grapevine clones were analyzed to select a set of candidate genes likely involved in the observed variation for bunch compactness. Up to 183 genes were sequenced in a grapevine collection, and 7032 single nucleotide polymorphisms (SNPs) were detected in more than 100 varieties with a frequency of the minor allele over 5%. They were used to test their association in three consecutive seasons with bunch compactness and two of its most influencing factors: total berry number and length of the first ramification of the rachis. Only one SNP was associated with berry number in two seasons, suggesting the high sensitiveness of this trait to seasonal environmental changes. On the other hand, we found a set of SNPs associated with both the first ramification length and bunch compactness in various seasons, in several genes which had not previously related to bunch compactness or bunch compactness-related traits. They are proposed as interesting candidates for further functional analyses aimed to verify the results obtained in this work, as a previous step to their inclusion in marker-assisted selection strategies.

Structural and functional annotation of the MADS-box transcription factor family in grapevine

Background

MADS-box genes encode transcription factors that are involved in developmental control and signal transduction in eukaryotes. In plants, they are associated to numerous development processes most notably those related to reproductive development: flowering induction, specification of inflorescence and flower meristems, establishment of flower organ identity, as well as regulation of fruit, seed and embryo development. Genomic analyses of MADS-box genes in different plant species are providing new relevant information on the function and evolution of this transcriptional factor family. We have performed a true genome-wide analysis of the complete set of MADS-box genes in grapevine (Vitis vinifera), analyzed their expression pattern and establish their phylogenetic relationships (including MIKC* and type I MADS-box) with genes from 16 other plant species. This study was integrated to previous works on the family in grapevine.

Results

A total of 90 MADS-box genes were detected in the grapevine reference genome by completing current gene annotations with a genome-wide analysis based on sequence similarity. We performed a thorough in-depth curation of all gene models and combined the results with gene expression information including RNAseq data to clarifying the expression of newly identified genes and improve their functional characterization. Curated data were uploaded to the ORCAE database for grapevine in the frame of the grapevine genome curation effort. This approach resulted in the identification of 30 additional MADS box genes. Among them, ten new MIKC^C genes were identified, including a potential new group of short proteins similar to the SVP protein subfamily. The MIKC* subgroup contains six genes in grapevine that can be grouped in the S (4 genes) and P (2 genes) clades, showing less redundancy than that observed in Arabidopsis thaliana. Expression pattern of these genes in grapevine is compatible with a role in male gametophyte development. Most of the identified new genes belong to the type I MADS-box genes and were classified as members of the Mα and Mγ subclasses. Ours analyses indicate that only few members of type I genes in grapevine have homology in other species and that species-specific clades appeared both in the Mα and Mγ subclasses. On the other hand, as deduced from the phylogenetic analysis with other plant species, genes that can be crucial for development of central cell, endosperm and embryos seems to be conserved in plants.

Conclusions

The genome analysis of MADS-box genes in grapevine, the characterization of their pattern of expression and the phylogenetic analysis with other plant species allowed the identification of new MADS-box genes not yet described in other plant species as well as basic characterization of their possible role, particularly in the case of type I and MIKC* genes.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-2398-7) contains supplementary material, which is available to authorized users.

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.

Suppression of the D-class MADS-box AGL11 gene triggers seedlessness in fleshy fruits

Seedlessness, one of the most desired traits in fleshy fruits, can be obtained altering solely AGL11 gene, a D -class MADS-box. Opposite to overlapping functions described for ovule identity. AGAMOUS like-11 (AGL11) is a D-class MADS-box gene that determines ovule identity in model species. In grapevine, VviAGL11 has been proposed as the main candidate gene responsible for seedlessness because ovules develop into seeds after fertilization. Here, we demonstrate that AGL11 has a direct role in the determination of the seedless phenotype. In grapevine, broad expression analysis revealed very low expression levels of the seedless allele compared to the seeded allele at the pea-size berry stage. Heterozygous genotypes have lower transcript accumulation than expected considering the diploid nature of grapevine, thereby revealing that the dominant phenotype previously described for seedlessness is based on its expression level. In a seeded somatic variant of Sultanina (Thompson Seedless) that has well-developed seeds, Sultanine Monococco, structural differences were identified in the regulatory region of VviAGL11. These differences affect transcript accumulation levels and explain the phenotypic differences between the two varieties. Functional experiments in tomato demonstrated that SlyAGL11 gene silencing produces seedless fruits and that the degree of seed development is proportional to transcript accumulation levels. Furthermore, the genes involved in seed coat development, SlyVPE1 and SlyVPE2 in tomato and VviVPE in grapevine, that are putatively controlled by SlyAGL11 and VviAGL11, respectively, are expressed at lower levels in silenced tomato lines and in seedless grapevine genotypes. In conclusion, this work provides evidence that the D-class MADS-box AGL11 plays a major and direct role in seed development in fleshy fruits, providing a valuable tool for further analysis of fruit development.

The phenylpropanoid pathway is controlled at different branches by a set of R2R3-MYB C2 repressors in grapevine

Because of the vast range of functions that phenylpropanoids possess, their synthesis requires precise spatiotemporal coordination throughout plant development and in response to the environment. The accumulation of these secondary metabolites is transcriptionally controlled by positive and negative regulators from the MYB and basic helix-loop-helix protein families. We characterized four grapevine (Vitis vinifera) R2R3-MYB proteins from the C2 repressor motif clade, all of which harbor the ethylene response factor-associated amphiphilic repression domain but differ in the presence of an additional TLLLFR repression motif found in the strong flavonoid repressor Arabidopsis (Arabidopsis thaliana) AtMYBL2. Constitutive expression of VvMYB4a and VvMYB4b in petunia (Petunia hybrida) repressed general phenylpropanoid biosynthetic genes and selectively reduced the amount of small-weight phenolic compounds. Conversely, transgenic petunia lines expressing VvMYBC2-L1 and VvMYBC2-L3 showed a severe reduction in petal anthocyanins and seed proanthocyanidins together with a higher pH of crude petal extracts. The distinct function of these regulators was further confirmed by transient expression in tobacco (Nicotiana benthamiana) leaves and grapevine plantlets. Finally, VvMYBC2-L3 was ectopically expressed in grapevine hairy roots, showing a reduction in proanthocyanidin content together with the down-regulation of structural and regulatory genes of the flavonoid pathway as revealed by a transcriptomic analysis. The physiological role of these repressors was inferred by combining the results of the functional analyses and their expression patterns in grapevine during development and in response to ultraviolet B radiation. Our results indicate that VvMYB4a and VvMYB4b may play a key role in negatively regulating the synthesis of small-weight phenolic compounds, whereas VvMYBC2-L1 and VvMYBC2-L3 may additionally fine tune flavonoid levels, balancing the inductive effects of transcriptional activators.