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

Antibody array-based proteome approach reveals proteins involved in grape seed development

Grape (Vitis vinifera) is one of the most widely cultivated fruits globally, primarily used for processing and fresh consumption. Seedless grapes are favored by consumers for their convenience, making the study of seedlessness a subject of great interest to scientists. To identify regulators involved in this process in grape, a monoclonal antibody (mAb)-array-based proteomics approach, which contains 21,120 mAbs, was employed for screening proteins/antigens differentially accumulated in grape during development. Differences in antigen signals were detected between seeded and seedless grapes revealing the differential accumulation of 2,587 proteins. After immunoblotting validation, 71 antigens were further immunoprecipitated and identified by mass spectrometry (MS). An in planta protein-protein interaction (PPI) network of those differentially accumulated proteins was established using mAb antibody by immunoprecipitation (IP)-MS, which reveals the alteration of pathways related to carbon metabolism and glycolysis. To validate our result, a seedless-related protein, DUF642 domain-containing protein (VvDUF642), which is functionally uncharacterized in grapes, was ectopically overexpressed in tomato (Solanum lycopersicum "MicroTom") and led to a reduction in seed production. PPI network indicated that VvDUF642 interacts with pectin acetylesterase (VvPAE) in grapes, which was validated by BiFC and Co-IP. As anticipated, overexpression of VvPAE substantially reduced seed production in tomato. Moreover, S. lycopersicum colourless non-ripening expression was altered in VvDUF642- and VvPAE-overexpressing plants. Taken together, we provided a high-throughput method for the identification of proteins involved in the seed formation process. Among those, VvDUF642 and VvPAE are potential targets for breeding seedless grapes and other important fruits in the future.

Comparative RNA-Seq Analysis between Monoecious and Androecious Plants Reveals Regulatory Mechanisms Controlling Female Flowering in Cucurbita pepo

In the monoecious Cucurbita pepo, the transition to female flowering is the time at which the plant starts the production of female flowers after an initial male phase of development. Ethylene plays an essential role in this process since some ethylene deficient and ethylene-insensitive mutants are androecious and only produce male flowers. To gain insight into the molecular mechanisms regulating the specification and early development of female flowers, we have compared the transcriptomic changes occurring in the shoot apices of WT and androecious ethylene-insensitive etr1b mutant plants upon female flowering transition. There were 1160 female flowering-specific DEGs identified in WT plants upon female flowering, and 284 of them were found to be modulated by the ethylene-insensitive etr1b mutation. The function of these DEGs indicated that female flower specification depends on the adoption of a transcriptional program that includes previously identified sex-determining genes in the ethylene pathway, but also genes controlling the biosynthesis and signaling pathways of other phytohormones, and those encoding for many different transcription factors. The transcriptomic changes suggested that gibberellins play a negative role in female flowering, while ethylene, auxins, ABA and cytokinins are positive regulators. Transcription factors from 34 families, including NAC, ERF, bHLH, bZIP, MYB and C2H2/CH3, were found to be regulating female flowering in an ethylene-dependent or -independent manner. Our data open a new perspective of the molecular mechanisms that control the specification and development of female flowers in C. pepo.

Molecular, hormonal, and metabolic mechanisms of fruit set, the ovary-to-fruit transition, in horticultural crops

Fruit set is the process by which the ovary develops into a fruit and is an important factor in determining fruit yield. Fruit set is induced by two hormones, auxin and gibberellin, and the activation of their signaling pathways, partly by suppressing various negative regulators. Many studies have investigated the structural changes and gene networks in the ovary during fruit set, revealing the cytological and molecular mechanisms. In tomato (Solanum lycopersicum), SlIAA9 and SlDELLA/PROCERA act as auxin and gibberellin signaling repressors, respectively, and are important regulators of the activity of transcription factors and downstream gene expression involved in fruit set. Upon pollination, SlIAA9 and SlDELLA are degraded, which subsequently activates downstream cascades and mainly contributes to active cell division and cell elongation, respectively, in ovaries during fruit setting. According to current knowledge, the gibberellin pathway functions as the most downstream signal in fruit set induction, and therefore its role in fruit set has been extensively explored. Furthermore, multi-omics analysis has revealed the detailed dynamics of gene expression and metabolites downstream of gibberellins, highlighting the rapid activation of central carbon metabolism. This review will outline the relevant mechanisms at the molecular and metabolic levels during fruit set, particularly focusing on tomato.

Nuclear phylogeny and insights into whole-genome duplications and reproductive development of Solanaceae plants

Solanaceae, the nightshade family, have ∼2700 species, including the important crops potato and tomato, ornamentals, and medicinal plants. Several sequenced Solanaceae genomes show evidence for whole-genome duplication (WGD), providing an excellent opportunity to investigate WGD and its impacts. Here, we generated 93 transcriptomes/genomes and combined them with 87 public datasets, for a total of 180 Solanaceae species representing all four subfamilies and 14 of 15 tribes. Nearly 1700 nuclear genes from these transcriptomic/genomic datasets were used to reconstruct a highly resolved Solanaceae phylogenetic tree with six major clades. The Solanaceae tree supports four previously recognized subfamilies (Goetzeioideae, Cestroideae, Nicotianoideae, and Solanoideae) and the designation of three other subfamilies (Schizanthoideae, Schwenckioideae, and Petunioideae), with the placement of several previously unassigned genera. We placed a Solanaceae-specific whole-genome triplication (WGT1) at ∼81 million years ago (mya), before the divergence of Schizanthoideae from other Solanaceae subfamilies at ∼73 mya. In addition, we detected two gene duplication bursts (GDBs) supporting proposed WGD events and four other GDBs. An investigation of the evolutionary histories of homologs of carpel and fruit developmental genes in 14 gene (sub)families revealed that 21 gene clades have retained gene duplicates. These were likely generated by the Solanaceae WGT1 and may have promoted fleshy fruit development. This study presents a well-resolved Solanaceae phylogeny and a new perspective on retained gene duplicates and carpel/fruit development, providing an improved understanding of Solanaceae evolution.

Genome-Wide Analysis of the Mads-Box Transcription Factor Family in Solanum melongena

The MADS-box transcription factors are known to be involved in several aspects of plant growth and development, especially in floral organ specification. However, little is known in eggplant. Here, 120 eggplant MADS-box genes were identified and categorized into type II (MIKCC and MIKC*) and type I (Mα, Mβ, and Mγ) subfamilies based on phylogenetic relationships. The exon number in type II SmMADS-box genes was greater than that in type I SmMADS-box genes, and the K-box domain was unique to type II MADS-box TFs. Gene duplication analysis revealed that segmental duplications were the sole contributor to the expansion of type II genes. Cis-elements of MYB binding sites related to flavonoid biosynthesis were identified in three SmMADS-box promoters. Flower tissue-specific expression profiles showed that 46, 44, 38, and 40 MADS-box genes were expressed in the stamens, stigmas, petals, and pedicels, respectively. In the flowers of SmMYB113-overexpression transgenic plants, the expression levels of 3 SmMADS-box genes were co-regulated in different tissues with the same pattern. Correlation and protein interaction predictive analysis revealed six SmMADS-box genes that might be involved in the SmMYB113-regulated anthocyanin biosynthesis pathway. This study will aid future studies aimed at functionally characterizing important members of the MADS-box gene family.

Genic male and female sterility in vegetable crops

Vegetable crops are greatly appreciated for their beneficial nutritional and health components. Hybrid seeds are widely used in vegetable crops for advantages such as high yield and improved resistance, which require the participation of male (stamen) and female (pistil) reproductive organs. Male- or female-sterile plants are commonly used for production of hybrid seeds or seedless fruits in vegetables. In this review we will focus on the types of genic male sterility and factors affecting female fertility, summarize typical gene function and research progress related to reproductive organ identity and sporophyte and gametophyte development in vegetable crops [mainly tomato (Solanum lycopersicum) and cucumber (Cucumis sativus)], and discuss the research trends and application perspectives of the sterile trait in vegetable breeding and hybrid production, in order to provide a reference for fertility-related germplasm innovation.

Multispecies transcriptomes reveal core fruit development genes

During angiosperm evolution there have been repeated transitions from an ancestral dry fruit to a derived fleshy fruit, often with dramatic ecological and economic consequences. Following the transition to fleshy fruits, domestication may also dramatically alter the fruit phenotype via artificial selection. Although the morphologies of these fruits are well documented, relatively less is known about the molecular basis of these developmental and evolutionary shifts. We generated RNA-seq libraries from pericarp tissue of desert tobacco and both cultivated and wild tomato species at common developmental time points and combined this with corresponding, publicly available data from Arabidopsis and melon. With this broadly sampled dataset consisting of dry/fleshy fruits and wild/domesticated species, we applied novel bioinformatic methods to investigate conserved and divergent patterns of gene expression during fruit development and evolution. A small set of 121 orthologous "core" fruit development genes show a common pattern of expression across all five species. These include key players in developmental patterning such as orthologs of KNOLLE, PERIANTHIA, and ARGONAUTE7. GO term enrichment suggests that these genes function in basic cell division processes, cell wall biosynthesis, and developmental patterning. We furthermore uncovered a number of "accessory" genes with conserved expression patterns within but not among fruit types, and whose functional enrichment highlights the conspicuous differences between these phenotypic classes. We observe striking conservation of gene expression patterns despite large evolutionary distances, and dramatic phenotypic shifts, suggesting a conserved function for a small subset of core fruit development genes.

SlMBP3 Knockout/down in Tomato: Normal-Sized Fruit with Increased Dry Matter Content through Non-Liquefied Locular Tissue by Altered Cell Wall Formation

The phenotypic effect of the knockdown/out of AGAMOUS clade MADS-box gene SlMBP3 in tomato was evaluated using a transferred DNA (T-DNA)-tagged mutant of SlMBP3 and SlMBP3-RNA interference lines. SlMBP3 was preferentially expressed in the locular tissue of fruit and the seed coat combined with the endoderm. Consistent with where SlMBP3 is expressed, the SlMBP3-knockout/down lines showed non-liquefied locular tissues and increased number of seed hairs than the wild type (WT). The early cell degradation of the locular tissue was not observed in the fruits of the SlMBP3-knockout/down lines, and the cells were elongated like placental cells resulting in non-liquefied locular tissues. As the result, the fruits of the SlMBP3-knockout/down lines exhibited higher dry matter contents and titratable acidity than those of the WT. During locular tissue cell development under the SlMBP3 knockout/down, the expression of cell-enlargement-related genes (beta-expansin gene SlEXPB1 and endo-beta-1,4-D-glucanase gene Cel8) and pectinase-inhibitor-related genes (pectin esterase inhibitor gene PE inhibitor and polygalacturonase inhibitor gene PG inhibitor) was upregulated and that of pectinase-encoding genes (polygalacturonase gene QRT3-like and pectin lyase gene PL2) was downregulated. In the seed coat of the SlMBP3-knockout/down lines, tomato trichome-formation-related genes such as MYB genes containing R2 and R3 repeats (R2R3-MYB) transcription factor SlMYB75, B-type cyclin SlCycB2 and Homeodomain Leucine Zipper (HD-Zip) IV transcription factor Woolly were downregulated. Our results demonstrate that SlMBP3 is involved in the liquefaction of the locular tissue through the modification of cell development and degradation processes and seed hair formation in tomato fruits, and the SlMBP3 knockout/down results in normal-sized fruit with increased dry matter content.

Options for the generation of seedless cherry, the ultimate snacking product

This manuscript identifies cherry orthologues of genes implicated in the development of pericarpic fruit and pinpoints potential options and restrictions in the use of these targets for commercial exploitation of parthenocarpic cherry fruit. Cherry fruit contain a large stone and seed, making processing of the fruit laborious and consumption by the consumer challenging, inconvenient to eat 'on the move' and potentially dangerous for children. Availability of fruit lacking the stone and seed would be potentially transformative for the cherry industry, since such fruit would be easier to process and would increase consumer demand because of the potential reduction in costs. This review will explore the background of seedless fruit, in the context of the ambition to produce the first seedless cherry, carry out an in-depth analysis of the current literature around parthenocarpy in fruit, and discuss the available technology and potential for producing seedless cherry fruit as an 'ultimate snacking product' for the twenty-first century.

VviAGL11 self-regulates and targets hormone- and secondary metabolism-related genes during seed development

VviAGL11, the Arabidopsis SEEDSTICK homolog, has been proposed to have a causative role in grapevine stenospermocarpy. An association between a mutation in the coding sequence (CDS) and the seedless phenotype was reported, however, no working mechanisms have been demonstrated yet. We performed a deep investigation of the full VviAGL11 gene sequence in a collection of grapevine varieties belonging to several seedlessness classes that revealed three different promoter-CDS combinations. By investigating the expression of the three VviAGL11 alleles, and by evaluating their ability to activate the promoter region, we observed that VviAGL11 self-activates in a specific promoter-CDS combination manner. Furthermore, by transcriptomic analyses on ovule and developing seeds in seeded and seedless varieties and co-expression approaches, candidate VviAGL11 targets were identified and further validated through luciferase assay and in situ hybridization. We demonstrated that VviAGL11 Wild Type CDS activates Methyl jasmonate esterase and Indole-3-acetate beta-glucosyltransferase, both involved in hormone signaling and Isoflavone reductase, involved in secondary metabolism. The dominant-negative effect of the mutated CDS was also functionally ectopically validated in target induction. VviAGL11 was shown to co-localize with its targets in the outer seed coat integument, supporting its direct involvement in seed development, possibly by orchestrating the crosstalk among MeJA, auxin, and isoflavonoids synthesis. In conclusion, the VviAGL11 expression level depends on the promoter-CDS allelic combination, and this will likely affect its ability to activate important triggers of the seed coat development. The dominant-negative effect of the mutated VviAGL11 CDS on the target genes activation was molecularly validated. A new regulatory mechanism correlating VviAGL11 haplotype assortment and seedlessness class in grapevine is proposed.

Programmed Cell Death May Be Involved in the Seedless Phenotype Formation of Oil Palm

Oil palm (Elaeis guineensis Jacq.) is a well-known vegetable oil-yielding crop. Seedlessness is one of the most prominent traits in oil palm due to its low processing costs and high oil content. Nevertheless, an extensive study on molecular mechanisms regulating seedless phenotype formation in oil palm is very limited so far. In this study, stigma, style, and ovary from seedless and seeded (Tenera and Pisifera) oil palm trees were used to investigate the possible mechanism. Results showed that non-pollination resulted in no fruits, and self- and cross-pollinations resulted in seedless fruits, while boron treatment had no effect on seedless phenotype formation, implying that seedless trees have incomplete self and outcrossing incompatibility. Furthermore, the transcriptome data analysis highlighted eight programmed cell death (PCD) genes and three groups of PCD-related genes: 4-coumarate-CoA ligase (4CL), S-RNase, and MADS-box. The majority of these genes were significantly up-regulated in the stigma and style of Seedless palm trees compared to Tenera and Pisifera. In addition, the co-expression network analysis confirmed the significant correlation among these genes. Moreover, two simple sequence repeats (SSR) markers (S41 and S44) were developed to identify the seedless phenotype. The up-regulation of 4CL and MADS-box TFs activated the expression of PCD genes; on the other hand, S-RNase resulted in pollen tube RNA degradation and triggered PCD. While the link between PCD and seedless phenotype formation in oil palm has not been extensively studied to date, these findings suggest a role of PCD in pollen tube lethality, leading to double fertilization failure and the seedless phenotype.

Overexpression of BnaAGL11, a MADS-Box Transcription Factor, Regulates Leaf Morphogenesis and Senescence in Brassica napus

Previous studies have reported that SEEDSTICK/AGAMOUS-LIKE 11 (AtSTK/AtAGL11), a MADS-box transcription factor, plays important roles in many biological processes in Arabidopsis thaliana. However, the function of BnaAGL11, an AtAGL11 homologous gene from Brassica napus, in leaf development remains unknown. Here, we found that the ectopic expression of any copy of Bna.C09.AGL11, Bna.A03.AGL11, and Bna.A09.AGL11 in A. thaliana led to smaller and curly leaves and promoted leaf senescence. Consistently, the overexpression of Bna.C09.AGL11 in B. napus also caused smaller and curly leaves and accelerated leaf senescence. Furthermore, we demonstrated that Bna.C09.AGL11 controlled leaf morphogenesis by indirectly downregulating the genes of Bna.A01.DWF4 and Bna.C07.PGX3 and promoted leaf senescence by indirectly upregulating the genes of Bna.A04.ABI5, Bna.A05.ABI5, Bna.C04.ABI5-1, and Bna.C01.SEN4 and directly activating the transcription of Bna.C04.ABI5-2 and Bna.C03.SEN4 genes. Our results provide new insights into the underlying regulatory mechanism of BnaAGL11 during leaf development in B. napus.

Gene regulation network analyses of pistil development in papaya

BACKGROUND

The pistil is an essential part of flowers that functions in the differentiation of the sexes and reproduction in plants. The stigma on the pistil can accept pollen to allow fertilization and seed development. Papaya (Carica papaya L.) is a dioecious plant, where female flowers exhibit normal pistil, while the male flowers exhibit aborted pistil at a late stage of pistil development.

RESULTS

The developmental stages of papaya pistil were analyzed after first dividing it into slices representing the primordium stage 1 (S1), the pre-meiotic stages S2, post-meiotic stage S3, and the mitotic stage S4. The SS scoring algorithm analysis of genes preferentially expressed at different stages revealed differentially expressed genes between male and female flowers. A transcription factor regulatory network for each stage based on the genes that are differentially expressed between male and female flowers was constructed. Some transcription factors related to pistil development were revealed based on the analysis of regulatory networks such as CpAGL11, CpHEC2, and CpSUPL. Based on the specific expression of genes, constructed a gene regulatory subnetwork with CpAGL11-CpSUPL-CpHEC2 functioning as the core. Analysis of the functionally enriched terms in this network reveals several differentially expressed genes related to auxin/ brassinosteroid signal transduction in the plant hormone signal transduction pathway. At the same time, significant differences in the expression of auxin and brassinosteroid synthesis-related genes between male and female flowers at different developmental stages were detected.

CONCLUSIONS

The pistil abortion of papaya might be caused by the lack of expression or decreased expression of some transcription factors and hormone-related genes, affecting hormone signal transduction or hormone biosynthesis. Analysis of aborted and normally developing pistil in papaya provided new insights into the molecular mechanism of pistil development and sex differentiation in dioecious papaya.

Firming up your tomato: a natural promoter variation in a MADS-box gene is causing all-flesh tomatoes

This article comments on: Liu L, Zhang K, Bai JR, Lu J, Lu X, Hu J, Pan C, He S, Yuan J, Zhang Y, Zhang M, Guo Y, Wang X, Huang Z, Du Y, Cheng F, Li J. 2022. All-flesh fruit in tomato is controlled by reduced expression dosage of AFF through a structural variant mutation in the promoter. Journal of Experimental Botany 73, 123–138.

All-flesh fruit in tomato is controlled by reduced expression dosage of AFF through a structural variant mutation in the promoter

The formation of locule gel is an important process in tomato and is a typical characteristic of berry fruit. In this study, we examined a natural tomato mutant that produces all-flesh fruit (AFF) in which the locule tissue remains in a solid state during fruit development. We constructed different genetic populations to fine-map the causal gene for this trait and identified SlMBP3 as the locus conferring the locule gel formation, which we rename as AFF. We determined the causal mutation as a 416-bp deletion in the promoter region of AFF, which reduces its expression dosage. Generally, this sequence is highly conserved among Solanaceae, as well as within the tomato germplasm. Using BC6 near-isogenic lines, we determined that the reduced expression dosage of AFF did not affect the normal development of seeds, whilst producing unique, non-liquefied locule tissue that was distinct from that of normal tomatoes in terms of metabolic components. Combined analysis using mRNA-seq and metabolomics indicated the importance of AFF in locule tissue liquefaction. Our findings provide insights into fruit-type differentiation in Solanaceae crops and also present the basis for future applications of AFF in tomato breeding programs.

Whole-transcriptome analysis of differentially expressed genes between ray and disc florets and identification of flowering regulatory genes in Chrysanthemum morifolium

Chrysanthemum morifolium has ornamental and economic values. However, there has been minimal research on the morphology of the chrysanthemum florets and related genes. In this study, we used the leaves as a control to screen for differentially expressed genes between ray and disc florets in chrysanthemum flowers. A total of 8,359 genes were differentially expressed between the ray and disc florets, of which 3,005 were upregulated and 5,354 were downregulated in the disc florets. Important regulatory genes that control flower development and flowering determination were identified. Among them, we identified a TM6 gene (CmTM6-mu) that belongs to the Class B floral homeotic MADS-box transcription factor family, which was specifically expressed in disc florets. We isolated this gene and found it was highly similar to other typical TM6 lineage genes, but a single-base deletion at the 3' end of the open reading frame caused a frame shift that generated a protein in which the TM6-specific paleoAP3 motif was missing at the C terminus. The CmTM6-mu gene was ectopically expressed in Arabidopsis thaliana. Petal and stamen developmental processes were unaffected in transgenic A. thaliana lines; however, the flowering time was earlier than in the wild-type control. Thus, the C-terminal of paleoAP3 appears to be necessary for the functional performance in regulating the development of petals or stamens and CmTM6-mu may be involved in the regulation of flowering time in chrysanthemum. The results of this study will be useful for future research on flowering molecular mechanisms and for the breeding of novel flower types.

Integrative Analyses of Metabolomes and Transcriptomes Provide Insights into Flavonoid Variation in Grape Berries

Flavonoids in grapes contribute the quality of the berry, but the flavonoid diversity and the regulatory networks underlying the variation require a further investigation. In this study, we integrated multi-omics data to systematically explore the global metabolic and transcriptional profiles in the skins and pulps of three grape cultivars. The results revealed large-scale differences involved in the flavonoid metabolic pathway. A total of 133 flavonoids, including flavone and flavone C-glycosides, were identified. Beyond the visible differences of anthocyanins, there was large variation in other sub-branched flavonoids, most of which were positively correlated with anthocyanins in grapes. The expressions of most flavonoid biosynthetic genes and the major regulators MYBA1 were strongly consistent with the changes in flavonoids. Integrative analysis identified two novel transcription factors (MYB24 and MADS5) and two ubiquitin proteins (RHA2) as promising regulatory candidates for flavonoid biosynthesis in grapes. Further verification in various grape accessions indicated that five major genes including flavonol 3'5'-hydroxylase (F3'5'H), UDP-glucose:flavonoid 3-O-glycosyl-transferase, anthocyanin O-methyltransferase, acyltransferase (3AT), and glutathione S-transferase (GST4) controlled flavonoid variation in grape berries. These findings provide valuable information for understanding the mechanism of flavonoid biosynthesis in grape berries and the further development of grape health products.

The co-expression of genes involved in seed coat and endosperm development promotes seed abortion in grapevine

The seed coat gene VviAGL11 coordinates with endosperm development genes FIS2, PHERESE1 and IKU2 and functions as the key regulator in seed development and abortion processes in grapevine. Seed development is essential for the reproduction of flowering plants. Seed abortion is a specific characteristic that produces seedless berries and is often observed in cultivated grapevines. Although seedlessness is an important trait for table and dried grapevine production, the mechanism of seed abortion remains poorly understood. This research aimed to analyze the co-expression of the seed coat development gene VviAGL11 and the endosperm development genes FERTILIZATION INDEPENDENT SEED2 (FIS2), PHERESE1 and HAIKU2 (IKU2) that regulate seedless fruit development in grapevine. The transcript levels of VviAGL11, FIS2, PHERESE1 and IKU2 all decreased during seed abortion in the seedless grape 'Thompson Seedless' plants, compared to those of the seeded grape 'Pinot Noir'. The transcript levels of the salicylic acid (SA)-dependent defense response genes EDS1, NPR1, NDR1 and SID2 were higher in 'Thompson Seedless' than 'Pinot Noir' during seed development. Also, WRKY3, WRKY6 and WRKY52, which participate in the SA pathway, were higher expressed in 'Thompson Seedless' than in 'Pinot Noir', indicating that SA-dependent defense responses may regulate seed abortion. The genes related to synthesis and metabolism of gibberellic acid (GA) and abscisic acid (ABA) also showed differential expression between 'Thompson Seedless' and 'Pinot Noir'. Exogenous applications of plant growth regulators (PGRs) to inflorescences of three stenospermocarpy grapevines before flowering showed that GA₃ was critical prominently in seed development. Therefore, the co-expression of seed coat and endosperm development-related genes, SA pathway genes, and genes for the synthesis and metabolism of GA₃ together enhance seed abortion in seedless grapes.

VvHDZ28 positively regulate salicylic acid biosynthesis during seed abortion in Thompson Seedless

Seedlessness in grapes is one of the features most appreciated by consumers. However, the mechanisms underlying seedlessness in grapes remain obscure. Here, we observe small globular embryos and globular embryos in Pinot Noir and Thompson Seedless from 20 to 30 days after flowering (DAF). From 40 to 50 DAF, we observe torpedo embryos and cotyledon embryos in Pinot Noir but aborted embryos and endosperm in Thompson Seedless. Thus, RNA-Seq analyses of seeds at these stages from Thompson Seedless and Pinot Noir were performed. A total of 6442 differentially expressed genes were identified. Among these, genes involved in SA biosynthesis, VvEDS1 and VvSARD1, were more highly expressed in Thompson Seedless than in Pinot Noir. Moreover, the content of endogenous SA is at least five times higher in Thompson Seedless than in Pinot Noir. Increased trimethylation of H3K27 of VvEDS1 and VvSARD1 may be correlated with lower SA content in Pinot Noir. We also demonstrate that VvHDZ28 positively regulates the expression of VvEDS1. Moreover, over-expression of VvHDZ28 results in seedless fruit and increased SA contents in Solanum lycopersicum. Our results reveal the potential role of SA and feedback regulation of VvHDZ28 in seedless grapes.

Integrative genomics reveals paths to sex dimorphism in Salix purpurea L

Sex dimorphism and gene expression were studied in developing catkins in 159 F2 individuals from the bioenergy crop Salix purpurea, and potential mechanisms and pathways for regulating sex development were explored. Differential expression, eQTL, bisulfite sequencing, and network analysis were used to characterize sex dimorphism, detect candidate master regulator genes, and identify pathways through which the sex determination region (SDR) may mediate sex dimorphism. Eleven genes are presented as candidates for master regulators of sex, supported by gene expression and network analyses. These include genes putatively involved in hormone signaling, epigenetic modification, and regulation of transcription. eQTL analysis revealed a suite of transcription factors and genes involved in secondary metabolism and floral development that were predicted to be under direct control of the sex determination region. Furthermore, data from bisulfite sequencing and small RNA sequencing revealed strong differences in expression between males and females that would implicate both of these processes in sex dimorphism pathways. These data indicate that the mechanism of sex determination in Salix purpurea is likely different from that observed in the related genus Populus. This further demonstrates the dynamic nature of SDRs in plants, which involves a multitude of mechanisms of sex determination and a high rate of turnover.

Molecular Characterization and Phylogenetic Analysis of MADS-Box Gene VroAGL11 Associated with Stenospermocarpic Seedlessness in Muscadine Grapes

Reduced expression of MADS-box gene AGAMOUS-LIKE11 (VviAGL11) is responsible for stenospermocarpic seedlessness in bunch grapes. This study is aimed to characterize the VviAGL11 orthologous gene (VroAGL11) in native muscadine grapes (Vitis rotundifolia) at the molecular level and analyze its divergence from other plants. The VroAGL11 transcripts were found in all muscadine cultivars tested and highly expressed in berries while barely detectable in leaves. RT-PCR and sequencing of predicted ORFs from diverse grape species showed that AGL11 transcripts were conservatively spliced. The encoded VroAGL11 protein contains highly conserved MADS-MEF2-like domain, MADS domain, K box, putative phosphorylation site and two sumoylation motifs. The muscadine VroAGL11 proteins are almost identical (99%) to that of seeded bunch cultivar, Chardonnay, except in one amino acid (A79G), but differs from mutant protein of seedless bunch grape, Sultanina, in two amino acids, R197L and T210A. Phylogenetic analysis showed that AGL11 gene of muscadine and other Vitis species formed a separate clade than that of other eudicots and monocots. Muscadine grape cultivar "Jane Bell" containing the highest percentage of seed content in berry (7.2% of berry weight) had the highest VroAGL11 expression, but almost none to nominal expression in seedless cultivars Fry Seedless (muscadine) and Reliance Seedless (bunch). These findings suggest that VroAGL11 gene controls the seed morphogenesis in muscadine grapes like in bunch grape and can be manipulated to induce stenospermocarpic seedlessness using gene editing technology.

ZbAGL11, a class D MADS-box transcription factor of Zanthoxylum bungeanum, is involved in sporophytic apomixis

Apomixis is a reproductive model that bypasses sexual reproduction, so it does not require the combination of paternal and maternal gametes but instead results in the production of offspring directly from maternal tissues. This reproductive mode results in the same genetic material in the mother and the offspring and has significant applications in agricultural breeding. Molecular and cytological methods were used to identify the reproductive type of Zanthoxylum bungeanum (ZB). Fluorescence detection of the amplified products of 12 pairs of polymorphic SSR primers showed consistent fluorescence signals for mother and offspring, indicating that no trait separation occurred during reproduction. In addition, the cytological observation results showed differentiation of ZB embryos (2n) from nucellar cells (2n) to form indefinite embryonic primordia and then form adventitious embryos (2n), indicating that the apomictic type of ZB is sporophytic apomixis. The MADS-box transcription factor ZbAGL11 was highly expressed during the critical period of nucellar embryo development in ZB. Unpollinated ZbAGL11-OE Arabidopsis produced fertile offspring and exhibited an apomictic phenotype. The overexpression of ZbAGL11 increased the callus induction rate of ZB tissue. In addition, the results of the yeast two-hybrid experiment showed that ZbAGL11 could interact with the ZbCYP450 and ZbCAD11 proteins. Our results demonstrate that ZbAGL11 can cause developmental disorders of Arabidopsis flower organs and result in apomixis-like phenotypes.

Bulk RNA-Seq analysis to dissect the regulation of stigma position in tomato

Transcriptomic analysis of tomato genotypes contrasting for stigma position suggests that stigma insertion occurred by the disruption of a process that finds a parallel in Arabidopsis gynoecium development. Domestication of cultivated tomato (Solanum lycopersicum L.) included the transition from allogamy to autogamy that occurred through the loss of self-incompatibilty and the retraction of the stigma within the antheridial cone. Although the inserted stigma is an established phenotype in modern tomatoes, an exserted stigma is still present in several landraces or vintage varieties. Moreover, exsertion of the stigma is a frequent response to high temperature stress and, being a cause of reduced fertility, a trait of increasing importance. Few QTLs for stigma position have been described and only one of the underlying genes identified. To gain insights on genes involved in stigma position in tomato, a bulk RNA sequencing (RNA-Seq) approach was adopted, using two groups of contrasting genotypes. Phenotypic analysis confirmed the extent and the stability of stigma position in the selected genotypes, whereas they were highly heterogeneous for other reproductive and productive traits. The RNA-Seq analysis yielded 801 differentially expressed genes (DEGs), 566 up-regulated and 235 down-regulated in the genotypes with exserted stigma. Validation by quantitative PCR indicated a high reliability of the RNA-Seq data. Up-regulated DEGs were enriched for genes involved in the cell wall metabolism, lipid transport, auxin response and flavonoid biosynthesis. Down-regulated DEGs were enriched for genes involved in translation. Validation of selected genes on pistil tissue of the 26 single genotypes revealed that differences between bulks could both be due to a general trend of the bulk or to the behaviour of single genotypes. Novel candidate genes potentially involved in the control of stigma position in tomato are discussed.

Identification, characterization and functional analysis of AGAMOUS subfamily genes associated with floral organs and seed development in Marigold (Tagetes erecta)

BACKGROUND

AGAMOUS (AG) subfamily genes regulate the floral organs initiation and development, fruit and seed development. At present, there has been insufficient study of the function of AG subfamily genes in Asteraceae. Marigold (Tagetes erecta) belongs to Asteraceae family whose unique inflorescence structure makes it an important research target for understanding floral organ development in plants.

RESULTS

Four AG subfamily genes of marigold were isolated and phylogenetically grouped into class C (TeAG1 and TeAG2) and class D (TeAGL11-1 and TeAGL11-2) genes. Expression profile analysis demonstrated that these four genes were highly expressed in reproductive organs of marigold. Subcellular localization analysis suggested that all these four proteins were located in the nucleus. Protein-protein interactions analysis indicated that class C proteins had a wider interaction manner than class D proteins. Function analysis of ectopic expression in Arabidopsis thaliana revealed that TeAG1 displayed a C function specifying the stamen identity and carpel identity, and that TeAGL11-1 exhibited a D function regulating seed development and petal development. In addition, overexpression of both TeAG1 and TeAGL11-1 leaded to curling rosette leaf and early flowering in Arabidopsis thaliana.

CONCLUSIONS

This study provides an insight into molecular mechanism of AG subfamily genes in Asteraceae species and technical support for improvement of several floral traits.

Unraveling the Deep Genetic Architecture for Seedlessness in Grapevine and the Development and Validation of a New Set of Markers for VviAGL11-Based Gene-Assisted Selection

Seedless inheritance has been considered a quasi-monogenic trait based on the VvAGL11 gene. An intragenic simple sequence repeat (SSR) marker, p3_VvAGL11, is currently used to opportunely discard seeded progeny, which represents up to 50% of seedlings to be established in the field. However, the rate of false positives remains significant, and this lack of accuracy might be due to a more complex genetic architecture, some intrinsic flaws of p3_VvAGL11, or potential recombination events between p3_VvAGL11 and the causal SNP located in the coding region. The purpose of this study was to update the genetic architecture of this trait in order to better understand its implications in breeding strategies. A total of 573 F1 individuals that segregate for seedlessness were genotyped with a 20K SNP chip and characterized phenotypically during four seasons for a fine QTL mapping analysis. Based on the molecular diversity of p3_VvAGL11 alleles, we redesigned this marker, and based on the causal SNP, we developed a qPCR-HRM marker for high-throughput and a Tetra-ARMS-PCR for simple predictive analyses. Up to 10 new QTLs were identified that describe the complex nature of seedlessness, corresponding to small but stable effects. The positive predictive value, based on VvAGL11 alone (0.647), was improved up to 0.814 when adding three small-effect QTLs in a multi-QTL additive model as a proof of concept. The new SSR, 5U_VviAGL11, is more informative and robust, and easier to analyze. However, we demonstrated that the association can be lost by intragenic recombination and that the e7_VviAGL11 SNP-based marker is thus more reliable and decreases the occurrence of false positives. This study highlights the bases of prediction failure based solely on a major gene and a reduced set of candidate genes, in addition to opportunities for molecular breeding following further and larger validation studies.

New disease-resistant, seedless grapes are developed using embryo rescue and molecular markers

Improving the operation of embryo rescue technology is a highly efficient way to breed new high-quality cultivars of seedless, disease-resistant grapes when using a stenospermocarpic Vitis vinifera L. (female parents) hybrid with Chinese wild Vitis (male parents). In this study, sampling time had a significant effect on embryo recovery. Four crosses were investigated to improve the embryo rescue efficiency by determining the best sampling time, which was found to be 40, 50, 55, and 57 days after pollination (DAP) for 'Flame seedless' × 'Ruby seedless', 'Kunxiang seedless' × 'Flame seedless', 'Ruby seedless' self-pollination and 'Ruby seedless' × 'Flame seedless', respectively. The highest percentage embryo germination ranged from 60.83 to 89.10% for four cross-combinations when the embryo was germinated on woody plant medium (WPM), with 1.0-μM thidiazuron (TDZ, a potent cytokinin). For 11 cross-combinations, the embryo recovery rate varied from 4.8 to 29.6% and the plant development rate varied from 17.1 to 78.9%. 'Ruby seedless' was the best female parent followed by 'Flame seedless'. The Grape Seedless gene Probe 1 (GSLP1) and SCF27 molecular markers were used to assist the identification of the seedless traits of the 388 progeny. A total of 309 plantlets were amplified, with the specific bands at 569-bp and 2k-bp being preliminarily considered as seedless. The S382-615 marker was used to identify the downy mildew resistance of the 'Ruby seedless' × 'Beichun' cross. Two F1 progeny were amplified, with the specific band at 615-bp being identified as downy mildew resistance.

The grapevine homeobox gene VvHB58 influences seed and fruit development through multiple hormonal signaling pathways

BACKGROUND

The homeobox transcription factor has a diversity of functions during plant growth and development process. Previous transcriptome analyses of seed development in grape hybrids suggested that specific homeodomain transcription factors are involved in seed development in seedless cultivars. However, the molecular mechanism of homeobox gene regulating seed development in grape is rarely reported.

RESULTS

Here, we report that the grapevine VvHB58 gene, encoding a homeodomain-leucine zipper (HD-Zip I) transcription factor, participates in regulating fruit size and seed number. The VvHB58 gene was differentially expressed during seed development between seedless and seeded cultivars. Subcellular localization assays revealed that the VvHB58 protein was located in the nucleus. Transgenic expression of VvHB58 in tomato led to loss of apical dominance, a reduction in fruit pericarp expansion, reduced fruit size and seed number, and larger endosperm cells. Analysis of the cytosine methylation levels within the VvHB58 promoter indicated that the differential expression during seed development between seedless and seeded grapes may be caused by different transcriptional regulatory mechanisms rather than promoter DNA methylation. Measurements of five classic endogenous hormones and expression analysis of hormone-related genes between VvHB58 transgenic and nontransgenic control plants showed that expression of VvHB58 resulted in significant changes in auxin, gibberellin and ethylene signaling pathways. Additionally, several DNA methylation-related genes were expressed differentially during seed development stages in seedless and seeded grapes, suggesting changes in methylation levels during seed development may be associated with seed abortion.

CONCLUSION

VvHB58 has a potential function in regulating fruit and seed development by impacting multiple hormonal pathways. These results expand understanding of homeodomain transcription factors and potential regulatory mechanism of seed development in grapevine, and provided insights into molecular breeding for grapes.

Pollination Type Recognition from a Distance by the Ovary Is Revealed Through a Global Transcriptomic Analysis

Sexual reproduction in flowering plants involves intimate contact and continuous interactions between the growing pollen tube and the female reproductive structures. These interactions can trigger responses in distal regions of the flower well ahead of fertilization. While pollination-induced petal senescence has been studied extensively, less is known about how pollination is perceived at a distance in the ovary, and how specific this response is to various pollen genotypes. To address this question, we performed a global transcriptomic analysis in the ovary of a wild potato species, Solanum chacoense, at various time points following compatible, incompatible, and heterospecific pollinations. In all cases, pollen tube penetration in the stigma was initially perceived as a wounding aggression. Then, as the pollen tubes grew in the style, a growing number of genes became specific to each pollen genotype. Functional classification analyses revealed sharp differences in the response to compatible and heterospecific pollinations. For instance, the former induced reactive oxygen species (ROS)-related genes while the latter affected genes associated to ethylene signaling. In contrast, incompatible pollination remained more akin to a wound response. Our analysis reveals that every pollination type produces a specific molecular signature generating diversified and specific responses at a distance in the ovary in preparation for fertilization.

RNA interference suppression of AGAMOUS and SEEDSTICK alters floral organ identity and impairs floral organ determinacy, ovule differentiation, and seed-hair development in Populus

The role of the floral homeotic gene AGAMOUS (AG) and its close homologues in development of anemophilous, unisexual catkins has not previously been studied. We transformed two RNA interference (RNAi) constructs, PTG and its matrix-attachment-region flanked version MPG, into the early-flowering female poplar clone 6K10 (Populus alba) to suppress the expression of its two duplicate AG orthologues. By early 2018, six out of 22 flowering PTG events and 11 out of 12 flowering MPG events showed modified floral phenotypes in a field trial in Oregon, USA. Flowers in catkins from modified events had 'carpel-inside-carpel' phenotypes. Complete disruption of seed production was observed in seven events, and sterile anther-like organs in 10 events. Events with strong co-suppression of both the two AG and two SEEDSTICK (STK) paralogues lacked both seeds and associated seed hairs. Alterations in all of the modified floral phenotypes were stable over 4 yr of study. Trees from floral-modified events did not differ significantly (P < 0.05) from nonmodified transgenic or nontransgenic controls in biomass growth or leaf morphology. AG and STK genes show strong conservation of gene function during poplar catkin development and are promising targets for genetic containment of exotic or genetically engineered trees.

An AGAMOUS MADS-box protein, SlMBP3, regulates the speed of placenta liquefaction and controls seed formation in tomato

AGAMOUS (AG) MADS-box transcription factors have been shown to play crucial roles in floral organ and fruit development in angiosperms. Here, we isolated a tomato (Solanum lycopersicum) AG MADS-box gene SlMBP3 and found that it is preferentially expressed in flowers and during early fruit developmental stages in the wild-type (WT), and in the Nr (never ripe) and rin (ripening inhibitor) mutants. Its transcripts are notably accumulated in the pistils; transcripts abundance decrease during seed and placental development, increasing again during flower development. SlMBP3-RNAi tomato plants displayed fleshy placenta without locular gel and extremely malformed seeds with no seed coat, while SlMBP3-overexpressing plants exhibited advanced liquefaction of the placenta and larger seeds. Enzymatic activities related to cell wall modification, and the contents of cell wall components and pigments were dramatically altered in the placentas of SlMBP3-RNAi compared with the WT. Alterations in these physiological features were also observed in the placentas of SlMBP3-overexpressing plants. The lignin content of mature seeds in SlMBP3-RNAi lines was markedly lower than that in the WT. RNA-seq and qRT-PCR analyses revealed that genes involved in seed development and the biosynthesis of enzymes related to cell wall modification, namely gibberellin, indole-3-acetic acid, and abscisic acid were down-regulated in the SlMBP3-RNAi lines. Taking together, our results demonstrate that SlMBP3 is involved in the regulation of placenta and seed development in tomato.

The parthenocarpic gene Pat-k is generated by a natural mutation of SlAGL6 affecting fruit development in tomato (Solanum lycopersicum L.)

BACKGROUND

Parthenocarpy is a desired trait in tomato because it can overcome problems with fruit setting under unfavorable environmental conditions. A parthenocarpic tomato cultivar, 'MPK-1', with a parthenocarpic gene, Pat-k, exhibits stable parthenocarpy that produces few seeds. Because 'MPK-1' produces few seeds, seedlings are propagated inefficiently via cuttings. It was reported that Pat-k is located on chromosome 1. However, the gene had not been isolated and the relationship between the parthenocarpy and low seed set in 'MPK-1' remained unclear. In this study, we isolated Pat-k to clarify the relationship between parthenocarpy and low seed set in 'MPK-1'.

RESULTS

Using quantitative trait locus (QTL) analysis for parthenocarpy and seed production, we detected a major QTL for each trait on nearly the same region of the Pat-k locus on chromosome 1. To isolate Pat-k, we performed fine mapping using an F₄ population following the cross between a non-parthenocarpic cultivar, 'Micro-Tom' and 'MPK-1'. The results showed that Pat-k was located in the 529 kb interval between two markers, where 60 genes exist. By using data from a whole genome re-sequencing and genome sequence analysis of 'MPK-1', we could identify that the SlAGAMOUS-LIKE 6 (SlAGL6) gene of 'MPK-1' was mutated by a retrotransposon insertion. The transcript level of SlAGL6 was significantly lower in ovaries of 'MPK-1' than a non-parthenocarpic cultivar. From these results, we could conclude that Pat-k is SlAGL6, and its down-regulation in 'MPK-1' causes parthenocarpy and low seed set. In addition, we observed abnormal micropyles only in plants homozygous for the 'MPK-1' allele at the Pat-k/SlAGL6 locus. This result suggests that Pat-k/SlAGL6 is also related to ovule formation and that the low seed set in 'MPK-1' is likely caused by abnormal ovule formation through down-regulation of Pat-k/SlAGL6.

CONCLUSIONS

Pat-k is identical to SlAGL6, and its down-regulation causes parthenocarpy and low seed set in 'MPK-1'. Moreover, down-regulation of Pat-k/SlAGL6 could cause abnormal ovule formation, leading to a reduction in the number of seeds.

MADS-box genes and crop domestication: the jack of all traits

MADS-box genes are key regulators of virtually every aspect of plant reproductive development. They play especially prominent roles in flowering time control, inflorescence architecture, floral organ identity determination, and seed development. The developmental and evolutionary importance of MADS-box genes is widely acknowledged. However, their role during flowering plant domestication is less well recognized. Here, we provide an overview illustrating that MADS-box genes have been important targets of selection during crop domestication and improvement. Numerous examples from a diversity of crop plants show that various developmental processes have been shaped by allelic variations in MADS-box genes. We propose that new genomic and genome editing resources provide an excellent starting point for further harnessing the potential of MADS-box genes to improve a variety of reproductive traits in crops. We also suggest that the biophysics of MADS-domain protein-protein and protein-DNA interactions, which is becoming increasingly well characterized, makes them especially suited to exploit coding sequence variations for targeted breeding approaches.

Overexpression of the class D MADS-box gene Sl-AGL11 impacts fleshy tissue differentiation and structure in tomato fruits

MADS-box transcription factors are key elements of the genetic networks controlling flower and fruit development. Among these, the class D clade gathers AGAMOUS-like genes which are involved in seed, ovule, and funiculus development. The tomato genome comprises two class D genes, Sl-AGL11 and Sl-MBP3, both displaying high expression levels in seeds and in central tissues of young fruits. The potential effects of Sl-AGL11 on fruit development were addressed through RNAi silencing and ectopic expression strategies. Sl-AGL11-down-regulated tomato lines failed to show obvious phenotypes except a slight reduction in seed size. In contrast, Sl-AGL11 overexpression triggered dramatic modifications of flower and fruit structure that include: the conversion of sepals into fleshy organs undergoing ethylene-dependent ripening, a placenta hypertrophy to the detriment of locular space, starch and sugar accumulation, and an extreme softening that occurs well before the onset of ripening. RNA-Seq transcriptomic profiling highlighted substantial metabolic reprogramming occurring in sepals and fruits, with major impacts on cell wall-related genes. While several Sl-AGL11-related phenotypes are reminiscent of class C MADS-box genes (TAG1 and TAGL1), the modifications observed on the placenta and cell wall and the Sl-AGL11 expression pattern suggest an action of this class D MADS-box factor on early fleshy fruit development.

Genome-wide identification of pistil-specific genes expressed during fruit set initiation in tomato (Solanum lycopersicum)

Fruit set involves the developmental transition of an unfertilized quiescent ovary in the pistil into a fruit. While fruit set is known to involve the activation of signals (including various plant hormones) in the ovary, many biological aspects of this process remain elusive. To further expand our understanding of this process, we identified genes that are specifically expressed in tomato (Solanum lycopersicum L.) pistils during fruit set through comprehensive RNA-seq-based transcriptome analysis using 17 different tissues including pistils at six different developmental stages. First, we identified 532 candidate genes that are preferentially expressed in the pistil based on their tissue-specific expression profiles. Next, we compared our RNA-seq data with publically available transcriptome data, further refining the candidate genes that are specifically expressed within the pistil. As a result, 108 pistil-specific genes were identified, including several transcription factor genes that function in reproductive development. We also identified genes encoding hormone-like peptides with a secretion signal and cysteine-rich residues that are conserved among some Solanaceae species, suggesting that peptide hormones may function as signaling molecules during fruit set initiation. This study provides important information about pistil-specific genes, which may play specific roles in regulating pistil development in relation to fruit set.

Silencing SlAGL6, a tomato AGAMOUS-LIKE6 lineage gene, generates fused sepal and green petal

Silencing SlAGL6 in tomato leads to fused sepal and green petal by influencing the expression of A-, B-class genes. AGAMOUS-LIKE6 (AGL6) lineage is an important clade MADS-box transcription factor and plays essential roles in various developmental programs especially in flower meristem and floral organ development. Here, we isolated a tomato AGL6 lineage gene SlAGL6 and successfully obtained several RNA interference (RNAi) lines. Silencing SlAGL6 led to abnormal fused sepals and light green petals with smaller size. The total chlorophyll content in transgenic petals increased and the morphology of epidermis cells altered. Further analysis showed that A-class gene MACROCALYX (MC) participating in sepal development and a NAC-domain gene GOBLET involving in boundary establishment were down-regulated in transgenic lines. In transgenic petals, two chlorophyll synthesis genes, Golden2-like1 (SlGLK1) and Golden2-like2 (SlGLK2), two photosystem-related genes, ribulose bisphosphate carboxylase small chain 3B (SlrbcS3B) and chlorophyll a/b-binding protein 7 (SlCab-7) were induced and three B-class genes TM6, TAP3 and SlGLO1 were repressed. These results suggest that SlAGL6 involves in tomato sepal and petal development.

The MADS-box gene Agamous-like 11 is essential for seed morphogenesis in grapevine

Despite the wide appreciation of seedless grapes, little is known about the molecular mechanisms that drive the stenospermocarpic seedless-type phenotype in grapevine. In order to address the molecular mechanisms that control seedlessness in grapevine, our study aimed to characterize VviAGL11, a class D MADS-box transcription factor gene that has been proposed as the major candidate gene involved in Vitis vinifera seed morphogenesis. VviAGL11 allelic variations in seeded and seedless grapevine cultivars were determined, and its correlations with allele-specific steady-state mRNA levels were investigated. VviAGL11 relative expression was significantly higher in seeds at 2, 4, and 6 weeks after fruit set, whereas in the seedless grape its transcript levels were extremely low in all stages analyzed. In situ hybridization revealed transcript accumulation specifically in the dual endotesta layer of the seeds, which is responsible for elongation and an increase of cell number, a necessary step to determine the lignification and the final seed size. No hybridization signals were visible in the seedless grapevine tissues, and a morphoanatomical analysis showed an apparent loss of identity of the endotesta layer of the seed traces. Ectopic expression of VviAGL11 in the Arabidopsis SEEDSTICK mutant background restored the wild-type phenotype and confirmed the direct role of VviAGL11 in seed morphogenesis, suggesting that depletion of its expression is responsible for the erroneous development of a highly essential seed layer, therefore culminating in the typical apirenic phenotype.

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.