Cytokinin-induced parthenocarpic fruit development in tomato is partly dependent on enhanced gibberellin and auxin biosynthesis

New Advances in the Study of Regulation of Tomato Flowering-Related Genes Using Biotechnological Approaches

The tomato is a convenient object for studying reproductive processes, which has become a classic. Such complex processes as flowering and fruit setting require an understanding of the fundamental principles of molecular interaction, the structures of genes and proteins, the construction of signaling pathways for transcription regulation, including the synchronous actions of cis-regulatory elements (promoter and enhancer), trans-regulatory elements (transcription factors and regulatory RNAs), and transposable elements and epigenetic regulators (DNA methylation and acetylation, chromatin structure). Here, we discuss the current state of research on tomatoes (2017-2023) devoted to studying the function of genes that regulate flowering and signal regulation systems using genome-editing technologies, RNA interference gene silencing, and gene overexpression, including heterologous expression. Although the central candidate genes for these regulatory components have been identified, a complete picture of their relationship has yet to be formed. Therefore, this review summarizes the latest achievements related to studying the processes of flowering and fruit set. This work attempts to display the gene interaction scheme to better understand the events under consideration.

Loss of S-nitrosoglutathione reductase disturbs phytohormone homeostasis and regulates shoot side branching and fruit growth in tomato

S-Nitrosoglutathione plays a central role in nitric oxide (NO) homeostasis, and S-nitrosoglutathione reductase (GSNOR) regulates the cellular levels of S-nitrosoglutathione across kingdoms. Here, we investigated the role of endogenous NO in shaping shoot architecture and controlling fruit set and growth in tomato (Solanum lycopersicum). SlGSNOR silencing promoted shoot side branching and led to reduced fruit size, negatively impacting fruit yield. Greatly intensified in slgsnor knockout plants, these phenotypical changes were virtually unaffected by SlGSNOR overexpression. Silencing or knocking out of SlGSNOR intensified protein tyrosine nitration and S-nitrosation and led to aberrant auxin production and signaling in leaf primordia and fruit-setting ovaries, besides restricting the shoot basipetal polar auxin transport stream. SlGSNOR deficiency triggered extensive transcriptional reprogramming at early fruit development, reducing pericarp cell proliferation due to restrictions on auxin, gibberellin, and cytokinin production and signaling. Abnormal chloroplast development and carbon metabolism were also detected in early-developing NO-overaccumulating fruits, possibly limiting energy supply and building blocks for fruit growth. These findings provide new insights into the mechanisms by which endogenous NO fine-tunes the delicate hormonal network controlling shoot architecture, fruit set, and post-anthesis fruit development, emphasizing the relevance of NO-auxin interaction for plant development and productivity.

Exogenous spraying of 4-chlorophenoxyacetic acid sodium salt promotes growth and flavonoid biosynthesis of mulberry leaves (Morus alba L.)

Mulberry (Morus alba L.) leaves are known as an ideal vegetable with good antioxidant effect, which can bring delicious taste and multiple health benefits. In the present study, the effects of 4-Chlorophenoxyacetic acid sodium salt (4-CPANa) treatment on growth and content of flavonoid compounds in mulberry leaves were investigated. Moreover, the changes in the expression levels of genes involved in flavonoid biosynthetic pathways, and the accumulation of important secondary metabolites including rutin (Rut), chlorogenic acid (ChA), isoquercitrin (IQ) and astragalin (Ast), were investigated in mulberry leaves. The results showed that 4-CPANa treatment could significantly promote the differentiation and growth of mulberry, increased shoot number, bud number, leaf fresh weight and leaf area of mulberry compared with control. Besides, the contents of ChA, Rut, IQ and Ast were significantly increased after 4-CPANa (5 mg/L) treatment. Further analysis revealed that 5 mg/L 4-CPANa strongly induced the expression of flavonoid biosynthesis-related genes including flavonoid 3-O-glucosyltransferase (F3GT) gene, chalcone synthase (CHS) gene, 4-xoumarate-CoA ligase (4CL) and phenylalanine ammonia lyase (PAL) gene. In conclusion, exogenous spraying of 4-CPANa provides a new way to improve the medicinal quality and development of mulberry leaf food with high value.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-023-01339-z.

Effect of nitrogen application on enhancing high-temperature stress tolerance of tomato plants during the flowering and fruiting stage

This study was conducted to investigate the effects of nitrogen application on growth, photosynthetic performance, nitrogen metabolism activities, and fruit quality of tomato plants under high-temperature (HT) stress. Three levels of daily minimum/daily maximum temperature were adopted during the flowering and fruiting stage, namely control (CK; 18°C/28°C), sub-high temperature (SHT; 25°C/35°C), and high-temperature (HT; 30°C/40°C) stress. The levels of nitrogen (urea, 46% N) were set as 0 (N₁), 125 (N₂), 187.5 (N₃), 250 (N₄), and 312.5 (N₅) kg hm², respectively, and the duration lasted for 5 days (short-term). HT stress inhibited the growth, yield, and fruit quality of tomato plants. Interestingly, short-term SHT stress improved growth and yield via higher photosynthetic efficiency and nitrogen metabolism whereas fruit quality was reduced. Appropriate nitrogen application can enhance the high-temperature stress tolerance of tomato plants. The maximum net photosynthetic rate (P _Nmax), stomatal conductance (g _s), stomatal limit value (L_S), water-use efficiency (WUE), nitrate reductase (NR), glutamine synthetase (GS), soluble protein, and free amino acids were the highest in N₃, N₃, and N₂, respectively, for CK, SHT, and HT stress, whereas carbon dioxide concentration (C _i), was the lowest. In addition, maximum SPAD value, plant morphology, yield, Vitamin C, soluble sugar, lycopene, and soluble solids occurred at N₃-N₄, N₃-N₄, and N₂-N₃, respectively, for CK, SHT, and HT stress. Based on the principal component analysis and comprehensive evaluation, we found that the optimum nitrogen application for tomato growth, yield, and fruit quality was 230.23 kg hm² (N₃-N₄), 230.02 kg hm² (N₃-N₄), and 115.32 kg hm² (N₂), respectively, at CK, SHT, and HT stress. Results revealed that the high yield and good fruit quality of tomato plants at high temperatures can be maintained by higher photosynthesis, nitrogen efficiency, and nutrients with moderate nitrogen.

Genome-wide identification and characterization of parthenocarpic fruit set-related gene homologs in cucumber (Cucumis sativus L.)

Cucumber (Cucumis sativus L.), a major horticultural crop, in the family Cucurbitaceae is grown and consumed globally. Parthenocarpy is an ideal trait for many fruit and vegetables which produces seedless fruit desired by consumers. The seedlessness occurs when fruit develops without fertilization which can be either natural or induced. So far, a limited number of genes regulating parthenocarpic fruit set have been reported in several fruit or vegetable crops, most of which are involved in hormone biosynthesis or signalling. Although parthenocarpic cucumber has been widely used in commercial production for a long time; its genetic basis is not well understood. In this study, we retrieved thirty five parthenocarpy fruit-set related genes (PRGs) from bibliomic data in various plants. Thirty-five PRG homologs were identified in the cucumber genome via homology-based search. An in silico analysis was performed on phylogenetic tree, exon-intron structure, cis-regulatory elements in the promoter region, and conserved domains of their deduced proteins, which provided insights into the genetic make-up of parthenocarpy-related genes in cucumber. Simple sequence repeat (SSR) sequences were mined in these PRGs, and 31 SSR markers were designed. SSR genotyping identified three SSRs in two polymorphic genes. Quantitative real-time PCR of selected genes was conducted in five cucumber lines with varying degrees of parthenocarpic fruit set capacities, which revealed possible association of their expression with parthenocarpy. The results revealed that homologs CsWD40 and CsPIN-4 could be considered potential genes for determination of parthenocarpy as these genes showed parental polymorphism and differential gene expression in case of parthenocarpic and non-parthenocarpic parents.

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.

Identification and Characterization of AUXIN Response Factor Gene Family Reveals Their Regulatory Network to Respond the Multi-Hormones Crosstalk during GA-Induced Grape Parthenocarpic Berry

Exogenous gibberellin (GA) was widely used to improve berry quality through inducing parthenocarpic seedless berries in grapes. We revealed that auxin response factors (ARFs), the key transcription factors in response to auxin, might respond to GA involving modulation of grape parthenocarpy. However, the underlying molecular mechanism in this process remains yet unclear. Here, a total of 19 VvARF members were identified in the ovaries during GA-induced grapes’ parthenocarpy. Interestingly, almost all members were GA-responsive factors, of which 9 could be classified in plant hormone signal transduction (KO04075) and involved in the tryptophan metabolic pathway (K14486). Moreover, VvARFs were predicted to have 310 interacted proteins involved in 19 KEGG pathways. Of them, 32 interacted proteins participated in the KO04075 pathway, including auxin (IAA), salicylic acid (SA), abscisic acid (ABA), cytokinin (CTK), and ethylene signaling pathways by responding to GA-mediated multi-hormone crosstalk. Further analysis demonstrated that VvARF4-2 might be the major factor in the modulation of GA-induced parthenocarpy via the crosstalk of IAA, CTK, SA, and ethylene signaling, followed by VvARF6-1 and VvARF9 involved in SA and ABA signaling pathways, respectively. Finally, we developed a VvARFs-mediated regulatory network by responding to GA-mediated multi-hormone crosstalk during grape parthenocarpy. Collectively, our findings provided novel insights into the regulatory network of VvARFs in GA-guided multi-hormone signaling to modulate grape parthenocarpy, which has great implications for the molecular breeding of high quality seedless grape berries.

Auxin Coordinates Achene and Receptacle Development During Fruit Initiation in Fragaria vesca

In strawberries, fruit set is considered as the transition from the quiescent ovary to a rapidly growing fruit. Auxin, which is produced from the fertilized ovule in the achenes, plays a key role in promoting the enlargement of receptacles. However, detailed regulatory mechanisms for fruit set and the mutual regulation between achenes and receptacles are largely unknown. In this study, we found that pollination promoted fruit development (both achene and receptacle), which could be stimulated by exogenous auxin treatment. Interestingly, auxin was highly accumulated in achenes, but not in receptacles, after pollination. Further transcriptome analysis showed that only a small portion of the differentially expressed genes induced by pollination overlapped with those by exogenous auxin treatment. Auxin, but not pollination, was able to activate the expression of growth-related genes, especially in receptacles, which resulted in fast growth. Meanwhile, those genes involved in the pathways of other hormones, such as GA and cytokinin, were also regulated by exogenous auxin treatment, but not pollination. This suggested that pollination was not able to activate auxin responses in receptacles but produced auxin in fertilized achenes, and then auxin might be able to transport or transduce from achenes to receptacles and promote fast fruit growth at the early stage of fruit initiation. Our work revealed a potential coordination between achenes and receptacles during fruit set, and auxin might be a key coordinator.

Cytokinins is involved in regulation of tomato pericarp thickness and fruit size

Although cytokinins (CKs) regulate fruit development, no direct genetic evidence supports the role of endogenous CKs in pericarp growth or development or fruit size. Here, we report that the reduction in endogenous active CKs level via overexpression of a CKs-inactivating enzyme gene AtCKX2 specifically in fruit tissues resulted in reduced pericarp thickness and smaller fruit size, compared to wild-type control fruits. The pericarp thickness and single fruit weight in transgenic plants were significantly reduced. Analysis of paraffin sections showed that the reduced pericarp thickness was due largely to a decreased number of cells, and thus decreased cell division. Transcriptome profiling showed that the expression of cell division- and expansion-related genes was reduced in AtCKX2-overexpressing fruits. In addition, the expression of auxin-signaling and gibberellin-biosynthetic genes was repressed, whereas that of gibberellin-inactivating genes was enhanced, in AtCKX2-overexpressing fruits. These results demonstrate that endogenous CKs regulate pericarp cell division and, subsequently, fruit size. They also suggest that CKs interact with auxin and gibberellins in regulating tomato pericarp thickness and fruit size.

Interplays between auxin and GA signaling coordinate early fruit development

Phytohormones and their interactions are critical for fruit development and, are key topics in horticulture research. Auxin, together with gibberellic acid (GA), promotes cell division and expansion, thus subsequently regulates fruit development and enlargement after fertilization. Auxin and GA related mutants show parthenocarpy (fruit formation without fertilization of ovule) in many plant species, indicating that these hormones and possibly their interactions play a key role in the regulation of fruit initiation and development. Recent studies have shown clear molecular and genetic evidence that ARF/IAA and DELLA protein interact each other and regulate both auxin and GA signaling pathways in response to auxin and GA during fruit growth in horticultural plants, tomato (the most studied freshy fruit) and strawberry (the model of Rosaceae). These recent findings provide new insights into the mechanisms by which plant hormones auxin and GA regulate fruit development.

Hormonal interactions underlying parthenocarpic fruit formation in horticultural crops

In some horticultural crops, such as Cucurbitaceae, Solanaceae, and Rosaceae species, fruit set and development can occur without the fertilization of ovules, a process known as parthenocarpy. Parthenocarpy is an important agricultural trait that can not only mitigate fruit yield losses caused by environmental stresses but can also induce the development of seedless fruit, which is a desirable trait for consumers. In the present review, the induction of parthenocarpic fruit by the application of hormones such as auxins (2,4 dichlorophenoxyacetic acid; naphthaleneacetic acid), cytokinins (forchlorfenuron; 6-benzylaminopurine), gibberellic acids, and brassinosteroids is first presented. Then, the molecular mechanisms of parthenocarpic fruit formation, mainly related to plant hormones, are presented. Auxins, gibberellic acids, and cytokinins are categorized as primary players in initiating fruit set. Other hormones, such as ethylene, brassinosteroids, and melatonin, also participate in parthenocarpic fruit formation. Additionally, synergistic and antagonistic crosstalk between these hormones is crucial for deciding the fate of fruit set. Finally, we highlight knowledge gaps and suggest future directions of research on parthenocarpic fruit formation in horticultural crops.

Fine mapping and identification of the candidate gene BFS for fruit shape in wax gourd (Benincasa hispida)

Non-synonymous mutations in the BFS gene, which encodes the IQD protein, are responsible for the shape of wax gourd fruits. Fruit shape is an important agronomic trait in wax gourds. Therefore, in this study, we employed bulked segregant analysis (BSA) to identify a candidate gene for fruit shape in wax gourds within F₂ populations derived by crossing GX-71 (long cylindrical fruit, fruit shape index = 4.56) and MY-1 (round fruit, fruit shape index = 1.06) genotypes. According to BSA, the candidate gene is located in the 17.18 Mb region on chromosome 2. Meanwhile, kompetitive allele-specific PCR (KASP) markers were used to reduce it to a 19.6 Kb region. Only one gene was present within the corresponding region of the reference genome, namely Bch02G016830 (designated BFS). Subsequently, BFS was sequenced in six wax gourd varieties with different fruit shapes. Sequence analysis revealed two non-synonymous mutations in the round wax gourd and one non-synonymous mutation in the cylindrical wax gourd. Quantitative real‑time PCR (qRT-PCR) analysis further showed that the expression of BFS in round fruits was significantly higher than in long cylindrical fruits at the ovary formation stage. Therefore, BFS is a candidate gene for determination wax gourd shape. The predicted protein encoded by the BFS gene belongs to the IQ67-domain protein family, which have the structural characteristics of scaffold proteins and coordinate Ca²⁺ CaM signaling from the membrane to the nucleus. Ultimately, two derived cleaved amplified polymorphic sequence (dCAPS) markers were developed to facilitate marker-assisted selection for wax gourds breeding.

Downstream of GA4, PbCYP78A6 participates in regulating cell cycle-related genes and parthenogenesis in pear (Pyrus bretshneideri Rehd.)

BACKGROUND

Parthenocarpy results in traits attractive to both consumers and breeders, and it overcomes the obstacle of self-incompatibility in the fruit set of horticultural crops, including pear (Pyrus bretshneider). However, there is limited knowledge regarding the genetic and molecular mechanisms that regulate parthenogenesis.

RESULTS

Here, in a transcriptional comparison between pollination-dependent fruit and GA₄-induced parthenocarpy, PbCYP78A6 was identified and proposed as a candidate gene involved in parthenocarpy. PbCYP78A6 is similar to Arabidopsis thaliana CYP78A6 and highly expressed in pear hypanthia. The increased PbCYP78A6 expression, as assessed by RT-qPCR, was induced by pollination and GA₄ exposure. The ectopic overexpression of PbCYP78A6 contributed to parthenocarpic fruit production in tomato. The PbCYP78A6 expression coincided with fertilized and parthenocarpic fruitlets development and the expression of fruit development-related genes as assessed by cytological observations and RT-qPCR, respectively. PbCYP78A6 RNA interference and overexpression in pear calli revealed that the gene is an upstream regulator of specific fruit development-related genes in pear.

CONCLUSIONS

Our findings indicate that PbCYP78A6 plays a critical role in fruit formation and provide insights into controlling parthenocarpy.

Molecular and Hormonal Mechanisms Regulating Fleshy Fruit Ripening

This article focuses on the molecular and hormonal mechanisms underlying the control of fleshy fruit ripening and quality. Recent research on tomato shows that ethylene, acting through transcription factors, is responsible for the initiation of tomato ripening. Several other hormones, including abscisic acid (ABA), jasmonic acid (JA) and brassinosteroids (BR), promote ripening by upregulating ethylene biosynthesis genes in different fruits. Changes to histone marks and DNA methylation are associated with the activation of ripening genes and are necessary for ripening initiation. Light, detected by different photoreceptors and operating through ELONGATED HYPOCOTYL 5(HY5), also modulates ripening. Re-evaluation of the roles of 'master regulators' indicates that MADS-RIN, NAC-NOR, Nor-like1 and other MADS and NAC genes, together with ethylene, promote the full expression of genes required for further ethylene synthesis and change in colour, flavour, texture and progression of ripening. Several different types of non-coding RNAs are involved in regulating expression of ripening genes, but further clarification of their diverse mechanisms of action is required. We discuss a model that integrates the main hormonal and genetic regulatory interactions governing the ripening of tomato fruit and consider variations in ripening regulatory circuits that operate in other fruits.

SlTPL1 Silencing Induces Facultative Parthenocarpy in Tomato

Facultative parthenocarpy is of great practical value. However, the molecular mechanism underlying facultative parthenocarpy remains elusive. Transcriptional co-repressors (TPL) act as a central regulatory hub controlling all nine phytohormone pathways. Previously, we proved that SlTPLs participate in the auxin signaling pathway by interacting with auxin/indole acetic acid (Aux/IAAs) in tomato; however, their function in fruit development has not been studied. In addition to their high expression levels during flower development, the interaction between SlTPL1 and SlIAA9 stimulated the investigation of its functional significance via RNA interference (RNAi) technology, whereby the translation of a protein is prevented by selective degradation of its encoded mRNA. Down-regulation of SlTPL1 resulted in facultative parthenocarpy. Plants of SlTPL1-RNAi transgenic lines produced similar fruits which did not show any pleiotropic effects under normal conditions. However, they produced seedless fruits upon emasculation and under heat stress conditions. Furthermore, SlTPL1-RNAi flower buds contained higher levels of cytokinins and lower levels of abscisic acid. To reveal how SlTPL1 regulates facultative parthenocarpy, RNA-seq was performed to identify genes regulated by SlTPL1 in ovaries before and after fruit set. The results showed that down-regulation of SlTPL1 resulted in reduced expression levels of cytokinin metabolism-related genes, and all transcription factors such as MYB, CDF, and ERFs. Conversely, down-regulation of SlTPL1 induced the expression of genes related to cell wall and cytoskeleton organization. These data provide novel insights into the molecular mechanism of facultative tomato parthenocarpy and identify SlTPL1 as a key factor regulating these processes.

How Hormones and MADS-Box Transcription Factors Are Involved in Controlling Fruit Set and Parthenocarpy in Tomato

Fruit set is the earliest phase of fruit growth and represents the onset of ovary growth after successful fertilization. In parthenocarpy, fruit formation is less affected by environmental factors because it occurs in the absence of pollination and fertilization, making parthenocarpy a highly desired agronomic trait. Elucidating the genetic program controlling parthenocarpy, and more generally fruit set, may have important implications in agriculture, considering the need for crops to be adaptable to climate changes. Several phytohormones play an important role in the transition from flower to fruit. Further complexity emerges from functional analysis of floral homeotic genes. Some homeotic MADS-box genes are implicated in fruit growth and development, displaying an expression pattern commonly observed for ovary growth repressors. Here, we provide an overview of recent discoveries on the molecular regulatory gene network underlying fruit set in tomato, the model organism for fleshy fruit development due to the many genetic and genomic resources available. We describe how the genetic modification of components of this network can cause parthenocarpy, discussing the contribution of hormonal signals and MADS-box transcription factors.

Applications of Cytokinins in Horticultural Fruit Crops: Trends and Future Prospects

Cytokinins (CKs) are a chemically diverse class of plant growth regulators, exhibiting wide-ranging actions on plant growth and development, hence their exploitation in agriculture for crop improvement and management. Their coordinated regulatory effects and cross-talk interactions with other phytohormones and signaling networks are highly sophisticated, eliciting and controlling varied biological processes at the cellular to organismal levels. In this review, we briefly introduce the mode of action and general molecular biological effects of naturally occurring CKs before highlighting the great variability in the response of fruit crops to CK-based innovations. We present a comprehensive compilation of research linked to the application of CKs in non-model crop species in different phases of fruit production and management. By doing so, it is clear that the effects of CKs on fruit set, development, maturation, and ripening are not necessarily generic, even for cultivars within the same species, illustrating the magnitude of yet unknown intricate biochemical and genetic mechanisms regulating these processes in different fruit crops. Current approaches using genomic-to-metabolomic analysis are providing new insights into the in planta mechanisms of CKs, pinpointing the underlying CK-derived actions that may serve as potential targets for improving crop-specific traits and the development of new solutions for the preharvest and postharvest management of fruit crops. Where information is available, CK molecular biology is discussed in the context of its present and future implications in the applications of CKs to fruits of horticultural significance.

CPPU may induce gibberellin-independent parthenocarpy associated with PbRR9 in 'Dangshansu' pear

Parthenocarpy is a valuable trait in self-incompatible plants, such as pear. N-(2-chloro-4-pyridyl)-N'-phenylurea (CPPU), a synthetic cytokinin analog, can induce parthenocarpy in pear (Pyrus spp.), but the mechanism of induction is unclear. To investigate the role of gibberellin in CPPU-induced parthenocarpy in pear, CPPU supplemented with paclobutrazol (PAC) was sprayed onto 'Dangshansu' pear. We found that the fruit set rate of pear treated with CPPU supplemented with PAC was identical to that in a CPPU-alone treatment group. In regard to cell development, CPPU mainly promoted hypanthium cell division and expansion, and PAC application had no influence on CPPU-induced cell development. RNA sequencing revealed that gibberellin 20 oxidase and gibberellin 3 oxidase genes were not differentially expressed following CPPU treatment. According to the analysis of fruit phytohormone content, the CPPU treatments did not induce gibberellin biosynthesis. These results suggest that CPPU-induced parthenocarpy may be gibberellin independent in 'Dangshansu' pear. After CPPU treatment, the indole acetic acid (IAA) content in fruit was significantly increased, and the abscisic acid (ABA) content was significantly decreased. Similarly, RNA sequencing revealed that many genes involved in the auxin and ABA pathways were significantly differentially expressed in the CPPU treatment groups; among them, indole-3-pyruvate monooxygenase (YUCCA) was significantly upregulated and 9-cis-epoxycarotenoid dioxygenase (NCED) was significantly downregulated. IAA and ABA may thus play important roles in CPPU-induced parthenocarpy. PbTwo-component response regulator9 (PbRR9), PbYUCCA4, and PbNCED6 were then selected to further elucidate the mechanism of CPPU-induced parthenocarpy. A yeast one-hybrid assay indicated that PbRR9 can combine with the PbYUCCA4 and PbNCED6 promoters. Dual luciferase assays revealed that PbRR9 can promote and repress the activities of the PbYUCCA4 and PbNCED6 promoters, respectively. After the transient expression of PbRR9 in fruits, PbYUCCA4 expression was significantly upregulated, and PbNCED6 expression was significantly downregulated. This study uncovered a CPPU-induced parthenocarpy mechanism that is different from that in tomato. CPPU may upregulate PbYUCCA4 and downregulate PbNCED6 by upregulating PbRR9, thereby increasing IAA content and decreasing ABA content to ultimately induce parthenocarpy in 'Dangshansu' pear. However, because only a single time point was used and because 'botanical' and 'accessory' fruits have different structures, this conclusion is still preliminary.

PbGA20ox2 Regulates Fruit Set and Induces Parthenocarpy by Enhancing GA4 Content

Fruit set and development occur following successful fertilization. Parthenocarpy, a valuable trait in some self-incompatible species, produces seedless fruit without fertilization. Gibberellin (GA) is a crucial hormone in fruit-set regulation and development. While investigating the development of parthenocarpy in pear (Pyrus bretschneideri Rehd.), we determined that GA 20-oxidases (GA20ox) may play key roles in seedless pear fruit development. Sequence analysis revealed three PbGA20ox genes: PbGA20ox1, PbGA20ox2, and PbGA20ox3. We analyzed the expression patterns of candidate genes and found that PbGA20ox2 levels significantly changed in pollinated fruits. Tissue-specific expression assays revealed that PbGA20ox2 is highly expressed in young fruit and leaves. Subcellular localization assays showed it was located in the cytoplasm, nucleus, and plasma membrane. Overexpressed PbGA20ox2 tomato plants were taller and had longer hypocotyls and internodes, and the emasculated flowers produced parthenocarpic fruit. In pear, the transient overexpression of PbGA20ox2 promoted fruit development and delayed the drop of nonpollinated fruit. Furthermore, the fruit of PbGA20ox2-overexpressing tomato and transient PbGA20ox2-overexpressing pear had increased GA₄ (but not GA₃ and GA₁) contents. This result provided evidence that PbGA20ox2 was necessary for GA₄-dependent pear fruit development. Our study revealed that PbGA20ox2 altered the GA biosynthetic pathway and enhanced GA₄ synthesis, thereby promoting fruit set and parthenocarpic fruit development.

Downregulation of SlGRAS15 manipulates plant architecture in tomato (Solanum lycopersicum)

GRAS family transcription factors (TF) are involved in multiple biological processes in plants. In recent years among the 54 identified GRAS proteins, only few have been studied functionally in tomato (Solanum lycopersicum). In the present study, a novel and previously uncharacterized member of tomato GRAS transcription factors family SlGRAS15 was isolated and functionally characterized. It was observed that SlGRAS15 preferably expressed in roots, followed by young leaves, stem, and comparatively low transcripts levels were noticed in all other tissues. To explore the SlGRAS15 function in detail, an RNA interference (RNAi) vector targeting SlGRAS15 was constructed and transformed into tomato plants. The transgenic plants carrying SlGRAS15-RNAi displayed pleiotropic phenotypes associated with multiple agronomical traits including reduced plant height and small leaf size with pointed margins, increased node number, lateral shoots, and petiolules length. In addition, transcriptional analysis revealed that silencing SlGRAS15 altered vegetative growth by downregulating gibberellin (GA) biosynthesis genes and stimulating the GA deactivating genes, thus lowering the endogenous GA content in tomato transgenic lines. Moreover, the GA signaling downstream gene (SlGAST1) was downregulated but the negative regulator of GA signaling (SlDELLA) was upregulated by SlGRAS15 silencing. The root and hypocotyl length in SlGRAS15-RNAi lines showed reduced growth under normal conditions (Mock) as compared with the wild type (WT) control plants. Taken together, these findings enhanced our understanding that suppression of SlGRAS15 lead to a series of developmental processes by modulating gibberellin signaling and demonstrate an association between the SlGRAS15 and GA signaling pathway during vegetative growth in tomato.

Tomato Fruit Development and Metabolism

Tomato (Solanum lycopersicum L.) belongs to the Solanaceae family and is the second most important fruit or vegetable crop next to potato (Solanum tuberosum L.). It is cultivated for fresh fruit and processed products. Tomatoes contain many health-promoting compounds including vitamins, carotenoids, and phenolic compounds. In addition to its economic and nutritional importance, tomatoes have become the model for the study of fleshy fruit development. Tomato is a climacteric fruit and dramatic metabolic changes occur during its fruit development. In this review, we provide an overview of our current understanding of tomato fruit metabolism. We begin by detailing the genetic and hormonal control of fruit development and ripening, after which we document the primary metabolism of tomato fruits, with a special focus on sugar, organic acid, and amino acid metabolism. Links between primary and secondary metabolic pathways are further highlighted by the importance of pigments, flavonoids, and volatiles for tomato fruit quality. Finally, as tomato plants are sensitive to several abiotic stresses, we briefly summarize the effects of adverse environmental conditions on tomato fruit metabolism and quality.

Alq mutation increases fruit set rate and allows the maintenance of fruit yield under moderate saline conditions

Arlequin (Alq) is a gain-of-function mutant whose most relevant feature is that sepals are able to become fruit-like organs due to the ectopic expression of the ALQ-TAGL1 gene. The role of this gene in tomato fruit ripening was previously demonstrated. To discover new functional roles for ALQ-TAGL1, and most particularly its involvement in the fruit set process, a detailed characterization of Alq yield-related traits was performed. Under standard conditions, the Alq mutant showed a much higher fruit set rate than the wild type. A significant percentage of Alq fruits were seedless. The results showed that pollination-independent fruit set in Alq is due to early transition from flower to fruit. Analysis of endogenous hormones in Alq suggests that increased content of cytokinins and decreased level of abscisic acid may account for precocious fruit set. Comparative expression analysis showed relevant changes of several genes involved in cell division, gibberellin metabolism, and the auxin signalling pathway. Since pollination-independent fruit set may be a very useful strategy for maintaining fruit production under adverse conditions, fruit set and yield in Alq plants under moderate salinity were assessed. Interestingly, Alq mutant plants showed a high yield under saline conditions, similar to that of Alq and the wild type under unstressed conditions.

Heracleum sosnowskyi seed development under the effect of exogenous application of GA3

Numerous studies have demonstrated the impact of exogenous gibberellin on fleshy fruit formation, but the effect on dry fruits is not yet well known. To test the role of gibberellin (GA₃) in dry fruit formation, we analysed the impact of exogenous GA₃ on the invasive plant Sosnowsky’s hogweed (H. sosnowskyi Manden.) seed development and germination. Treatment of GA₃ concentrations of 0.07 mM, 0.14 mM, 0.28 mM, 0.43 mM was applied to flowers at the early stage of development. Seeds were collected from treated satellite umbels. It was observed that GA₃treatment did not have a significant effect on the size of H. sosnowskyi seeds, but caused various changes in their shape. The data on semi-thin longitudinal sections of H. sosnowskyi mericarps and SEM micrographs of embryos showed that the embryos in GA₃ (0.43 mM) treated variants were at torpedo stage, while in control variants—mature embryos. The germination of seeds of each variant was estimated by burying them in the soil. Our studies indicated that GA₃ application reduced the germination of H. sosnowskyi seed from 98.0% (control) to 16.5% (GA₃ concentration 0.43 mM). It was assumed that exogenous application of GA₃ had influence on the development of dry Sosnowsky’s hogweed seeds and could be used to inhibit the spread of this invasive plant.

Gibberellins modulate auxin responses during tomato (Solanum lycopersicum L.) fruit development

In tomato, auxin and gibberellins (GAs) interact with each other to drive fruit growth and development. While the role of auxin in directing GA biosynthesis and signal is already known, very little information has been obtained about GA-mediated control of auxin signalling and response. Interestingly, we show that gibberellic acid (GA₃ ) is able to modify the expression of several auxin signalling genes in the partial auxin-insensitive diageotropica (dgt) mutant, suggesting that GAs may override the control of DGT on auxin signal. Procera (pro) mutation, which confers a constitutively active GA signal, enhances the effects of exogenous auxin, indicating that PRO may act as a negative effector of auxin responses in fruits. Indeed, transcript modulation of some auxin/indole acetic acid and auxin response factor genes in auxin-treated dgt/pro fruits suggests that PRO controls their expression possibly bypassing DGT. It was also shown that GA biosynthesis, in response to auxin treatment, is largely controlled by DGT. It is therefore conceivable that the DGT-mediated increase of active GAs in auxin-treated or pollinated fruits would promote PRO degradation, which in turn activates part of the auxin signalling cascade.

Cytokinin-induced parthenocarpy of San Pedro type fig (Ficus carica L.) main crop: explained by phytohormone assay and transcriptomic network comparison

CPPU-induced San Pedro type fig main crop parthenocarpy exhibited constantly increasing IAA content and more significantly enriched KEGG pathways in the receptacle than in female flowers. N-(2-chloro-4-pyridyl)-N-phenylurea (CPPU) was applied to San Pedro fig (Ficus carica L.) main crop to induce parthenocarpy; the optimal effect was obtained with 25 mg L^-1 application to syconia when female flowers were at anthesis. To elucidate the key expression changes in parthenocarpy conversion, significant changes in phytohormone level and transcriptome of fig female flowers and receptacles were monitored. HPLC-MS revealed increased IAA content in female flowers and receptacle 2, 4 and 10 days after treatment (DAT), decreased zeatin level in the receptacle 2, 4 and 10 DAT, decreased GA₃ content 2 and 4 DAT, and increased GA₃ content 10 DAT. ABA level increased 2 and 4 DAT, and decreased 10 DAT. CPPU-treated syconia released more ethylene than the control except 2 DAT. RNA-Seq and bioinformatics analysis revealed notably more differentially expressed KEGG pathways in the receptacle than in female flowers. In the phytohormone gene network, GA-biosynthesis genes GA20ox and GA3ox were upregulated, along with GA signal-transduction genes GID1 and GID2, and IAA-signaling genes AUX/IAA and GH3. ABA-biosynthesis gene NCED and signaling genes PP2C and ABF were downregulated 10 DAT. One ACO gene showed consistent upregulation in both female flowers and receptacle after CPPU treatment, and more than a dozen of ERFs demonstrated opposing changes in expression. Our results revealed early-stage spatiotemporal phytohormone and transcriptomic responses in CPPU-induced San Pedro fig main crop parthenocarpy, which could be valuable for further understanding the nature of the parthenocarpy of different fig types.

Functional Disruption of the Tomato Putative Ortholog of HAWAIIAN SKIRT Results in Facultative Parthenocarpy, Reduced Fertility and Leaf Morphological Defects

A number of plant microRNAs have been demonstrated to regulate developmental processes by integrating internal and environmental cues. Recently, the Arabidopsis thaliana F-box protein HAWAIIAN SKIRT (HWS) gene has been described for its role in miRNA biogenesis. We have isolated in a forward genetic screen a tomato (Solanum lycopersicum) line mutated in the putative ortholog of HWS. We show that the tomato hws-1 mutant exhibits reduction in leaflet serration, leaflet fusion, some degree of floral organ fusion, and alteration in miRNA levels, similarly to the original A. thaliana hws-1 mutant. We also describe novel phenotypes for hws such as facultative parthenocarpy, reduction in fertility and flowering delay. In slhws-1, the parthenocarpy trait is influenced by temperature, with higher parthenocarpy rate in warmer environmental conditions. Conversely, slhws-1 is able to produce seeds when grown in cooler environment. We show that the reduction in seed production in the mutant is mainly due to a defective male function and that the levels of several miRNAs are increased, in accordance with previous HWS studies, accounting for the abnormal leaf and floral phenotypes as well as the altered flowering and fruit development processes. This is the first study of HWS in fleshy fruit plant, providing new insights in the function of this gene in fruit development.

Aberrant Stamen Development is Associated with Parthenocarpic Fruit Set Through Up-Regulation of Gibberellin Biosynthesis in Tomato

Parthenocarpy, a process in which fruit set occurs without fertilization, leads to the production of seedless fruit. A number of floral homeotic mutants with abnormal stamen development exhibit parthenocarpic fruit set. Flower development is thought to repress ovary growth before anthesis. However, the mechanism of parthenocarpic fruit development caused by aberrant flower formation is poorly understood. To investigate the molecular mechanism of parthenocarpic fruit development in floral homeotic mutants, we performed functional analysis of Tomato APETALA3 (TAP3) by loss-of-function approaches. Organ-specific promoter was used to induce organ-specific loss of function in stamen and ovary/fruit. We observed increased cell expansion in tap3 mutants and TAP3-RNAi lines during parthenocarpic fruit growth. These were predominantly accompanied by the up-regulation of GA biosynthesis genes, including SlGA20ox1, SlGA20ox2, and SlGA20ox3, as well as reduced expression of the GA-inactivating gene SlGA2ox1 and the auxin signaling gene SlARF7 involved in a crosstalk between GA and auxin. These transcriptional profiles are in agreement with the GA levels in these lines. These results suggest that stamen development negatively regulates fruit set by repressing the GA biosynthesis.

Transcriptome analysis of oil palm inflorescences revealed candidate genes for an auxin signaling pathway involved in parthenocarpy

Oil palm parthenocarpic fruits, which are produced without fertilization, can be targeted to increase oil content because the majority of the fruit is occupied by mesocarp, the part in which palm oil is stored. Consequently, gaining an understanding of the parthenocarpic mechanism would be instrumental for producing parthenocarpic oil palm. This study aims to determine effects of auxin treatment and analyze differentially expressed genes in oil palm pistils at the pollination/anthesis stage, using an RNA sequencing (RNA seq) approach. The auxin treatment caused 100% parthenocarpy when auxin was sprayed before stigmas opened. The parthenocarpy decreased to 55%, 8% and 5% when the auxin was sprayed 1, 2 and 3 days after the opening of stigmas, respectively. Oil palm plants used for RNA seq were plants untreated with auxin as controls and auxin-treated plants on the day before pollination and 1 day after pollination. The number of raw reads ranged from 8,425,859 to 11,811,166 reads, with an average size ranging from 99 to 137 base pairs (bp). When compared with the oil palm transcriptome, the mapped reads ranged from 8,179,948 to 11,320,799 reads, representing 95.85–98.01% of the oil palm matching. Based on five comparisons between RNA seq of treatments and controls, and confirmation using reverse transcription polymerase chain reaction and quantitative real-time RT-PCR expression, five candidate genes, including probable indole-3-acetic acid (IAA)-amido synthetase GH3.8 (EgGH3.8), IAA-amido synthetase GH3.1 (EgGH3.1), IAA induced ARG7 like (EgARG7), tryptophan amino transferase-related protein 3-like (EgTAA3) and flavin-containing monooxygenase 1 (EgFMO1), were differentially expressed between auxin-treated and untreated samples. This evidence suggests a pathway of parthenocarpic fruit development at the beginning of fruit development. However, more research is needed to identify which genes are definitely involved in parthenocarpy.

The molecular events of IAA inhibiting citrus fruitlet abscission revealed by digital gene expression profiling

Citrus fruits possess two abscission zones (AZ), AZ A and AZ C located at the pedicel and calyx, respectively. Early citrus fruitlet abscission (CFA) exclusively occurs at AZ A. Previous data have shown that indole-3-acetic acid (IAA) could inhibit fruitlet abscission. However, its role in CFA remains vague. In this study, we first removed the ovaries of fruitlets in order to exclude their interferences. Then, the calyxes were treated with IAA, gibberellin 3 (GA₃) and 6-benzylaminopurine (6-BA), respectively. The results have shown that IAA could prevent CFA from taking place, while either GA₃ or 6-BA could not. When IAA concentration decreased to a value between 30 mg/L and 40 mg/L, CFA occurred, showing a concentration-dependent manner. Digital gene expression analysis revealed that 2317 corresponded to IAA treatment, of which 1226 genes were closely related to CFA. The most affected genes included those related to biosynthesis, transport and signaling of phytohormones, primarily ethylene (ET), abscisic acid (ABA) and auxin as well as protein ubiquitination, ROS response, calcium signal transduction, cell wall and transcription factors (TFs). The results obtained in this study suggested that the IAA in AZ A could suppress ethylene biosynthesis and signaling, and then inhibit abscission signaling. To our knowledge, it is the first time to reveal the key role of IAA in CFA, which will contribute to a better understanding for the mechanism underlying CFA.

Putting primary metabolism into perspective to obtain better fruits

Background

One of the key goals of fruit biology is to understand the factors that influence fruit growth and quality, ultimately with a view to manipulating them for improvement of fruit traits.

Scope

Primary metabolism, which is not only essential for growth but is also a major component of fruit quality, is an obvious target for improvement. However, metabolism is a moving target that undergoes marked changes throughout fruit growth and ripening.

Conclusions

Agricultural practice and breeding have successfully improved fruit metabolic traits, but both face the complexity of the interplay between development, metabolism and the environment. Thus, more fundamental knowledge is needed to identify further strategies for the manipulation of fruit metabolism. Nearly two decades of post-genomics approaches involving transcriptomics, proteomics and/or metabolomics have generated a lot of information about the behaviour of fruit metabolic networks. Today, the emergence of modelling tools is providing the opportunity to turn this information into a mechanistic understanding of fruits, and ultimately to design better fruits. Since high-quality data are a key requirement in modelling, a range of must-have parameters and variables is proposed.

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

BACKGROUND

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

RESULTS

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

CONCLUSIONS

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

The making of virgin fruit: the molecular and genetic basis of parthenocarpy

Fruit set-the commitment of an angiosperm plant to develop fruit-is a key developmental process that normally occurs following successful fertilization. Parthenocarpy arises when fruit automatically develop in the absence of fertilization. This review uses parthenocarpic fruit development as a focal device through which to recapitulate and understand the molecular effectors that mediate and regulate fruit set. The review demonstrates that studies of parthenocarpy are providing vital insight into plant development, signaling and, potentially, high-value agricultural products.

Histological, hormonal and transcriptomic reveal the changes upon gibberellin-induced parthenocarpy in pear fruit

Phytohormones play crucial roles in fruit set regulation and development. Here, gibberellins (GA₄₊₇), but not GA₃, induced pear parthenocarpy. To systematically investigate the changes upon GA₄₊₇ induced pear parthenocarpy, dynamic changes in histology, hormone and transcript levels were observed and identified in unpollinated, pollinated and GA₄₊₇-treated ovaries. Mesocarp cells continued developing in both GA₄₊₇-treated and pollinated ovaries. In unpollinated ovaries, mesocarp cells stopped developing 14 days after anthesis. During fruit set process, GA₄₊₇, but not GA₁₊₃, increased after pollination. Abscisic acid (ABA) accumulation was significantly repressed by GA₄₊₇ or pollination, but under unpollinated conditions, ABA was produced in large quantities. Moreover, indole-3-acetic acid biosynthesis was not induced by GA₄₊₇ or pollination treatments. Details of this GA-auxin-ABA cross-linked gene network were determined by a comparative transcriptome analysis. The indole-3-acetic acid transport-related genes, mainly auxin efflux carrier component genes, were induced in both GA₄₊₇-treated and pollinated ovaries. ABA biosynthetic genes of the 9-cis-epoxycarotenoid dioxygenase family were repressed by GA₄₊₇ and pollination. Moreover, directly related genes in the downstream parthenocarpy network involved in cell division and expansion (upregulated), and MADS-box family genes (downregulated), were also identified. Thus, a model of GA-induced hormonal balance and its effects on parthenocarpy were established.

Proteomic insight into fruit set of cucumber (Cucumis sativus L.) suggests the cues of hormone-independent parthenocarpy

BACKGROUND

Parthenocarpy is an excellent agronomic trait that enables crops to set fruit in the absence of pollination and fertilization, and therefore to produce seedless fruit. Although parthenocarpy is widely recognized as a hormone-dependent process, hormone-insensitive parthenocarpy can also be observed in cucumber; however, its mechanism is poorly understood. To improve the global understanding of parthenocarpy and address the hormone-insensitive parthenocarpy shown in cucumber, we conducted a physiological and proteomic analysis of differently developed fruits.

RESULTS

Physiological analysis indicated that the natural hormone-insensitive parthenocarpy of 'EC1' has broad hormone-inhibitor resistance, and the endogenous hormones in the natural parthenocarpy (NP) fruits were stable and relatively lower than those of the non-parthenocarpic cultivar '8419 s-1.' Based on the iTRAQ technique, 683 fruit developmental proteins were identified from NP, cytokinin-induced parthenocarpic (CP), pollinated and unpollinated fruits. Gene Ontology (GO) analysis showed that proteins detected from both set and aborted fruits were involved in similar biological processes, such as cell growth, the cell cycle, cell death and communication. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that 'protein synthesis' was the major biological process that differed between fruit set and fruit abortion. Clustering analysis revealed that different protein expression patterns were involved in CP and NP fruits. Forty-one parthenocarpy-specialized DEPs (differentially expressed proteins) were screened and divided into two distinctive groups: NP-specialized proteins and CP-specialized proteins. Furthermore, qRT-PCR and western blot analysis indicated that NP-specialized proteins showed hormone- or hormone-inhibitor insensitive expression patterns in both ovaries and seedlings.

CONCLUSIONS

In this study, the global molecular regulation of fruit development in cucumber was revealed at the protein level. Physiological and proteomic comparisons indicated the presence of hormone-independent parthenocarpy and suppression of fruit abortion in cucumber. The proteomic analysis suggested that hormone-independent parthenocarpy is regulated by hormone-insensitive proteins such as the NP-specialized proteins. Moreover, the regulation of fruit abortion suppression may be closely related to protein synthesis pathways.

Dynamic transcriptomic analysis of the early response of female flowers of Populus alba × P. glandulosa to pollination

Pollination is an important event in plant sexual reproduction, and post-pollination response is an essential process for reproduction. Populus alba × P. glandulosa is used widely in scientific research, especially in cross breeding as parents. Adult female P. alba × P. glandulosa flowers are highly compatible with pollen from male P. tomentosa, but the early post-pollination response of flowers at the molecular levels is unclear. In this study, RNA-seq was employed to comprehensively understand the response of female P. alba × P. glandulosa flowers to pollination. Enrichment analysis reveals that the 'plant hormone signal transduction' pathway is enhanced during pollen-pistil interaction. Moreover, genes related to auxin, gibberellin and ethylene biosynthesis were significantly up-regulated. Ca2+ and H+-related genes and cell wall-related genes are interrelated, and all of them are essential for pollen tube elongation in pistil, especially, free Ca2+ providing a concentration gradient for pollen tube guidance and involved in signal transduction. Furthermore, RNA-seq results indicate that genes involved in the adhesion and guidance for pollen germination and pollen tube growth are abundantly present in the extracellular matrix. Our study provides an overview and detailed information for understanding the molecular mechanism of early post-pollination response in this hybrid poplar reproduction.

Comparative transcriptome analysis provides insights into molecular mechanisms for parthenocarpic fruit development in eggplant (Solanum melongena L.)

Genetic control of parthenocarpy, a desirable trait in edible fruit with hard seeds, has been extensively studied. However, the molecular mechanism of parthenocarpic fruit development in eggplant (Solanum melongena L.) is still unclear. To provide insights into eggplant parthenocarpy, the transcriptomic profiles of a natural parthenocarpic (PP05) and two non-parthenocarpic (PnP05 and GnP05) eggplant lines were analyzed using RNA-sequencing (RNA-seq) technology. These sequences were assembled into 38925 unigenes, of which 22683 had an annotated function and 3419 were predicted as novel genes or from alternative splicing. 4864 and 1592 unigenes that were identified as DEGs between comparison groups PP05 vs PnP05 and PP05 vs GnP05, respectively. 506 common DEGs were found contained in both comparison groups, including 258 up-regulated and 248 down-regulated genes. Functional enrichment analyses identified many common or specific biological processes and gene set potentially associated with plant development. The most pronounced findings are that differentially regulated genes potentially-related with auxin signaling between parthenocarpic and non-parthenocarpic eggplants, e.g. calcium-binding protein PBP1 and transcription factor E2FB, which mediate the auxin distribution and auxin-dependent cell division, respectively, are up-regulated in the PP05; whereas homologs of GH3.1 and AUX/IAA, which are involved in inactivation of IAA and interference of auxin signaling, respectively, are down-regulated in PP05. Furthermore, gibberellin and cytokinin signaling genes and genes related to flower development were found differentially regulated between these eggplant lines. The present study provides comprehensive transcriptomic profiles of eggplants with or without parthenocarpic capacity. The information will deepen our understanding of the molecular mechanisms of eggplant parthenocarpy. The DEGs, especially these filtered from PP05 vs PnP05 + GnP05, will be valuable for further investigation of key genes involved in the parthenocarpic fruit development and genomics-assisted breeding.

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

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

SlTIR1 is involved in crosstalk of phytohormones, regulates auxin-induced root growth and stimulates stenospermocarpic fruit formation in tomato

TIR1 and its homologs act as auxin receptors and play important roles in plant growth and development in Arabidopsis thaliana. An auxin receptor homolog Solanum lycopersicum TIR1 (SlTIR1) has been isolated from tomato cultivar Micro-Tom, and SlTIR1 over-expression results in parthenocarpic fruit formation. In this study, the promoter driving the β-glucuronidase (GUS) expression vector was constructed and stably transformed into Micro-Tom seedlings. The SlTIR1 promoter driving GUS expression accumulated predominantly in the leaf and vasculature in transgenic seedlings. Promoter analysis identified an auxin-response element (AuxRE) and two gibberellic acid (GA)-response elements in the SlTIR1 promoter. Quantitative PCR showed that SlTIR1 transcript level was down-regulated by naphthaleneacetic acid, ethephon and abscisic acid and up-regulated by GA. Furthermore, because of the lack of ability to form reproductive seeds in SlTIR1 over-expressing Micro-Tom, this limits further exploration of potential roles of SlTIR1 in auxin signaling. Here, an antisense vector and an over-expression vector of the SlTIR1 gene were stably transformed into Micro-Tom and Ailsa Craig tomato, respectively. Phenotypes and physiological analyses indicated that SlTIR1 regulated primary root growth and auxin-associated lateral root formation in Micro-Tom. Meanwhile, SlTIR1 also stimulated abnormal seed development, so-called stenospermocarpy, in Ailsa Craig. Transcript accumulations of auxin-signaling genes determined by quantitative PCR were consistent with the idea that SlTIR1 regulated plant growth and development, partially mediated by controlling the mRNA levels of auxin-signaling genes. Our work demonstrates that SlTIR1 regulated auxin-induced root growth and stimulated stenospermocarpic fruit formation. SlTIR1 may be a key mediator of the crosstalk among auxin and other hormones to co-regulate plant growth and development.

Silencing SlGID2, a putative F-box protein gene, generates a dwarf plant and dark-green leaves in tomato

In plant, F-box protein participates in various signal transduction systems and plays an important role in signaling pathways. Here, a putative F-box protein, namely SlGID2, was isolated from tomato (Solanum lycopersicum). Bioinformatics analyses suggested that SlGID2 shows high identity with F-box proteins from other plant species. Expression pattern analysis showed that SlGID2 gene is ubiquitously expressed in tomato tissues. To study the function of SlGID2 in tomato, SlGID2-silenced (SlGID2i) tomato by RNA interference (RNAi) was generated and displayed a dwarf plant and dark-green leaf phenotypes. The defective stem elongation of SlGID2i lines was not rescued by exogenous GA and its endogenous GA level was higher than wild type, further supporting the observation that SlGID2i transgenic plants are GA insensitive. Furthermore, SlGAST1, the downstream gene of GA signaling, and some cell expansion, division related genes (SlCycB1;1, SlCycD2;1, SlCycA3;1, SlXTH2, SlEXP2, SlKRP4) were down-regulated by SlGID2 silencing. In addition, the expression levels of SlDELLA (a negative regulator of GA signaling) and SlGA2ox1 were decreased, while SlGA3ox1 and SlGA20ox2 transcripts were increased in SlGID2i lines. Thus, we conclude that SlGID2 may be a positive regulator of GA signaling and promotes the GA signal pathway.

Overexpression of INCREASED CAMBIAL ACTIVITY, a putative methyltransferase, increases cambial activity and plant growth

Cambial activity is a prerequisite for secondary growth in plants; however, regulatory factors controlling the activity of the secondary meristem in radial growth remain elusive. Here, we identified INCREASED CAMBIAL ACTIVITY (ICA), a gene encoding a putative pectin methyltransferase, which could function as a modulator for the meristematic activity of fascicular and interfascicular cambium in Arabidopsis. An overexpressing transgenic line, 35S::ICA, showed accelerated stem elongation and radial thickening, resulting in increased accumulation of biomass, and increased levels of cytokinins (CKs) and gibberellins (GAs). Expression of genes encoding pectin methylesterases involved in pectin modification together with pectin methyltransferases was highly induced in 35S::ICA, which might contribute to an increase of methanol emission as a byproduct in 35S::ICA. Methanol treatment induced the expression of GA- or CK-responsive genes and stimulated plant growth. Overall, we propose that ectopic expression of ICA increases cambial activity by regulating CK and GA homeostasis, and methanol emission, eventually leading to stem elongation and radial growth in the inflorescence stem.

Translating the "Banana Genome" to Delineate Stress Resistance, Dwarfing, Parthenocarpy and Mechanisms of Fruit Ripening

Evolutionary frozen, genetically sterile and globally iconic fruit "Banana" remained untouched by the green revolution and, as of today, researchers face intrinsic impediments for its varietal improvement. Recently, this wonder crop entered the genomics era with decoding of structural genome of double haploid Pahang (AA genome constitution) genotype of Musa acuminata. Its complex genome decoded by hybrid sequencing strategies revealed panoply of genes and transcription factors involved in the process of sucrose conversion that imparts sweetness to its fruit. Historically, banana has faced the wrath of pandemic bacterial, fungal, and viral diseases and multitude of abiotic stresses that has ruined the livelihood of small/marginal farmers' and destroyed commercial plantations. Decoding structural genome of this climacteric fruit has given impetus to a deeper understanding of the repertoire of genes involved in disease resistance, understanding the mechanism of dwarfing to develop an ideal plant type, unraveling the process of parthenocarpy, and fruit ripening for better fruit quality. Further, injunction of comparative genomics will usher in integration of information from its decoded genome and other monocots into field applications in banana related but not limited to yield enhancement, food security, livelihood assurance, and energy sustainability. In this mini review, we discuss pre- and post-genomic discoveries and highlight accomplishments in structural genomics, genetic engineering and forward genetic accomplishments with an aim to target genes and transcription factors for translational research in banana.

Identification of a stable major-effect QTL (Parth 2.1) controlling parthenocarpy in cucumber and associated candidate gene analysis via whole genome re-sequencing

BACKGROUND

Parthenocarpy is an important trait for yield and quality in many plants. But due to its complex interactions with genetic and physiological factors, it has not been adequately understood and applied to breeding and production. Finding novel and effective quantitative trait loci (QTLs) is a critical step towards understanding its genetic mechanism. Cucumber (Cucumis sativus L.) is a typical parthenocarpic plant but the QTLs controlling parthenocarpy in cucumber were not mapped on chromosomes, and the linked markers were neither user-friendly nor confirmed by previous studies. Hence, we conducted a two-season QTL study of parthenocarpy based on the cucumber genome with 145 F2:3 families derived from a cross between EC1 (a parthenocarpic inbred line) and 8419 s-1 (a non-parthenocarpic inbred line) in order to map novel QTLs. Whole genome re-sequencing was also performed both to develop effective linked markers and to predict candidate genes.

RESULTS

A genetic linkage map, employing 133 Simple Sequence Repeats (SSR) markers and nine Insertion/Deletion (InDel) markers spanning 808.1 cM on seven chromosomes, was constructed from an F2 population. Seven novel QTLs were identified on chromosomes 1, 2, 3, 5 and 7. Parthenocarpy 2.1 (Parth2.1), a QTL on chromosome 2, was a major-effect QTL with a logarithm of odds (LOD) score of 9.0 and phenotypic variance explained (PVE) of 17.0 % in the spring season and with a LOD score of 6.2 and PVE of 10.2 % in the fall season. We confirmed this QTL using a residual heterozygous line97-5 (RHL97-5). Effectiveness of linked markers of the Parth2.1 was validated in F3:4 population and in 21 inbred lines. Within this region, there were 57 genes with nonsynonymous SNPs/InDels in the coding sequence. Based on further combined analysis with transcriptome data between two parents, CsARF19, CsWD40, CsEIN1, CsPPR, CsHEXO3, CsMDL, CsDJC77 and CsSMAX1 were predicted as potential candidate genes controlling parthenocarpy.

CONCLUSIONS

A major-effect QTL Parth2.1 and six minor-effect QTLs mainly contribute to the genetic architecture of parthenocarpy in cucumber. SSR16226 and Indel-T-39 can be used in marker-assisted selection (MAS) of cucumber breeding. Whole genome re-sequencing enhances the efficiency of polymorphic marker development and prediction of candidate genes.

A Genome-Wide Association Study on the Seedless Phenotype in Banana (Musa spp.) Reveals the Potential of a Selected Panel to Detect Candidate Genes in a Vegetatively Propagated Crop

Banana (Musa sp.) is a vegetatively propagated, low fertility, potentially hybrid and polyploid crop. These qualities make the breeding and targeted genetic improvement of this crop a difficult and long process. The Genome-Wide Association Study (GWAS) approach is becoming widely used in crop plants and has proven efficient to detecting candidate genes for traits of interest, especially in cereals. GWAS has not been applied yet to a vegetatively propagated crop. However, successful GWAS in banana would considerably help unravel the genomic basis of traits of interest and therefore speed up this crop improvement. We present here a dedicated panel of 105 accessions of banana, freely available upon request, and their corresponding GBS data. A set of 5,544 highly reliable markers revealed high levels of admixture in most accessions, except for a subset of 33 individuals from Papua. A GWAS on the seedless phenotype was then successfully applied to the panel. By applying the Mixed Linear Model corrected for both kinship and structure as implemented in TASSEL, we detected 13 candidate genomic regions in which we found a number of genes potentially linked with the seedless phenotype (i.e. parthenocarpy combined with female sterility). An additional GWAS performed on the unstructured Papuan subset composed of 33 accessions confirmed six of these regions as candidate. Out of both sets of analyses, one strong candidate gene for female sterility, a putative orthologous gene to Histidine Kinase CKI1, was identified. The results presented here confirmed the feasibility and potential of GWAS when applied to small sets of banana accessions, at least for traits underpinned by a few loci. As phenotyping in banana is extremely space and time-consuming, this latest finding is of particular importance in the context of banana improvement.

Spatiotemporal transcriptome provides insights into early fruit development of tomato (Solanum lycopersicum)

Early fruit development is crucial for crop production in tomato. After fertilization, the ovary undergoes cell division and cell expansion before maturation. Although the roles of regulatory signals such as hormone and carbohydrate during early fruit development have been studied, the spatial distribution and the sequential initiation of these regulatory signals still need to be explored. Using the tomato cultivar 'Moneymaker', we analyzed the transcriptome of the ovule and the ovary wall/pericarp dissected from four different stages of the early developing fruits by stereoscope. These datasets give us the whole picture about the spatial and temporal signal distribution in early development of ovule and pericarp. Our results indicate that the hormone signal was initiated in both ovule and pericarp after fertilization. After that, different signals were activated in ovule and pericarp due to their distinct developmental processes. Our study provides spatiotemporal regulatory landscape of gene expression with sequential information which was not studied by previous work and further strengthens the comprehension of the regulatory and metabolic events controlling early fruit development.

Identification and characterization of tomato gibberellin 2-oxidases (GA2oxs) and effects of fruit-specific SlGA2ox1 overexpression on fruit and seed growth and development

Gibberellins (GAs) play a crucial role in growth and development of the tomato fruit. Previously published studies focusing on the effect of GAs on tomato fruits used chemical treatments, constitutive overexpression or silencing of GA biosynthetic and catabolic genes globally throughout the plant. Fruit-specific overexpression of GA catabolic enzyme genes GA2-oxidases (GA2oxs), however, may provide an alternative method to study the role of endogenous GAs on the fruit development. In this study, we have identified 11 SlGA2ox proteins in tomato that are classified into three subgroups. Motif analysis and multiple sequence alignments have demonstrated that all SlGA2oxs, except SlGA2ox10, have similar motif compositions and high-sequence conservation. Quantitative reverse transcription-PCR analysis has showed that SlGA2oxs exhibit differential expression patterns in tomato fruits at different developmental stages. When the fruit-specific promoter TFM7 was used to control the expression of SlGA2ox1, we observed no changes in growth and development of vegetative organs. However, fruit weight, seed number and germination rate were significantly affected. We also treated tomato fruits with GA biosynthesis inhibitor and observed phenotypes similar to those of the transgenic fruits. Furthermore, we have demonstrated that expression of cell expansion and GA responsive genes were downregulated in transgenic tomato fruits, supporting that overexpression of the SlGA2ox1 leads to reduction in endogenous GAs. This study provides additional evidence that endogenous GAs and the SlGA2ox1 gene play an important role in controlling on fruit weight, seed development and germination in tomato plant.

Transcriptome Analysis Reveals Candidate Genes Involved in Gibberellin-Induced Fruit Setting in Triploid Loquat (Eriobotrya japonica)

The triploid loquat (Eriobotrya japonica) is a new germplasm with a high edible fruit rate. Under natural conditions, the triploid loquat has a low fruit setting ratio (not more than 10 fruits in a tree), reflecting fertilization failure. To unravel the molecular mechanism of gibberellin (GA) treatment to induce parthenocarpy in triploid loquats, a transcriptome analysis of fruit setting induced by GA₃ was analyzed using RNA-seq at four different stages during the development of young fruit. Approximately 344 million high quality reads in seven libraries were de novo assembled, yielding 153,900 unique transcripts with more than 79.9% functionally annotated transcripts. A total of 2,220, 2,974, and 1,614 differentially expressed genes (DEGs) were observed at 3, 7, and 14 days after GA treatment, respectively. The weighted gene co-expression network and Venn diagram analysis of DEGs revealed that sixteen candidate genes may play critical roles in the fruit setting after GA treatment. Five genes were related to auxin, in which one auxin synthesis gene of yucca was upregulated, suggesting that auxin may act as a signal for fruit setting. Furthermore, ABA 8'-hydroxylase was upregulated, while ethylene-forming enzyme was downregulated, suggesting that multiple hormones may be involved in GA signaling. Four transcription factors, NAC7, NAC23, bHLH35, and HD16, were potentially negatively regulated in fruit setting, and two cell division-related genes, arr9 and CYCA3, were upregulated. In addition, the expression of the GA receptor gid1 was downregulated by GA treatment, suggesting that the negative feedback mechanism in GA signaling may be regulated by gid1. Altogether, the results of the present study provide information from a comprehensive gene expression analysis and insight into the molecular mechanism underlying fruit setting under GA treatment in E. japonica.

A transcriptomic approach to identify regulatory genes involved in fruit set of wild-type and parthenocarpic tomato genotypes

The tomato parthenocarpic fruit (pat) mutation associates a strong competence for parthenocarpy with homeotic transformation of anthers and aberrancy of ovules. To dissect this complex floral phenotype, genes involved in the pollination-independent fruit set of the pat mutant were investigated by microarray analysis using wild-type and mutant ovaries. Normalized expression data were subjected to one-way ANOVA and 2499 differentially expressed genes (DEGs) displaying a >1.5 log-fold change in at least one of the pairwise comparisons analyzed were detected. DEGs were categorized into 20 clusters and clusters classified into five groups representing transcripts with similar expression dynamics. The "regulatory function" group (685 DEGs) contained putative negative or positive fruit set regulators, "pollination-dependent" (411 DEGs) included genes activated by pollination, "fruit growth-related" (815 DEGs) genes activated at early fruit growth. The last groups listed genes with different or similar expression pattern at all stages in the two genotypes. qRT-PCR validation of 20 DEGs plus other four selected genes assessed the high reliability of microarray expression data; the average correlation coefficient for the 20 DEGs was 0.90. In all the groups were evidenced relevant transcription factors encoding proteins regulating meristem differentiation and floral organ development, genes involved in metabolism, transport and response of hormones, genes involved in cell division and in primary and secondary metabolism. Among pathways related to secondary metabolites emerged genes related to the synthesis of flavonoids, supporting the recent evidence that these compounds are important at the fruit set phase. Selected genes showing a de-regulated expression pattern in pat were studied in other four parthenocarpic genotypes either genetically anonymous or carrying lesions in known gene sequences. This comparative approach offered novel insights for improving the present molecular understanding of fruit set and parthenocarpy in tomato.

Ethylene suppresses tomato (Solanum lycopersicum) fruit set through modification of gibberellin metabolism

Fruit set in angiosperms marks the transition from flowering to fruit production and a commitment to seed dispersal. Studies with Solanum lycopersicum (tomato) fruit have shown that pollination and subsequent fertilization induce the biosynthesis of several hormones, including auxin and gibberellins (GAs), which stimulate fruit set. Circumstantial evidence suggests that the gaseous hormone ethylene may also influence fruit set, but this has yet to be substantiated with molecular or mechanistic data. Here, we examined fruit set at the biochemical and genetic levels, using hormone and inhibitor treatments, and mutants that affect auxin or ethylene signaling. The expression of system-1 ethylene biosynthetic genes and the production of ethylene decreased during pollination-dependent fruit set in wild-type tomato and during pollination-independent fruit set in the auxin hypersensitive mutant iaa9-3. Blocking ethylene perception in emasculated flowers, using either the ethylene-insensitive Sletr1-1 mutation or 1-methylcyclopropene (1-MCP), resulted in elongated parthenocarpic fruit and increased cell expansion, whereas simultaneous treatment with the GA biosynthesis inhibitor paclobutrazol (PAC) inhibited parthenocarpy. Additionally, the application of the ethylene precursor 1-aminocyclopropane-1-carboxylic acid (ACC) to pollinated ovaries reduced fruit set. Furthermore, Sletr1-1 parthenocarpic fruits did not exhibit increased auxin accumulation, but rather had elevated levels of bioactive GAs, most likely reflecting an increase in transcripts encoding the GA-biosynthetic enzyme SlGA20ox3, as well as a reduction in the levels of transcripts encoding the GA-inactivating enzymes SlGA2ox4 and SlGA2ox5. Taken together, our results suggest that ethylene plays a role in tomato fruit set by suppressing GA metabolism.

Transcriptome profiling reveals the regulatory mechanism underlying pollination dependent and parthenocarpic fruit set mainly mediated by auxin and gibberellin

BACKGROUND

Fruit set is a key process for crop production in tomato which occurs after successful pollination and fertilization naturally. However, parthenocarpic fruit development can be uncoupled from fertilization triggered by exogenous auxin or gibberellins (GAs). Global transcriptome knowledge during fruit initiation would help to characterize the molecular mechanisms by which these two hormones regulate pollination-dependent and -independent fruit set.

PRINCIPAL FINDINGS

In this work, digital gene expression tag profiling (DGE) technology was applied to compare the transcriptomes from pollinated and 2, 4-D/GA3-treated ovaries. Activation of carbohydrate metabolism, cell division and expansion as well as the down-regulation of MADS-box is a comprehensive regulatory pathway during pollination-dependent and parthenocarpic fruit set. The signaling cascades of auxin and GA are significantly modulated. The feedback regulations of Aux/IAAs and DELLA genes which functioned to fine-tune auxin and GA response respectively play fundamental roles in triggering fruit initiation. In addition, auxin regulates GA synthesis via up-regulation of GA20ox1 and down-regulation of KNOX. Accordingly, the effect of auxin on fruit set is mediated by GA via ARF2 and IAA9 down-regulation, suggesting that both pollination-dependent and parthenocarpic fruit set depend on the crosstalk between auxin and GA.

SIGNIFICANCE

This study characterizes the transcriptomic features of ovary development and more importantly unravels the integral roles of auxin and GA on pollination-dependent and parthenocarpic fruit set.