Changes in tomato ovary transcriptome demonstrate complex hormonal regulation of fruit set

Comparative transcriptome analysis of two pomelo accessions with different parthenocarpic ability provides insight into the molecular mechanisms of parthenocarpy in pomelo (Citrus grandis)

Parthenocarpy is an important way for seedless fruit production in citrus. However, the molecular mechanism(s) of parthenocarpy in pomelo is still unknown. Our initial study found significantly different parthenocarpic abilities in Guanximiyou (G) and Shatianyou (S) pomelo following emasculation, and an endogenous hormone content assay revealed that indole-3-acetic acid (IAA), gibberellic acid (GA3) and zeatin (ZT) jointly promoted fruit expansion and cell division in parthenocarpic pomelo (G pomelo). To unravel the underlying molecular mechanism(s), we conducted the first transcriptome analysis on the two pomelo accessions at these two critical stages: the fruit initiation stage and the rapid expansion stage, in order to identify genes associated with parthenocarpy. This analysis yielded approximately 7.86 Gb of high-quality reads, and the subsequent de novo assembly resulted in the identification of 5,792 DEGs (Differentially Expressed Genes). Among these, a range of transcription factor families such as CgERF, CgC2H2, CgbHLH, CgNAC and CgMYB, along with genes like CgLAX2, CgGH3.6 and CgGH3, emerged as potential candidates contributing to pomelo parthenocarpy, as confirmed by qRT-PCR analysis. The present study provides comprehensive transcriptomic profiles of both parthenocarpic and non-parthenocarpic pomelos, reveals several metabolic pathways linked to parthenocarpy, and highlights the significant role of plant hormones in its regulation. These findings deepen our understanding of the molecular mechanisms underlying parthenocarpy in pomelo.

The hormone regulatory mechanism underlying parthenocarpic fruit formation in tomato

Parthenocarpic fruits, known for their superior taste and reliable yields in adverse conditions, develop without the need for fertilization or pollination. Exploring the physiological and molecular mechanisms behind parthenocarpic fruit development holds both theoretical and practical significance, making it a crucial area of study. This review examines how plant hormones and MADS-box transcription factors control parthenocarpic fruit formation. It delves into various aspects of plant hormones-including auxin, gibberellic acid, cytokinins, ethylene, and abscisic acid-ranging from external application to biosynthesis, metabolism, signaling pathways, and their interplay in influencing parthenocarpic fruit development. The review also explores the involvement of MADS family gene functions in these processes. Lastly, we highlight existing knowledge gaps and propose directions for future research on parthenocarpy.

A long noncoding RNA functions in pumpkin fruit development through S-adenosyl-L-methionine synthetase

Long noncoding RNAs (lncRNAs) play important roles in various biological processes. However, the regulatory roles of lncRNAs underlying fruit development have not been extensively studied. The pumpkin (Cucurbita spp.) is a preferred model for understanding the molecular mechanisms regulating fruit development because of its variable shape and size and large inferior ovary. Here, we performed strand-specific transcriptome sequencing on pumpkin (Cucurbita maxima "Rimu") fruits at 6 developmental stages and identified 5,425 reliably expressed lncRNAs. Among the 332 lncRNAs that were differentially expressed during fruit development, the lncRNA MSTRG.44863.1 was identified as a negative regulator of pumpkin fruit development. MSTRG.44863.1 showed a relatively high expression level and an obvious period-specific expression pattern. Transient overexpression and silencing of MSTRG.44863.1 significantly increased and decreased the content of 1-aminocyclopropane carboxylic acid (a precursor of ethylene) and ethylene production, respectively. RNA pull-down and microscale thermophoresis assays further revealed that MSTRG.44863.1 can interact with S-adenosyl-L-methionine synthetase (SAMS), an enzyme in the ethylene synthesis pathway. Considering that ethylene negatively regulates fruit development, these results indicate that MSTRG.44863.1 plays an important role in the regulation of pumpkin fruit development, possibly through interacting with SAMS and affecting ethylene synthesis. Overall, our findings provide a rich resource for further study of fruit-related lncRNAs while offering insights into the regulation of fruit development in plants.

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.

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.

Parthenocarpy in Cucurbitaceae: Advances for Economic and Environmental Sustainability

Parthenocarpy is an important agricultural trait that not only produces seedless fruits, but also increases the rate of the fruit set under adverse environmental conditions. The study of parthenocarpy in Cucurbitaceae crops has considerable implications for cultivar improvement. This article provides a comprehensive review of relevant studies on the parthenocarpic traits of several major Cucurbitaceae crops and offers a perspective on future developments and research directions.

Transcriptome Analysis Reveals Candidate Genes Involved in Gibberellin-Induced Fruit Development in Rosa roxburghii

Gibberellins (GAs) play indispensable roles in the fruit development of horticultural plants. Unfortunately, the molecular basis behind GAs regulating fruit development in R. roxburghii remains obscure. Here, GA3 spraying to R. roxburghii 'Guinong 5' at full-bloom promoted fruit size and weight, prickle development, seed abortion, ascorbic acid accumulation, and reduction in total soluble sugar. RNA-Seq analysis was conducted to generate 45.75 Gb clean reads from GA3- and non-treated fruits at 120 days after pollination. We obtained 4275 unigenes belonging to differently expressed genes (DEGs). Gene ontology and the Kyoto Encyclopedia of Genes and Genomes displayed that carbon metabolism and oxidative phosphorylation were highly enriched. The increased critical genes of DEGs related to pentose phosphate, glycolysis/gluconeogenesis, and citrate cycle pathways might be essential for soluble sugar degradation. Analysis of DEGs implicated in ascorbate revealed the myoinositol pathway required to accumulate ascorbic acid. Finally, DEGs involved in endogenous phytohormones and transcription factors, including R2R3 MYB, bHLH, and WRKY, were determined. These findings indicated that GA3-trigged morphological alterations might be related to the primary metabolites, hormone signaling, and transcription factors, providing potential candidate genes that could be guided to enhance the fruit development of R. roxburghii in practical approaches.

Amomum tsaoko DRM1 regulate seed germination and improve heat tolerance in Arabidopsis

Seed dormancy and germination are critical to medicinal plant reproduction. Dormancy-associated gene (DRM1) has been involved in the regulation of dormancy in Arabidopsis meristematic tissues or organs. However, research on molecular functions and regulations of DRM1 in Amomum tsaoko, an important medicinal plant, is rare. In this study, the DRM1 was isolated from embryos of A. tsaoko, and the results of protein subcellular localization in Arabidopsis protoplast indicated that DRM1 was mainly nucleus and cytoplasm. Expression analysis showed that DRM1 especially exhibited the highest transcript level in dormant seed and short-time stratification while displaying a high response of hormone and abiotic stress. Further investigation showed that ectopic expression of DRM1 in Arabidopsis exhibited delayed seed germination and germination capability to high temperatures. Additionally, DRM1 transgenic Arabidopsis exhibited increased tolerance to heat stress by enhancing antioxidative capacities and regulating stress-associated genes (AtHsp25.3-P, AtHsp18.2-CI, AtHsp70B, AtHsp101, AtGolS1, AtMBF1c, AtHsfA2, AtHsfB1 and AtHsfB2). Overall, our results reveal the role of DRM1 in seed germination and abiotic stress response.

Seedlessness Trait and Genome Editing—A Review

Parthenocarpy and stenospermocarpy are the two mechanisms underlying the seedless fruit set program. Seedless fruit occurs naturally and can be produced using hormone application, crossbreeding, or ploidy breeding. However, the two types of breeding are time-consuming and sometimes ineffective due to interspecies hybridization barriers or the absence of appropriate parental genotypes to use in the breeding process. The genetic engineering approach provides a better prospect, which can be explored based on an understanding of the genetic causes underlying the seedlessness trait. For instance, CRISPR/Cas is a comprehensive and precise technology. The prerequisite for using the strategy to induce seedlessness is identifying the crucial master gene or transcription factor liable for seed formation/development. In this review, we primarily explored the seedlessness mechanisms and identified the potential candidate genes underlying seed development. We also discussed the CRISPR/Cas-mediated genome editing approaches and their improvements.

A multifaceted comparison between the fruit-abscission and fruit-retention cultivars in ornamental crabapple

The ornamental crabapple is a multipurpose landscaping tree that bears brilliant fruit throughout the winter. However, whether or not its fruit persists after maturation is specifically correlated to cultivar characteristics. In this work, we screened two different types that display fruit-retention ("Donald Wyman," "Red Jewel," and "Sugar Tyme") and fruit-abscission ("Radiant" and "Flame") in Northern China across the whole winter using multi-year successional records. Fruit-abscission was determined predominantly by the abscission zone established at the base of the pedicel, regardless of fruit size and pedicel length, according to the results of the comparative research. The primary physiological rationale was the accumulation of hydrolases activity (pectinesterase, cellulase, polygalacturonase, and β-glucosidase). Comparative transcriptomics further identified a number of upregulated DEGs involved in the synthesis pathways of canonical phytohormones, such as ethylene, jasmonic acid, abscisic acid, and cytokinin, as well as 12 transcription factors linked in downstream signaling in fruit-abscission cultivars. Finally, a model incorporating multi-layered modulation was proposed for the fruit abscission of ornamental crabapple. This study will serve as the foundation for the development of fruit-viewing crabapples that have an extended ornamental lifetime.

A molecular framework of ethylene-mediated fruit growth and ripening processes in tomato

Although the role of ethylene in tomato (Solanum lycopersicum) fruit ripening has been intensively studied, its role in tomato fruit growth remains poorly understood. In addition, the relationship between ethylene and the developmental factors NON-RIPENING (NOR) and RIPENING INHIBITOR (RIN) during ripening is under debate. Here, we carried out comprehensive genetic analyses of genome-edited mutants of tomato ETHYLENE INSENSITIVE 2 (SlEIN2), four EIN3-like genes (SlEIL1-4), and three EIN3 BINDING F-box protein genes (SlEBF1-3). Both slein2-1 and the high-order sleil mutant (sleil1 sleil2 sleil3/SlEIL3 sleil4) showed reduced fruit size, mainly due to decreased auxin biosynthesis. During fruit maturation, slein2 mutants displayed the complete cessation of ripening, which was partially rescued by slebf1 but not slebf2 or slebf3. We also discovered that ethylene directly activates the expression of the developmental genes NOR, RIN, and FRUITFULL1 (FUL1) via SlEIL proteins. Indeed, overexpressing these genes partially rescued the ripening defects of slein2-1. Finally, the signal intensity of the ethylene burst during fruit maturation was intimately connected with the progression of full ripeness. Collectively, our work uncovers a critical role of ethylene in fruit growth and supports a molecular framework of ripening control in which the developmental factors NOR, RIN, and FUL1 act downstream of ethylene signaling.

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.

Fruit Development in Sweet Cherry

Fruits are an important source of vitamins, minerals and nutrients in the human diet. They also contain several compounds of nutraceutical importance that have significant antioxidant and anti-inflammatory roles, which can protect the consumer from diseases, such as cancer, and cardiovascular disease as well as having roles in reducing the build-up of LDL-cholesterol in blood plasma and generally reduce the risks of disease and age-related decline in health. Cherries contain high concentrations of bioactive compounds and minerals, including calcium, phosphorous, potassium and magnesium, and it is, therefore, unsurprising that cherry consumption has a positive impact on health. This review highlights the development of sweet cherry fruit, the health benefits of cherry consumption, and the options for increasing consumer acceptance and consumption.

Gene Expression in Zucchini Fruit Development

The study of fruit development in zucchini via gene expression has proven to be applicable in breeding programs. Phenotypic and transcriptomic studies of fruit set and parthenocarpy have been previously developed and some relevant genes have been reported. From these studies, three genotypes (MUCU-16, Whitaker, and Cavili) and six genes (CpAUX22, CpIAA4, CpIAMT-1, CpPIN5, CpCYCD6-1, and CpEXPLB1) were selected. The expression of these genes was analyzed in each genotype under three different treatments (pollination, auxin-treatment and non-treatment) during one week post anthesis. Also, a phenotyping analysis was conducted. The different nature of the samples and the genes selected allowed associations between different fruit traits and fruit development stages. There was a rapid response of CpAUX22 and CpIAA4 to the auxin treatment. Also, these genes and the CpIAMT-1 became more overexpressed in pollinated samples over time. The CpPIN5 gene increased its expression over time in all genotypes while CpCYCD6-1 was overexpressed in the early stages of fruit development in all samples. The CpEXPLB1 was highly up-regulated in non-treated samples, suggesting a relationship with fruit abortion. The overexpression of CpAUX22 and the non-overexpression of CpEXPLB1 in early stages may be associated with fruit growth in zucchini.

The Ethylene Biosynthesis Gene CpACO1A: A New Player in the Regulation of Sex Determination and Female Flower Development in Cucurbita pepo

A methanesulfonate-generated mutant has been identified in Cucurbita pepo that alters sex determination. The mutation converts female into hermaphrodite flowers and disrupts the growth rate and maturation of petals and carpels, delaying female flower opening, and promoting the growth rate of ovaries and the parthenocarpic development of the fruit. Whole-genome resequencing allowed identification of the causal mutation of the phenotypes as a missense mutation in the coding region of CpACO1A, which encodes for a type I ACO enzyme that shares a high identity with Cucumis sativus CsACO3 and Cucumis melo CmACO1. The so-called aco1a reduced ACO1 activity and ethylene production in the different organs where the gene is expressed, and reduced ethylene sensitivity in flowers. Other sex-determining genes, such as CpACO2B, CpACS11A, and CpACS27A, were differentially expressed in the mutant, indicating that ethylene provided by CpACO1A but also the transcriptional regulation of CpACO1A, CpACO2B, CpACS11A, and CpACS27A are responsible for determining the fate of the floral meristem toward a female flower, promoting the development of carpels and arresting the development of stamens. The positive regulation of ethylene on petal maturation and flower opening can be mediated by inducing the biosynthesis of JA, while its negative control on ovary growth and fruit set could be mediated by its repressive effect on IAA biosynthesis.

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.

Comparative Analysis of the Transcriptomes of Persisting and Abscised Fruitlets: Insights into Plant Hormone and Carbohydrate Metabolism Regulated Self-Thinning of Pecan Fruitlets during the Early Stage

Pecan is one of the most popular nut species in the world. The fruit drop rate of the pecan ‘Pawnee’ is more than 57%, with four fruit drop stages, which is very serious. In this study, we conducted transcriptomic profiling of persisting and abscised fruitlets in early fruit development by RNA-seq. A total of 11,976 differentially expressed genes (DEGs) were identified, 3012 upregulated and 8964 downregulated, in a comparison of abscised vs. persisting fruitlets at 35 days after anthesis (DAA). Our transcriptomic data suggest that gene subsets encoding elements involving the biosynthesis, metabolism, perception, signal transduction, and crosstalk of the plant hormones abscisic acid (ABA), auxin, cytokinin, ethylene, and gibberellin (GA) and plant growth regulators jasmonates, salicylic acid, and brassinosteroids were differentially expressed. In addition, the majority of transcriptionally activated genes involved in hormone signaling (except for ethylene and salicylic acid signaling) were downregulated in abscised fruitlets. The differential expression of transcripts coding for enzymes involved in sucrose, glucose, trehalose, starch, galactose, and galactinol metabolism shows that sucrose, galactinol, and glucose synthesis and starch content were reduced as starch biosynthesis was blocked, and retrogradation and degradation intensified. These results suggest that the abscised pecan fruitlets stopped growing and developing for some time before dropping, further indicating that their sugar supply was reduced or stopped. The transcriptome characterization described in this paper contributes to unravelling the molecular mechanisms and pathways involved in the physiological abscission of pecan fruits.

Pollination promotes ABA synthesis but not sexual reproduction in the apomictic species Zanthoxylum bungeanum Maxim

Apomixis is a form of reproduction that does not involve the fertilization of female gametes by male gametes but instead involves the production of offspring directly from the female parent. The offspring of apomixis are genetically identical to the female parent and inherit its traits. Therefore, apomixis has great potential for application to agricultural genetic breeding. However, it remains unclear whether apomictic species require pollination, and the impacts of pollination on such species are poorly understood. We investigated the effects of pollination on the apomictic species Zanthoxylum bungeanum Maxim. by analyzing its fertilization process, assembling its transcriptome, and measuring hormone concentrations, fruit setting rate and gene expression levels. Transcriptome sequencing of pollinated and unpollinated fruits resulted in a total of 69,131 PacBio reads. Of these, 7102 genes were up-regulated and 6491 genes were down-regulated. Analysis of the differentially expressed genes (DEGs) and construction of a weighted gene co-expression network showed that many DEGs were involved in plant hormone signal transduction, suggesting that hormonal signaling during development differs between pollinated and unpollinated fruit. The germination rate of Z. bungeanum pollen in vitro was only 11%, and pollen could not germinate in the embryo sac to complete fertilization. Although pollination did not enable Z. bungeanum to complete the sexual reproduction process, it significantly increased abscisic acid (ABA) concentration and fruit setting rate. Spraying 100 μg l-1 ABA also significantly increased the fruit setting rate. Therefore, ABA appears to be a key factor in the regulation of fruit setting in apomictic Z. bungeanum. Based on these results, we suggest that some male plants be cultivated in Z. bungeanum plantations or exogenous ABA be sprayed to increase the likelihood of pollination and thereby increase the fruit setting rate.

Auxin Metabolism Is Involved in Fruit Set and Early Fruit Development in the Parthenocarpic Tomato "R35-P"

Parthenocarpic tomato can set fruit and develop without pollination and exogenous hormone treatments under unfavorable environmental conditions, which is beneficial to tomato production from late fall to early spring in greenhouses. In this study, the endogenous hormones in the ovaries of the parthenocarpic tomato line "R35-P" (stigma removed or self-pollination) and the non-parthenocarpic tomato line "R35-N" (self-pollination) at four stages between preanthesis and postanthesis investigated, using high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS). A nearly twofold IAA (indoleacetic acid) content was found in "R35-P" rather than in "R35-N" at -2 and 0 days after anthesis (DAA). Except at -2 DAA, a lower ABA (abscisic acid) content was observed in Pe (stigma removed in "R35-P") compared to that in Ps (self-pollination in "R35-P") or CK (self-pollination in "R35-N"). After pollination, although the content of GA₁ (gibberellins acid 1) in CK increased, the levels of GAs (gibberellins acids) were notably low. At all four stages, a lower SA (salicylic acid) content was found in Ps and CK than in Pe, while the content and the change trend were similar in Ps and CK. The variation tendencies of JA (jasmonic acid) varied among Pe, Ps, and CK at the studied periods. Furthermore, KEGG (Kyoto Encyclopedia of Genes and Genomes) enrichment analyses of transcriptomic data identified 175 differentially expressed genes (DEGs) related to plant hormone signal transduction, including 63 auxin-related genes, 27 abscisic acid-related genes, 22 ethylene-related genes, 16 cytokinin-related genes, 16 salicylic acid-related genes, 14 brassinosteroid-related genes, 13 jasmonic acid-related genes, and 4 gibberellin-related genes at -2 DAA and 0 DAA. Our results suggest that the fate of a fruit set or degeneration occurred before anthesis in tomato. Auxins, whose levels were independent of pollination and fertilization, play prominent roles in controlling a fruit set in "R35-P," and other hormones are integrated in a synergistic or antagonistic way.

Genetic diversity of tomato response to heat stress at the QTL and transcriptome levels

Tomato is a widely cultivated crop, which can grow in many environments. However, temperature above 30°C impairs its reproduction, subsequently impacting fruit yield. We assessed the impact of high-temperature stress (HS) in two tomato experimental populations, a multi-parental advanced generation intercross (MAGIC) population and a core-collection (CC) of small-fruited tomato accessions. Both populations were evaluated for 11 traits related to yield components, phenology and fruit quality in optimal and HS conditions. HS significantly impacted all traits in both populations, but a few genotypes with stable yield under HS were identified. A plasticity index was computed for each individual to measure the extent of the heat impact for each trait. Quantitative trait loci (QTL) were detected in control and HS conditions as well as for plasticity index. Linkage and genome-wide association analyses in the MAGIC and CC populations identified a total of 98 and 166 QTLs, respectively. Taking the two populations together, 69 plasticity QTLs (pQTLs) were involved in tomato heat response for 11 traits. The transcriptome changes in the ovary of six genotypes with contrasted responses to HS were studied, and 837 genes differentially expressed according to the conditions were detected. Combined with previous transcriptome studies, these results were used to propose candidate genes for HS response QTLs.

Tomato agamous-like6 parthenocarpy is facilitated by ovule integument reprogramming involving the growth regulator KLUH

Fruit set is established during and soon after fertilization of the ovules inside the quiescent ovary, but the signaling pathways involved remain obscure. The tomato (Solanum lycopersicum) CRISPR loss-of-function mutant of the transcription factor gene AGAMOUS-like6 (SlAGL6; slagl6CR-sg1) is capable of fertilization-independent setting of normal, yet seedless (parthenocarpic), fruit. To gain insight into the mechanism of fleshy fruit set, in this study, we investigated how slagl6CR-sg1 uncouples fruit set from fertilization. We found that mutant ovules were enlarged due to integument over-proliferation and failed to differentiate an endothelium, the integument's innermost layer, upon maturation. A causal relationship between slagl6 loss-of-function and these abnormal phenotypes is inferred from the observation that SlAGL6 is predominantly expressed in the immature ovule integument, and upon ovule maturation, its expression shifts to the endothelium. The transcriptome of unfertilized mutant ovules profoundly differs from that of wild-type and exhibits substantial overlap with the transcriptomes of fertilized ovules sporophytic tissues. One prominent upregulated gene was the fertilization-induced cytochrome P450 cell proliferation regulator SlKLUH. Indeed, ectopic overexpression of SlKLUH stimulated both integument growth in unfertilized ovules and parthenocarpy, suggesting that its suppression by SlAGL6 is paramount for preventing fertilization-independent fruit set. Taken together, our study informs on the transcriptional programs that are regulated by SlAGL6 and demonstrates that it acts from within the ovule integument to inhibit ovary growth beyond anthesis. That by suppressing components of the fertilization-induced ovule reprogramming underlying fruit set.

Histone posttranslational modifications rather than DNA methylation underlie gene reprogramming in pollination-dependent and pollination-independent fruit set in tomato

Fruit formation comprises a series of developmental transitions among which the fruit set process is essential in determining crop yield. Yet, our understanding of the epigenetic landscape remodelling associated with the flower-to-fruit transition remains poor. We investigated the epigenetic and transcriptomic reprogramming underlying pollination-dependent and auxin-induced flower-to-fruit transitions in the tomato (Solanum lycopersicum) using combined genomewide transcriptomic profiling, global ChIP-sequencing and whole genomic DNA bisulfite sequencing (WGBS). Variation in the expression of the overwhelming majority of genes was associated with change in histone mark distribution, whereas changes in DNA methylation concerned a minor fraction of differentially expressed genes. Reprogramming of genes involved in processes instrumental to fruit set correlated with their H3K9ac or H3K4me3 marking status but not with changes in cytosine methylation, indicating that histone posttranslational modifications rather than DNA methylation are associated with the remodelling of the epigenetic landscape underpinning the flower-to-fruit transition. Given the prominent role previously assigned to DNA methylation in reprogramming key genes of the transition to ripening, the outcome of the present study supports the idea that the two main developmental transitions in fleshy fruit and the underlying transcriptomic reprogramming are associated with different modes of epigenetic regulations.

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.

Transcriptome sequencing and endogenous phytohormone analysis reveal new insights in CPPU controlling fruit development in kiwifruit (Actinidia chinensis)

Kiwifruit (Actinidia chinensis) is a rich nutritious fruit crop owing to a markedly higher content of vitamin C and minerals. To promote fruit set and to increase the yield of kiwifruit, forchlorfenuron (CPPU) has been widely applied. However, the molecular details regarding CPPU controlling kiwifruit development, especially at the fastest fruit growth stage, remain unknown. In the present study, we measured the effect of CPPU on developmental regulation in red-fleshed kiwifruit (Actinidia chinensis 'Hongyang'). Additionally, a cytological analysis was performed to clarify the precise changes in the cell structure of the CPPU-treated kiwifruits. Moreover, the concentration of endogenous phytohormones, including indoleacetic acid (IAA), zeatin (ZT), gibberellic acid 3 (GA3), and abscisic acid (ABA), were measured by Enzyme-linked Immunosorbent Assay (ELISA). Furthermore, RNA-Seq was performed to dissect the complicated molecular mechanisms, with a focus on biosynthesis, metabolism, and signaling compounds, such as endogenous hormones, sugars, and L-ascorbic acid. Our results demonstrated that CPPU treatment not only regulates the size and weight of a single fruit but also improves the quality in 'Hongyang' kiwifruit through the accumulation of both soluble sugar and vitamin C. It was also seen that CPPU regulates kiwifruit development by enhancing cell expansion of epidermal cells and parenchyma cells, while, promoting cell division of subepidermal cells. Additionally, CPPU significantly increased the gibberellin and cytokinin biosynthetic pathway and signaling, while repressing auxin and ABA biosynthetic pathway; thus, signaling plays an essential role in CPPU controlling kiwifruit development. Notably, transcriptomic analysis revealed that a total of 2244 genes, including 352 unannotated genes, were differentially expressed in kiwifruits because of CPPU treatment, including 127 transcription factors. These genes are mainly enriched in plant hormone signal transduction, photosynthesis, MAPK signaling pathway, starch and sucrose metabolism, and phenylpropanoid biosynthesis. Overall, our results highlight that CPPU regulation of kiwifruit development is mainly associated with an antagonistic and/or synergistic regulatory role of endogenous phytohormones, and enhancing the energy supply. This provides new insights into the molecular details of CPPU controlling kiwifruit development at the fastest fruit growth stage, which is of agricultural importance for kiwifruit breeding and crop improvement.

Fruit setting rewires central metabolism via gibberellin cascades

Fruit set is the process whereby ovaries develop into fruits after pollination and fertilization. The process is induced by the phytohormone gibberellin (GA) in tomatoes, as determined by the constitutive GA response mutant procera However, the role of GA on the metabolic behavior in fruit-setting ovaries remains largely unknown. This study explored the biochemical mechanisms of fruit set using a network analysis of integrated transcriptome, proteome, metabolome, and enzyme activity data. Our results revealed that fruit set involves the activation of central carbon metabolism, with increased hexoses, hexose phosphates, and downstream metabolites, including intermediates and derivatives of glycolysis, the tricarboxylic acid cycle, and associated organic and amino acids. The network analysis also identified the transcriptional hub gene SlHB15A, that coordinated metabolic activation. Furthermore, a kinetic model of sucrose metabolism predicted that the sucrose cycle had high activity levels in unpollinated ovaries, whereas it was shut down when sugars rapidly accumulated in vacuoles in fruit-setting ovaries, in a time-dependent manner via tonoplastic sugar carriers. Moreover, fruit set at least partly required the activity of fructokinase, which may pull fructose out of the vacuole, and this could feed the downstream pathways. Collectively, our results indicate that GA cascades enhance sink capacities, by up-regulating central metabolic enzyme capacities at both transcriptional and posttranscriptional levels. This leads to increased sucrose uptake and carbon fluxes for the production of the constituents of biomass and energy that are essential for rapid ovary growth during the initiation of fruit set.

The inhibition of SlIAA9 mimics an increase in endogenous auxin and mediates changes in auxin and gibberellin signalling during parthenocarpic fruit development in tomato

Parthenocarpic fruit formation can be achieved through the inhibition of SlIAA9, a negative regulator of auxin signalling in tomato plant. During early fruit development under SlIAA9 inhibition, cell division and cell expansion were observed. Bioactive gibberellin (GA) accumulated, but indole-3-acetic acid (IAA) and trans-zeatin did not accumulate substantially. Furthermore, under SlIAA9 inhibition, auxin-responsive genes such as SlIAA2, -3, and -14 were upregulated, and SlARF7 was downregulated. These results indicate that SlIAA9 inhibition mimics an increase in auxin. The auxin biosynthesis genes SlTAR1, ToFZY, and ToFZY5 were stimulated by an increase in auxin and by auxin mimicking under SlIAA9 inhibition. However, SlTAR2 and ToFZY2 were upregulated only by pollination followed by high IAA accumulation. These results suggest that SlTAR2 and ToFZY2 play an important role in IAA synthesis in growing ovaries. GA synthesis was also activated by SlIAA9 inhibition through both the early-13-hydroxylation (for GA₁ synthesis) and non-13-hydroxylation (GA₄) pathways, indicating that fruit set caused by SlIAA9 inhibition was partially mediated by the GA pathway. SlIAA9 inhibition induced the expression of GA inactivation genes as well as GA biosynthesis genes except SlCPS during early parthenocarpic fruit development in tomato. This result suggests that inactivation genes play a role in fine-tuning the regulation of bioactive GA accumulation.

Cucumber Fruit Size and Shape Variations Explored from the Aspects of Morphology, Histology, and Endogenous Hormones

Fruit size and shape are important qualities and yield traits in cucumber (Cucumis sativus L.), but the factors that influence fruit size and shape remain to be explored. In this study, we investigated the dynamic changes of fruit size and shape from the aspects of morphology, cellular levels and endogenous hormones for nine typical cucumber inbred lines. The results show that fruit length had a strong positive correlation to the cell number in the longitudinal section of fruit throughout the four stages of 0, 6, 12, and 30 DAA (days after anthesis). However, the significant negative correlations were found between fruit length and the fruit cell size at 12 and 30 DAA. Furthermore, fruit diameter was positively correlated to the cell number in the cross section at all the investigated fruit growth stages. The indole-3-acetic acid (IAA) content showed significant positive correlations to the fruit length at all fruit growth stages of −6, −3, 0, 3, 6, 9 and 12 DAA, but IAA content and fruit diameter showed significant negative correlations for all the stages except for at −6 DAA. The trans-zeatin riboside (tZR), zeatin (ZT), gibberellic acid (GA₃) and jasmonic acid (JA) content had a positive or negative correlation with fruit length or diameter only at certain stages. Neither fruit length nor diameter had significant correlations to abscisic acid (ABA) content. These results indicate that variations in fruit size and shape of different cucumber inbred lines mainly result from the differences in fruit cell number and endogenous IAA content. The present work is the first to propose cucumber fruit size and shape changes from the combined aspects of morphology, cellular levels, and endogenous hormones.

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.

Dissection of complex traits of tomato in the post-genome era

We present the main advances of dissection of complex traits in tomato by omics, the genes identified to control complex traits and the application of CRISPR/Cas9 in tomato breeding. Complex traits are believed to be under the control of multiple genes, each with different effects and interaction with environmental factors. Advance development of sequencing and molecular technologies has enabled the recognition of the genomic structure of most organisms and the identification of a nearly limitless number of markers that have made it to accelerate the speed of QTL identification and gene cloning. Meanwhile, multiomics have been used to identify the genetic variations among different tomato species, determine the expression profiles of genes in different tissues and at distinct developmental stages, and detect metabolites in different pathways and processes. The combination of these data facilitates to reveal mechanism underlying complex traits. Moreover, mutants generated by mutagens and genome editing provide relatively rich genetic variation for deciphering the complex traits and exploiting them in tomato breeding. In this article, we present the main advances of complex trait dissection in tomato by omics since the release of the tomato genome sequence in 2012. We provide further insight into some tomato complex traits because of the causal genetic variations discovered so far and explore the utilization of CRISPR/Cas9 for the modification of tomato complex traits.

Auxin and ethylene regulation of fruit set

With the forecasted fast increase in world population and global climate change, providing sufficient amounts of quality food becomes a major challenge for human society. Seed and fruit crop yield is determined by developmental processes including flower initiation, pollen fertility and fruit set. Fruit set is defined as the transition from flower to young fruit, a key step in the development of sexually reproducing higher plants. Plant hormones have important roles during flower pollination and fertilization, leading to fruit set. Moreover, it is well established that fruit set can be triggered by phytohormones like auxin and gibberellins (GAs), in the absence of fertilization, both hormones being commonly used to produce parthenocarpic fruits and to increase fruit yield. Additionally, a number of studies highlighted the role of ethylene in plant reproductive organ development. The present review integrates current knowledge on the roles of auxin and ethylene in different steps of the fruit set process with a specific emphasis on the interactions between the two hormones. A deeper understanding of the interplay between auxin and ethylene may provide new leads towards designing strategies for a better control of fruit initiation and ultimately yield.

Interplay between hormones and assimilates during pear development and ripening and its relationship with the fruit postharvest behaviour

The ability of European pears (Pyrus communis L.) to ripen immediately after harvest is cultivar-dependent and relies on a range of physiological and biochemical events occurring during fruit growth and development that remain largely unknown. To gain further knowledge on these events, changes in the content of sugars, acids, major hormones and ethylene precursors or related enzymes were studied in two pear varieties ('Blanquilla' and 'Conference') with known differences in their postharvest ripening behaviour. In both cultivars, low contents of abscisic acid (ABA) seemed to be a prerequisite to initiate on-tree fruit ripening including sugar accumulation and softening. In 'Blanquilla' pears, the enhanced potential to produce ethylene and thereby to ripen upon harvest was associated to a late increase in ABA content paralleled by an accumulation of indole 3-acetic acid (IAA). In turn, the inability of 'Conference' fruit to produce ethylene upon harvest appeared to be related to a coordinated action of gibberellins (more specifically GA₁), salicylic acid (SA) and jasmonic acid (JA), which remained at high concentrations during the latest phases of fruit growth. Collectively, our results highlight that a complex hormonal cross-talk during the development and on-tree ripening of pear fruit may finally determine the ability of the fruit to ripen upon harvest.

The Role of Major Transcription Factors in Solanaceous Food Crops under Different Stress Conditions: Current and Future Perspectives

Plant growth, development, and productivity are adversely affected by environmental stresses such as drought (osmotic stress), soil salinity, cold, oxidative stress, irradiation, and diverse diseases. These impacts are of increasing concern in light of climate change. Noticeably, plants have developed their adaptive mechanism to respond to environmental stresses by transcriptional activation of stress-responsive genes. Among the known transcription factors, DoF, WRKY, MYB, NAC, bZIP, ERF, ARF and HSF are those widely associated with abiotic and biotic stress response in plants. Genome-wide identification and characterization analyses of these transcription factors have been almost completed in major solanaceous food crops, emphasizing these transcription factor families which have much potential for the improvement of yield, stress tolerance, reducing marginal land and increase the water use efficiency of solanaceous crops in arid and semi-arid areas where plant demand more water. Most importantly, transcription factors are proteins that play a key role in improving crop yield under water-deficient areas and a place where the severity of pathogen is very high to withstand the ongoing climate change. Therefore, this review highlights the role of major transcription factors in solanaceous crops, current and future perspectives in improving the crop traits towards abiotic and biotic stress tolerance and beyond. We have tried to accentuate the importance of using genome editing molecular technologies like CRISPR/Cas9, Virus-induced gene silencing and some other methods to improve the plant potential in giving yield under unfavorable environmental conditions.

Functional analysis of SlNCED1 in pistil development and fruit set in tomato (Solanum lycopersicum L.)

Abscisic acid (ABA) is an important regulator of many plant developmental processes, although its regulation in the pistil during anthesis is unclear. We investigated the role of 9-cis-epoxycarotenoid dioxygenase (SlNCED1), a key ABA biosynthesis enzyme, through overexpression and transcriptome analysis in the tomato pistil. During pistil development, ABA accumulates and SlNCED1 expression increases continually, peaking one day before full bloom, when the maximum amount of ethylene is released in the pistil. ABA accumulation and SlNCED1 expression in the ovary remained high for three days before and after full bloom, but then both declined rapidly four days after full bloom following senescence and petal abscission and expansion of the young fruits. Overexpression of SlNCED1 significantly increased ABA levels and also up-regulated SlPP2C5 expression, which reduced ABA signaling activity. Overexpression of SlNCED1 caused up-regulation of pistil-specific Zinc finger transcription factor genes SlC3H29, SlC3H66, and SlC3HC4, which may have affected the expression of SlNCED1-mediated pistil development-related genes, causing major changes in ovary development. Increased ABA levels are due to SlNCED1 overexpresson which caused a hormonal imbalance resulting in the growth of parthenocarpic fruit. Our results indicate that SlNCED1 plays a crucial role in the regulation of ovary/pistil development and fruit set.

Transcriptome Analysis of Young Ovaries Reveals Candidate Genes Involved in Gamete Formation in Lantana camara

Lantana (Lantana camara L., Verbenaceae) is an important ornamental crop, yet can be a highly invasive species. The formation of unreduced female gametes (UFGs) is a major factor contributing to its invasiveness and has severely hindered the development of sterile cultivars. To enrich the genomic resources and gain insight into the genetic mechanisms of UFG formation in lantana, we investigated the transcriptomes of young ovaries of two lantana genotypes, GDGHOP-36 (GGO), producing 100% UFGs, and a cultivar Landmark White Lantana (LWL), not producing UFGs. The de novo transcriptome assembly resulted in a total of 90,641 unique transcript sequences with an N50 of 1692 bp, among which, 29,383 sequences contained full-length coding sequences (CDS). There were 214 transcripts associated with the biological processes of gamete production and 10 gene families orthologous to genes known to control unreduced gamete production in Arabidopsis. We identified 925 transcription factor (TF)-encoding sequences, 91 nucleotide-binding site (NBS)-containing genes, and gene families related to drought/salt tolerance and allelopathy. These genomic resources and candidate genes involved in gamete formation will be valuable for developing new tools to control the invasiveness in L. camara, protect native lantana species, and understand the formation of unreduced gametes in plants.

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.

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.

First RNA-seq approach to study fruit set and parthenocarpy in zucchini (Cucurbita pepo L.)

BACKGROUND

Zucchini fruit set can be limited due to unfavourable environmental conditions in off-seasons crops that caused ineffective pollination/fertilization. Parthenocarpy, the natural or artificial fruit development without fertilization, has been recognized as an important trait to avoid this problem, and is related to auxin signalling. Nevertheless, differences found in transcriptome analysis during early fruit development of zucchini suggest that other complementary pathways could regulate fruit formation in parthenocarpic cultivars of this species. The development of next-generation sequencing technologies (NGS) as RNA-sequencing (RNA-seq) opens a new horizon for mapping and quantifying transcriptome to understand the molecular basis of pathways that could regulate parthenocarpy in this species. The aim of the current study was to analyze fruit transcriptome of two cultivars of zucchini, a non-parthenocarpic cultivar and a parthenocarpic cultivar, in an attempt to identify key genes involved in parthenocarpy.

RESULTS

RNA-seq analysis of six libraries (unpollinated, pollinated and auxin treated fruit in a non-parthenocarpic and parthenocarpic cultivar) was performed mapping to a new version of C. pepo transcriptome, with a mean of 92% success rate of mapping. In the non-parthenocarpic cultivar, 6479 and 2186 genes were differentially expressed (DEGs) in pollinated fruit and auxin treated fruit, respectively. In the parthenocarpic cultivar, 10,497 in pollinated fruit and 5718 in auxin treated fruit. A comparison between transcriptome of the unpollinated fruit for each cultivar has been performed determining that 6120 genes were differentially expressed. Annotation analysis of these DEGs revealed that cell cycle, regulation of transcription, carbohydrate metabolism and coordination between auxin, ethylene and gibberellin were enriched biological processes during pollinated and parthenocarpic fruit set.

CONCLUSION

This analysis revealed the important role of hormones during fruit set, establishing the activating role of auxins and gibberellins against the inhibitory role of ethylene and different candidate genes that could be useful as markers for parthenocarpic selection in the current breeding programs of zucchini.

The Occurrence of Seedlessness in Higher Plants; Insights on Roles and Mechanisms of Parthenocarpy

Parthenocarpy in a broad sense includes those processes that allow the production of seedless fruits. Such fruits are favorable to growers, because they are set independently of successful pollination, and to processors and consumers, because they are easier to deal with and to eat. Seedless fruits however represent a biological paradox because they do not contribute to offspring production. In this work, the occurrence of parthenocarpy in Angiosperms was investigated by conducting a bibliographic survey. We distinguished monospermic (single seeded) from plurispermic (multiseeded) species and wild from cultivated taxa. Out of 96 seedless taxa, 66% belonged to plurispermic species. Of these, cultivated species were represented six times higher than wild species, suggesting a selective pressure for parthenocarpy during domestication and breeding. In monospermic taxa, wild and cultivated species were similarly represented. The occurrence of parthenocarpy in wild species suggests that seedlessness may have an adaptive role. In monospermic species, seedless fruits are proposed to reduce seed predation through deceptive mechanisms. In plurispermic fruit species, parthenocarpy may exert an adaptive advantage under suboptimal pollination regimes, when too few embryos are formed to support fruit growth. In this situation, parthenocarpy offers the opportunity to accomplish the production and dispersal of few seeds, thus representing a selective advantage. Approximately 20 sources of seedlessness have been described in tomato. Excluding the EMS induced mutation parthenocarpic fruit (pat), the parthenocarpic phenotype always emerged in biparental populations derived from wide crosses between cultivated tomato and wild relatives. Following a theory postulated for apomictic species, we argument that wide hybridization could also be the force driving parthenocarpy, following the disruption of synchrony in time and space of reproductive developmental events, from sporogenesis to fruit development. The high occurrence of polyploidy among parthenocarpic species supported this suggestion. Other commonalities between apomixis and parthenocarpy emerged from genetic and molecular studies of the two phenomena. Such insights may improve the understanding of the mechanisms underlying these two reproductive variants of great importance to modern breeding.

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.

Modulation of sphingolipid long-chain base composition and gene expression during early olive-fruit development, and putative role of brassinosteroid

Sphingolipids are abundant membrane components and signalling molecules in various aspects of plant development. However, the role of sphingolipids in early fleshy-fruit growth has rarely been investigated. In this study, we first investigated the temporal changes in sphingolipid long-chain base (LCB) content, composition, and gene expression that occurred during flower opening and early fruit development in olive (Olea europaea L. cv Picual). Moreover, the interaction between sphingolipid and the plant hormone, brassinosteroid (BR), during the early fruit development was also explored. For this, BR levels were manipulated through the application of exogenous BRs (24-epibrassinolide, EBR) or a BR biosynthesis inhibitor (brassinazole, Brz) and their effects on early fruit development, sphingolipid LCB content, and gene expression were examined in olive fruit at 14 days post-anthesis (DPA). We here show that sphingolipid with C-4 hydroxylation and Δ8 desaturation with a preference for (E)-isomer formation are quantitatively the most important sphingolipids in olive reproductive organs. In this work, the total LCB amount significantly decreased at the anthesis stage, but olive sphingosine-1-phosphate lyase (OeSPL) gene was expressed exclusively in flower and upregulated during the anthesis, revealing an association with the d18:1(8E) accumulation. However, the LCB content increased in parallel with the upregulation of the expression of genes for key sphingolipid biosynthetic and LCB modification enzymes during early fruit development in olive. Likewise, we found that EBR exogenously applied to olive trees significantly stimulated the fruit growth rate whereas Brz inhibited fruit growth rate after 7 and 14 days of treatment. In addition, this inhibitory effect could be counteracted by the application of EBR. The promotion of early fruit growth was accompanied by the down-regulation of sphingolipid LCB content and gene expression in olive fruit, whereas Brz application raised levels of sphingolipid LCB content and gene expression in olive fruit after 7 and 14 days of treatment. Thus, our data indicate that endogenous sphingolipid LCB and gene-expression levels are intricately controlled during early fruit development and also suggest a possible link between BR, the sphingolipid content/gene expression, and early fruit development in olive.

The sex-determining gene CitACS4 is a pleiotropic regulator of flower and fruit development in watermelon (Citrullus lanatus)

In the species of the Cucurbitaceae family, the occurrence of separate male and female flowers in the same plant (monoecy) is controlled by an ethylene biosynthesis ACS gene, which specifically suppresses the development of stamen in the female flower. In watermelon, a mutation of loss of function in CitACS4 promotes the conversion of female into hermaphrodite flowers, and of monoecious into andromonoecious plants. We have studied whether the ethylene produced by CitACS4 enzyme could also be involved in other ethylene-regulated traits, including pistillate flowering transition and the number of female flowers per plant, the development of floral organs other than stamens, as well as fruit and seed set, and fruit development. A linkage analysis approach was performed in three independent F2 populations segregating for the two alleles of the gene (M, monoecious; m, andromonoecious), and the different traits under study. The CitACS4m allele not only cosegregated with andromonoecy, but also with earlier pistillate transition, an increased number of pistillate flowers per plant, and a slower growth and maturation of petals and carpels, which delayed anthesis time in hermaphrodite flowers. The m allele was also found to be linked to a reduced fruit set, which was not caused by a deficiency in pollination or fertilization. The gene also affected the longitudinal and transverse growth rates of the ovary and fruit, which means that fruits from andromonoecious plants (mm) were rounder than those from monoecious (MM) ones. Taken together, these data indicate that the locus defined by the ethylene biosynthesis and sex-determining gene CitACS4 acts as a pleiotropic regulator of the complete development of the pistillate flower and the earlier development of the fruit.

Comparative Transcriptomic Profiling to Understand Pre- and Post-Ripening Hormonal Regulations and Anthocyanin Biosynthesis in Early Ripening Apple Fruit

The ‘Hongyu’ apple is an early ripening apple cultivar and usually used for fresh marketing. Due to the short ripening period, most of the fruit are harvested at the commercial maturity stage for proper marketing distribution and a longer shelf life. Fruit ripening involves delicate changes to its metabolic and physiological traits through well-organized synchronization of several hormones and regulatory steps. A clear understanding of these hormonal alterations is crucial for extending the period from commercial to physiological ripening. This study was intended to clarify the hormonal alterations and anthocyanin biosynthesis process prior to and immediate after, the harvesting of apple fruit considering the commercial maturity stage. Fruits harvested at 120 Days after flowering (DAF) (HY_4th) was considered as commercially ripened, 110 DAF (HY_3rd) as pre-ripening and 120 DAF followed by five days storage at 20 °C (HY_20 °C_5) as post-ripening samples. Three different stages of fruit were used for transcriptome assembly using RNA-Seq. Results revealed 9187 differentially expressed genes (DEGs) in the post-ripening samples, which was comparatively lower (922 DEGs) in the pre-ripening fruits. DEGs were subjected to Gene Ontology analysis and 31 categories were significantly enriched in the groups ‘biological process,’ ‘molecular function’ and ‘cellular component.’ The DEGs were involved in hormonal signaling pathways like ethylene, abscisic acid (ABA), auxin, gibberellin (GA), brassinosteroid (BR) and anthocyanin biosynthesis pathways such as PAL, 4CL, CHI, DFR, F3H, UFGT. Several transcription factors like the MADS-box gene, MYB, bHLH, NAC, WRKY and HSF were differentially expressed between the pre- and post-ripening fruits. Selected DEGs were subjected to gene expression analysis using quantitative RT-PCR (qRT-PCR) and the results were consistent with those of RNA-Seq. Our data suggested that in addition to ethylene, ABA and other hormones also play key roles in regulating apple fruit ripening and may interact with the ethylene signaling process. Additionally, our data provided an exhibition of the expression pattern of genes in the anthocyanin biosynthesis pathway.

Silencing GRAS2 reduces fruit weight in tomato

GRAS family transcription factors are involved in multiple biological processes in plants. Here, we report that GRAS2 plays a vital role in regulating fruit weight in tomato (Solanum lycopersicum). We establish that the expression of GRAS2 was elevated in ovaries and maintained at a constant level in fertilized ovules. Reduction of GRAS2 expression in transgenic plants reduced fruit weight through modulating ovary growth and cell size. At the metabolic level, downregulation of GRAS2 decreased activities of the gibberellic acid biosynthesis and signal transduction pathways, leading to insufficient levels of active gibberellic acid during the initial ovary development of tomato. Moreover, genotypic diversity of GRAS2 was consistent with the molecular basis of fruit weight evolution, suggesting that GRAS2 contributes to the molecular basis of the evolution of fruit weight in tomato. Collectively, these findings enhance our understanding of GRAS2 functions, in fruit development of tomato, and demonstrate a strong association between the GRAS gene family and fruit development.

The role of ethylene in the regulation of ovary senescence and fruit set in tomato (Solanum lycopersicum)

Fruit set is the developmental transition from ovary to young fruit, and generally requires pollination and fertilization. Although the mechanism for fruit set remains elusive, several lines of evidence have demonstrated that fruit set is triggered by activated metabolism of or increased sensitivity to the plant hormones auxin or gibberellins (GAs), which stimulate cell division and expansion within the ovary. Our recent study with tomato (Solanum lycopersicum) suggested that the gaseous hormone ethylene connects auxin and GA, suppressing initiation of fruit set by down-regulating GA accumulation. By contrast, reduced sensitivity to ethylene triggers accumulation of GA, but not auxin, through increasing bioactive GA biosynthesis and decreasing GA inactivation. These changes induce parthenocarpy accompanied by pollination-independent cell expansion in the ovary. Here, we provide evidence that ethylene likely promotes mRNA expression of the senescence-associated genes SlSAG12 and SlNAP in unpollinated ovaries. These results suggest that ethylene acts downstream of auxin and upstream of GA, and also suggest that ethylene promotes senescence of ovary that fail to set fruit in tomato.

Tomato AUXIN RESPONSE FACTOR 5 regulates fruit set and development via the mediation of auxin and gibberellin signaling

Auxin response factors (ARFs) encode transcriptional factors that function in the regulation of plant development processes. A tomato ARF gene, SlARF5, was observed to be expressed at high levels in emasculated ovaries but maintained low expression levels in pollinated ovaries. The amiRNA SlARF5 lines exhibited ovary growth and formed seedless fruits following emasculation. These parthenocarpic fruits developed fewer locular tissues, and the fruit size and weight were decreased in transgenic lines compared to those of wild-type fruits. Gene expression analysis demonstrated that several genes involved in the auxin-signaling pathway were downregulated, whereas some genes involved in the gibberellin-signaling pathway were enhanced by the decreased SlARF5 mRNA levels in transgenic plants, indicating that SlARF5 may play an important role in regulating both the auxin- and gibberellin-signaling pathways during fruit set and development.