Generation of parthenocarpic tomato plants in multiple elite cultivars using the CRISPR/Cas9 system

Tomato (Solanum lycopersicum L.) is one of the most important crops in the world for its fruit production. Advances in cutting-edge techniques have enabled the development of numerous critical traits related to the quality and quantity of tomatoes. Genetic engineering techniques, such as gene transformation and gene editing, have emerged as powerful tools for generating new plant varieties with superior traits. In this study, we induced parthenocarpic traits in a population of elite tomato (ET) lines. At first, the adaptability of ET lines to genetic transformation was evaluated to identify the best-performing lines by transforming the SlANT1 gene overexpression cassette and then later used to produce the SlIAA9 knockout lines using the CRISPR/Cas9 system. ET5 and ET8 emerged as excellent materials for these techniques and showed higher efficiency. Typical phenotypes of knockout sliaa9 were clearly visible in G0 and G1 plants, in which simple leaves and parthenocarpic fruits were observed. The high efficiency of the CRISPR/Cas9 system in developing new tomato varieties with desired traits in a short period was demonstrated by generating T-DNA-free homozygous sliaa9 knockout plants in the G1 generation. Additionally, a simple artificial fertilization method was successfully applied to recover seed production from parthenocarpic plants, securing the use of these varieties as breeding materials.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-024-01452-1.

MicroRNAs associated with AGL6 and IAA9 function in tomato fruit set

OBJECTIVE

Fruit set is triggered after ovule fertilization, as a consequence of the downregulation of ovary growth repressors, such as the tomato transcription factors Auxin/indole-3-acetic acid 9 (IAA9) and Agamous-like 6 (AGL6). In a recent work, we developed a method to silence IAA9 and AGL6 in tomato ovaries using exogenous dsRNAs. We also produced small RNA libraries from IAA9- and AGL6-silenced ovaries to confirm the presence of siRNAs, derived from exogenous dsRNA, targeting IAA9 and AGL6. The objective of this work is to exploit these sRNA libraries to identify miRNAs differentially expressed in IAA9- and AGL6-silenced ovaries as compared with unpollinated control ovaries.

RESULTS

We identified by RNA sequencing 125 and 104 known and 509 and 516 novel miRNAs from reads mapped to mature or hairpin sequences, respectively. Of the known miRNAs, 7 and 45 were differentially expressed in IAA9- and AGL6-silenced ovaries compared to control ones, respectively. Six miRNAs were common to both datasets, suggesting their importance in the fruit set process. The expression pattern of two of these (miR393 and miR482e-5p) was verified by stem-loop qRT-PCR. The identified miRNAs represent a pool of regulatory sRNAs potentially involved in tomato fruit initiation.

Transcriptome dataset from Solanum lycopersicum L. cv. Micro-Tom; wild type and two mutants of INDOLE-ACETIC-ACID (SlIAA9) using long-reads sequencing oxford nanopore technologies

OBJECTIVE

Tomatoes are the most widely consumed fruit vegetable and are relatively easy to cultivate. However, an increase in temperature causes some plants to respond with a decrease in fruit production. So, it is necessary to develop plants resistant to extreme temperature changes. The tomato cv. Micro-Tom has genetic variations in the gene of INDOLE-ACETIC-ACID, namely SlIAA9-3 and SlIAA9-5. However, the genetic information regarding the full-length transcript of the gene from this type of tomato plant is unknown. Therefore, this study aimed to determine the full-length transcript of the genes of these three types of tomatoes using long-reads sequencing technology from Oxford Nanopore.

DATA DESCRIPTION

The total RNA from three types of Micro-Tom was isolated with the RNeasy PowerPlant Kit. Then, the RNA sequencing process used PCR-cDNA Barcoding kit - SQK-PCB109 and continued with the processing of raw reads based on the protocol from microbepore protocol ( https://github.com/felixgrunberger/microbepore ). The resulting raw reads were 578 374, 409 905, and 851 948 for wildtype, iaa9-3, and iaa9-5, respectively. After obtaining cleaned reads, each sample was mapped to the tomato reference genome (S. lycopersicum ITAG4.0) with the Minimap2 program. In particular, 965 genes were expressed only in the iaa9-3 mutant, and 2332 genes were expressed only in the iaa9-5 mutant. Whereas in the wild type, 1536 genes are specifically expressed. In cluster analysis using the heatmap analysis, separate groups were obtained between the wild type and the two mutants. This proves an overall difference in transcript levels between the wild type and the mutants.

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.

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.

Somatic variants for seed and fruit set in grapevine

BACKGROUND

Grapevine reproductive development has direct implications on yield. It also impacts on berry and wine quality by affecting traits like seedlessness, berry and bunch size, cluster compactness and berry skin to pulp ratio. Seasonal fluctuations in yield, fruit composition and wine attributes, which are largely driven by climatic factors, are major challenges for worldwide table grape and wine industry. Accordingly, a better understanding of reproductive processes such as gamete development, fertilization, seed and fruit set is of paramount relevance for managing yield and quality. With the aim of providing new insights into this field, we searched for clones with contrasting seed content in two germplasm collections.

RESULTS

We identified eight variant pairs that seemingly differ only in seed-related characteristics while showing identical genotype when tested with the GrapeReSeq_Illumina_20K_SNP_chip and several microsatellites. We performed multi-year observations on seed and fruit set deriving from different pollination treatments, with special emphasis on the pair composed by Sangiovese and its seedless variant locally named Corinto Nero. The pollen of Corinto Nero failed to germinate in vitro and gave poor berry set when used to pollinate other varieties. Most berries from both open- and cross-pollinated Corinto Nero inflorescences did not contain seeds. The genetic analysis of seedlings derived from occasional Corinto Nero normal seeds revealed that the few Corinto Nero functional gametes are mostly unreduced. Moreover, three genotypes, including Sangiovese and Corinto Nero, were unexpectedly found to develop fruits without pollen contribution and occasionally showed normal-like seeds. Five missense single nucleotide polymorphisms were identified between Corinto Nero and Sangiovese from transcriptomic data.

CONCLUSIONS

Our observations allowed us to attribute a seedlessness type to some variants for which it was not documented in the literature. Interestingly, the VvAGL11 mutation responsible for Sultanina stenospermocarpy was also discovered in a seedless mutant of Gouais Blanc. We suggest that Corinto Nero parthenocarpy is driven by pollen and/or embryo sac defects, and both events likely arise from meiotic anomalies. The single nucleotide polymorphisms identified between Sangiovese and Corinto Nero are suitable for testing as traceability markers for propagated material and as functional candidates for the seedless phenotype.

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.

Melatonin in flowering, fruit set and fruit ripening

Melatonin induces a delay in flowering stabilizing DELLA proteins and also promotes the transcription of FLC. In fruit set, melatonin is able to induce parthenocarpy. Melatonin promotes ripening and retards senescence of fruits. Melatonin is an animal hormone involved in many regulatory processes such as those related to sleep. Melatonin was discovered in plants in 1995 and is called phytomelatonin. Also in plants, a great variety of physiological processes have been described in which melatonin plays a role. In plants, melatonin is mainly involved in stress situations but also in germination, plant growth, rhizogenesis, senescence and as a protector agent improving important processes such as photosynthesis, CO₂ uptake, cell water economy and primary and secondary metabolism. Melatonin has been related to changes in the majority of plant hormones. Many revisions of stress situations have been published. However, melatonin and plant reproductive development have been poorly studied. The aim of this review is to provide an overview of works related to flowering, fruit set and development, including parthenocarpy and fruit ripening/senescence, and the role played by melatonin in the same.

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.

Don) genes responding to parthenocarpy induced by GA3 through transcriptome analysis

Background

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

Results

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

Conclusions

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

Electronic supplementary material

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

The flower to fruit transition in Citrus is partially sustained by autonomous carbohydrate synthesis in the ovary

Why evergreen fruit tree species accumulate starch in the ovary during flower bud differentiation in spring, as deciduous species do during flower bud dormancy, is not fully understood. This is because in evergreen species carbon supply is assured by leaves during flower development. We suggest the existence of an autonomous mechanism in the flowers which counteracts the competition for photoassimilates with new leaves, until they become source organs. Our hypothesis is that starch accumulated during Citrus ovary ontogeny originates from 1) its own photosynthetic capacity and 2) the mobilization of reserves. Through defoliation experiments, we found that ovaries accumulate starch during flower ontogeny using a dual mechanism: 1) the autotrophic route of source organs activating Rubisco (RbcS) genes expression, and 2) the heterotrophic route of sink organs that hydrolyze sucrose in the cytosol. Defoliation 40 days before anthesis did not significantly reduce ovary growth, flower abscission or starch concentration up to 20 days after anthesis (i.e. 60 days later). Control flowers activated the energy depletion signaling system (i.e. SnRK1) and RbcS gene expression around athesis. Defoliation accelerated and boosted both activities, increasing SPS gene expression (sucrose synthesis), and SUS1, SUS3 and cwINV (sucrose hydrolysis) to maintain a glucose threshold which satisfied its need to avoid abscission.

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.

VvmiR160s/VvARFs interaction and their spatio-temporal expression/cleavage products during GA-induced grape parthenocarpy

BACKGROUND

Grape (Vitis vinifera) is highly sensitive to gibberellin (GA), which effectively induce grape parthenocarpy. Studies showed that miR160s and their target AUXIN RESPONSIVE FACTOR (ARF) responding hormones are indispensable for various aspects of plant growth and development, but their functions in GA-induced grape parthenocarpy remain elusive.

RESULTS

In this study, the morphological changes during flower development in response to GA treatments were examined in the 'Rosario Bianco' cultivar. The precise sequences of VvmiR160a/b/c/d/e and their VvARF10/16/17 target genes were cloned, sequenced and characterized. The phylogenetic relationship and intron-exon structure of VvARFs and other ARF family members derived from different species were investigated. All VvmiR160s (except VvmiR160b) and VvARF10/16/17 had the common cis-elements responsive to GA, which support their function in GA-mediated grape parthenocarpy. The cleavage role of VvmiR160s-mediated VvARF10/16/17 was verified in grape flowers. Moreover, spatio-temporal expression analysis demonstrated that among VvmiR160 family, VvmiR160a/b/c highly expressed at late stage of flower/berry development, while VvARF10/16/17showed a reverse expression trend. Interestingly, GA exhibited a long-term effect through inducing the expression of VvmiR160a/b/c/e to increase their cleavage product accumulations from 5 to 9 days after treatment, but GA enhanced the expressions of VvARF10/16/17 only at short term. Pearson correlation analysis based on expression data revealed a negative correlation between VvmiR160a/b/c and VvARF10/16/17 in flowers not berries during GA-induced grape parthenocarpy.

CONCLUSIONS

This work demonstrated that the negative regulation of VvARF10/16/17 expression by VvmiR160a/b/c as key regulatory factors is critical for GA-mediated grape parthenocarpy, and provide significant implications for molecular breeding of high-quality seedless berry.

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.

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.

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.

Abnormal development of floral meristem triggers defective morphogenesis of generative system in transgenic tomatoes

Parthenocarpy and fruit malformations are common among independent transgenic tomato lines, expressing genes encoding different pathogenesis-related (PR) protein and antimicrobal peptides. Abnormal phenotype developed independently of the expression and type of target genes, but distinctive features during flower and fruit development were detected in each transgenic line. We analyzed the morphology, anatomy, and cytoembryology of abnormal flowers and fruits from these transgenic tomato lines and compared them with flowers and fruits of wild tomatoes, line YaLF used for transformation, and transgenic plants with normal phenotype. We confirmed that the main cause of abnormal flower and fruit development was the alterations of determinate growth of generative meristem. These alterations triggered different types of anomalous growth, affecting the number of growing ectopic shoots and formation of new flowers. Investigation of the ovule ontogenesis did not show anomalies in embryo sac development, but fertilization did not occur and embryo sac degenerated. Nevertheless, the ovule continued to differentiate due to proliferation of endothelium cells. The latter substituted embryo sac and formed pseudoembryonic tissue. This process imitated embryogenesis and stimulated ovary growth, leading to the development of parthenocarpic fruit. We demonstrated that failed fertilization occurred due to defective male gametophyte formation, which was manifested in blocked division of the nucleus in the microspore and arrest of vegetative and generative cell formation. Maturing pollen grains were overgrown microspores, not competent for fertilization but capable to induce proliferation of endothelium and development of parthenocarpic ovary. Thus, our study provided new data on the structural transformations of reproductive organs during development of parthenocarpic fruits in transgenic tomato.

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

BACKGROUND

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

RESULTS

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

CONCLUSIONS

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

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.

Effects of exogenous application of CPPU, NAA and GA4+7 on parthenocarpy and fruit quality in cucumber (Cucumis sativus L.)

In protected vegetable fields, plant growth regulators are often used to improve cucumber fruit growth. However, the effects of plant growth regulators on the appearance and nutritional quality of cucumber (Cucumis sativus L.) remain largely unknown. In the present study, 100 mg/L N-(2-chloro-4-pyridyl)-N'-phenylurea (CPPU), naphthaleneacetic acid (NAA) or gibberellin A4+A7 (GA₄₊₇) was applied to the female cucumber flowers 1 day before anthesis and at anthesis. The CPPU, NAA and GA₄₊₇ treatments resulted in parthenocarpic fruits with similar weights, sizes and shapes as the pollinated fruits. NAA treatment did not affect the appearance and nutritional characteristics of cucumber at harvest and after storage. CPPU treatment increased the flesh firmness at harvest but decreased phenolic acid and vitamin C contents after storage. GA₄₊₇ treatment decreased the flesh firmness but increased total flavonoids and protein content after storage.

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.

Gibberellin reactivates and maintains ovary-wall cell division causing fruit set in parthenocarpic Citrus species

Citrus is a wide genus in which most of the cultivated species and cultivars are natural parthenocarpic mutants or hybrids (i.e. orange, mandarin, tangerine, grapefruit). The autonomous increase in GA1 ovary concentration during anthesis was suggested as being the stimulus responsible for parthenocarpy in Citrus regardless of the species. To determine the exact GA-role in parthenocarpic fruit set, the following hypothesis was tested: GA triggers and maintains cell division in ovary walls causing fruit set. Obligate and facultative parthenocarpic Citrus species were used as a model system because obligate parthenocarpic Citrus sp (i.e. Citrus unshiu) have higher GA levels and better natural parthenocarpic fruit set compared to other facultative parthenocarpic Citrus (i.e. Citrus clementina). The autonomous activation of GA synthesis in C. unshiu ovary preceded cell division and CYCA1.1 up-regulation (a G2-stage cell cycle regulator) at anthesis setting a high proportion of fruits, whereas C. clementina lacked this GA-biosynthesis and CYCA1.1 up-regulation failing in fruit set. In situ hybridization experiments revealed a tissue-specific expression of GA20ox2 only in the dividing tissues of the pericarp. Furthermore, CYCA1.1 expression correlated endogenous GA1 content with GA3 treatment, which stimulated cell division and ovary growth, mostly in C. clementina. Instead, paclobutrazol (GA biosynthesis inhibitor) negated cell division and reduced fruit set. Results suggest that in parthenocarpic citrus the specific GA synthesis in the ovary walls at anthesis triggers cell division and, thus, the necessary ovary growth rate to set fruit.

Transcriptome comparison of global distinctive features between pollination and parthenocarpic fruit set reveals transcriptional phytohormone cross-talk in cucumber (Cucumis sativus L.)

Parthenocarpy is an important trait determining yield and quality of fruit crops. However, the understanding of the mechanisms underlying parthenocarpy induction is limited. Cucumber (Cucumis sativus L.) is abundant in parthenocarpic germplasm resources and is an excellent model organism for parthenocarpy studies. In this study, the transcriptome of cucumber fruits was studied using RNA sequencing (RNA-Seq). Differentially expressed genes (DEGs) of set fruits were compared against aborted fruits. Distinctive features of parthenocarpic and pollinated fruits were revealed by combining the analysis of the transcriptome together with cytomorphological and physiological analysis. Cell division and the transcription of cell division genes were found to be more active in parthenocarpic fruit. The study also indicated that parthenocarpic fruit set is a high sugar-consuming process which is achieved via enhanced carbohydrate degradation through transcription of genes that lead to the breakdown of carbohydrates. Furthermore, the evidence provided by this work supports a hypothesis that parthenocarpic fruit set is induced by mimicking the processes of pollination/fertilization at the transcriptional level, i.e. by performing the same transcriptional patterns of genes inducing pollination and gametophyte development as in pollinated fruit. Based on the RNA-Seq and ovary transient expression results, 14 genes were predicted as putative parthenocarpic genes. The transcription analysis of these candidate genes revealed auxin, cytokinin and gibberellin cross-talk at the transcriptional level during parthenocarpic fruit set.