Gibberellic acid induced parthenocarpic 'Honeycrisp' apples (Malus domestica) exhibit reduced ovary width and lower acidity

Parthenocarpy, a pollination-independent fruit set mechanism to ensure yield stability

Fruit development is essential for flowering plants' reproduction and a significant food source. Climate change threatens fruit yields due to its impact on pollination and fertilization processes, especially vulnerable to extreme temperatures, insufficient light, and pollinator decline. Parthenocarpy, the development of fruit without fertilization, offers a solution, ensuring yield stability in adverse conditions and enhancing fruit quality. Parthenocarpic fruits not only secure agricultural production but also exhibit improved texture, appearance, and shelf life, making them desirable for food processing and other applications. Recent research unveils the molecular mechanisms behind parthenocarpy, implicating transcription factors (TFs), noncoding RNAs, and phytohormones such as auxin, gibberellin (GA), and cytokinin (CK). Here we review recent findings, construct regulatory models, and identify areas for further research.

Genome-wide gene network uncover temporal and spatial changes of genes in auxin homeostasis during fruit development in strawberry (F. × ananassa)

BACKGROUND

The plant hormone auxin plays a crucial role in regulating important functions in strawberry fruit development. Although a few studies have described the complex auxin biosynthetic and signaling pathway in wild diploid strawberry (Fragaria vesca), the molecular mechanisms underlying auxin biosynthesis and crosstalk in octoploid strawberry fruit development are not fully characterized. To address this knowledge gap, comprehensive transcriptomic analyses were conducted at different stages of fruit development and compared between the achene and receptacle to identify developmentally regulated auxin biosynthetic genes and transcription factors during the fruit ripening process. Similar to wild diploid strawberry, octoploid strawberry accumulates high levels of auxin in achene compared to receptacle.

RESULTS

Genes involved in auxin biosynthesis and conjugation, such as Tryptophan Aminotransferase of Arabidopsis (TAAs), YUCCA (YUCs), and Gretchen Hagen 3 (GH3s), were found to be primarily expressed in the achene, with low expression in the receptacle. Interestingly, several genes involved in auxin transport and signaling like Pin-Formed (PINs), Auxin/Indole-3-Acetic Acid Proteins (Aux/IAAs), Transport Inhibitor Response 1 / Auxin-Signaling F-Box (TIR/AFBs) and Auxin Response Factor (ARFs) were more abundantly expressed in the receptacle. Moreover, by examining DEGs and their transcriptional profiles across all six developmental stages, we identified key auxin-related genes co-clustered with transcription factors from the NAM-ATAF1,2-CUC2/ WRKYGQK motif (NAC/WYKY), Heat Shock Transcription Factor and Heat Shock Proteins (HSF/HSP), APETALA2/Ethylene Responsive Factor (AP2/ERF) and MYB transcription factor groups.

CONCLUSIONS

These results elucidate the complex regulatory network of auxin biosynthesis and its intricate crosstalk within the achene and receptacle, enriching our understanding of fruit development in octoploid strawberries.

Movement of ACC oxidase 3 mRNA from seeds to flesh promotes fruit ripening in apple

Xenia, the phenomenon in which the pollen genotype directly affects the phenotypic characteristics of maternal tissues (i.e., fruit ripening), has applications in crop production and breeding. However, the underlying molecular mechanism has yet to be elucidated. Here, we investigated whether mobile mRNAs from the pollen affect the ripening and quality-related characteristics of the fruit using cross-pollination between distinct Malus domestica (apple) cultivars. We demonstrated that hundreds of mobile mRNAs originating from the seeds are delivered to the fruit. We found that the movement of one of these mRNAs, ACC oxidase 3 (MdACO3), is coordinated with fruit ripening. Salicylic acid treatment, which can cause plasmodesmal closure, blocks MdACO3 movement, indicating that MdACO3 transcripts may move through the plasmodesmata. To assess the role of mobile MdACO3 transcripts in apple fruit, we created MdACO3-GFP-expressing apple seeds using MdACO3-GFP-overexpressing pollen for pollination and showed that MdACO3 transcripts in the transgenic seeds move to the flesh, where they promote fruit ripening. Furthermore, we demonstrated that MdACO3 can be transported from the seeds to fruit in the fleshy-fruited species tomato and strawberry. These results underscore the potential of mobile mRNAs from seeds to influence fruit characteristics, providing an explanation for the xenia phenomenon. Notably, our findings highlight the feasibility of leveraging diverse pollen genomic resources, without resorting to genome editing, to improve fruit quality.

Dataset describing the influence of preharvest gibberellic acid application on fruiting behavior, yield and fruit biochemical properties of rambutan (Nephelium lappaceum L.)

Rambutan (Nephelium lappaceum L.), an exotic non-climacteric tropical fruit in Bangladesh, has got wide acceptance to consumers as well as growers due to its attractive appearance, taste and nutrition, but the demerits of inadequate fruiting and yield as well as low edible properties at the farmers field requires to be addressed. Hence, an experiment was performed with gibberellic acid (GA3) and the obtained dataset demonstrates how GA3 application augmented the fruit set and retention, fruit yield and post-harvest biochemical properties of rambutan. Gibberellic acid was sprayed at seven various concentrations from 0 ppm (control) to 500 ppm at the mature panicles (inflorescence) during the pre-flowering and the early fruiting stages (three weeks after fruit set). The study was conducted in two sequential growing years (2020 and 2021) following a randomized complete block design (RCBD). Results revealed that 200-300 ppm doses had superiority over the lower (50-100 ppm) and higher (400-500 ppm) doses for promoting the fruit yield and quality. More specifically, fruit set and retention, fruit size and weight, pulp weight and thickness, pulp:peel ratio, edible portion and fruit yield as well as total soluble solids and total sugars contents in fruit were exhibited the best at 300 ppm being consonant with 200 ppm at majority cases, whereas GA3 doses from 200 ppm to 500 ppm performed similarly to enhance fruit physico-chemical qualities and shelf life of rambutan. Control treatment along with 50 ppm gibberellic acid dose demonstrated inferior results for yield and fruit quality promotion of rambutan. Thus, use of plant growth regulator at appropriate dose and time is imperative to rambutan improvement.

Morphological Changes to Fruit Development Induced by GA3 Application in Sweet Cherry (Prunus avium L.)

Cherry (Prunus avium) fruits are important sources of vitamins, minerals, and nutrients in the human diet; however, they contain a large stone, making them inconvenient to eat 'on the move' and process. The exogenous application of gibberellic acid (GA3) can induce parthenocarpy in a variety of fruits during development. Here, we showed that the application of GA3 to sweet cherry unpollinated pistils acted as a trigger for fruit set and permitted the normal formation of fruit up to a period of twenty-eight days, indicating that gibberellins are involved in the activation of the cell cycle in the ovary wall cells, leading to fruit initiation. However, after this period, fruit development ceased and developing fruit began to be excised from the branch by 35 days post treatment. This work also showed that additional signals are required for the continued development of fully mature parthenocarpic fruit in sweet cherry.

Identification of Key Genes of Fruit Shape Variation in Jujube with Integrating Elliptic Fourier Descriptors and Transcriptome

Jujube (Ziziphus jujuba) exhibits a rich diversity in fruit shape, with natural occurrences of gourd-like, flattened, and other special shapes. Despite the ongoing research into fruit shape, studies integrating elliptical Fourier descriptors (EFDs) with both Short Time-series Expression Miner (STEM) and weighted gene co-expression network analysis (WGCNA) for gene discovery remain scarce. In this study, six cultivars of jujube fruits with distinct shapes were selected, and samples were collected from the fruit set period to the white mature stage across five time points for shape analysis and transcriptome studies. By combining EFDs with WGCNA and STEM, the study aimed to identify the critical periods and key genes involved in the formation of jujube fruit shape. The findings indicated that the D25 (25 days after flowering) is crucial for the development of jujube fruit shape. Moreover, ZjAGL80, ZjABI3, and eight other genes have been implicated to regulate the shape development of jujubes at different periods of fruit development, through seed development and fruit development pathway. In this research, EFDs were employed to precisely delineate the shape of jujube fruits. This approach, in conjunction with transcriptome, enhanced the precision of gene identification, and offered an innovative methodology for fruit shape analysis. This integration facilitates the advancement of research into the morphological characteristics of plant fruits, underpinning the development of a refined framework for the genetic underpinnings of fruit shape variation.

Regulatory mechanism of GA3 application on grape (Vitis vinifera L.) berry size

Gibberellin A3 (GA3) is often used as a principal growth regulator to increase plant size. Here, we applied Tween-20 (2%)-formulated GA3 (T1:40 mg/L; T2:70 mg/L) by dipping the clusters at the initial expansion phase of 'Red Globe' grape (Vitis vinifera L.) in 2018 and 2019. Tween-20 (2%) was used as a control. The results showed that GA3 significantly increased fruit cell length, cell size, diameter, and volume. The hormone levels of auxin (IAA) and zeatin (ZT) were significantly increased at 2 h (0 d) -1 d after application (DAA0-1) and remained significantly higher at DAA1 until maturity. Conversely, ABA exhibited an opposite trend. The mRNA and non-coding sequencing results yielded 436 differentially expressed mRNA (DE_mRNAs), 79 DE_lncRNAs and 17 DE_miRNAs. These genes are linked to hormone pathways like cysteine and methionine metabolism (ko00270), glutathione metabolism (ko00480) and plant hormone signal transduction (ko04075). GA3 application reduced expression of insensitive dwarf 2 (GID2, VIT_07s0129g01000), small auxin-upregulated RNA (SAUR, VIT_08s0007g03120) and 1-aminocyclopropane-1-carboxylate synthase (ACS, VIT_18s0001g08520), but increased SAUR (VIT_04s0023g00560) expression. These four genes were predicted to be negatively regulated by vvi-miR156, vvi-miR172, vvi-miR396, and vvi-miR159, corresponding to specific lncRNAs. Therefore, miRNAs could affect grape size by regulating key genes GID2, ACS and SAUR. The R2R3 MYB family member VvRAX2 (VIT_08s0007g05030) was upregulated in response to GA3 application. Overexpression of VvRAX2 in tomato transgenic lines increased fruit size in contrast to the wild type. This study provides a basis and genetic resources for elucidating the novel role of ncRNAs in fruit development.

Evaluation of Plant Defense Inducers and Plant Growth Regulators for Fire Blight Management Using Transcriptome Studies and Field Assessments

Fire blight, caused by Erwinia amylovora, is a destructive disease of pome fruit trees. In the United States, apple and pear growers rely on applications of copper and antibiotics during bloom to control fire blight, but such methods have already led to regional instances of resistance. In this study, we used transcriptome analyses and field trials to evaluate the effectiveness of three commercially available plant defense elicitors and one plant growth regulator for fire blight management. Our data indicated that foliar applications of acibenzolar-S-methyl (ASM; Actigard 50WG) triggered a strong defense-related response in apple leaves, whereas applications of Bacillus mycoides isolate J (LifeGard WG) or Reynoutria sachalinensis extract (Regalia) did not. Genes upregulated by ASM were enriched in the biological processes associated with plant immunity, such as defense response and protein phosphorylation. The expression of several pathogenesis-related (PR) genes was induced by ASM as well. Surprisingly, many differentially expressed genes in ASM-treated apple leaves overlapped with those induced by treatment with prohexadione-calcium (ProCa; Apogee), a plant growth regulator that suppresses shoot elongation. Further analysis suggested that ProCa likely acts similarly to ASM to stimulate plant immunity because genes involved in plant defense were shared and significantly upregulated (more than twofold) by both treatments. Our field trials agreed with the transcriptome study, demonstrating that ASM and ProCa exhibit the best control performance relative to the other biopesticides. Taken together, these data are pivotal for the understanding of plant response and shed light on future improvements of strategies for fire blight management.

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.

Comparison of red raspberry and wild strawberry fruits reveals mechanisms of fruit type specification

Belonging to Rosaceae, red raspberry (Rubus idaeus) and wild strawberry (Fragaria vesca) are closely related species with distinct fruit types. While the numerous ovaries become the juicy drupelet fruits in raspberry, their strawberry counterparts become dry and tasteless achenes. In contrast, while the strawberry receptacle, the stem tip, enlarges to become a red fruit, the raspberry receptacle shrinks and dries. The distinct fruit-forming ability of homologous organs in these 2 species allows us to investigate fruit type determination. We assembled and annotated the genome of red raspberry (R. idaeus) and characterized its fruit development morphologically and physiologically. Subsequently, transcriptomes of dissected and staged raspberry fruit tissues were compared to those of strawberry from a prior study. Class B MADS box gene expression was negatively associated with fruit-forming ability, which suggested a conserved inhibitory role of class B heterodimers, PISTILLATA/TM6 or PISTILLATA/APETALA3, for fruit formation. Additionally, the inability of strawberry ovaries to develop into fruit flesh was associated with highly expressed lignification genes and extensive lignification of the ovary pericarp. Finally, coexpressed gene clusters preferentially expressed in the dry strawberry achenes were enriched in "cell wall biosynthesis" and "ABA signaling," while coexpressed clusters preferentially expressed in the fleshy raspberry drupelets were enriched in "protein translation." Our work provides extensive genomic resources as well as several potential mechanisms underlying fruit type specification. These findings provide the framework for understanding the evolution of different fruit types, a defining feature of angiosperms.

Parthenocarpy-related genes induced by naphthalene acetic acid in oil palm interspecific O × G [Elaeis oleifera (Kunth) Cortés × Elaeis guineensis Jacq.] hybrids

Parthenocarpy is the development without fertilization of seedless fruits. In the oil palm industry, the development of parthenocarpic fruits is considered an attractive option to increase palm oil production. Previous studies have shown the application of synthetic auxins in Elaeis guineensis, and interspecific O×G hybrids (Elaeis oleifera (Kunth) Cortés × E. guineensis Jacq.) induces parthenocarpy. The aim of this study was to identify the molecular mechanism through transcriptomics and biology system approach to responding to how the application of NAA induces parthenocarpic fruits in oil palm O×G hybrids. The transcriptome changes were studied in three phenological stages (PS) of the inflorescences: i) PS 603, pre-anthesis III, ii) PS 607, anthesis, and iii) PS 700, fertilized female flower. Each PS was treated with NAA, Pollen, and control (any application). The expression profile was studied at three separate times: five minutes (T0), 24 hours (T1), and 48 h post-treatment (T2). The RNA sequencing (RNA seq) approach was used with 27 oil palm O×G hybrids for a total of 81 raw samples. RNA-Seq showed around 445,920 genes. Numerous differentially expressed genes (DEGs) were involved in pollination, flowering, seed development, hormone biosynthesis, and signal transduction. The expression of the most relevant transcription factors (TF) families was variable and dependent on the stage and time post-treatment. In general, NAA treatment expressed differentially more genes than Pollen. Indeed, the gene co-expression network of Pollen was built with fewer nodes than the NAA treatment. The transcriptional profiles of Auxin-responsive protein and Gibberellin-regulated genes involved in parthenocarpy phenomena agreed with those previously reported in other species. The expression of 13 DEGs was validated by RT-qPCR analysis. This detailed knowledge about the molecular mechanisms involved in parthenocarpy could be used to facilitate the future development of genome editing techniques that enable the production of parthenocarpic O×G hybrid cultivars without growth regulator application.

A Flashforward Look into Solutions for Fruit and Vegetable Production

One of the most important challenges facing current and future generations is how climate change and continuous population growth adversely affect food security. To address this, the food system needs a complete transformation where more is produced in non-optimal and space-limited areas while reducing negative environmental impacts. Fruits and vegetables, essential for human health, are high-value-added crops, which are grown in both greenhouses and open field environments. Here, we review potential practices to reduce the impact of climate variation and ecosystem damages on fruit and vegetable crop yield, as well as highlight current bottlenecks for indoor and outdoor agrosystems. To obtain sustainability, high-tech greenhouses are increasingly important and biotechnological means are becoming instrumental in designing the crops of tomorrow. We discuss key traits that need to be studied to improve agrosystem sustainability and fruit yield.

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.

A phased, chromosome-scale genome of 'Honeycrisp' apple (Malus domestica)

The apple cultivar 'Honeycrisp' has superior fruit quality traits, cold hardiness, and disease resistance, making it a popular breeding parent. However, it suffers from several physiological disorders, production, and postharvest issues. Despite several available apple genome sequences, understanding of the genetic mechanisms underlying cultivar-specific traits remains lacking. Here, we present a highly contiguous, fully phased, chromosome-level genome of 'Honeycrisp' apples, using PacBio HiFi, Omni-C, and Illumina sequencing platforms, with two assembled haplomes of 674 Mbp and 660 Mbp, and contig N50 values of 32.8 Mbp and 31.6 Mbp, respectively. Overall, 47,563 and 48,655 protein-coding genes were annotated from each haplome, capturing 96.8-97.4% complete BUSCOs in the eudicot database. Gene family analysis reveals most 'Honeycrisp' genes are assigned into orthogroups shared with other genomes, with 121 'Honeycrisp'-specific orthogroups. This resource is valuable for understanding the genetic basis of important traits in apples and related Rosaceae species to enhance breeding efforts.

Comparative transcriptomic analysis of apple and peach fruits: insights into fruit type specification

Fruits represent key evolutionary innovations in angiosperms and exhibit diverse types adapted for seed dissemination. However, the mechanisms that underlie fruit type diversity are not understood. The Rosaceae family comprises many different fruit types, including 'pome' and 'drupe' fruits, and hence is an excellent family for investigating the genetic basis of fruit type specification. Using comparative transcriptomics, we investigated the molecular events that correlate with pome (apple) and drupe (peach) fleshy fruit development, focusing on the earliest stages of fruit initiation. We identified PI and TM6, MADS box genes whose expression negatively correlates with fruit flesh-forming tissues irrespective of fruit type. In addition, the MADS box gene FBP9 is expressed in fruit-forming tissues in both species, and was lost multiple times in the genomes of dry-fruit-forming eudicots including Arabidopsis. Network analysis reveals co-expression between FBP9 and photosynthesis genes in both apple and peach, suggesting that FBP9 and photosynthesis may both promote fleshy fruit development. The large transcriptomic datasets at the earliest stages of pome and drupe fruit development provide rich resources for comparative studies, and the work provides important insights into fruit-type specification.

Evaluation and Genetic Analysis of Parthenocarpic Germplasms in Cucumber

Parthenocarpy is an important agronomic trait in cucumber (Cucumis sativus L.) production. However, the systematic identification of parthenocarpic germplasms from national gene banks for cucumber improvement remains an international challenge. In this study, 201 cucumber lines were investigated, including different ecotypes. The percentages of parthenocarpic fruit set (PFS) and parthenocarpic fruit expansion (PFE) were evaluated in three experiments. In natural populations, the PFS rates fit a normal distribution, while PFE rates showed a skewed distribution, suggesting that both PFS and PFE rates are typical quantitative traits. Genetic analysis showed that parthenocarpy in different ecotypes was inherited in a similar incompletely dominant manner. A total of 5324 single nucleotide polymorphisms (SNPs) associated with parthenocarpy were detected in a Genome-wide association study (GWAS) of parthenocarpy in the 31 cucumber lines, from which six parthenocarpic loci, including two novel loci (Pfs1.1 and Pfs4.1), were identified. Consequently, fifteen of the elite lines that were screened presented relatively stronger parthenocarpy ability (PFS > 90%, PFE > 50%), among which six cucumber lines (18007s, 18008s, 18022s, 18076s, 18099s, and 18127s) exhibited weak first-fruit inhibition. Three lines (18011s, 18018s, and 18019s) were screened for super ovary parthenocarpy, which showed more attractive performance. Four low-temperature-enhanced parthenocarpy lines (18018s, 18022s, 18029s, and 18012s) were identified, which were suited for breeding for counter-season production. Our approaches could help increase efficiency and lead to parthenocarpy improvements for modern cucumber cultivars.

Gibberellic Acid (GA3) Applied to Flowering Heracleum sosnowskyi Decreases Seed Viability Even If Seed Development Is Not Inhibited

Sosnowsky’s hogweed (Heracleum sosnowskyi Manden.), an important invasive species in Eastern Europe, is a monocarpic perennial plant that propagates exclusively by seeds. Hence, interfering with seed viability could help control its spread. In the present study, we investigated the effect of exogenous GA₃ (25, 100 and 150 mg/L) sprayed twice onto flowering H. sosnowskyi plants on the development of fruits (mericarps) and their ability to germinate under field conditions over the growing seasons of 2018 and 2019. Mericarps from plants sprayed with GA₃ failed to develop normally. The width/length ratio of mericarps decreased by 23% to 25% after 150 mg/L GA₃ application and their average weight decreased between 7% and 39% under all GA₃ treatments. X-ray radiographs revealed that the internal structure was malformed, with many of the mericarps lacking well-developed seeds. Proportionally fewer well-developed mericarps were produced by GA₃-treated plants than water-sprayed control plants in 2018. Seed germination assessed outdoors in seeds buried in the ground was also severely reduced (from 58% to 99% after 150 mg/L GA₃ application). This indicates that exogenous GA₃ sprays result in incomplete seed development and a consequent decrease in viability and germination. As the highest GA₃ dose used resulted in significantly reduced propagation of Sosnowsky’s hogweed through seeds in the field, GA₃ provides a promising approach to the control of the spread of this invasive weed species.

Hormonal interactions underlying parthenocarpic fruit formation in horticultural crops

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

Decoding the molecular mechanism of parthenocarpy in Musa spp. through protein-protein interaction network

Banana, one of the most important staple fruit among global consumers is highly sterile owing to natural parthenocarpy. Identification of genetic factors responsible for parthenocarpy would facilitate the conventional breeders to improve the seeded accessions. We have constructed Protein-protein interaction (PPI) network through mining differentially expressed genes and the genes used for transgenic studies with respect to parthenocarpy. Based on the topological and pathway enrichment analysis of proteins in PPI network, 12 candidate genes were shortlisted. By further validating these candidate genes in seeded and seedless accession of Musa spp. we put forward MaAGL8, MaMADS16, MaGH3.8, MaMADS29, MaRGA1, MaEXPA1, MaGID1C, MaHK2 and MaBAM1 as possible target genes in the study of natural parthenocarpy. In contrary, expression profile of MaACLB-2 and MaZEP is anticipated to highlight the difference in artificially induced and natural parthenocarpy. By exploring the PPI of validated genes from the network, we postulated a putative pathway that bring insights into the significance of cytokinin mediated CLAVATA(CLV)-WUSHEL(WUS) signaling pathway in addition to gibberellin mediated auxin signaling in parthenocarpy. Our analysis is the first attempt to identify candidate genes and to hypothesize a putative mechanism that bridges the gaps in understanding natural parthenocarpy through PPI network.

Gibberellin and the plant growth retardant Paclobutrazol altered fruit shape and ripening in tomato

Fruit shape and ripening are major horticultural traits for many fruits and vegetable crops. Changes in fruit shape and ripening are often accomplished by altered cell division or cell expansion patterns. Gibberellic acids (GAs) are essential for tomato fruit development; however, the exact role and the underlying mechanism are still elusive. To elucidate the relationship between gibberellins and fruit shape and ripening in tomato, GA₃ and gibberellin biosynthesis inhibitor paclobutrazol (PAC) were applied to tomato. Fruit shape index was increased when GA₃ was applied, which was mainly attributed to the increased organ elongation. The expression levels of genes involved in cell elongation and expansion were altered at the same time. In addition, GA delayed the ripening time by regulating the transcript levels of ethylene-related genes. By contrast, PAC application decreased fruit shape index and shortened fruit ripening time. These results demonstrate that manipulation of GA levels can simultaneously influence tomato fruit shape and ripening. Further studies aimed to regulate fruit shape and ripening can be achieved by altering GA levels.

Developmental Mechanisms of Fleshy Fruit Diversity in Rosaceae

Rosaceae (the rose family) is an economically important family that includes species prized for high-value fruits and ornamentals. The family also exhibits diverse fruit types, including drupe (peach), pome (apple), drupetum (raspberry), and achenetum (strawberry). Phylogenetic analysis and ancestral fruit-type reconstruction suggest independent evolutionary paths of multiple fleshy fruit types from dry fruits. A recent whole genome duplication in the Maleae/Pyreae tribe (with apple, pear, hawthorn, and close relatives; referred to as Maleae here) may have contributed to the evolution of pome fruit. MADS-box genes, known to regulate floral organ identity, are emerging as important regulators of fruit development. The differential competence of floral organs to respond to fertilization signals may explain the different abilities of floral organs to form fleshy fruit. Future comparative genomics and functional studies in closely related Rosaceae species with distinct fruit types will test hypotheses and provide insights into mechanisms of fleshy fruit diversity. These efforts will be facilitated by the wealth of genome data and resources in Rosaceae.

Identification of early fruit development reference genes in plum

An RNAseq study of early fruit development and stone development in plum, Prunus domestica, was mined to identify sets of genes that could be used to normalize expression studies in early fruit development. The expression values of genes previously identified from Prunus as reference genes were first extracted and found to vary considerably in endocarp tissue relative to whole fruit tissue. Nine other genes were chosen that varied less than 2-fold amongst the 20 RNAseq libraries of early fruit development and endocarp tissues. These gene were tested on a series of developmental plum fruit samples to determine if any could be used as a reference gene in the analyses of fruit-based tissues in plum. The three most stable genes as determined using RefFinder were IPGD (imidazole glycerol-phosphate dehydratase), HAM1 (histone acetyltransferase) and SNX1 (sorting nexin 1). These were further tested to analyze genes expressed differentially in endocarp tissue between normal and minimal endocarp cultivars. To determine the universality of those nine genes as fruit development reference genes, three other data sets of RNAseq from peach and apple were analyzed to determine the reference gene expression. Multiple genes exhibited tissue specific patterns of expression while one gene, the SNX1, emerged as possessing a universal pattern between the Rosaceae species, at all developmental stages, and tissue types tested. The results suggest that the use of existing RNAseq data to identify standard genes can provide stable reference genes for a specific tissues or experimental conditions under exploration.

Selection of appropriate reference genes for RT-qPCR analysis under abiotic stress and hormone treatment in celery

Celery is one of the most important vegetable crop and its yield and quality is influenced by many environmental factors. Researches on gene expression not only help to unravel the molecular regulatory mechanism but also identify the key genes in the biological response. RT-qPCR is a commonly used technology to quantify the gene expression. Selecting an appropriate reference gene is an effective approach to improve the accuracy of RT-qPCR assay. To our knowledge, the evaluation of reference genes under different treatments in celery has not been reported yet. In this study, the expression stabilities of eight candidate reference genes (ACTIN, eIF-4α , GAPDH, TBP, TUB-A, UBC, TUB-B, and EF-1α ) under abiotic stresses (heat, cold, drought, and salt) and hormone treatments (SA, MeJA, GA, and ABA) were detected. The expression stabilities of candidate genes were compared and ranked by geNorm, NormFinder, BestKeeper, ΔCt, and RefFinder programs. The results calculated by different programs were not completely consistent. Considering the comprehensive analysis results, ACTIN was the most stable reference gene and TUB-B showed the worst expression stabilities under the selected abiotic stress and hormone treatments in celery. The reliability of reference genes was further confirmed by the normalization of CAT1 gene under drought stress. This study presented evidences and basis to select the appropriate reference genes under different treatments in celery.