Signaling pathways mediating the induction of apple fruitlet abscission

Extreme Hypoxic Conditions Induce Selective Molecular Responses and Metabolic Reset in Detached Apple Fruit

The ripening physiology of detached fruit is altered by low oxygen conditions with profound effects on quality parameters. To study hypoxia-related processes and regulatory mechanisms, apple (Malus domestica, cv Granny Smith) fruit, harvested at commercial ripening, were kept at 1°C under normoxic (control) and hypoxic (0.4 and 0.8 kPa oxygen) conditions for up to 60 days. NMR analyses of cortex tissue identified eight metabolites showing significantly different accumulations between samples, with ethanol and alanine displaying the most pronounced difference between hypoxic and normoxic treatments. A rapid up-regulation of alcohol dehydrogenase and pyruvate-related metabolism (lactate dehydrogenase, pyruvate decarboxylase, alanine aminotransferase) gene expression was detected under both hypoxic conditions with a more pronounced effect induced by the lowest (0.4 kPa) oxygen concentration. Both hypoxic conditions negatively affected ACC synthase and ACC oxidase transcript accumulation. Analysis of RNA-seq data of samples collected after 24 days of hypoxic treatment identified more than 1000 genes differentially expressed when comparing 0.4 vs. 0.8 kPa oxygen concentration samples. Genes involved in cell-wall, minor and major CHO, amino acid and secondary metabolisms, fermentation and glycolysis as well as genes involved in transport, defense responses, and oxidation-reduction appeared to be selectively affected by treatments. The lowest oxygen concentration induced a higher expression of transcription factors belonging to AUX/IAA, WRKY, HB, Zinc-finger families, while MADS box family genes were more expressed when apples were kept under 0.8 kPa oxygen. Out of the eight group VII ERF members present in apple genome, two genes showed a rapid up-regulation under hypoxia, and western blot analysis showed that apple MdRAP2.12 proteins were differentially accumulated in normoxic and hypoxic samples, with the highest level reached under 0.4 kPa oxygen. These data suggest that ripe apple tissues finely and specifically modulate sensing and regulatory mechanisms in response to different hypoxic stress conditions.

Transcriptome Profiling of Petal Abscission Zone and Functional Analysis of an Aux/IAA Family Gene RhIAA16 Involved in Petal Shedding in Rose

Roses are one of the most important cut flowers among ornamental plants. Rose flower longevity is largely dependent on the timing of petal shedding occurrence. To understand the molecular mechanism underlying petal abscission in rose, we performed transcriptome profiling of the petal abscission zone during petal shedding using Illumina technology. We identified a total of 2592 differentially transcribed genes (DTGs) during rose petal shedding. Gene ontology term enrichment and pathway analysis revealed that major biochemical pathways the DTGs were involved in included ethylene biosynthesis, starch degradation, superpathway of cytosolic glycolysis, pyruvate dehydrogenase and TCA cycle, photorespiration and the lactose degradation III pathway. This suggests that alterations in carbon metabolism are an important part of rose petal abscission. Among these DTGs, approximately 150 genes putatively encoding transcription factors were identified in rose abscission zone. These included zinc finger, WRKY, ERF, and Aux/IAA gene families, suggesting that petal abscission involves complex transcriptional reprogramming. Approximately 108 DTGs were related to hormone pathways, of which auxin and ethylene related DTGs were the largest groups including 52 and 41 genes, respectively. These also included 12 DTGs related to gibberellin and 6 DTGs in jasmonic acid pathway. Surprisingly, no DTGs involved in the biosynthesis/signaling of abscisic acid, cytokinin, brassinosteroid, and salicylic acid pathways were detected. Moreover, among DTGs related to auxin, we identified an Aux/IAA gene RhIAA16 that was up-regulated in response to petal shedding. Down-regulation of RhIAA16 by virus-induced gene silencing in rose promoted petal abscission, suggesting that RhIAA16 plays an important role in rose petal abscission.

Ethylene negatively regulates transcript abundance of ROP-GAP rheostat-encoding genes and affects apoplastic reactive oxygen species homeostasis in epicarps of cold stored apple fruits

Apple (Malus×domestica Borkh) fruits are stored for long periods of time at low temperatures (1 °C) leading to the occurrence of physiological disorders. 'Superficial scald' of Granny Smith apples, an economically important ethylene-dependent disorder, was used as a model to study relationships among ethylene action, the regulation of the ROP-GAP rheostat, and maintenance of H2O2 homeostasis in fruits during prolonged cold exposure. The ROP-GAP rheostat is a key module for adaptation to low oxygen in Arabidopsis through Respiratory Burst NADPH Oxidase Homologs (RBOH)-mediated and ROP GTPase-dependent regulation of reactive oxygen species (ROS) homeostasis. Here, it was shown that the transcriptional expression of several components of the apple ROP-GAP machinery, including genes encoding RBOHs, ROPs, and their ancillary proteins ROP-GEFs and ROP-GAPs, is coordinately and negatively regulated by ethylene in conjunction with the progressive impairment of apoplastic H2O2 homeostatic levels. RNA sequencing analyses showed that several components of the known ROP- and ROS-associated transcriptional networks are regulated along with the ROP-GAP rheostat in response to ethylene perception. These findings may extend the role of the ROP-GAP rheostat beyond hypoxic responses and suggest that it may be a functional regulatory node involved in the integration of ethylene and ROS signalling pathways in abiotic stress.

Ethephon induced abscission in mango: physiological fruitlet responses

Fruitlet abscission of mango is typically very severe, causing considerable production losses worldwide. Consequently, a detailed physiological and molecular characterization of fruitlet abscission in mango is required to describe the onset and time-dependent course of this process. To identify the underlying key mechanisms of abscission, ethephon, an ethylene releasing substance, was applied at two concentrations (600 and 7200 ppm) during the midseason drop stage of mango. The abscission process is triggered by ethylene diffusing to the abscission zone where it binds to specific receptors and thereby activating several key physiological responses at the cellular level. The treatments reduced significantly the capacity of polar auxin transport through the pedicel at 1 day after treatment and thereafter when compared to untreated pedicels. The transcript levels of the ethylene receptor genes MiETR1 and MiERS1 were significantly upregulated in the pedicel and pericarp at 1, 2, and 3 days after the ethephon application with 7200 ppm, except for MiETR1 in the pedicel, when compared to untreated fruitlet. In contrast, ethephon applications with 600 ppm did not affect expression levels of MiETR1 in the pedicel and of MiERS1 in the pericarp; however, MiETR1 in the pericarp at day 2 and MiERS1 in the pedicel at days 2 and 3 were significantly upregulated over the controls. Moreover, two novel short versions of the MiERS1 were identified and detected more often in the pedicel of treated than untreated fruitlets at all sampling times. Sucrose concentration in the fruitlet pericarp was significantly reduced to the control at 2 days after both ethephon treatments. In conclusion, it is postulated that the ethephon-induced abscission process commences with a reduction of the polar auxin transport capacity in the pedicel, followed by an upregulation of ethylene receptors and finally a decrease of the sucrose concentration in the fruitlets.

Roles of Ethylene Production and Ethylene Receptor Expression in Regulating Apple Fruitlet Abscission

Apple (Malus × domestica) is increasingly being considered an interesting model species for studying early fruit development, during which an extremely relevant phenomenon, fruitlet abscission, may occur as a response to both endogenous and/or exogenous cues. Several studies were carried out shedding light on the main physiological and molecular events leading to the selective release of lateral fruitlets within a corymb, either occurring naturally or as a result of a thinning treatment. Several studies pointed out a clear association between a rise of ethylene biosynthetic levels in the fruitlet and its tendency to abscise. A direct mechanistic link, however, has not yet been established between this gaseous hormone and the generation of the abscission signal within the fruit. In this work, the role of ethylene during the very early stages of abscission induction was investigated in fruitlet populations with different abscission potentials due either to the natural correlative inhibitions determining the so-called physiological fruit drop or to a well-tested thinning treatment performed with the cytokinin benzyladenine. A crucial role was ascribed to the ratio between the ethylene produced by the cortex and the expression of ethylene receptor genes in the seed. This ratio would determine the final probability to abscise. A working model has been proposed consistent with the differential distribution of four receptor transcripts within the seed, which resembles a spatially progressive cell-specific immune-like mechanism evolved by apple to protect the embryo from harmful ethylene.

Flower abscission in Vitis vinifera L. triggered by gibberellic acid and shade discloses differences in the underlying metabolic pathways

Understanding abscission is both a biological and an agronomic challenge. Flower abscission induced independently by shade and gibberellic acid (GAc) sprays was monitored in grapevine (Vitis vinifera L.) growing under a soilless greenhouse system during two seasonal growing conditions, in an early and late production cycle. Physiological and metabolic changes triggered by each of the two distinct stimuli were determined. Environmental conditions exerted a significant effect on fruit set as showed by the higher natural drop rate recorded in the late production cycle with respect to the early cycle. Shade and GAc treatments increased the percentage of flower drop compared to the control, and at a similar degree, during the late production cycle. The reduction of leaf gas exchanges under shade conditions was not observed in GAc treated vines. The metabolic profile assessed in samples collected during the late cycle differently affected primary and secondary metabolisms and showed that most of the treatment-resulting variations occurred in opposite trends in inflorescences unbalanced in either hormonal or energy deficit abscission-inducing signals. Particularly concerning carbohydrates metabolism, sucrose, glucose, tricarboxylic acid metabolites and intermediates of the raffinose family oligosaccharides pathway were lower in shaded and higher in GAc samples. Altered oxidative stress remediation mechanisms and indolacetic acid (IAA) concentration were identified as abscission signatures common to both stimuli. According to the global analysis performed, we report that grape flower abscission mechanisms triggered by GAc application and C-starvation are not based on the same metabolic pathways.

An improved fruit transcriptome and the identification of the candidate genes involved in fruit abscission induced by carbohydrate stress in litchi

Massive young fruit abscission usually causes low and unstable yield in litchi (Litchi chinensis Sonn.), an important fruit crop cultivated in tropical and subtropical areas. However, the molecular mechanism of fruit drop has not been fully characterized. This study aimed at identification of molecular components involved in fruitlet abscission in litchi, for which reference genome is not available at present. An improved de novo transcriptome assembly was firstly achieved by using an optimized assembly software, Trinity. Using improved transcriptome assembly as reference, digital transcript abundance (DTA) profiling was performed to screen and identify candidate genes involved in fruit abscission induced by girdling plus defoliation (GPD), a treatment significantly decreased the soluble sugar contents causing carbohydrate stress to fruit. Our results showed that the increasing fruit abscission rate after GPD treatment was associated with higher ethylene production and lower glucose levels in fruit. A total of 2,771 differentially expressed genes were identified as GPD-responsive genes, 857 of which were defined by GO and KEGG enrichment analyses as the candidate genes involved in fruit abscission process. These genes were involved in diverse metabolic processes and pathways, including carbohydrate metabolism, plant hormone synthesis, and signaling, transcription factor activity and cell wall modification that were rapidly induced in the early stages (within 2 days after treatment). qRT-PCR was used to explore the expression pattern of 15 selected candidate genes in the abscission zone, pericarp, and seed, which confirmed the accuracy of our DTA data. More detailed information for different functional categories was also analyzed. This study profiled the gene expression related to fruit abscission induced by carbohydrate stress at whole transcriptome level and thus provided a better understanding of the regulatory mechanism of young fruit abscission in litchi.

Apple SVP Family MADS-Box Proteins and the Tomato Pedicel Abscission Zone Regulator JOINTLESS have Similar Molecular Activities

Pedicel abscission occurs widely in fruit-bearing plants to detach ripe, senescent or diseased organs, and regulation of abscission plays a substantial role in regulating yield and quality in fruit crops. In tomato, development of pedicel abscission zones (AZs) requires the MADS-box genes JOINTLESS (J), MACROCALYX (MC) and SlMBP21. In other plants, however, the involvement of MADS-box genes in pedicel abscission remains unclear. Here, we used genetic and biochemical methods to characterize apple J homologs in the context of the regulation of abscission in tomato. We identified three genes encoding two J homologs, MdJa and MdJb. Similarly to J, MdJa and MdJb interacted with MC and SlMBP21, but their interactions differed slightly: like J, MdJb formed a multimer (probably a tetramer) with SlMBP21; however, MdJa formed multimers to a lesser extent. Ectopic expression of MdJb in a J-deficient tomato mutant restored development of functional pedicel AZs, but ectopic expression of MdJa did not complement j mutants. Introduction of MdJb also restored expression of J-dependent genes in the mutant, such as genes for polygalacturonase, cellulase and AZ-specific transcription factors. These results suggest a potentially conserved mechanism of pedicel AZ development in apple and other plants, regulated by MADS-box transcription factors.

Profiling gene expression in citrus fruit calyx abscission zone (AZ-C) treated with ethylene

On-tree storage and harvesting of mature fruit account for a large proportion of cost in the production of citrus, and a reduction of the cost would not be achieved without a thorough understanding of the mechani sm of the mature fruit abscission. Genome-wide gene expression changes in ethylene-treated fruit calyx abscission zone (AZ-C) of Citrus sinensis cv. Olinda were therefore investigated using a citrus genome array representing up to 33,879 citrus transcripts. In total, 1313 and 1044 differentially regulated genes were identified in AZ-C treated with ethylene for 4 and 24 h, respectively. The results showed that mature citrus fruit abscission commenced with the activation of ethylene signal transduction pathway that led to the activation of ethylene responsive transcription factors and the subsequent transcriptional regulation of a large set of ethylene responsive genes. Significantly down-regulated genes included those of starch/sugar biosynthesis, transportation of water and growth promoting hormone synthesis and signaling, whereas significantly up-regulated genes were those involved in defense, cell wall degradation, and secondary metabolism. Our data unraveled the underlying mechanisms of some known important biochemical events occurring at AZ-C and should provide informative suggestions for future manipulation of the events to achieve a controllable abscission for mature citrus fruit.

Cross-talk between environmental stresses and plant metabolism during reproductive organ abscission

In plants, flowering is a crucial process for reproductive success and continuity of the species through time. Fruit production requires the perfect development of reproductive structures. Abscission, a natural process, can occur to facilitate shedding of no longer needed, infected, or damaged organs. If stress occurs during flower development, abscission can intervene at flower level, leading to reduced yield. Flower abscission is a highly regulated developmental process simultaneously influenced and activated in response to exogenous (changing environmental conditions, interactions with microorganisms) and endogenous (physiological modifications) stimuli. During climate change, plant communities will be more susceptible to environmental stresses, leading to increased flower and fruit abscission, and consequently a decrease in fruit yield. Understanding the impacts of stress on the reproductive phase is therefore critical for managing future agricultural productivity. Here, current knowledge on flower/fruit abscission is summarized by focusing specifically on effects of environmental stresses leading to this process in woody plants. Many of these stresses impair hormonal balance and/or carbohydrate metabolism, but the exact mechanisms are far from completely known. Hormones are the abscission effectors and the auxin/ethylene balance is of particular importance. The carbohydrate pathway is the result of complex regulatory processes involving the balance between photosynthesis and mobilization of reserves. Hormones and carbohydrates together participate in complex signal transduction systems, especially in response to stress. The available data are discussed in relation to reproductive organ development and the process of abscission.

Transcriptomic signatures in seeds of apple (Malus domestica L. Borkh) during fruitlet abscission

Abscission is the regulated process of detachment of an organ from a plant. In apple the abscission of fruits occurs during their early development to control the fruit load depending on the nutritional state of the plant. In order to control production and obtain fruits with optimal market qualities, the horticultural procedure of thinning is performed to further reduce the number of fruitlets. In this study we have conducted a transcriptomic profiling of seeds from two different types of fruitlets, according to size and position in the fruit cluster. Transcriptomic profiles of central and lateral fruit seeds were obtained by RNAseq. Comparative analysis was performed by the functional categorization of differentially expressed genes by means of Gene Ontology (GO) annotation of the apple genome. Our results revealed the overexpression of genes involved in responses to stress, hormone biosynthesis and also the response and/or transport of auxin and ethylene. A smaller set of genes, mainly related to ion transport and homeostasis, were found to be down-regulated. The transcriptome characterization described in this manuscript contributes to unravelling the molecular mechanisms and pathways involved in the physiological abscission of apple fruits and suggests a role for seeds in this process.

De novo Transcriptome Sequencing and Development of Abscission Zone-Specific Microarray as a New Molecular Tool for Analysis of Tomato Organ Abscission

Abscission of flower pedicels and leaf petioles of tomato (Solanum lycopersicum) can be induced by flower removal or leaf deblading, respectively, which leads to auxin depletion, resulting in increased sensitivity of the abscission zone (AZ) to ethylene. However, the molecular mechanisms that drive the acquisition of abscission competence and its modulation by auxin gradients are not yet known. We used RNA-Sequencing (RNA-Seq) to obtain a comprehensive transcriptome of tomato flower AZ (FAZ) and leaf AZ (LAZ) during abscission. RNA-Seq was performed on a pool of total RNA extracted from tomato FAZ and LAZ, at different abscission stages, followed by de novo assembly. The assembled clusters contained transcripts that are already known in the Solanaceae (SOL) genomics and NCBI databases, and over 8823 identified novel tomato transcripts of varying sizes. An AZ-specific microarray, encompassing the novel transcripts identified in this study and all known transcripts from the SOL genomics and NCBI databases, was constructed to study the abscission process. Multiple probes for longer genes and key AZ-specific genes, including antisense probes for all transcripts, make this array a unique tool for studying abscission with a comprehensive set of transcripts, and for mining for naturally occurring antisense transcripts. We focused on comparing the global transcriptomes generated from the FAZ and the LAZ to establish the divergences and similarities in their transcriptional networks, and particularly to characterize the processes and transcriptional regulators enriched in gene clusters that are differentially regulated in these two AZs. This study is the first attempt to analyze the global gene expression in different AZs in tomato by combining the RNA-Seq technique with oligonucleotide microarrays. Our AZ-specific microarray chip provides a cost-effective approach for expression profiling and robust analysis of multiple samples in a rapid succession.

Burst of reactive oxygen species in pedicel-mediated fruit abscission after carbohydrate supply was cut off in longan (Dimocarpus longan)

Cutting off carbohydrate supply to longan (Dimocarpus longan Lour.) fruit by girdling and defoliation or by detachment induced 100% abscission within a few days. We used these treatments to study the involvement of reactive oxygen species (ROS) in fruit abscission. Girdling plus defoliation decreased sugar concentrations in the fruit and pedicel and depleted starch grains in the chloroplasts in the cells of abscission zone. Prior to the occurrence of intensive fruit abscission, there was a burst in ROS in the pedicel, which peaked at 1 day after treatment (DAT), when H2O2 in the abscission zone was found to be chiefly located along the plasma membrane (PM). H2O2 was found exclusively in the cell walls 2 DAT, almost disappeared 3 DAT, and reappeared in the mitochondria and cell walls 4 DAT. Signs of cell death such as cytoplasm breakdown were apparent from 3 DAT. The burst of ROS coincided with a sharp increase in the activity of PM-bound NADPH oxidase in the pedicel. At the same time, activities of antioxidant enzymes including superoxide dismutase (SOD), catalase, and peroxidase (POD) were all increased by the treatment and maintained higher than those in the control. Accompanying the reduction in H2O2 abundance, there was a sharp decrease in PM-bound NADPH oxidase activity after 1 DAT in the treated fruit. H2O2 scavenger dimethylthiourea (DMTU, 1 g L(-1)) significantly inhibited fruit abscission in detached fruit clusters and suppressed the increase in cellulase activity in the abscission zone. These results suggest that fruit abscission induced by carbohydrate stress is mediated by ROS. Roles of ROS in regulating fruit abscission were discussed in relation to its subcellular distribution.

Multiscale investigation of mealiness in apple: an atypical role for a pectin methylesterase during fruit maturation

BACKGROUND

Apple fruit mealiness is one of the most important textural problems that results from an undesirable ripening process during storage. This phenotype is characterized by textural deterioration described as soft, grainy and dry fruit. Despite several studies, little is known about mealiness development and the associated molecular events. In this study, we integrated phenotypic, microscopic, transcriptomic and biochemical analyses to gain insights into the molecular basis of mealiness development.

RESULTS

Instrumental texture characterization allowed the refinement of the definition of apple mealiness. In parallel, a new and simple quantitative test to assess this phenotype was developed.

CONCLUSIONS

These data support the role of PME in cell wall remodelling during apple fruit development and ripening and suggest a local action of these enzymes. Mealiness may partially result from qualitative and spatial variations of pectin microarchitecture rather than quantitative pectin differences, and these changes may occur early in fruit development. The specific MdPME2 gene highlighted in this study could be a good early marker of texture unfavourable trait in apple.

Differential behavior within a grapevine cluster: decreased ethylene-related gene expression dependent on auxin transport is correlated with low abscission of first developed berries

In grapevine, fruit abscission is known to occur within the first two to three weeks after flowering, but the reason why some berries in a cluster persist and others abscise is not yet understood. Ethylene sensitivity modulates abscission in several fruit species, based on a mechanism where continuous polar auxin transport across the pedicel results in a decrease in ethylene perception, which prevents abscission. In grapevine, flowering takes about four to seven days in a single cluster, thus while some flowers are developing into berries, others are just starting to open. So, in this work it was assessed whether uneven flowering accounted for differences in berry abscission dependent on polar auxin transport and ethylene-related gene expression. For this, flowers that opened in a cluster were tagged daily, which allowed to separately analyze berries, regarding their ability to persist. It was found that berries derived from flowers that opened the day that flowering started – named as “first berries” – had lower abscission rate than berries derived from flowers that opened during the following days – named as “late berries”. Use of radiolabeled auxin showed that “first berries” had higher polar auxin transport, correlated with lower ethylene content and lower ethylene-related transcript abundance than “late berries”. When “first berries” were treated with a polar auxin transport inhibitor they showed higher ethylene-related transcript abundance and were more prone to abscise than control berries. This study provides new insights on fruit abscission control. Our results indicate that polar auxin transport sustains the ability of “first berries” to persist in the cluster during grapevine abscission and also suggest that this could be associated with changes in ethylene-related gene expression.

Involvements of PCD and changes in gene expression profile during self-pruning of spring shoots in sweet orange (Citrus sinensis)

Background

Citrus shoot tips abscise at an anatomically distinct abscission zone (AZ) that separates the top part of the shoots into basal and apical portions (citrus self-pruning). Cell separation occurs only at the AZ, which suggests its cells have distinctive molecular regulation. Although several studies have looked into the morphological aspects of self-pruning process, the underlying molecular mechanisms remain unknown.

Results

In this study, the hallmarks of programmed cell death (PCD) were identified by TUNEL experiments, transmission electron microscopy (TEM) and histochemical staining for reactive oxygen species (ROS) during self-pruning of the spring shoots in sweet orange. Our results indicated that PCD occurred systematically and progressively and may play an important role in the control of self-pruning of citrus. Microarray analysis was used to examine transcriptome changes at three stages of self-pruning, and 1,378 differentially expressed genes were identified. Some genes were related to PCD, while others were associated with cell wall biosynthesis or metabolism. These results strongly suggest that abscission layers activate both catabolic and anabolic wall modification pathways during the self-pruning process. In addition, a strong correlation was observed between self-pruning and the expression of hormone-related genes. Self-pruning plays an important role in citrus floral bud initiation. Therefore, several key flowering homologs of Arabidopsis and tomato shoot apical meristem (SAM) activity genes were investigated in sweet orange by real-time PCR and in situ hybridization, and the results indicated that these genes were preferentially expressed in SAM as well as axillary meristem.

Conclusion

Based on these findings, a model for sweet orange spring shoot self-pruning is proposed, which will enable us to better understand the mechanism of self-pruning and abscission.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-892) contains supplementary material, which is available to authorized users.

Isoprene production in transgenic tobacco alters isoprenoid, non-structural carbohydrate and phenylpropanoid metabolism, and protects photosynthesis from drought stress

Isoprene strengthens thylakoid membranes and scavenges stress-induced oxidative species. The idea that isoprene production might also influence isoprenoid and phenylpropanoid pathways under stress conditions was tested. We used transgenic tobacco to compare physiological and biochemical traits of isoprene-emitting (IE) and non-emitting (NE) plants exposed to severe drought and subsequent re-watering. Photosynthesis was less affected by drought in IE than in NE plants, and higher rates were also observed in IE than in NE plants recovering from drought. Isoprene emission was stimulated by mild drought. Under severe drought, isoprene emission declined, and levels of non-volatile isoprenoids, specifically de-epoxidated xanthophylls and abscisic acid (ABA), were higher in IE than in NE plants. Soluble sugars and phenylpropanoids were also higher in IE plants. After re-watering, IE plants maintained higher levels of metabolites, but isoprene emission was again higher than in unstressed plants. We suggest that isoprene production in transgenic tobacco triggered different responses, depending upon drought severity. Under drought, the observed trade-off between isoprene and non-volatile isoprenoids suggests that in IE plants isoprene acts as a short-term protectant, whereas non-volatile isoprenoids protect against severe, long-term damage. After drought, it is suggested that the capacity to emit isoprene might up-regulate production of non-volatile isoprenoids and phenylpropanoids, which may further protect IE leaves.

Target metabolite and gene transcription profiling during the development of superficial scald in apple (Malus x domestica Borkh)

BACKGROUND

Fruit quality features resulting from ripening processes need to be preserved throughout storage for economical reasons. However, during this period several physiological disorders can occur, of which superficial scald is one of the most important, due to the development of large brown areas on the fruit skin surface.

RESULTS

This study examined the variation in polyphenolic content with the progress of superficial scald in apple, also with respect to 1-MCP, an ethylene competitor interacting with the hormone receptors and known to interfere with this etiology. The change in the accumulation of these metabolites was further correlated with the gene set involved in this pathway, together with two specific VOCs (Volatile Organic Compounds), α-farnesene and its oxidative form, 6-methyl-5-hepten-2-one. Metabolite profiling and qRT-PCR assay showed these volatiles are more heavily involved in the signalling system, while the browning coloration would seem to be due more to a specific accumulation of chlorogenic acid (as a consequence of the activation of MdPAL and MdC3H), and its further oxidation carried out by a polyphenol oxidase gene (MdPPO). In this physiological scenario, new evidence regarding the involvement of an anti-apoptotic regulatory mechanism for the compartmentation of this phenomenon in the skin alone was also hypothesized, as suggested by the expression profile of the MdDAD1, MdDND1 and MdLSD1 genes.

CONCLUSIONS

The results presented in this work represent a step forward in understanding the physiological mechanisms of superficial scald in apple, shedding light on the regulation of the specific physiological cascade.

Additional amphivasal bundles in pedicel pith exacerbate central fruit dominance and induce self-thinning of lateral fruitlets in apple

Apple (Malus × domestica) trees naturally produce an excess of fruitlets that negatively affect the commercial value of fruits brought to maturity and impact their capacity to develop flower buds the following season. Therefore, chemical thinning has become an important cultural practice, allowing the selective removal of unwanted fruitlets. As the public pressure to limit the use of chemical agents increases, the control of thinning becomes a major issue. Here, we characterized the self-thinning capacity of an apple hybrid genotype from the tree scale to the molecular level. Additional amphivasal vascular bundles were identified in the pith of pedicels supporting the fruitlets with the lowest abscission potential (central fruitlet), indicating that these bundles might have a role in the acquisition of dominance over lateral fruitlets. Sugar content analysis revealed that central fruitlets were better supplied in sorbitol than lateral fruitlets. Transcriptomic profiles allowed us to identify genes potentially involved in the overproduction of vascular tissues in central pedicels. In addition, histological and transcriptomic data permitted a detailed characterization of abscission zone development and the identification of key genes involved in this process. Our data confirm the major role of ethylene, auxin, and cell wall-remodeling enzymes in abscission zone formation. The shedding process in this hybrid appears to be triggered by a naturally exacerbated dominance of central fruitlets over lateral ones, brought about by an increased supply of sugars, possibly through additional amphivasal vascular bundles. The characterization of this genotype opens new perspectives for the selection of elite apple cultivars.

Genomic resources in fruit plants: an assessment of current status

The availability of many genomic resources such as genome sequences, functional genomics resources including microarrays and RNA-seq, sufficient numbers of molecular markers, express sequence tags (ESTs) and high-density genetic maps is causing a rapid acceleration of genetics and genomic research of many fruit plants. This is leading to an increase in our knowledge of the genes that are linked to many horticultural and agronomically important traits. Recently, some progress has also been made on the identification and functional analysis of miRNAs in some fruit plants. This is one of the most active research fields in plant sciences. The last decade has witnessed development of genomic resources in many fruit plants such as apple, banana, citrus, grapes, papaya, pears, strawberry etc.; however, many of them are still not being exploited. Furthermore, owing to lack of resources, infrastructure and research facilities in many lesser-developed countries, development of genomic resources in many underutilized or less-studied fruit crops, which grow in these countries, is limited. Thus, research emphasis should be given to those fruit crops for which genomic resources are relatively scarce. The development of genomic databases of these less-studied fruit crops will enable biotechnologists to identify target genes that underlie key horticultural and agronomical traits. This review presents an overview of the current status of the development of genomic resources in fruit plants with the main emphasis being on genome sequencing, EST resources, functional genomics resources including microarray and RNA-seq, identification of quantitative trait loci and construction of genetic maps as well as efforts made on the identification and functional analysis of miRNAs in fruit plants.

Fruit self-thinning: a trait to consider for genetic improvement of apple tree

In apple (Malus×domestica Borkh), as in many fruiting crops, fruit maintenance vs abscission is a major criteria for production profitability. Growers routinely make use of chemical thinning agents to control total fruit load. However, serious threats for the environment lead to the demand for new apple cultivars with self-thinning properties. In this project, we studied the genetic determinism of this trait using a F1 progeny derived from the cross between the hybrid INRA X3263, assumed to possess the self-thinning trait, and the cultivar 'Belrène'. Both counting and percentage variables were considered to capture the fruiting behaviour on different shoot types and over three consecutive years. Besides low to moderate but significant genetic effects, mixed models showed considerable effects of the year and the shoot type, as well as an interaction effect. Year effect resulted mainly from biennial fruiting. Eight Quantitative Trait Locus (QTL) were detected on several linkage groups (LG), either independent or specific of the year of observation or the shoot type. The QTL with highest LOD value was located on the top third of LG10. The screening of three QTL zones for candidate genes revealed a list of transcription factors and genes involved in fruit nutrition, xylem differentiation, plant responses to starvation and organ abscission that open new avenues for further molecular investigations. The detailed phenotyping performed revealed the dependency between the self-thinning trait and the fruiting status of the trees. Despite a moderate genetic control of the self-thinning trait, QTL and candidate genes were identified which will need further analyses involving other progenies and molecular investigations.

Genomics and bioinformatics resources for translational science in Rosaceae

Recent technological advances in biology promise unprecedented opportunities for rapid and sustainable advancement of crop quality. Following this trend, the Rosaceae research community continues to generate large amounts of genomic, genetic and breeding data. These include annotated whole genome sequences, transcriptome and expression data, proteomic and metabolomic data, genotypic and phenotypic data, and genetic and physical maps. Analysis, storage, integration and dissemination of these data using bioinformatics tools and databases are essential to provide utility of the data for basic, translational and applied research. This review discusses the currently available genomics and bioinformatics resources for the Rosaceae family.

Comparative transcriptional profiling analysis of olive ripe-fruit pericarp and abscission zone tissues shows expression differences and distinct patterns of transcriptional regulation

BACKGROUND

In fleshy fruit, abscission of fully ripe fruit is a process intimately linked to the ripening process. In many fruit-tree species, such as olive (Olea europaea L. cv. Picual), there is a coupling of the full ripening and the activation of the abscission-zone (AZ). Although fully ripe fruit have marked physiological differences with respect to their AZs, dissimilarities in gene expression have not been thoroughly investigated. The present study examines the transcriptome of olive fruit and their AZ tissues at the last stage of ripening, monitored using mRNA-Seq.

RESULTS

Roche-454 massive parallel pyrosequencing enabled us to generate 397,457 high-quality EST sequences, among which 199,075 were from ripe-fruit pericarp and 198,382 from AZ tissues. We assembled these sequences into 19,062 contigs, grouped as 17,048 isotigs. Using the read amounts for each annotated isotig (from a total of 15,671), we identified 7,756 transcripts. A comparative analysis of the transcription profiles conducted in ripe-fruit pericarp and AZ evidenced that 4,391 genes were differentially expressed genes (DEGs) in fruit and AZ. Functional categorization of the DEGs revealed that AZ tissue has an apparently higher response to external stimuli than does that of ripe fruit, revealing a higher expression of auxin-signaling genes, as well as lignin catabolic and biosynthetic pathway, aromatic amino acid biosynthetic pathway, isoprenoid biosynthetic pathway, protein amino acid dephosphorylation, amino acid transport, and photosynthesis. By contrast, fruit-enriched transcripts are involved in ATP synthesis coupled proton transport, glycolysis, and cell-wall organization. Furthermore, over 150 transcripts encoding putative transcription-factors (TFs) were identified (37 fruit TFs and 113 AZ TFs), of which we randomly selected eight genes and we confirmed their expression patterns using quantitative RT-PCR.

CONCLUSION

We generated a set of EST sequences from olive fruit at full ripening, and DEGs between two different olive tissues, ripe fruit and their AZ, were also identified. Regarding the cross-talk between fruit and AZ, using qRT-PCR, we confirmed a set of TF genes that were differentially expressed, revealing profiles of expression that have not previously been reported, this offering a promising beginning for studies on the different transcription regulation in such tissues.

Evidence for regulation of columnar habit in apple by a putative 2OG-Fe(II) oxygenase

Understanding the genetic mechanisms controlling columnar-type growth in the apple mutant 'Wijcik' will provide insights on how tree architecture and growth are regulated in fruit trees. In apple, columnar-type growth is controlled by a single major gene at the Columnar (Co) locus. By comparing the genomic sequence of the Co region of 'Wijcik' with its wild-type 'McIntosh', a novel non-coding DNA element of 1956 bp specific to Pyreae was found to be inserted in an intergenic region of 'Wijcik'. Expression analysis of selected genes located in the vicinity of the insertion revealed the upregulation of the MdCo31 gene encoding a putative 2OG-Fe(II) oxygenase in axillary buds of 'Wijcik'. Constitutive expression of MdCo31 in Arabidopsis thaliana resulted in compact plants with shortened floral internodes, a phenotype reminiscent of the one observed in columnar apple trees. We conclude that MdCo31 is a strong candidate gene for the control of columnar growth in 'Wijcik'.

Letting go is never easy: abscission and receptor-like protein kinases

Abscission is the process by which plants discard organs in response to environmental cues/stressors, or as part of their normal development. Abscission has been studied throughout the history of the plant sciences and in numerous species. Although long studied at the anatomical and physiological levels, abscission has only been elucidated at the molecular and genetic levels within the last two decades, primarily with the use of the model plant Arabidopsis thaliana. This has led to the discovery of numerous genes involved at all steps of abscission, including key pathways involving receptor-like protein kinases (RLKs). This review covers the current knowledge of abscission research, highlighting the role of RLKs. [Figure: see text] John C. Walker (Corresponding author).

Identifying the candidate genes involved in the calyx abscission process of 'Kuerlexiangli' (Pyrus sinkiangensis Yu) by digital transcript abundance measurements

Background

'Kuerlexiangli’ (Pyrus sinkiangensis Yu), a native pear of Xinjiang, China, is an important agricultural fruit and primary export to the international market. However, fruit with persistent calyxes affect fruit shape and quality. Although several studies have looked into the physiological aspects of the calyx abscission process, the underlying molecular mechanisms remain unknown. In order to better understand the molecular basis of the process of calyx abscission, materials at three critical stages of regulation, with 6000 × Flusilazole plus 300 × PBO treatment (calyx abscising treatment) and 50 mg^.L^-1GA₃ treatment (calyx persisting treatment), were collected and cDNA fragments were sequenced using digital transcript abundance measurements to identify candidate genes.

Results

Digital transcript abundance measurements was performed using high-throughput Illumina GAII sequencing on seven samples that were collected at three important stages of the calyx abscission process with chemical agent treatments promoting calyx abscission and persistence. Altogether more than 251,123,845 high quality reads were obtained with approximately 8.0 M raw data for each library. The values of 69.85%-71.90% of clean data in the digital transcript abundance measurements could be mapped to the pear genome database. There were 12,054 differentially expressed genes having Gene Ontology (GO) terms and associating with 251 Kyoto Encyclopedia of Genes and Genomes (KEGG) defined pathways. The differentially expressed genes correlated with calyx abscission were mainly involved in photosynthesis, plant hormone signal transduction, cell wall modification, transcriptional regulation, and carbohydrate metabolism. Furthermore, candidate calyx abscission-specific genes, e.g. Inflorescence deficient in abscission gene, were identified. Quantitative real-time PCR was used to confirm the digital transcript abundance measurements results.

Conclusions

We identified candidate genes that showed highly dynamic changes in expression during the calyx abscission process. These genes are potential targets for future functional characterization and should be valuable for exploration of the mechanisms of calyx abscission, and eventually for developing methods based on small molecule application to induce calyx abscission in fruit production.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-14-727) contains supplementary material, which is available to authorized users.

De novo assembly and characterization of fruit transcriptome in Litchi chinensis Sonn and analysis of differentially regulated genes in fruit in response to shading

BACKGROUND

Litchi (Litchi chinensis Sonn.) is one of the most important fruit trees cultivated in tropical and subtropical areas. However, a lack of transcriptomic and genomic information hinders our understanding of the molecular mechanisms underlying fruit set and fruit development in litchi. Shading during early fruit development decreases fruit growth and induces fruit abscission. Here, high-throughput RNA sequencing (RNA-Seq) was employed for the de novo assembly and characterization of the fruit transcriptome in litchi, and differentially regulated genes, which are responsive to shading, were also investigated using digital transcript abundance(DTA)profiling.

RESULTS

More than 53 million paired-end reads were generated and assembled into 57,050 unigenes with an average length of 601 bp. These unigenes were annotated by querying against various public databases, with 34,029 unigenes found to be homologous to genes in the NCBI GenBank database and 22,945 unigenes annotated based on known proteins in the Swiss-Prot database. In further orthologous analyses, 5,885 unigenes were assigned with one or more Gene Ontology terms, 10,234 hits were aligned to the 24 Clusters of Orthologous Groups classifications and 15,330 unigenes were classified into 266 Kyoto Encyclopedia of Genes and Genomes pathways. Based on the newly assembled transcriptome, the DTA profiling approach was applied to investigate the differentially expressed genes related to shading stress. A total of 3.6 million and 3.5 million high-quality tags were generated from shaded and non-shaded libraries, respectively. As many as 1,039 unigenes were shown to be significantly differentially regulated. Eleven of the 14 differentially regulated unigenes, which were randomly selected for more detailed expression comparison during the course of shading treatment, were identified as being likely to be involved in the process of fruitlet abscission in litchi.

CONCLUSIONS

The assembled transcriptome of litchi fruit provides a global description of expressed genes in litchi fruit development, and could serve as an ideal repository for future functional characterization of specific genes. The DTA analysis revealed that more than 1000 differentially regulated unigenes respond to the shading signal, some of which might be involved in the fruitlet abscission process in litchi, shedding new light on the molecular mechanisms underlying organ abscission.

Constraints to obtaining consistent annual yields in perennial tree crops. I: Heavy fruit load dominates over vegetative growth

Farmers lack effective methods to achieve and maintain stable production from year to year in many commercial fruit crops. Annual fruit yield within a region often alternates between high and low fruit load and is termed alternate bearing. The underlying cause of alternate bearing is the negative impact of high fruit load on vegetative growth and next year's flowering. In this review, we emphasize common responses of diverse perennials to heavy crop load. We present botanical, ecological and horticultural perspectives on irregular bearing. The later part of this review focuses on understanding how high fruit load dominates over vegetative growth. We discuss sink strengths and putative mobile signals (hormones), perhaps seed-derived. We highlight gaps in current understanding of alternate bearing, and discuss new approaches to better understand fruit load dominance. Assuming the effect of high fruit load may be related to other mechanisms of sink partitioning, other forms of dominance are presented such as apical, first fruit and king fruit dominance. Dominance seems to be enforced, in independent cases through the establishment of a polar auxin transport system from the stronger sink. Once established this somehow perturbs the transport of auxin out of weaker sinks. Possibly, fruit derived auxin may alter the polar auxin transport system of the shoot to inhibit shoot growth.

Early induction of apple fruitlet abscission is characterized by an increase of both isoprene emission and abscisic acid content

Apple (Malus domestica) fruitlet abscission represents an interesting model system to study the early phases of the shedding process, during which major transcriptomic changes and metabolic rearrangements occur within the fruit. In apple, the drop of fruits at different positions within the cluster can be selectively magnified through chemical thinners, such as benzyladenine and metamitron, acting as abscission enhancers. In this study, different abscission potentials were obtained within the apple fruitlet population by means of the above-cited thinners. A metabolomic study was conducted on the volatile organic compounds emitted by abscising fruitlets, allowing for identification of isoprene as an early marker of abscission induction. A strong correlation was also observed between isoprene production and abscisic acid (ABA) levels in the fruit cortex, which were shown to increase in abscising fruitlets with respect to nonabscising ones. Transcriptomic evidence indicated that abscission-related ABA is biologically active, and its increased biosynthesis is associated with the induction of a specific ABA-responsive 9-cis-epoxycarotenoid dioxygenase gene. According to a hypothetical model, ABA may transiently cooperate with other hormones and secondary messengers in the generation of an intrafruit signal leading to the downstream activation of the abscission zone. The shedding process therefore appears to be triggered by multiple interdependent pathways, whose fine regulation, exerted within a very short temporal window by both endogenous and exogenous factors, determines the final destiny of the fruitlets.

Transcriptomic events involved in melon mature-fruit abscission comprise the sequential induction of cell-wall degrading genes coupled to a stimulation of endo and exocytosis

BACKGROUND

Mature-fruit abscission (MFA) in fleshy-fruit is a genetically controlled process with mechanisms that, contrary to immature-fruit abscission, has not been fully characterized. Here, we use pyrosequencing to characterize the transcriptomes of melon abscission zone (AZ) at three stages during AZ-cell separation in order to understand MFA control at an early stage of AZ-activation.

PRINCIPAL FINDINGS

The results show that by early induction of MFA, the melon AZ exhibits major gene induction, while by late induction of MFA, melon AZ shows major gene repression. Although some genes displayed similar regulation in both early and late induction of abscission, such as EXT1-EXT4, EGase1, IAA2, ERF1, AP2D15, FLC, MADS2, ERAF17, SAP5 and SCL13 genes, the majority had different expression patterns. This implies that time-specific events occur during MFA, and emphasizes the value of characterizing multiple time-specific abscission transcriptomes. Analysis of gene-expression from these AZs reveal that a sequential induction of cell-wall-degrading genes is associated with the upregulation of genes involved in endo and exocytosis, and a shift in plant-hormone metabolism and signaling genes during MFA. This is accompanied by transcriptional activity of small-GTPases and synthaxins together with tubulins, dynamins, V-type ATPases and kinesin-like proteins potentially involved in MFA signaling. Early events are potentially controlled by down-regulation of MADS-box, AP2/ERF and Aux/IAA transcription-factors, and up-regulation of homeobox, zinc finger, bZIP, and WRKY transcription-factors, while late events may be controlled by up-regulation of MYB transcription-factors.

SIGNIFICANCE

Overall, the data provide a comprehensive view on MFA in fleshy-fruit, identifying candidate genes and pathways associated with early induction of MFA. Our comprehensive gene-expression profile will be very useful for elucidating gene regulatory networks of the MFA in fleshy-fruit.

Elucidating mechanisms underlying organ abscission

Abscission consists in the detachment of entire vegetative and reproductive organs due to cell separation processes occurring at the abscission zones (AZs) at specific positions of the plant body. From an evolutionary point of view, abscission is a highly advantageous process resulting into fruit and seed dispersal as well as the shedding of no longer useful organs. In an agricultural context, however, abscission may become a major limiting factor for crop productivity. Domestication of major crops included the selection of plants that did not naturally shed ripe fruits or seeds. The understanding of abscission is of great importance to control seed and fruit production and to improve breeding and harvesting practices. Thus, advances made on model plants and crops are of major importance since they may provide potential candidate genes for further biotechnological applications. Here, we review the current knowledge of the physiological, genetic and genomic aspects related to abscission including the most recently disclosed putative regulators that appear to be implicated in the development and/or activation of the AZs.

Grape berry ripening delay induced by a pre-véraison NAA treatment is paralleled by a shift in the expression pattern of auxin- and ethylene-related genes

BACKGROUND

Auxins act as repressors of ripening inception in grape (véraison), while ethylene and abscisic acid (ABA) play a positive role as inducers of the syndrome. Despite the increasing amount of information made available on this topic, the complex network of interactions among these hormones remains elusive. In order to shed light on these aspects, a holistic approach was adopted to evaluate, at the transcriptomic level, the crosstalk between hormones in grape berries, whose ripening progression was delayed by applying naphtalenacetic acid (NAA) one week before véraison.

RESULTS

The NAA treatment caused significant changes in the transcription rate of about 1,500 genes, indicating that auxin delayed grape berry ripening also at the transcriptional level, along with the recovery of a steady state of its intracellular concentration. Hormone indices analysis carried out with the HORMONOMETER tool suggests that biologically active concentrations of auxins were achieved throughout a homeostatic recovery. This occurred within 7 days after the treatment, during which the physiological response was mainly unspecific and due to a likely pharmacological effect of NAA. This hypothesis is strongly supported by the up-regulation of genes involved in auxin conjugation (GH3-like) and action (IAA4- and IAA31-like). A strong antagonistic effect between auxin and ethylene was also observed, along with a substantial 'synergism' between auxins and ABA, although to a lesser extent.

CONCLUSIONS

This study suggests that, in presence of altered levels of auxins, the crosstalk between hormones involves diverse mechanisms, acting at both the hormone response and biosynthesis levels, creating a complex response network.

Comparative transcriptomics and proteomics analysis of citrus fruit, to improve understanding of the effect of low temperature on maintaining fruit quality during lengthy post-harvest storage

Fruit quality is a very complex trait that is affected by both genetic and non-genetic factors. Generally, low temperature (LT) is used to delay fruit senescence and maintain fruit quality during post-harvest storage but the molecular mechanisms involved are poorly understood. Hirado Buntan Pummelo (HBP; Citrus grandis × C. paradis) fruit were chosen to explore the mechanisms that maintain citrus fruit quality during lengthy LT storage using transcriptome and proteome studies based on digital gene expression (DGE) profiling and two-dimensional gel electrophoresis (2-DE), respectively. Results showed that LT up-regulated stress-responsive genes, arrested signal transduction, and inhibited primary metabolism, secondary metabolism and the transportation of metabolites. Calcineurin B-like protein (CBL)-CBL-interacting protein kinase complexes might be involved in the signal transduction of LT stress, and fruit quality is likely to be regulated by sugar-mediated auxin and abscisic acid (ABA) signalling. Furthermore, ABA was specific to the regulation of citrus fruit senescence and was not involved in the LT stress response. In addition, the accumulation of limonin, nomilin, methanol, and aldehyde, together with the up-regulated heat shock proteins, COR15, and cold response-related genes, provided a comprehensive proteomics and transcriptomics view on the coordination of fruit LT stress responses.

Comprehensive QTL mapping survey dissects the complex fruit texture physiology in apple (Malus x domestica Borkh.)

Fruit ripening is a complex physiological process in plants whereby cell wall programmed changes occur mainly to promote seed dispersal. Cell wall modification also directly regulates the textural properties, a fundamental aspect of fruit quality. In this study, two full-sib populations of apple, with 'Fuji' as the common maternal parent, crossed with 'Delearly' and 'Pink Lady', were used to understand the control of fruit texture by QTL mapping and in silico gene mining. Texture was dissected with a novel high resolution phenomics strategy, simultaneously profiling both mechanical and acoustic fruit texture components. In 'Fuji × Delearly' nine linkage groups were associated with QTLs accounting from 15.6% to 49% of the total variance, and a highly significant QTL cluster for both textural components was mapped on chromosome 10 and co-located with Md-PG1, a polygalacturonase gene that, in apple, is known to be involved in cell wall metabolism processes. In addition, other candidate genes related to Md-NOR and Md-RIN transcription factors, Md-Pel (pectate lyase), and Md-ACS1 were mapped within statistical intervals. In 'Fuji × Pink Lady', a smaller set of linkage groups associated with the QTLs identified for fruit texture (15.9-34.6% variance) was observed. The analysis of the phenotypic variance over a two-dimensional PCA plot highlighted a transgressive segregation for this progeny, revealing two QTL sets distinctively related to both mechanical and acoustic texture components. The mining of the apple genome allowed the discovery of the gene inventory underlying each QTL, and functional profile assessment unravelled specific gene expression patterns of these candidate genes.

MACROCALYX and JOINTLESS interact in the transcriptional regulation of tomato fruit abscission zone development

Abscission in plants is a crucial process used to shed organs such as leaves, flowers, and fruits when they are senescent, damaged, or mature. Abscission occurs at predetermined positions called abscission zones (AZs). Although the regulation of fruit abscission is essential for agriculture, the developmental mechanisms remain unclear. Here, we describe a novel transcription factor regulating the development of tomato (Solanum lycopersicum) pedicel AZs. We found that the development of tomato pedicel AZs requires the gene MACROCALYX (MC), which was previously identified as a sepal size regulator and encodes a MADS-box transcription factor. MC has significant sequence similarity to Arabidopsis (Arabidopsis thaliana) FRUITFULL, which is involved in the regulation of fruit dehiscent zone development. The MC protein interacted physically with another MADS-box protein, JOINTLESS, which is known as a regulator of fruit abscission; the resulting heterodimer acquired a specific DNA-binding activity. Transcriptome analyses of pedicels at the preabscission stage revealed that the expression of the genes involved in phytohormone-related functions, cell wall modifications, fatty acid metabolism, and transcription factors is regulated by MC and JOINTLESS. The regulated genes include homologs of Arabidopsis WUSCHEL, REGULATOR OF AXILLARY MERISTEMS, CUP-SHAPED COTYLEDON, and LATERAL SUPPRESSOR. These Arabidopsis genes encode well-characterized transcription factors regulating meristem maintenance, axillary meristem development, and boundary formation in plant tissues. The tomato homologs were specifically expressed in AZs but not in other pedicel tissues, suggesting that these transcription factors may play key roles in pedicel AZ development.

Transcriptomics of shading-induced and NAA-induced abscission in apple (Malus domestica) reveals a shared pathway involving reduced photosynthesis, alterations in carbohydrate transport and signaling and hormone crosstalk

BACKGROUND

Naphthaleneacetic acid (NAA), a synthetic auxin analogue, is widely used as an effective thinner in apple orchards. When applied shortly after fruit set, some fruit abscise leading to improved fruit size and quality. However, the thinning results of NAA are inconsistent and difficult to predict, sometimes leading to excess fruit drop or insufficient thinning which are costly to growers. This unpredictability reflects our incomplete understanding of the mode of action of NAA in promoting fruit abscission.

RESULTS

Here we compared NAA-induced fruit drop with that caused by shading via gene expression profiling performed on the fruit abscission zone (FAZ), sampled 1, 3, and 5 d after treatment. More than 700 genes with significant changes in transcript abundance were identified from NAA-treated FAZ. Combining results from both treatments, we found that genes associated with photosynthesis, cell cycle and membrane/cellular trafficking were downregulated. On the other hand, there was up-regulation of genes related to ABA, ethylene biosynthesis and signaling, cell wall degradation and programmed cell death. While the differentially expressed gene sets for NAA and shading treatments shared only 25% identity, NAA and shading showed substantial similarity with respect to the classes of genes identified. Specifically, photosynthesis, carbon utilization, ABA and ethylene pathways were affected in both NAA- and shading-induced young fruit abscission. Moreover, we found that NAA, similar to shading, directly interfered with leaf photosynthesis by repressing photosystem II (PSII) efficiency within 10 minutes of treatment, suggesting that NAA and shading induced some of the same early responses due to reduced photosynthesis, which concurred with changes in hormone signaling pathways and triggered fruit abscission.

CONCLUSIONS

This study provides an extensive transcriptome study and a good platform for further investigation of possible regulatory genes involved in the induction of young fruit abscission in apple, which will enable us to better understand the mechanism of fruit thinning and facilitate the selection of potential chemicals for the thinning programs in apple.

A microarray approach to identify genes involved in seed-pericarp cross-talk and development in peach

BACKGROUND

Field observations and a few physiological studies have demonstrated that peach embryogenesis and fruit development are tightly coupled. In fact, attempts to stimulate parthenocarpic fruit development by means of external tools have failed. Moreover, physiological disturbances during early embryo development lead to seed abortion and fruitlet abscission. Later in embryo development, the interactions between seed and fruit development become less strict. As there is limited genetic and molecular information about seed-pericarp cross-talk and development in peach, a massive gene approach based on the use of the μPEACH 1.0 array platform and quantitative real time RT-PCR (qRT-PCR) was used to study this process.

RESULTS

A comparative analysis of the transcription profiles conducted in seed and mesocarp (cv Fantasia) throughout different developmental stages (S1, S2, S3 and S4) evidenced that 455 genes are differentially expressed in seed and fruit. Among differentially expressed genes some were validated as markers in two subsequent years and in three different genotypes. Seed markers were a LTP1 (lipid transfer protein), a PR (pathogenesis-related) protein, a prunin and LEA (Late Embryogenesis Abundant) protein, for S1, S2, S3 and S4, respectively. Mesocarp markers were a RD22-like protein, a serin-carboxypeptidase, a senescence related protein and an Aux/IAA, for S1, S2, S3 and S4, respectively.The microarray data, analyzed by using the HORMONOMETER platform, allowed the identification of hormone-responsive genes, some of them putatively involved in seed-pericarp crosstalk. Results indicated that auxin, cytokinins, and gibberellins are good candidates, acting either directly (auxin) or indirectly as signals during early development, when the cross-talk is more active and vital for fruit set, whereas abscisic acid and ethylene may be involved later on.

CONCLUSIONS

In this research, genes were identified marking different phases of seed and mesocarp development. The selected genes behaved as good seed markers, while for mesocarp their reliability appeared to be dependent upon developmental and ripening traits. Regarding the cross-talk between seed and pericarp, possible candidate signals were identified among hormones.Further investigations relying upon the availability of whole genome platforms will allow the enrichment of a marker genes repertoire and the elucidation of players other than hormones that are involved in seed-pericarp cross-talk (i.e. hormone peptides and microRNAs).