Fruitlet abscission: A cDNA-AFLP approach to study genes differentially expressed during shedding of immature fruits reveals the involvement of a putative auxin hydrogen symporter in apple (Malus domestica L. Borkh)

KNOX protein KNAT1 regulates fruitlet abscission in litchi by repressing ethylene biosynthetic genes

Abscission is triggered by multiple environmental and developmental cues, including endogenous plant hormones. KNOTTED-LIKE HOMEOBOX (KNOX) transcription factors (TFs) play an important role in controlling abscission in plants. However, the underlying molecular mechanism of KNOX TFs in abscission is largely unknown. Here, we identified LcKNAT1, a KNOTTED-LIKE FROM ARABIDOPSIS THALIANA1 (KNAT1)-like protein from litchi, which regulates abscission by modulating ethylene biosynthesis. LcKNAT1 is expressed in the fruit abscission zone and its expression decreases during fruitlet abscission. Furthermore, the expression of the ethylene biosynthetic genes LcACS1, LcACS7, and LcACO2 increases in the fruit abscission zone, in parallel with the emission of ethylene in fruitlets. In vitro and in vivo assays revealed that LcKNAT1 inhibits the expression of LcACS/ACO genes by directly binding to their promoters. Moreover, ectopic expression of LcKNAT1 represses flower abscission in tomatoes. Transgenic plants expressing LcKNAT1 also showed consistently decreased expression of ACS/ACO genes. Collectively, these results indicate that LcKNAT1 represses abscission via the negative regulation of ethylene biosynthesis.

Validation of MADS-box genes from apple fruit pedicels during early fruit abscission by transcriptome analysis and real-time PCR

BACKGROUND

Fruit abscission in an isolated region called abscission zone (AZ) is regulated by several genes including JOINTLESS, MACROCALYX and SEPALLATA, MADS-box genes, in tomato.

OBJECTIVE

The surviving central pedicels and the abscised lateral pedicels were examined in fruit clusters in order to investigate apple MADS-box genes from fruit pedicels of self-abscising apple 'Saika' during early fruit abscission.

METHODS

After performing RNA-Seq, transcription profiling was conducted on the MADS-box genes from apple central and lateral pedicels. The JOINTLESS homolog of apple (MdJOINTLESS) was amplified using degenerate primers annealing to a highly conserved domain based on the orthologous genes of various crops, including JOINTLESS gene of tomato. The expression pattern of MdJOINTLESS was investigated in central and lateral pedicles by real-time PCR.

RESULTS

Some homologs were found which similar to JOINTLESS, MACROCALYX and SEPALLATA of tomato MADS-box genes from transcriptome analysis and RACE. Using phylogenetic analyses with the MADS-box gene family, MdJOINTLESS was classified into the SHORT VEGETATIVE PHASE (SVP) clade that included Arabidopsis and other crops. The expression level of MdJOINTLESS in central pedicel was more than twice as high as that of lateral pedicel.

CONCLUSION

In the current study, we could find apple homologs of JOINTLESS, MACROCALYX, SEPALLATA, which were known to regulate pedicel AZ development in tomato. Furthermore, MdJOINTLESS might contribute to auxin gradation, influencing hierarchical ranking of auxin transport between fruit pedicels of self-abscising apple.

Photosynthetic limitation as a factor influencing yield in highbush blueberries (Vaccinium corymbosum) grown in a northern European environment

Published evidence indicates that nearly 60% of blueberry-producing countries experience yield instability. Yield is a complex trait determined by genetic and environmental factors. Here, using physiological and biochemical approaches, we tested the hypothesis that yield instability results from year-to-year environmental variation that limits carbon assimilation, storage and partitioning. The data indicate that fruit development depends primarily on the daily production of non-structural carbohydrates by leaves, and there is no accumulation of a starch buffer to allow continuous ripening under conditions limiting for photosynthesis. Photosynthesis was saturated at moderate light irradiance and this was mainly due to stomatal and biochemical limitations. In a dynamic light environment, photosynthesis was further limited by slow stomatal response to increasing light. Finally, labelling with 13CO2 at specific stages of fruit development revealed a relatively even distribution of newly assimilated carbon between stems, roots and fruits, suggesting that the fruit is not a strong sink. We conclude that a significant component of yield variability results from limitations in photosynthetic efficiency that are compounded by an inability to accumulate starch reserves in blueberry storage tissues in a typical northern European environment. This work informs techniques for improving agronomic management and indicates key traits required for yield stability in such environments.

A MADS-box transcription factor of 'Kuerlexiangli'(Pyrus sinkiangensis Yu) PsJOINTLESS gene functions in floral organ abscission

MADS-box proteins have been implicated in many biological processes. However, plant MADS-box proteins functioning in floral organ abscission and the underlying physiological mechanisms remain poorly understood. Here, we report the identification and functional characterization of PsJOINTLESS isolated from 'Kuerlexiangli'. PsJOINTLESS had a complete open reading frame of 672bp, encoding a 224 amino acid peptide, and shared high sequence identities with MADS-box from other plants. PsJOINTLESS was subcellularly targeted to the nucleus, supporting its role as a transcription factor. Expression levels of PsJOINTLESS in the calyx tube were strongly induced by calyx abscission treatment at 6d after full bloom. Overexpression of PsJOINTLESS in tomato enhanced the rate of pedicel abscission rate. Of special note, the transgenic plants increased the abscission zone cell layer compared with wild type. Furthermore, the tomato transgenic lines showed thinner flower pedicels, more cell number and small pedicel cell size. The cellulase activity in pedicel abscission zone of transgenic plants was higher than that of wild type. In addition, steady-state mRNA levels of five cell wall hydrolase genes coding for either functional or regulatory proteins were induced to higher levels in the transgenic lines. These results clearly demonstrate that PsJOINTLESS may affect pedicel abscission zone development.

Ethephon induced oxidative stress in the olive leaf abscission zone enables development of a selective abscission compound

BACKGROUND

Table olives (Olea europaea L.), despite their widespread production, are still harvested manually. The low efficiency of manual harvesting and the rising costs of labor have reduced the profitability of this crop. A selective abscission treatment, inducing abscission of fruits but not leaves, is crucial for the adoption of mechanical harvesting of table olives. In the present work we studied the anatomical and molecular differences between the three abscission zones (AZs) of olive fruits and leaves.

RESULTS

The fruit abscission zone 3 (FAZ3), located between the fruit and the pedicel, was found to be the active AZ in mature fruits and is sensitive to ethephon, whereas FAZ2, between the pedicel and the rachis, is the flower active AZ as well as functioning as the most ethephon induced fruit AZ. We found anatomical differences between the leaf AZ (LAZ) and the two FAZs. Unlike the FAZs, the LAZ is characterized by small cells with less pectin compared to neighboring cells. In an attempt to differentiate between the fruit and leaf AZs, we examined the effect of treating olive-bearing trees with ethephon, an ethylene-releasing compound, with or without antioxidants, on the detachment force (DF) of fruits and leaves 5 days after the treatment. Ethephon treatment enhanced pectinase activity and reduced DF in all the three olive AZs. A transcriptomic analysis of the three olive AZs after ethephon treatment revealed induction of several genes encoding for hormones (ethylene, auxin and ABA), as well as for several cell wall degrading enzymes. However, up-regulation of cellulase genes was found only in the LAZ. Many genes involved in oxidative stress were induced by the ethephon treatment in the LAZ alone. In addition, we found that reactive oxygen species (ROS) mediated abscission in response to ethephon only in leaves. Thus, adding antioxidants such as ascorbic acid or butyric acid to the ethephon inhibited leaf abscission but enhanced fruit abscission.

CONCLUSION

Our findings suggest that treating olive-bearing trees with a combination of ethephon and antioxidants reduces the detachment force (DF) of fruit without weakening that of the leaves. Hence, this selective abscission treatment may be used in turn to promote mechanized harvest of olives.

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 analyses reveal species-specific light-induced anthocyanin biosynthesis in chrysanthemum

BACKGROUND

The flower colour of agricultural products is very important for their commercial value, which is mainly attributed to the accumulation of anthocyanins. Light is one of the key environmental factors that affect the anthocyanin biosynthesis. However, the deep molecular mechanism remains elusive, and many problems regarding the phenotypic change and the corresponding gene regulation are still unclear. In the present study, Chrysanthemum × morifolium 'Purple Reagan', a light-responding pigmentation cultivar, was selected to investigate the mechanism of light-induced anthocyanin biosynthesis using transcriptomic analyses.

RESULTS

Only cyanidin derivatives were identified based on the analyses of the pigmentation in ray florets. Shading experiments revealed that the capitulum was the key organ and that its bud stage was the key phase responding to light. These results were used to design five libraries for transcriptomic analyses, including three capitulum developmental stages and two light conditions. RNA sequences were de novo assembled into 103,517 unigenes, of which 60,712 were annotated against four public protein databases. As many as 2,135 unigenes were differentially expressed between the light and dark libraries with 923 up-regulated and 1,212 down-regulated unigenes in response to shading. Next, interactive pathway analysis showed that the anthocyanin biosynthetic pathway was the only complete metabolic pathway both modulated in response to light and related to capitulum development. Following the shading treatment, nearly all structural genes involved in the anthocyanin biosynthetic pathway were down-regulated. Moreover, three CmMYB genes and one CmbHLH gene were identified as key transcription factors that might participate in the regulation of anthocyanin biosynthesis under light conditions based on clustering analysis and validation by RT-qPCR. Finally, a light-induced anthocyanin biosynthesis pathway in chrysanthemums was inferred.

CONCLUSION

The pigmentation of the ray florets of chrysanthemum cultivar 'Purple Reagan' is dependent on light. During the light-induced pigmentation process, the expression of seven structural genes in the anthocyanin biosynthetic pathway (regulated by at least four transcription factors in response to light) are the main contributors to the pigmentation of chrysanthemums. This information will further our understanding of the molecular mechanisms governing light-induced anthocyanin biosynthesis in ornamental plants.

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.

Gene expression profiling by cDNA-AFLP reveals potential candidate genes for partial resistance of 'Président Roulin' against Venturia inaequalis

Background

Scab, caused by the fungus Venturia inaequalis, is one of the most important diseases of cultivated apple. While a few scab resistance genes (R genes) governing qualitative resistance have been isolated and characterized, the biological roles of genes governing quantitative resistance, supposed to be more durable, are still unknown. This study aims to investigate the molecular mechanisms involved in the partial resistance of the old Belgian apple cultivar ‘Président Roulin’ against V. inaequalis.

Results

A global gene expression analysis was conducted in ‘Président Roulin’ (partially resistant) and in ‘Gala’ (susceptible) challenged by V. inaequalis by using the cDNA-AFLP method (cDNA-Amplified Fragment Length Polymorphism). Transcriptome analysis revealed significant modulation (up- or down-regulation) of 281 out of approximately 20,500 transcript derived fragments (TDFs) in ‘Président Roulin’ 48 hours after inoculation. Sequence annotation revealed similarities to several genes encoding for proteins belonging to the NBS-LRR and LRR-RLK classes of plant R genes and to other defense-related proteins. Differentially expressed genes were sorted into functional categories according to their gene ontology annotation and this expression signature was compared to published apple cDNA libraries by Gene Enrichment Analysis. The first comparison was made with two cDNA libraries from Malus x domestica uninfected leaves, and revealed in both libraries a signature of enhanced expression in ‘Président Roulin’ of genes involved in response to stress and photosynthesis. In the second comparison, the pathogen-responsive TDFs from the partially resistant cultivar were compared to the cDNA library from inoculated leaves of Rvi6 (HcrVf2)-transformed ‘Gala’ lines (complete disease resistance) and revealed both common physiological events, and notably differences in the regulation of defense response, the regulation of hydrolase activity, and response to DNA damage. TDFs were in silico mapped on the ‘Golden Delicious’ apple reference genome and significant co-localizations with major scab R genes, but not with quantitative trait loci (QTLs) for scab resistance nor resistance gene analogues (RGAs) were found.

Conclusions

This study highlights possible candidate genes that may play a role in the partial scab resistance mechanisms of ‘Président Roulin’ and increase our understanding of the molecular mechanisms involved in the partial resistance against apple scab.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-1043) contains supplementary material, which is available to authorized users.

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.

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.

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.

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.

Analysis of ripening-related gene expression in papaya using an Arabidopsis-based microarray

BACKGROUND

Papaya (Carica papaya L.) is a commercially important crop that produces climacteric fruits with a soft and sweet pulp that contain a wide range of health promoting phytochemicals. Despite its importance, little is known about transcriptional modifications during papaya fruit ripening and their control. In this study we report the analysis of ripe papaya transcriptome by using a cross-species (XSpecies) microarray technique based on the phylogenetic proximity between papaya and Arabidopsis thaliana.

RESULTS

Papaya transcriptome analyses resulted in the identification of 414 ripening-related genes with some having their expression validated by qPCR. The transcription profile was compared with that from ripening tomato and grape. There were many similarities between papaya and tomato especially with respect to the expression of genes encoding proteins involved in primary metabolism, regulation of transcription, biotic and abiotic stress and cell wall metabolism. XSpecies microarray data indicated that transcription factors (TFs) of the MADS-box, NAC and AP2/ERF gene families were involved in the control of papaya ripening and revealed that cell wall-related gene expression in papaya had similarities to the expression profiles seen in Arabidopsis during hypocotyl development.

CONCLUSION

The cross-species array experiment identified a ripening-related set of genes in papaya allowing the comparison of transcription control between papaya and other fruit bearing taxa during the ripening process.

dHPLC efficiency for semi-automated cDNA-AFLP analyses and fragment collection in the apple scab-resistance gene model

cDNA-AFLP analysis for transcript profiling has been successfully applied to study many plant biological systems, particularly plant-microbe interactions. However, the separation of cDNA-AFLP fragments by gel electrophoresis is reported to be labor-intensive with only limited potential for automation, and the collection of differential bands for gene identification is even more cumbersome. In this work, we present the use of dHPLC (denaturing high performance liquid chromatography) and automated DNA fragment collection using the WAVE(®) System to analyze and recover cDNA-AFLP fragments. The method is successfully applied to the Malus-Venturia inaequalis interaction, making it possible to collect 66 different transcript-derived fragments for apple genes putatively involved in the defense response activated by the HcrVf2 resistance gene. The results, validated by real time quantitative RT-PCR, were consistent with the plant-pathogen interaction under investigation and this further supports the suitability of dHPLC for cDNA-AFLP transcript profiling. Features and advantages of this new approach are discussed, evincing that it is an almost fully automatable and cost-effective solution for processing large numbers of samples and collecting differential genes involved in other biological processes and non-model plants.

Signaling pathways mediating the induction of apple fruitlet abscission

Apple (Malus × domestica) represents an interesting model tree crop for studying fruit abscission. The physiological fruitlet drop occurring in this species can be easily magnified by using thinning chemicals, such as benzyladenine (BA), to obtain fruits with improved quality and marketability. Despite the economic importance of this process, the molecular determinants of apple fruitlet abscission are still unknown. In this research, BA was used to obtain fruitlet populations with different abscission potentials to be analyzed by means of a newly released 30K oligonucleotide microarray. RNAs were extracted from cortex and seed of apple fruitlets sampled over a 4-d time course, during which BA triggers fruit drop, and used for microarray hybridization. Transcriptomic profiles of persisting and abscising fruitlets were tested for statistical association with abscission potential, allowing us to identify molecular signatures strictly related to fruit destiny. A hypothetical model for apple fruitlet abscission was obtained by putting together available transcriptomic and metabolomic data. According to this model, BA treatment would establish a nutritional stress within the tree that is primarily perceived by the fruitlet cortex whose growth is blocked by resembling the ovary growth inhibition found in other species. In weaker fruits, this stress is soon visible also at the seed level, likely transduced via reactive oxygen species/sugar and hormones signaling cross talk, and followed by a block of embryogenesis and the consequent activation of the abscission zone.

Mature fruit abscission is associated with up-regulation of polyamine metabolism in the olive abscission zone

This study investigates whether, and how, polyamines (PAs) are involved in mature fruit abscission of olive (Olea europaea L.). Physiological abscission was studied in relation to the activation of the abscission zone (AZ), located between fruit and peduncle, from two olive cultivars where the breakstrength profiles and the scanning electron micrographs illustrated differences in the abscission program, under natural conditions, of mature fruit. The localization and activities of diamine oxidase (DAO), polyamine oxidase (PAO) and PA biosynthetic enzymes, together with PA content were investigated in the fruit AZ during development and abscission. The activities of arginine decarboxylase and S-adenosyl-l-methionine decarboxylase in the fruit AZ were significantly increased and decreased, respectively, by mature fruit abscission, in good agreement with the rise in free putrescine (Put), and content in uncommon PAs there, such as homospermidine and cadaverine, while no significant differences in free spermidine (Spd) and spermine (Spm) contents were detected. By contrast, an abscission-induced decrease was noted in the contents of insoluble conjugated Put, Spd and Spm. The maximum activity of PAO coincided with the maximum content of Spd and Spm, and it was localized mainly in parenchyma cells of pith, while DAO was present mainly in parenchyma cells of pith and cortex as well as at the base of the vascular tissue. These results suggest a clear correlation between the PA distribution and mature fruit abscission. The regulation of PA metabolism is discussed in relation to mature fruit abscission.

AFLP-based transcript profiling for cassava genome-wide expression analysis in the onset of storage root formation

Cassava (Manihot esculenta Crantz) is a root crop that accumulates large quantities of starch, and it is an important source of carbohydrate. Study on gene expressions during storage root development provides important information on storage root formation and starch accumulation as well as unlock new traits for improving of starch yield. cDNA-Amplified Fragment Length Polymorphism (AFLP) was used to compare gene expression profiles in fibrous and storage roots of cassava cultivar Kasetsart 50. Total of 155 differentially expressed transcript-derived fragments with undetectable or low expression in leaves were characterized and classified into 11 groups regarding to their functions. The four major groups were no similarity (20%), hypothetical or unknown proteins (17%), cellular metabolism and biosynthesis (17%) and cellular communication and signaling (14%). Interestingly, sulfite reductase (MeKD82), calcium-dependent protein kinase (CDPK) (MeKD83), ent-kaurene synthase (KS) (MeKD106) and hexose transporter (HT) (MeKD154) showed root-specific expression patterns. This finding is consistent with previously reported genes involved in the initiation of potato tuber. Semi-quantitative reverse transcription polymerase chain reaction of early-developed root samples confirmed that those four genes exhibited significant expression with similar pattern in the storage root initiation and early developmental stages. We proposed that KS and HT may involve in transient induction of CDPK expression, which may play an important role in the signaling pathway of storage root initiation. Sulfite reductase, on the other hand, may involve in storage root development by facilitating sulfur-containing protein biosynthesis or detoxifying the cyanogenic glucoside content through aspartate biosynthesis.