Unknown,Transcriptomics,Genomics,Proteomics

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A Transcript and Metabolite Atlas of Blackcurrant Fruit Development Highlights Hormonal Regulation and Reveals the Role of Key Transcription Factors

ABSTRACT: Blackcurrant fruit collected at six stages of development were assessed for changes in gene expression using custom whole transcriptome microarrays and for variation in metabolite content using a combination of liquid chromatography-mass spectrometry and gas chromatography-mass spectrometry. Principal components analysis demonstrated that fruit development could be clearly defined according to their transcript or metabolite profiles. During early developmental stages, metabolite profiles were dominated by amino acids and tannins, whilst transcript profiles were enriched in functions associated with cell division, anatomical structure morphogenesis and cell wall metabolism. During mid fruit development, fatty acids accumulated and transcript profiles were consistent with seed and embryo development. At the later stages, sugars and anthocyanins accumulated consistent with transcript profiles that were associated with secondary metabolism. Transcript data also indicated active signalling during later stages of fruit development. A targeted analysis of signalling networks revealed a dynamic activation and repression of almost 60 different transcripts encoding transcription factors across the course of fruit development, many of which have been demonstrated as pivotal to controlling such processes in other species. Transcripts associated with cytokinin and gibberellin were highly abundant at early fruit development, whilst those associated with ABA and ethylene tended to be more abundant at later stages. The data presented here provides an insight into fruit development in blackcurrant and provides a foundation for further work in the elucidation of the genetic basis of fruit quality.

INSTRUMENT(S): Agilent G2505B scanner

ORGANISM(S): Ribes nigrum

SUBMITTER: Pete Hedley

PROVIDER: E-MTAB-6973 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Background Field observations and a few physiological studies pointed out that peach embryogenesis and fruit development are strictly related. In fact, attempts to stimulate parthenocarpic fruit development by means of external tools failed. Moreover, physiological disturbances during the early embryo development lead to seed abortion and fruitlet abscission. Later on, the interactions between seed and fruit development become less stringent. Genetic and molecular information about seed and fruit development in peach is limited. Results The isolation of 455 genes differentially expressed in seed and fruit was done by means of a comparative analysis of the transcription profiles carried out in peach (Prunus persica, cv Fantasia) seed and mesocarp throughout development by means of µPEACH 1.0, the first peach microarray. Genes differentially expressed in the two organs and specific of developmental stages had been identified, and some were validated as markers. Genes representative of the main functional categories are present, among which several transcription factors such as MADS-box, bZIP, Aux/IAA, AP2, WRKY, and HD. Some of these showed a similar transcription profile in the two organs, while others displayed an opposite pattern, being more expressed in embryo at early development and in mesocarp at ripening. Conclusions The µPEACH1.0, although developed from ripe fruit ESTs, resulted in being suitable for studying seed/mesocarp interactions. Among the differentially expressed genes, marker genes specific for organ and stage of development have been selected. Comparisons were carried out by pooling stage 1 and 2 (named early development, e) and stage 3 and 4 (named late development, l), separately for mesocarp (M) and seed (S) of cultivar Fantasia, and using a simple loop experimental design. RNA has been extracted from fruit harvest at above-mentioned stages of development. At least four hybridizations have been conducted for a total of four technical replicates (with dye-swap).

Project description:The conservation of plant genetic resources (PGRs) is contingent on their current or potential use, so extending the knowledge about them is crucial for their valorization. The valorization and conservation of wild fruit PGRs are critical to ensure the maintenance of genetic and cultural heritage and to promote and develop of new perspectives on resource use. New strategies for characterizing PGRs are needed, and the omics approach can provide profound information that is still largely unknown. The strawberry tree (Arbutus unedo L.) is an underutilized, drought and fire-resistant species distributed in the Mediterranean area and its berries have large ethnobotanical use but were not usually consumed as fresh fruits. Although their phenolic profile and antioxidant capacity are known, they are not well characterised, particularly from a proteomic perspective. The aim of this work is the characterisation from a molecular viewpoint of two ecotypes of A. unedo (Campania and Sicily) to valorise a less known wild fruit PGR to encourage its preservation. Samples were collected from two different geographical areas to assess whether different geographical conditions could influence the characteristics of leaves and fruits at the three stages of ripening (green, veraison, red). Proteomic analysis identified 904 proteins, of which 122 showed significance along the ripening process. Some of these differentially abundant proteins, such as chalcone synthase, show a marked increase during ripening. From a proteomic perspective, there are no differences between the fruits from the two regions compared by the ripening stage. However, the pedoclimatic metabolic imprinting allowed the observation of good diversity in the metabolomic profiles between the two ecotypes, especially for anthocyanins and catechins, generally more abundant in Sicilian fruit, or the phenolic compounds more abundant in Campania fruit. Multi-omic characterisation enhanced the knowledge on a wild fruit plant species which shows specific adaptations and responses to the environment to be considered when addressing the issue of local agrobiodiversity.

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A Transcript and Metabolite Atlas of Blackcurrant Fruit Development Highlights Hormonal Regulation and Reveals the Role of Key Transcription Factors

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