Blackcurrant (Ribes nigrum L.) is a perennial shrub grown for its black piquant berries, rich in a variety of nutrients, phytochemicals and antioxidants. Blackcurrants are commercially grown in 21 countries mainly across temperate zones of Europe, Russia, and New Zealand and to a lesser extent North America. The berries can be harvested by hand and consumed raw, however the main market lies within the mechanically harvested crop used for processing. Demand for juices, and fruit juices in particular, continues to rise mainly due to increasing consumer awareness of the health benefits of a balanced diet. The rich nutritional content of blackcurrant makes it a desired commodity for production of juice and other innovative products. Breeding of new blackcurrant cultivars is dominated by the processing industry and the emphasis in recent years has been to increase the nutritional value of the crop. New berry fruit cultivars in the UK have recently focused more on fruit quality traits than agronomic characters (Brennan and Graham, 2009), and the main quality traits of blackcurrant have been associated with antioxidant, colour and flavour properties. Quality-focused breeding is challenging due to long timescales and low precision as quality traits are complex, show continuous variation, polygenic control, genes of small effects and strong influence by the growing environment; additionally, blackcurrant is a minor crop with no reference genome and existing sequence annotation is based on homology to Arabidopsis. In this study high throughput phenotyping, and metabolome and transcriptome profiling analysis contributed to a comprehensive overview of blackcurrant physiology and regulation during fruit development. Combination of a novel correlation platform and database mining of metabolite and transcript abundances contributed to identification of genes associated with anthocyanin content in blackcurrant and provided functional gene annotation for Ribes sp. Sixty three genes were identified as having major roles in blackcurrant anthocyanin accumulation with putative functions of catalytic proteins, transporters and regulatory proteins; a number of cytochrome P450 family proteins were also implicated. Moreover, a range of proteins with unknown functions in Arabidopsis were shown to correlate strongly with flavonoid accumulation in blackcurrant. The developed approach for functional gene orthology annotation (genes with similar functions) can also be utilised for several other (~200) traits analysed in this study and can provide a functional systems biology platform for other woody perennial species with no reference genome. In parallel, mapping population analysis and a new high-density quality-specific genetic linkage map and quantitative trait loci association with major quality compounds such as anthocyanins, sugars, organic acids and other polyphenols were developed. This contributed to the identification of significant associations between 28 quality traits and 978 markers present on genetic linkage map and created a functional tool for future quality-orientated blackcurrant breeding. The genetic linkage map assisted further functional annotation of several new Ribes SNP based markers obtained through GbS technology through their association with quality traits for which polymorphism can be analysed using existing blackcurrant genomic resources. Integration of functional candidate genes identified in fruit ripening analysis and on genetic linkage map with several blackcurrant genomic resources formed a platform for assisting further developments in quality-orientated blackcurrant breeding at The James Hutton Institute. This platform provides a holistic view of the mechanisms that underlie fruit compositional quality and may provide a means for germplasm selection with no prior phenotypic information. Knowledge and tools developed in this study can be further developed with new developing genomic technologies.