Nutritionists have recommended an increased consumption of fruits and vegetables, as sources of dietary compounds such as fibre, micronutrients and antioxidant compounds that are beneficial to human health . Apple (Malus x domestica Borkh.) is considered to be part of such a healthy diet, being very low in total calories and a good source of dietary fibre (2 g/100 g fresh fruit) [2, 3]. While apples are lower in vitamin C than other fruits (5-25 mg/100 g depending on the cultivar ), they have very high concentrations of other antioxidant phytochemicals, especially polyphenolic compounds such as quercetin, epicatechin, and procyanidin polymers [2, 5, 6].
Numerous epidemiological studies have suggested that polyphenolic compounds are involved in the prevention of degenerative diseases such as epithelial (but not hormone-related) cancers and cardiovascular diseases, type-2 diabetes, thrombotic stroke, obesity, neurodegenerative diseases associated with aging and infections . Although polyphenolic compounds have long been studied for their antioxidant properties, which are now well characterized in vitro, recent studies have stressed that the mechanisms of biological actions of polyphenols extend beyond their antioxidant properties . It is now believed that polyphenols may exert their beneficial action through the modulation of gene expression and the activity of a wide range of enzymes and cell receptors [9, 10]. However, the health effects of dietary polyphenols depend on the amounts consumed and on their bioavailability. Previous studies suggest that the bioavailability of polyphenols is related to their chemical structure . For instance, the nature of the sugar conjugate and the phenolic aglycone are both important for anthocyanin absorption and excretion.
Several thousand compounds having a polyphenolic structure have been identified in higher plants [12, 13]. These compounds are secondary metabolites involved in defence against aggression by pathogens or ultraviolet radiation. The most important groups of polyphenols in plants are the flavonoids, phenolic acids, lignans and stilbenes. The flavonoid group can be subdivided into seven subgroups: flavonols, flavones, isoflavones, flavanols, flavanones, anthocyanins and dihydrochalcones of which flavonols, flavanols, anthocyanins and dihydrochalcones are found in apple . The flavonols' main representatives, quercetin and kaempferol, are present in glycosylated forms and the associated sugar moiety is often glucose or rhamnose. Flavanols are not glycosylated, and exist in both the monomer form (catechins) and the polymer form (procyanidins or condensed tannins). Catechin and epicatechin are the main flavanols in fruits and are the building blocks for dimeric, oligomeric and polymeric procyanidins. Anthocyanins are pigments dissolved in the vacuolar sap of usually the epidermal tissues of fruits and exist in a range of chemical forms that are blue, red, purple, pink or colourless according to pH. They are highly unstable as aglycones and in plants are found in glycosylated forms that are stable under light, pH and oxidizing conditions. Cyanidin and pelargonidin are the most common anthocyanins in foods. Finally, dihydrochalcones are a family of the bicyclic flavonoids, defined by the presence of two benzenoid rings joined by a three-carbon bridge. Phloridzin, which belongs to the dihydrochalcone family, is present in apple fruits .
Two classes of phenolic acids can be distinguished: derivatives of benzoic acid, and derivatives of cinnamic acid. These acids are found in plants both free and esterified with sugars or other organic acids . Hydroxycinnamic acids are more common than hydroxybenzoic acids, with the main compounds of the hydroxycinnamic acid class being p-coumaric, caffeic, and chlorogenic acids. Hydroxybenzoic and hydroxycinnamic acids are also components of complex structures such as hydrolysable tannins (gallotannins and ellagitannins) and lignins, respectively.
Polyphenolic content and identity can vary according to location within the fruit (e.g. skin v. cortex), stage of fruit maturity, location of the fruit within the plant structure and time since harvest. Fruit polyphenolic concentration varies among apple cultivars , making this character a potential breeding target. However, current apple breeding programmes emphasize appearance (skin colour, pattern and amount of fruit covered with colour, size and shape of the fruit), eating quality (flavour and texture), and storage ability. Breeding for pest and disease resistances is the second major objective . We are not aware of a breeding programme for apple that includes phytochemical properties and antioxidant content, despite the importance of healthy nutraceutical compounds from apple and other fruit. Consequently genetic mapping studies have focused on fruit quality and disease resistance and only a few have dealt with apple phytochemical content. Quantitative trait loci (QTL) for vitamin C have been identified following analysis of a 'Telamon' × 'Braeburn' segregating population  and a major locus for anthocyanin content in apple flesh has been mapped to linkage group (LG) 9 . Expression of this locus has been characterised as being controlled by MYB10 [18, 19].
This study analyses the genetic control of fruit polyphenolic concentrations using a segregating F1 population obtained from a cross between apple cultivars 'Royal Gala' and 'Braeburn', together with information from the apple whole genome sequence (Velasco et al. 2010). Once quantitative trait loci (QTL) were defined, candidate genes coding for enzymes involved in the synthesis of polyphenolic compounds were identified using genome sequencing and confirmed by genetic mapping. On the basis of our results, we suggest that a mutation in LAR1 is the probable cause of the variation in the concentration of flavanols in the fruit cortex and skin and that a similar change in HQT/HCT possibly causes variation in chlorogenic acid.