In relation to their antioxidant potential, phenolic compounds are usually associated with a protective effect on the human health of a diet rich in fruits and vegetables. They are also widely associated to the organoleptic quality of ciders since they affect bitterness, astringency, color and aroma. Two studies have recently been published on QTL detection for the phenolic content of dessert apple. No study has yet been published for cider apple, even though they are usually more concentrated in phenolic compounds The objective of this work was to identify genomic regions involved in the phenolic content for a cider apple progeny. In a first time, two quantification methods were developed and compared in UHPLC-UV and UHPLC-MS/MS for major phenolic compounds in juices. Even overestimation of some compounds with one detector were observed, these two methods were highly correlated. Phenolic compounds of whole fruits were also quantified at the INRA station of Rennes. A high variability was observed in both fruits and juices of this progeny, representative of major cider apple varieties grown in Europe. 48 QTL were detected on nine linkage groups (LG). Nine clusters seem particularly stable according to the year or material study. Enzymes of the polyphenol pathway and transcription factors were targeted as candidate gene and identified in silico under major QTL. This work offers new targets for the marker-assisted selection like the QTL for chlorogenic acid on LG17 to improve cider apple varieties.
