Fruit juice browning and fruit acidity, which are important characteristics for the determination of marketability and processability of apple fruit, are becoming major targets for apple breeding. To identify the genetic basis of these two traits, quantitative trait locus (QTL) analysis was carried out using a 79 progenies of ‘Fuji’ × ‘Maypole’ F1 population. The maternal parent ‘Fuji’ was characterized by low acidity and high browning, whereas the paternal parent ‘Maypole’ showed opposite phenotypes—high acidity and low browning—resulting in an F1 population with a wide range of phenotypes. QTL analysis identified the major QTLs for both traits on the upper part of linkage group (LG) 16 of ‘Fuji’. The effects of these QTLs explained 57.5% and 49.7 % of observed variation in fruit juice browning and fruit acidity, respectively. These two QTLs co-segregated with each other, with the allele for high acidity associated with the allele for low browning and vice versa in this population. To physically map the QTL region, recombinant progeny were genotyped with newly designed DNA markers; both QTLs were delimited to a 514-kb region including 105 annotated genes on apple chromosome 16. Several candidate genes were predicted in this region and their associations with fruit juice browning and fruit acidity were considered.
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