Genetic characterization of flesh browning trait in apple using the non-browning cultivar ‘Aori 27’

Market demand for non-browning apple (Malus × domestica Borkh.) fruit is expected to increase. To facilitate development of non-browning cultivars, we investigated the origin, inheritance pattern, and causal genomic region of the non-browning trait through genetic and quantitative trait loci (QTL) analysis of two F1 populations (165A27 and KA27) derived from crosses between the non-browning cultivar ‘Aori 27’ and different browning lines. One third of the 165A27 population showed the non-browning trait. By QTL analysis using constructed genetic linkage maps, we detected major QTLs for multiple browning-related traits—flesh browning, juice browning, total polyphenols, and polyphenol oxidase activity—on almost the same region (i.e., upper part of LG 16) in the browning parents of both populations, but few on the ‘Aori 27’ maps. The QTL for flesh browning detected in the 165A27 population explained the majority of phenotypic variance, suggesting that the non-browning trait was mostly inherited through a single recessive locus or gene. Leucoanthocyanidin reductase 1 (LAR1), the key gene in polyphenol synthesis, which resides in the flesh browning QTL region, is the most probable candidate gene. To determine the origin of the non-browning alleles, we analyzed haplotypes around this major QTL in the two populations and their ancestors, and showed that ‘Aori 27’ and non-browning F1 individuals were functionally homozygous for non-browning alleles either derived from ‘Golden Delicious’, ‘Delicious’, or ‘Indo’. We consider the non-browning allele from ‘Indo’ to be a valuable resource, because unlike the alleles from the other cultivars, it is not linked with high acidity.