Institute of Fruit Tree and Tea Science, NARO

Identification of chromosomal regions regulating apple flesh browning

- Accelerate the breeding of non-browning apple cultivars -

The National Agricultural Food Research Organization (NARO) and the Aomori Prefectural Industrial Technology Research Center (AITC) have identified three chromosomal regions regulating apple flesh browning through large-scale genetic analysis and developed a DNA-marker to select non-browning factor on these regions. It is expected that this research result will significantly accelerate the breeding of non-browning apple cultivars.


Most apple cultivars including "Fuji" turn brown in a short time after cutting, resulting in impaired appearance and commodity value. Therefore, before apples are distributed in the market as cut fruits, special treatment or packaging is necessary to inhibit the oxidation of polyphenols in the flesh, which causes browning. To reduce these difficulties and costs for processing, it is required to develop apple cultivars resistant to browning after cutting.
Although two non-browning apple cultivars "Aori 27" and "EdenTM" have been registered in the world to date, the genetic information (of those cultivars) related to fruit flesh browning is unknown. NARO and AITC have identified chromosomal regions regulating apple flesh browning through large-scale genetic analysis.
Fruits harvested from hundreds of apple trees bred by the cross of 28 cultivars, e.g. 'Aori 27' and 'Shinano Gold', as breeding parents were used for analysis. By 'grating' test materials to get severer and uniform oxidative condition, the browning intensity was evaluated. Genetic analysis was performed on 10,000 sites spanning all chromosomal regions of apple, and three chromosomal regions regulating flesh browning were identified. We also developed DNA markers to select non-browning factors on these three regions. In validation using the existing cultivars and breeding populations, the flesh browning intensity predicted from the genotypes of the three chromosomal regions matched to the observed browning intensity well.
The use of the developed DNA markers enables the selection of individuals resistant to browning at the stage of young seedlings, so the breeding efficiency will be greatly improved. This research result is expected to accelerate the breeding of the new non-browning apple cultivars, leading to the development of new demand for apples.

Relevant information

Budget: Strategic Innovation Promotion Program 2 (SIP2), Smart Bioindustry and Agricultural Infrastructure Technology, Agriculture, Forestry and Fisheries Research Promotion Project consignment study (Horticultural needs), Operational cost grant

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Published paper

Kunihisa M, Hayashi T, Hatsuyama Y, Fukasawa-Akada T, Uenishi H, Matsumoto T, Kon T, Kasai S, Kudo T, Oshino H, Yamamoto T & Tazawa J. (2021) Genome-wide association study for apple flesh browning: detection, validation, and physiological roles of QTLs. Tree Genetics & Genomes 17: 11.