Combined transcriptomic and targeted metabolomic analysis reveals the mechanism of flesh browning in cold stored ‘Fuji’ apple fruit

•Flesh browning (FB) tissue had the lowest flavonoids and sugars content.•Browned fruit had lower organic acids levels and higher lactic acid/malic acid.•Low temperature induced the synthesis of jasmonic acid and its signal transduction.•Most of the ERF and WRKY family transcription factors were up-regulated in FB tissue.