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‘Akane’ apple cultivar has a characteristic of naturally drastic early season drop in the lateral fruitlets, not in the central fruitlets, while ‘Fuji’ cultivar has no such characteristic. To get information about molecular mechanism on lateral fruitlet drop in ‘Akane’, we firstly carried out polymerase chain reaction (PCR) subtraction using ‘Akane’ and ‘Fuji’ fruitlets mRNAs. Through dot blot analysis using ‘Akane’ and ‘Fuji’ cDNA probe in the plasmid pool, we isolated several up-regulated cDNAs including cellulase, -1,3-glucanase, phosphate transporter (APT), chitinase, nuclease, protein serine/threonine kinase (ASK), and RING finger protein, and several down-regulated cDNAs including glycerol kinase (AGK), nitrilase, and hemolysin from ‘Akane’. Most of up-regulated cDNAs were stress-responsive genes. ASK and APT in ‘Akane’ lateral fruits were strongly expressed, while AGK was weakly expressed when the expression patterns were investigated on the clones showing the strongest signal in dot blots by reverse transcription-PCR. The 5'-flanking region of the APT genomic DNA was shown to contain a number of putative hormonal and stress responsive elements. The research on the physiological functions including early season lateral de-fruiting in apple is under progress.