Abscission is an important developmental process used to shed organs such as leaves, flowers and fruits. Despite the detailed characterization of growth dynamics and hormonal balance during the early steps of fruit development, the molecular aspects remain unclear. Abscission of young fruit occurs by separation of cells in anatomically distinct regions between the pedicel and junction. Differences of gene expression between central pedicel and lateral pedicel were investigated by NGS. Partial cDNAs from 15 clones from both the central pedicel and lateral pedicel were selected for nucleotide sequence determination and homology searches, and 12 clones were subsequently selected for further analysis. In preliminary series of Real Time PCR analysis, 9 genes were confirmed as showing a higher expression level in lateral pedicel than in central pedicel. Many of these genes are expressed in a central or lateral pedicel in specific manner, and the expression profiles of the representative genes were confirmed. To clarify the mechanism of MdIAA14 transcription factor gene underlying abscission zone development, we are investigating the expression patterns between central and lateral pedicels in different apple cultivar using real-time PCR and constructing the vector for transformation into apple.