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<p>Abstract</p> <p>Background</p> <p>Apple fruitlet abscission is induced by dominance, a process in which hormones such as auxin, cytokinins and strigolactone play a pivotal role. The response to these hormones is controlled by transcription regulators such as Aux/IAA and ARR, whereas auxin transport is controlled by influx and efflux carriers.</p> <p>Results</p> <p>Seven partial clones encoding auxin efflux carriers (<it>MdPIN1_A</it>, <it>MdPIN1_B</it>, <it>MdPIN10_A</it>, <it>MdPIN10_B</it>, <it>MdPIN4</it>, <it>MdPIN7_A </it>and <it>MdPIN7_B</it>), three encoding auxin influx carriers (<it>MdLAX1</it>, <it>MdLAX2 </it>and <it>MdLAX3</it>) and three encoding type A ARR cytokinin response regulators (<it>MdARR3</it>, <it>MdARR4 </it>and <it>MdARR6</it>) were isolated by the use of degenerate primers. The organization of the PIN multigene family in apple is closer to <it>Medicago truncatula </it>than to <it>Arabidopsis thaliana</it>. The genes are differentially expressed in diverse plant organs and at different developmental stages. <it>MdPIN1 </it>and <it>MdPIN7 </it>are largely more expressed than <it>MdPIN10 </it>and <it>MdPIN4</it>. During abscission, the transcription of these genes increased in the cortex whereas in the seed a sharp fall was observed. The expression of these genes was found to be at least partially controlled by ethylene and auxin.</p> <p>Conclusion</p> <p>The ethylene burst preceding abscission of fruitlets may be responsible for the decrease in transcript level of <it>MDPIN1</it>, <it>MDARR5 </it>and <it>MDIAA3 </it>in seed. This situation modulates the status of the fruitlet and its fate by hampering the PAT from the seeds down through the abscission zone (AZ) and this brings about the shedding of the fruitlet.</p>