To investigate the global gene expression change caused by csi-miR156a overexpression which enhanced soamtic embryogenesis in citrus, we cpmpared gene expression profiles of trangenic and wild type callus prior to and at the stage of soamtic embryos presence (40 and 60 days after somatic embryos induction, referref to 40 and 60 DAI, respectively). A total of 3020 and 1452 differentially expressed genes were found between trangenic and wild type at 40 and 60 DAI, respectively. Our result indicated that csi-miR156a overexpression could cause large-scale gene expression alteration. Overall design: Two lines of citrus callus overexpressing csi-miR156a were compared with two that from wild type at 40 and 60 DAI, respectively.