Dynamic changes of miR166s at both the transcriptional and post-transcriptional levels during somatic embryogenesis in Lilium

•We have studied the key target gene LMBR1 for miR166s in plants for the first time，it may regulate the formation of early embryonic cells.•Pre-miR166 family members of the same species are relatively diverse, but those among different lily species are closely related.•LpLMBR1, LpIDD1, LdLMBR1 and LdPHB are confirmed targets of lpu-miR166a, lpu-miR166b, lda-miR166a and lda-miR166b, respectively.•The expression profiles of miR166 precursors and targets are negatively regulated by miR166.•lpu-miR166a shows extremely high expression in globular embryos, while other miR166s are highly expressed in the late stages of SE.