Genome-wide identification of the LdBBM subfamily in Lilium davidii var. unicolor and functional analysis of LdBBM13 during the regeneration process

Baby boom (BBM) subfamily genes belong to the AP2/ERF superfamily, and play an essential role in plant cell totipotency. However, research on BBM genes in bulbous plants during regeneration of de novo shoot organogenesis and somatic embryogenesis (SE) remains limited. Here, 15 LdBBM subfamily genes are distributed across eight chromosomes in Lanzhou lily (Lilium davidii var. unicolor) genome. Gene structure analysis showed that five LdBBMs belong to ultra-long genes that contain ultra-long introns. The analysis of conserved motifs, phylogenetic and protein three-dimensional structure, and protein interaction network prediction showed that LdBBM genes were classified into three groups. Transcription start sites (TSSs) analysis revealed that the largest number of bases being "A". Cis-acting elements analysis showed that LdBBMs promoters might influence hormone signaling, tissue regeneration and development, and abiotic stress. Moreover, six LdBBMs were significantly differentially expressed in the regeneration of bulblet and SE, LdBBM13 was upregulated in early bulblet regeneration and early SE of lily. Furthermore, the functional experiment of LdBBM13 suggested that LdBBM13 located in the nucleus, significantly promoted the regeneration process of scale-induced somatic embryos and callus induction. Meanwhile, in pTRV2-LdBBM13 silencing scales, other embryonic- and auxin-related genes were significantly upregulated, and auxin content was also significantly increased, which demonstrated the importance of LdBBM13 in regulating scale-induced SE regeneration. In brief, this study provided new insights into the functions of LdBBM genes during the regeneration of lily bulblet, and laid the foundation for the development of marker genes for organogenesis-related transgenic lily bulbs using LdBBM13 in the future.