Understanding of auxin regulation during somatic embryogenesis in cotton by RNA-seq and sRNA-seq

Somatic embryogenesis (SE), by which somatic cells of higher plants can dedifferentiate and reorganize into new plants, is a notable illustration of cell totipotency. However, the precise molecular mechanisms regulating SE remain unclear. To characterize the molecular events of this unique process, transcriptome analysis, small RNA, and degradome sequencing were conducted in cotton, a typical plant species in SE. The results indicated that transcripts associated with auxin biosynthesis, conjugation, transport, and signal transduction were regulated during the whole developmental process. The complex auxin pathways with differentially regulated genes revealed that the auxin-related transcripts belonged to indoleacetic acid-induced protein (Aux/IAA), auxin response factor (ARF), small auxin-up RNA (SAUR), and other auxin-related proteins, which allow an intricate system of auxin utilization to achieve multiple purposes in SE. Additionally, we identified some small RNAs with their targets related to the auxin signaling pathway during cotton SE, and demonstrated that some sRNA regulate cotton SE by participating in auxin signaling pathways.