Genome-wide identification of transcripts and miRNAs during somatic embryogenesis in Pinellia ternata

As a bulk traditional Chinese medicinal material native to China, Pinellia ternata has long relied on asexual propagation via tubers, which gives rise to prominent problems such as low propagation efficiency and germplasm degeneration. Somatic embryogenesis(SEG) constitutes the primary pathway for plant regeneration. Nevertheless, the molecular mechanisms underlying SEG in P.ternata remain poorly elucidated. We performed genome-wide mRNA and small RNA sequencing analyses on samples collected from three key stages of SEG, namely explants, calli and protocorm-like bodies. The results indicated that the elevated levels of auxins indole-3-carboxylic acid (I3CA) and indole-3-carboxaldehyde (ICA1d) promoted the regeneration of P. ternata . Transcriptome revealed that SEG of P. ternata adopted stage-specific regulatory patterns and auxin synthesis and signaling pathway genes played a significant role in the process of P. ternata SEG. small RNA sequencing identified a total of 663 miRNAs and we discovered that miR396 were the key miRNAs involved in regulating P. ternat a SEG by targeting GRF genes. This study is the first to elucidate transcriptome and dynamic miRNA expression profiles during SEG in P. ternata . I3CA and ICA1d were identified as the key auxin metabolites governing SEG progression. The miR396-GRFs module may function as a core regulatory factor controlling P. ternata SEG. Collectively, these findings provide a solid theoretical basis for overcoming the technical bottleneck of low propagation efficiency in P. ternata .