Transcriptome analysis reveals the molecular patterns regulating prickle reduction in grafted Zanthoxylum armatum

Grafting has been found to effectively reduce the prickly nature of Zanthoxylum armatum seedlings, but the molecular mechanisms are unclear. A comparative transcriptome analysis was performed on stems (JJ) and leaves (JY) of grafted stems (SJ) and leaves (SY) of non-grafted Zanthoxylum armatum seedlings. The authors obtained 3097, 2124, 5995, and 5043 differentially expressed genes from JJ vs. SJ, JY vs. SY, JY vs. JJ, and SY vs. SJ with 17 co-expressed genes. The RNA-seq results were confirmed by qRT-PCR analysis. Function annotations showed that many DEGs enriched plant hormone signal transduction, phenylpropanoid biosynthesis, and plant-pathogen interaction. Secondary metabolites associated with stress-related hormones and defense were noticeably up-regulated in grafted plants. However, key enzymes regulating lignin synthesis were slightly down-regulated in grafted plants. Additionally, grafted plants had several noticeable up-regulated stress-response TFs (transcription factors), including NAC (NAM, ATAF1/2, CUC1/2), ERF (ethylene response factor), MYB (v-myb avian myeloblastosis viral oncogene homolog), bHLH (basic helix-loop-helix), and WRKY. This study generated abundant sequences for elucidating the genetic differences between grafted and non-grafted Z. armatum.