Comprehensive analysis of RNA-seq data reveals novel insight in the formation of bamboo embryogenic callus in Bambusa changningensis

Bamboo usually undergoes a prolonged vegetative growth period for several decades. Additionally, not all bamboo species produce seeds, and the regulatory mechanisms governing embryogenic callus formation remain unclear, which constrains molecular breeding progress in bamboo. Here, we used buds of Bambusa changningensis Yi et B. X. Li as explants for callus induction. The results revealed that bamboo embryogenic callus (EC) on media added coconut powder, 2,4-D and proline increased faster than that on other media. The content of EC increased with the increase of 2,4-D concentration on different media. The concentrations of auxin and gibberellin (GA) in non-embryogenic callus (NE) were significantly higher than those in EC. Furthermore, RNA-seq analysis revealed that 795 DEGs were mainly enriched in pathways of starch synthase and amyloplast metabolism. Gene set analysis revealed that genes associated with amylopectin synthesis and metabolism pathways were upregulated in EC, and several starch synthesis-related genes were significantly enriched in EC. We then observed that EC exhibited more clearly amyloplast, higher starch content, and three starch metabolism related genes (SS1, SBE1, STP-1) showed higher expression levels compared to NE. Collectively, these results identified that the transition from NE to EC was associated with amyloplast synthesis and metabolism, and it providing new insights into the establishment of callus regeneration and genetic transformation systems in bamboo.