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

Bamboo usually going through a prolonged vegetative growth period for several decades, not all bamboo species produce seeds, and the regulating mechanism of embryogenic callus formation remain unclear, which restricts the molecular breeding in bamboo. Here, we used buds of Bambusa changningensis Yi et B. X. Li as explants to induce callus formation. We found that bamboo embryogenic callus (EC) on mediums added coconut powder, 2,4-D and proline increased faster than that on other mediums. The contents of EC were increased with the increase of 2,4-D concentration on different mediums. The levels of auxin and GA in non-embryogenic callus (NE) were much higher than that in EC. Furthermore, RNA-seq showed that 795 DEGs were mainly enriched in pathways of starch synthase and amyloplast metabolism. The gene sets analysis illustrated that genes involving pathways of amylopectin synthesis/metabolism were upregulated in EC, several starch synthesis related genes were remarkedly enriched in EC. We then found that there were more clearly amyloplast, higher starch contents and three starch metabolism related genes (SS1, SBE1, STP-1) showed higher expression levels in EC than that in NE. Collectively, these results identified that the transition of NE to EC were associated with the synthesis and metabolism of amyloplast, and it providing new insights into the systems establishment of callus regeneration and genetic transformation in bamboo.