Deciphering the stem variations in ginseng plant using RNA-Seq

Abstract

Ginseng is an important herb widely grown in East Asia that has medicinal and nutritional uses. Multi-stem ginseng plants undergo rapid growth, are of good quality, and have a high main-root yield. The multi-stem trait is important in ginseng breeding. To understand the molecular mechanisms responsible for the multi-stem formation, the physiological changes before and after overwintering bud formation, we analysed the transcriptomes of multi- and single-stem ginseng plants. RNA sequencing of overwintering buds from multi- and single-stem ginseng plants was performed using high-throughput second-generation sequencing. We obtained 47.66 million high quality reads at a sequencing efficiency of greater than 99% from the multi- and single-stem transcriptome. An analysis of significantly enriched gene ontology functions and comparisons with Kyoto Encyclopedia of Genes and Genomes pathways revealed expression level changes in genes associated with plant hormones, photosynthesis, steroids biosynthesis, and sugar metabolism. Plant hormones are involved in multi-stem formation in ginseng. Auxin, cytokinin, brassinolide, and strigolactone have positive effects on multi-stem formation, but further research is needed to elucidate their mechanisms. Our results have important implications in ginseng cultivation and breeding.