Aralia elata cultivar:Yeongchun Genome sequencing
Aralia elata is one of the Araliaceae species which is a famous food ingredient and rich of saponins in Korea, Japan and some regions of China. A. elata is widely distributed in Northeast Asian region including China, Korea and Japan. In nature, A. elata has thorns on its epidermal tissues which hinders utility. Thus, breeding effort have been made to select A. elata cultivar with better nutrient value or tastes and thornless or less thorned cultivars for decades. However, it was uncertain that how population structure of A. elata cultivars were distributed and how the structure of population correlates with actual phenotype. Here, we performed de novo genome assembly of A. elata cv. Yeongchun to generate Korean representative A. elata genome. We identified de novo assembled genome of Yeongchun shared many of the genomic compartments with public A. elata genome assembled with Chinese cultivar yet to have many differences. To identify population structure of Korean and Japanese cultivars comprised of 32 cultivars, we identified 44 SSR markers by comparing de novo assembled genome and public A. elata genome. We identified three sub-clusters by K analysis. However, we identified one isolated cultivar and three sub-clusters. Meanwhile, we measured thorn-related phenotypes and performed machine learning based clustering of 32 cultivars based on the phenotypes. As a result, we identified thorn-related phenotypes were not strongly correlated with population structure which suggests multi-layered genetic regulation on thorn-related phenotypes. Thus, we revealed thorn-related phenotypes are able to inbred in addition to enhance other traits such as enhanced accumulation of saponins or young leaf sizes.