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.

辽东楤木（Aralia elata）是五加科（Araliaceae）物种之一，在韩国、日本及中国部分地区是知名食用食材，且富含皂苷（saponins）。该物种广泛分布于包括中国、韩国、日本在内的东北亚区域。自然状态下，辽东楤木的表皮组织带有尖刺，这一特性制约了其开发利用。因此，数十年来科研人员一直致力于育种工作，以筛选兼具更高营养价值或风味、无刺或少刺的辽东楤木栽培品种。此前，关于辽东楤木栽培品种的种群结构分布规律，以及种群结构与实际表型的关联机制，仍不明晰。本研究对辽东楤木‘春荣’（cv. Yeongchun）品种开展从头基因组组装（de novo genome assembly），以构建具有代表性的韩国辽东楤木参考基因组。通过比对本次从头组装的‘春荣’基因组与已公开的中国栽培品种辽东楤木基因组，发现二者共享大量基因组区域，但同时也存在诸多差异。为解析包含32个栽培品种的韩日辽东楤木种群结构，本研究基于上述组装基因组与公开的辽东楤木基因组，筛选得到44个简单序列重复（Simple Sequence Repeat，SSR）标记。通过K值分析，本研究将供试种群划分为3个亚簇，但同时也发现了1个孤立的栽培品种与3个亚簇并存的情况。与此同时，本研究测定了与尖刺相关的表型性状，并基于这些表型对32个栽培品种开展了基于机器学习（machine learning）的聚类分析。结果显示，尖刺相关表型与种群结构并无显著关联，这表明尖刺相关性状的遗传调控具有多层次性。综上，本研究揭示，与尖刺相关的表型可通过近交选育获得，同时还可强化皂苷积累、幼叶尺寸等其他优良性状。