Jiao Si-Qian, Dong Ai-Xiang, Shi Tian-Le, Liu Hui, Porth Ilga, Xin Hai-Bo, Mao Jian-Feng
Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.
Beijing Key Laboratory of Greening Plants Breeding, Beijing Institute of Landscape Architecture, Beijing, China.
Front Genet. 2020 May 21;11:504. doi: 10.3389/fgene.2020.00504. eCollection 2020.
, scarlet or tropical sage, is a tender perennial herbaceous flowering plant popularly grown in public and private gardens all over the world. In this study, we developed a set of simple sequence repeats (SSRs) from genome-wide sequences to assess the genetic diversity and population structure among 112 cultivars. We obtained 364,379 SSRs by mining scarlet sage's recently published whole genome sequence; 14,545 gene-associated SSR loci were identified in 2 kb gene flanking regions. Among the 768 gene-associated SSR primer sets we screened, 576 loci successfully amplified in DNA pools of 3-4 different cultivars, of which 271 remained polymorphic when tested across eight individual plants. We searched for the related gene functions attributable to these gene-associated SSRs using diverse databases, resulting in 259 Non-redundant matching sequences, 205 individual Gene Ontology (GO) terms, 236 assigned to eukaryotic orthologous groups, and 67 KEGG-annotated (Kyoto Encyclopedia of Genes and Genomes) sequences. We finally selected 41 polymorphic SSR loci to infer genetic diversity and population structure among 112 accessions. Based on the developed gene-associated SSRs, clustering analyses consistently revealed two distinct genetic groups within the core collection of cultivars. This work developed and characterized an exhaustive set of genome-wide gene-associated SSR markers for scarlet sage. These SSRs can provide species identification, genetic diversity and population structure information for , and will therefore be important tools for the management and protection of germplasm.
朱唇，又称热带鼠尾草，是一种多年生草本开花植物，在世界各地的公共和私人花园中广泛种植。在本研究中，我们从全基因组序列中开发了一组简单序列重复（SSR），以评估112个品种之间的遗传多样性和种群结构。通过挖掘朱唇最近发表的全基因组序列，我们获得了364,379个SSR；在2 kb基因侧翼区域鉴定出14,545个基因相关的SSR位点。在我们筛选的768个基因相关SSR引物组中，576个位点在3 - 4个不同品种的DNA池中成功扩增，其中271个位点在对8株单株进行测试时仍具有多态性。我们使用各种数据库搜索这些基因相关SSR的相关基因功能，得到259个非冗余匹配序列、205个单独的基因本体（GO）术语、236个分配给真核直系同源组的序列和67个KEGG注释（京都基因与基因组百科全书）序列。我们最终选择了41个多态性SSR位点来推断112份种质之间的遗传多样性和种群结构。基于开发的基因相关SSR，聚类分析始终揭示了品种核心收集内的两个不同遗传组。这项工作为朱唇开发并表征了一套详尽的全基因组基因相关SSR标记。这些SSR可以为朱唇提供物种鉴定、遗传多样性和种群结构信息，因此将成为管理和保护朱唇种质的重要工具。
