Gil Jinsu, Um Yurry, Kim Serim, Kim Ok Tae, Koo Sung Cheol, Reddy Chinreddy Subramanyam, Kim Seong-Cheol, Hong Chang Pyo, Park Sin-Gi, Kim Ho Bang, Lee Dong Hoon, Jeong Byung-Hoon, Chung Jong-Wook, Lee Yi
Department of Industrial Plant Science & Technology, Chungbuk National University, Chungju 28644, Korea.
Forest Medicinal Resources Research Center, National Institute of Forest Science, Yeongju 36040, Korea.
Genes (Basel). 2017 Sep 21;8(10):238. doi: 10.3390/genes8100238.
Nakai is an important medicinal herb, widely utilized in Asian countries especially in Korea, Japan, and China. Although it is a vital medicinal herb, the lack of sequencing data and efficient molecular markers has limited the application of a genetic approach for horticultural improvements. Simple sequence repeats (SSRs) are universally accepted molecular markers for population structure study. In this study, we found over 130,000 SSRs, ranging from di- to deca-nucleotide motifs, using the genome sequence of Manchu variety (MV) of derived from next generation sequencing (NGS). From the putative SSR regions identified, a total of 16,496 primer sets were successfully designed. Among them, we selected 848 SSR markers that showed polymorphism from in silico analysis and contained tri- to hexa-nucleotide motifs. We tested 36 SSR primer sets for polymorphism in 16 accessions. The average polymorphism information content (PIC) was 0.69; the average observed heterozygosity () values, and the expected heterozygosity () values were 0.53 and 0.73, respectively. These newly developed SSR markers would be useful tools for molecular genetics, genotype identification, genetic mapping, molecular breeding, and studying species relationships of the genus.
中井是一种重要的药用植物，在亚洲国家尤其是韩国、日本和中国被广泛使用。尽管它是一种重要的药用植物，但测序数据的缺乏和有效的分子标记限制了遗传方法在园艺改良中的应用。简单序列重复（SSRs）是用于群体结构研究的普遍接受的分子标记。在本研究中，我们利用下一代测序（NGS）获得的满族品种（MV）的基因组序列，发现了超过130,000个SSRs，其基序范围从二核苷酸到十核苷酸。从鉴定出的假定SSR区域中，成功设计了总共16,496对引物。其中，我们从电子分析中选择了848个显示多态性且包含三到六核苷酸基序的SSR标记。我们测试了36对SSR引物在16个种质中的多态性。平均多态性信息含量（PIC）为0.69；平均观察杂合度（）值和预期杂合度（）值分别为0.53和0.73。这些新开发的SSR标记将成为分子遗传学、基因型鉴定、遗传图谱构建、分子育种以及研究该属物种关系的有用工具。
