Development of genomic SSR markers and genetic diversity analysis in cultivated radish (Raphanus sativus L.)
Development of genomic SSR markers and genetic diversity analysis in cultivated radish (Raphanus sativus L.)
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DOI：
10.1007/s13580-015-0089-y
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发表时间：
2015-04-01
影响因子：
2.4
通讯作者：
Kwon, Yong-Sham
中科院分区：
文献类型：
--
作者：
Bae, Kyung-Mi;Sim, Sung-Chur;Kwon, Yong-Sham
萝卜（Raphanus sativus L.）是一种世界性的主要蔬菜。作为芸苔科的一员，本种根系形态特征多样。萝卜品种是根据根系形状和颜色等形态特征进行分类的。尽管萝卜在亚洲具有重要的经济意义，但相对于萝卜的近亲油菜，对萝卜的基因组研究还不够发达。本研究利用一个SSR富集文库开发了基因组简单序列重复（SSR）标记，并对144个萝卜品种的遗传多样性进行了研究。共设计ssr引物237对，产生扩增产物184对（77.6%）。在11个品种的亚群中选择27个SSR标记（占14.7%）进行遗传关系评价。每个标记的等位基因数为2 ~ 18个，平均为7.77个，多态性信息含量（PIC）值为0.491 ~ 0.906。两两F （st）估计显示135个萝卜品种（74个大品种，15个小品种，29个幼品种，12个小品种和5个加工品种）的5个市场类别之间存在显著的遗传分化。利用NTSYS-pc和STRUCTURE软件进行聚类分析，也发现74个大萝卜被划分为5-7个簇。此外，27个SSR标记均能根据UPGMA树图识别64个大萝卜品种，且每个标记独立鉴定1 ~ 17个大萝卜品种。这些结果表明，栽培萝卜具有不同的遗传变异模式，育种做法应成为市场类别之间和内部遗传分化的驱动力。本研究开发的SSR标记将为遗传研究和植物育种家通过品种鉴定保护知识产权提供有用的资源。
Radish (Raphanus sativus L.) is a major vegetable cultivated worldwide. As a member of the family Brassicaceae, this species has diverse morphological characteristics in root. Radish cultivars have been classified based on morphological traits, including root shape and color. Despite its economic importance in Asia, genomic research in radish is less well developed relative to Brassica rapa, a close relative of radish. In this study, we developed genomic simple sequence repeat (SSR) markers using a SSR-enriched library and investigated genetic diversity in a collection of 144 radish cultivars. A total of 237 primer pairs for SSRs were designed and 184 (77.6%) primer pairs produced PCR amplicons. Of these, we selected 27 SSR markers (14.7%) based on polymorphism in a subset of 11 cultivars and then used to assess genetic relationships in the germplasm panel. For these markers, the number of alleles per marker ranged from 2 to 18 with an average of 7.77 alleles and the polymorphism information content (PIC) values ranged from 0.491 to 0.906. The estimates of pairwise F (st) revealed significant genetic differentiation between the five market classes of 135 radish cultivars (74 big, 15 small, 29 young, 12 Altari, and 5 processing). Clustering analysis using NTSYS-pc and STRUCTURE software also found that the 74 big radishes were divided into 5-7 clusters. In addition, all 27 SSR markers were able to differentiate 64 big radish cultivars based on the UPGMA dendrogram and each of the 23 markers independently identified 1 to 17 big radish cultivars. These results suggest that cultivated radishes have different patterns of genetic variation and breeding practices should be a driving force for the genetic differentiation between and within market classes. The SSR markers developed in this study will be a useful resource for genetic study and protection of plant breeder's intellectual property right through cultivar identification.