摘要
SSR是应用于金钗石斛鉴定和遗传多样性研究的重要分子标记之一。为开发新的SSR标记,寻求快速鉴别金钗石斛的方法,该文通过生物信息学手段对金钗石斛转录组序列进行SSR位点搜索、分析,并设计出SSR特异性引物。结果显示,从金钗石斛转录组中搜索到32 709个SSR,分布与26 742条unigenes中,SSR位点发生频率为12.90%,平均每3 748 bp含1个SSR位点。其中,单核苷酸是最主要重复类型,占SSR总数的72.18%,其次是二核苷酸和三核苷酸,分别占SSR总数的15.97%,11.19%。而在所有重复基元中,A/T出现频率最高,AG/CT次之。通过设计、筛选,该研究共获得62 157对SSR位点特异性引物。从中随机挑选20对引物进行PCR扩增,17对扩增出清晰、可重复的条带,扩增率为85.0%。选择3种石斛检测引物多态性,共获得多态性引物13条。以上结果表明,金钗石斛转录组测序产生的unigenes信息可作为开发SSR标记的有效来源,其中的SSR位点出现密度大、类型丰富、多态性潜能高,在金钗石斛及其近缘种的分子鉴定、遗传多样性与分子育种等方面具有较好的应用前景。
SSR is one of the most important molecular markers used in molecular identification and genetic diversity research of Dendrobium nobile. In order to enrich the library of SSR and establish a method for rapid identification of D. nobile, the SSR informa- tion was analyzed in the transcriptome of D. nobile. A total of 32 709 SSRs were obtained from the transcriptome of D. nobile, distribu- ted in 26 742 unigenes with the distribution frequency of 12. 90%. SSR loci occurred every 3 748 bp. Mono-nucleotide repeat was the main type, account for as much as 72. 18% of all SSRs, followed by di-nucleotide （ 15.97% ） and tri-nucleotide （ 11.19% ）. Among all repeat types, A/T was the predominant one followed by AG/CT. Finally a total of 62 157 primer pairs were designed for marker de- velopment. Randomly 20 pairs of primers were selected for PCR amplification, 17 amplified on clear and reproducible bands, the am- plification rate was 85.0%. Thirteen pairs were polymorphic among the 3 Dendrobium plants. The results indicated that the unigenes generated from transcriptome sequencing in D. nobile can be used as effective source to develop SSR markers. The SSR loci in the tran- scriptome of D. nobile have the characteristics of type riches, high density and high potential of polymorphism, and these characteris- tics might applied in the study of molecular identification, genetic diversity and marker-assisted breeding of D. nobile and its closely re- lated species.
出处
《中国中药杂志》
CAS
CSCD
北大核心
2017年第1期63-69,共7页
China Journal of Chinese Materia Medica
基金
国家自然科学基金项目(31170314
81473331)
关键词
金钗石斛
转录组
SSR
位点信息
Dendrobium nobile
transcriptome
SSR
inibrmation of loci
