Population genetic variation of microsatellite markers developed for Siberian fir (Abies sibirica Ledeb.) and European silver fir (Abies alba Mill.) using whole genome sequencing data

IF 16.4 1区 化学 Q1 CHEMISTRY, MULTIDISCIPLINARY
N. Oreshkova, E. I. Bondar, V. V. Sharov, Sudha P. Dhungana, O. Gailing, K. Krutovsky
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引用次数: 1

Abstract

The article presents the results of the search for microsatellite or simple sequence repeat (SSR) loci with tri-, tetra-, penta- and hexanucleotide tandem repeat motifs in the draft de novo assembly of the Siberian fir (Abies sibirica Ledeb.) genome and the development of convenient relatively highly and moderately polymorphic markers that can be easily genotyped even by simple gel electrophoresis. In total, 64 pairs of oligonucleotide polymerase chain reaction (PCR) primers for 32 detected microsatellite loci were designed and tested. Based on the testing results, 10 most promising polymorphic loci were selected and genotyped in eight natural populations of Siberian fir. Homologous microsatellite loci in the genome of European silver fir (Abies alba Mill.) were also identified by mapping Siberian fir contigs, containing SSR loci to the European silver fir genome assembly. A multiplex panel of 14 universal microsatellite loci was developed and genotyped in samples from four natural populations of A. alba and a small sample of eight Nordmann fir (Abies nordmanniana (Steven) Spach) trees.
利用全基因组测序数据对西伯利亚冷杉(Abies sibirica Ledeb.)和欧洲银杉(Abies alba Mill.)微卫星标记进行群体遗传变异分析
本文介绍了在西伯利亚冷杉(Abies sibirica Ledeb.)基因组重新组装草图中寻找具有三、四、五和六核苷酸串联重复序列的微卫星或简单序列重复(SSR)位点的结果,并开发了方便的相对高多态性和中等多态性的标记,即使通过简单的凝胶电泳也可以很容易地进行基因分型。共设计64对PCR引物,检测了32个检测到的微卫星基因座。在此基础上,从8个西伯利亚冷杉自然居群中筛选出10个最有潜力的多态性位点并进行基因分型。通过对西伯利亚冷杉基因组序列进行定位,发现欧洲银杉基因组序列中存在同源微卫星位点,其中SSR位点与欧洲银杉基因组序列同源。在4个白桦自然居群和8个北冷杉(Abies nordmanniana (Steven) Spach)小样本中建立了14个通用微卫星位点的多重组合,并进行了基因分型。
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来源期刊
Accounts of Chemical Research
Accounts of Chemical Research 化学-化学综合
CiteScore
31.40
自引率
1.10%
发文量
312
审稿时长
2 months
期刊介绍: Accounts of Chemical Research presents short, concise and critical articles offering easy-to-read overviews of basic research and applications in all areas of chemistry and biochemistry. These short reviews focus on research from the author’s own laboratory and are designed to teach the reader about a research project. In addition, Accounts of Chemical Research publishes commentaries that give an informed opinion on a current research problem. Special Issues online are devoted to a single topic of unusual activity and significance. Accounts of Chemical Research replaces the traditional article abstract with an article "Conspectus." These entries synopsize the research affording the reader a closer look at the content and significance of an article. Through this provision of a more detailed description of the article contents, the Conspectus enhances the article's discoverability by search engines and the exposure for the research.
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