基于转录组序列的楠木SSR分子标记开发

doi:10.11707/j.1001-7488.20161109

摘要/Abstract

摘要： [目的] 通过对楠木转录组数据的分析，开发楠木SSR分子标记技术，为楠木遗传多样性分析和资源保护提供保障。[方法] 将楠木高通量转录组测序获得的67 331条Unigene进行简单重复序列（SSR）位点挖掘和分析，并结合引物验证，初步证明其可行性。[结果] 通过软件分析，共获得9 405个SSR位点，出现频率为13.97%，涉及序列数量为6 667条，发生频率为9.90%。SSR序列中包括166种重复基元类型，其中，单核苷酸、二核苷酸和三核苷酸为优势重复类型，SSR位点数分别为3 890（41.36%），2 885（30.68%），2 489（26.46%）。SSR位点重复次数差别较大，其中重复10次比例最高，SSR位点数为1 621（17.24%），其次是5次（1 549，16.47%）和6次（1 495，15.90%）。主导重复基元类型为A/T（40.67%），AG/CT（27.59%），AAG/CTT（11.29%）。运用多态性分析的方式初步验证了SSR位点在楠木标记中的可行性。同时，利用Primer 3.0 进行引物设计，随机筛选18对进行验证，9对引物可以扩增出预期大小的条带。[结论] 通过对楠木高通量转录组序列的SSR信息的研究，获得6 667条SSR序列，主导重复类型为A/T，AG/CT和AAG/CTT。同时随机挑选18对引物对SSR分子标记方法进行验证。本文对楠木SSR标记的研究将有助于楠木基因挖掘、分子标记育种和资源保护。

关键词: 楠木, 转录组, SSR

Abstract: [Objective] SSR (simple sequence repeat) markers is a very useful method for species identification, molecular linkage mapping, and genetic diversity studies. In order to develop molecular markers of Phoebe zhennan, SSR markers were developed based on transcriptome sequence. This study provided a basis for studies of genetic diversity and conservation of genetic resources of P. zhennan. [Method] A total of 67 331 unigenes obtained by transcriptome sequencing were used to develop SSRs. And it was feasible to develop molecular markers of P. zhennan by primers analysis.[Result] A total of 9 405 SSRs were identified through software analysis, at a frequency of 13.97%. Meanwhile, the number of sequences involved in these SSRs was 6 667, accounting for 9.90% of the total number of sequences. A total of 166 repeat types of SSRs were identified. Among them, mononucleotide, dinucleotide and trinucleotide were the dominant repeat types, and the number of SSRs was 3 890 (41.36%), 2 885 (30.68%), 2 489 (26.46%), respectively. SSR repeat frequencies were largely different, the largest number of repeats was 10, accounting for 17.24% of the total repeat types, followed by 5 repeats (16.47%) and 6 repeats (15.90%). Additionally, the dominant repeat type was A/T, AG/CT and AAG/CTT, and the distribution frequency was 40.67%, 27.59% and 11.29%. The results indicated the feasibility of developing SSR markers for P. zhennan by polymorphism analysis. Meanwhile, a total of 18 primer pairs were randomly selected and verified by PCR amplification, and 9 primer pairs of them were able to amplify expected products. [Conclusion] A total of 9 405 SSRs were identified from transcriptome sequencing of P. zhennan, with A/T, AG/CT and AAG/CTT the most common repeats. 18 primer pairs were chosen for verification through their amplification in P. zhennan. The SSR markers developed for P. zhennan will benefit studies in candidate gene mining, marker-assisted breeding and resources protection.

Key words: Phoebe zhennan, transcriptome, SSR

中图分类号:

S718.46

时小东, 朱学慧, 盛玉珍, 庄国庆, 陈放. 基于转录组序列的楠木SSR分子标记开发[J]. 林业科学, 2016, 52(11): 71-78.

Shi Xiaodong, Zhu Xuehui, Sheng Yuzhen, Zhuang Guoqing, Chen Fang. Development of SSR Markers Based on Transcriptome Sequence of Phoebe zhennan[J]. Scientia Silvae Sinicae, 2016, 52(11): 71-78.

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