基于转录组序列的楠木SSR分子标记开发

doi:10.11707/j.1001-7488.20161109

Abstract

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

CLC Number:

S718.46

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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Development of SSR Markers Based on Transcriptome Sequence of Phoebe zhennan

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