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The development of SSR markers from the endangered plant Tetracentron sinense Oliv. (Tetracentraceae) based on RAD–seq technique

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Abstract

Conservation genetics research of Tetracentron sinense, an endangered tree species in China used as medicine, ornament, and for its timber, depends on development of fast–evolving and reliable genetic markers. A simplified genome sequence was obtained by restrictive–site associated DNA sequencing based on high throughput sequencing and used to develop primers for identification of simple sequence repeat (SSR) molecular markers suitable for T. sinense. The results showed that 121,022 SSR loci obtained in 114,350 SSR containing sequences, which included mononucleotide repeats (59.14%), dinucleotide repeats (28.71%), and trinucleotide repeats (9.97%). These SSR sequences were used to design 1212 primers to detect the polymorphism. Therein, 67 pairs of primers containing 2–6 nucleotide repeats were selected for PCR amplification of 16 samples collected from four populations. Forty–eight primers were polymorphic, and the PIC values varied from 0 to 0.9297, with the average of 0.7168. Finally, 21 pairs of SSR primers suitable for T. sinense were screened. These results suggest that the species of T. sinense which without genomic information, the newly developed SSR primers provide a foundation for the analysis of genetic diversity, genetic variation, genetic structure, population dynamic history and development of effective conservation and management technology of T. sinense germplasm resources.

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All data generated or analysed during this study are included in this published article.

Abbreviations

HTS:

High throughput sequencing.

SSR:

Simple sequence repeat.

RAD–seq:

Restriction site–Associated DNA sequencing.

PCR:

Polymerase Chain Reaction.

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Acknowledgements

We thank all students who helped to collect materials and analyze data: Wei–Li Mao, Huan Zhang, Yang Chen, Xue–Mei Xu and Shan Li. This work was supported by National Natural Science Foundation of China (NO. 32070371).

Funding

This work was supported by National Natural Science Foundation of China (NO. 32070371).

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Authors and Affiliations

  1. Institute of Biodiversity Science and Geobiology, College of Science, Tibet University, 850012, Lhasa, China

    Zhong–Qiong Tian

  2. Institute of plant adaptation and utilization in southwest mountain, China West Normal University, 637000, Nanchong, China

    Fan Duan

  3. Key laboratory of southwest China wildlife resources conservation (Ministry of Education), No.1 Shida Road, Nanchong City, Sichuan Province, China

    Zhong–Qiong Tian, Shan Li & Xiao-Hong Gan

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  1. Zhong–Qiong Tian
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  2. Fan Duan
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  4. Xiao-Hong Gan
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Contributions

Conceptualization: [Zhong–Qiong Tian], Methodology: [Zhong–Qiong Tian], Formal analysis and investigation: [Fan Duan], Writing-original draft preparation: [Zhong–Qiong Tian], Writing-review and editing: [Xiao–Hong Gan], Funding acquisition: [Xiao–Hong Gan], Resources: [Xiao–Hong Gan], Supervision: [Shan Li ].

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Correspondence to Xiao-Hong Gan.

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Tian, Z., Duan, F., Li, S. et al. The development of SSR markers from the endangered plant Tetracentron sinense Oliv. (Tetracentraceae) based on RAD–seq technique. Biologia 78, 15–22 (2023). https://doi.org/10.1007/s11756-022-01109-4

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  • DOI: https://doi.org/10.1007/s11756-022-01109-4

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