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Development of 105 SNP markers in endangered turtle species Pelodiscus sinensis using RAD-seq

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Abstract

Restriction site-associated DNA sequencing (RAD-seq) was used to develop single nucleotide polymorphisms (SNP) marker for the Pelodiscus sinensis, which is a commercially important species in China. A total of 105 high-quality SNP markers were identified. The genetic statistics showed that the minor allele frequency varied from 0.0571 to 0.3382 and the observed heterozygosity and the expected heterozygosity ranged from 0.1143 to 0.6765 and 0.1078 to 0.4477, respectively. These novel SNP markers will serve as a valuable genetic tool for future conservation and population genetics studies for P. sinensis.

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Data availability

The RAD-seq data are openly available in NCBI at https://www.ncbi.nlm.nih.gov/sra, PRJNA680995.

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Acknowledgements

We thank Yang Li for providing computer resources.

Funding

This work was supported by the Hefei Independent Innovation Policy ‘loan to supplement’ project (No. J2019G37) and Fishery Industrial System of Anhui Province, China, No. [2021] 711.

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Authors and Affiliations

Authors

Contributions

QX and SS conceived of the presented idea. QX and FL experimented. QX developed the theory and performed the computations. JZ and XL verified the analytical methods. QX wrote the manuscript with support from FL, JZ, and XL. GF and RM provided the experiment samples. SS supervised the findings of this work. All authors discussed the results and contributed to the final manuscript.

Corresponding author

Correspondence to Shiping Su.

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Conflict of interest

The authors declare that they have no conflict of interest.

Ethical approval

This study was followed by the ethical standard of China (GB/T 35892-2018).

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Supplementary Information

Below is the link to the electronic supplementary material.

12686_2021_1238_MOESM1_ESM.docx

Supplementary file1 (DOCX 732 kb) The detailed process of data analysis and genetic information of 105 SNP markers can be found in Supplementary Materials 1 and 2.

Supplementary file2 (XLSX 40 kb)

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Xie, Q., Liu, F., Zhang, J. et al. Development of 105 SNP markers in endangered turtle species Pelodiscus sinensis using RAD-seq. Conservation Genet Resour 14, 27–30 (2022). https://doi.org/10.1007/s12686-021-01238-z

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  • DOI: https://doi.org/10.1007/s12686-021-01238-z

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