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Development and application of simple sequence repeat markers based on whole-genome sequencing in Codonopsis lanceolata

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Abstract

The content of medicinal components of Codonopsis pilosula differ greatly in various habitats. The development of specific molecular markers is of great significance for the identification of different cultivars of C. pilosula. In this study, 1,379,041 primer pairs were designed based on the whole genome of C. lanceolata. Of these, six pairs of primers were able to amplify polymorphic bands. We performed genetic diversity analysis and constructed a cluster tree and DNA fingerprint of the three groups: mixed, wild and cultivated C. pilosula materials. The results were as follows: first, the mixed materials had an average observed number of alleles (Na) of 7.6667, an average effective number of alleles (Ne) of 4.6058, an average Shannon's information index (I) of 1.7128, an average expected homozygosty (Exp Hom) of 0.2118, an average expected heterozygosity (Exp Het) of 0.7882, an average expected heterozygosity of Nei’s (Ht) of 0.7798, and an average gene flow (Nm) of 0.1281. Second, the cultivated accessions were as follows: Na = 4.6667, Ne = 2.5956, I = 1.0702, Exp Hom = 0.4234, Exp Het = 0.5766, Ht = 0.5755, and Nm = 0.5253. Finally, the accessions of the wild materials were as follows: Na = 5.333, Ne = 2.8769, I = 1.2771, Exp Hom = 0.3556, Exp Het = 0.6444, Ht = 0.6433, and Nm = 0.5314. In addition, the results of cluster analysis showed that mixed, wild and cultivated materials were clustered into 4, 4 and 3 subgroups, respectively. Furthermore, we performed DNA fingerprinting of 47 mixed materials. These results are valuable for the identification and genetic analysis of C. pilosula from different sources in Shanxi Province.

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Funding

This work was supported by Shanxi Provincial Program of key R & D projects (China) (No. 201903D221053), Applied Basic Research Programs of Shanxi Province (China) (No. 201901D211540), the earmarked fund for Modern Agro-industry Technology Research System (China) (No. 2021–11) and Doctoral foundation of Shanxi University of Chinese Medicine (China) (2020BK05).

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  1. Institute of Pharmaceutical and Food Engineering, Shanxi University of Chinese Medicine, Jinzhong, 030619, China

    Dan Zhang, Xiaoli Liu, Yuerong Zhang, Hui Li & Haixian Zhan

  2. Institute of Economic Crops, Shanxi Agricultural University, Fenyang, 032200, China

    Hongling Tian

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  1. Dan Zhang
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  3. Xiaoli Liu
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HZ: Conceptualization, data curation, review, editing. DZ: collection, investigation, data curation, writing-original draft. HT: collection, YZ: collection. XL: data curation. HL: data curation.

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Correspondence to Haixian Zhan.

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Zhang, D., Tian, H., Liu, X. et al. Development and application of simple sequence repeat markers based on whole-genome sequencing in Codonopsis lanceolata. Genet Resour Crop Evol 71, 651–664 (2024). https://doi.org/10.1007/s10722-023-01647-z

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