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Genotyping-by-sequencing to determine the genetic structure of a Tibetan medicinal plant Swertia mussotii Franch.

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Abstract

Swertia mussotii Franch. has been widely used in Tibetan folk medicine as an important drug ingredient for the treatment of hepatitis and hepatobiliary disease and for homeopathic purposes. But the lacking natural resources of S. mussotii is becoming more obvious with increasing market demands. The main objective of this work was to examine genetic differentiation among S. mussotii populations from different geographical locations and use the knowledge gained to facilitate future selection of the species suitable for large-scale cultivation to meet the increasing demand for medicinal use of this plant. In this study, 68 S. mussotii Franch samples collected from Zhongda (16), Chengduo (16), and Xiewu (8) County in Qinghai Province, Xiaojin (14) and Jinchuan (14) County in Sichuan Province, China and 4 samples from related species, were genotyped using genotyping-by-sequencing (GBS) technique. GBS scored 4095 SNPs with a minor-allele frequency > 0.25 and an average read depth < 200 based on the 72 samples examined. Analyses of all SNPs provided evidence of genetic differentiation among populations. Structural and phylogenetic topological analyses supported the genetic differentiations among populations. Gene ontology annotation results revealed that genetic differentiations often occurred in genes known or hypothesized to be involved in various metabolic processes such as catalytic and transferase activity, cellular component, nucleus, biological, cellular and metabolic process. The present results also revealed a significant positive correlation between the genetic similarity and geographical distance (P = 0.032). Moreover, the adaptability of S. mussotii to the environment had a strong effect on its chemical composition and phenotypic changes. Therefore, we hypothesize that the population structure is strongly influenced by local adaptive pressure. The adaptive evolution of S. mussotii species in heterogeneous environments may play an important role in inducing genetic differentiation among different geographical populations. This is evidenced by the observed changes in phenotypic traits and chemical compounds in S. mussotii plants from different geographic locations.

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Availability of data and materials

The datasets used and analysed in the current study are available from the corresponding author upon reasonable request.

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Acknowledgements

Financial support for this study came from the National Natural Science Foundation of China (No. 81274185; 81573535; 81873397), Young and Middle-aged Talents of the National Ethnic Affairs Commission of the People’s Republic of China (2016-3-01), New Century Excellent Talents in University of China (NCET-13-0624), the Programme of Introducing Talents of Discipline to University of China (No. 111-B08044), Natural Science Foundation of Beijing (7202109), the Foundation of Key Laboratory of Ethnomedicine (Minzu University of China), Ministry of Education (No. KLEM-ZZ201807; KLEM-ZZ201805; KLEM-ZZ201904), Minzu University of China (Collaborative Innovation Center for Ethnic Minority Development and yldxxk201819), National Innovation Training Program for College Students (GCCX2018110022), and the Innovation Class Project of Minzu University of China (SHSY2016120021).

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Authors and Affiliations

  1. College of Life and Environmental Sciences, Minzu University of China, Beijing, 100081, China

    Yan Qiao, Fengxian Guo, Lin Zhan, Jiaqing Sun, Xixi Zuo, Zeguang Guo & Yue Liu

  2. Key Laboratory of Ethnomedicine (Minzu University of China), Ministry of Education, Beijing, 10081, China

    Yan Qiao, Fengxian Guo, Jiaqing Sun, Xixi Zuo & Yue Liu

  3. USDA-ARS, Western Regional Research Center, Albany, CA, 94710, USA

    Naxin Huo & Yong Q. Gu

  4. Department of Plant Science, University of California Davis, Davis, CA, 95616, USA

    Naxin Huo

  5. Biological Science Research Center, Southwest University, Chongqing, 400715, China

    Yi Wang

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  1. Yan Qiao
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Contributions

YL and YQG conceived and designed the experiments. YL, LZ and JS collected the materials. YL, FG, NH, and JS performed the experiments. YQ, YW and YL compiled and interpreted the data. YQ, YL, YW, and YQG wrote the manuscript. All authors reviewed and discussed the manuscript.

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Correspondence to Yi Wang or Yue Liu.

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Qiao, Y., Guo, F., Huo, N. et al. Genotyping-by-sequencing to determine the genetic structure of a Tibetan medicinal plant Swertia mussotii Franch.. Genet Resour Crop Evol 68, 469–484 (2021). https://doi.org/10.1007/s10722-020-00993-6

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