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

Authors: QIAO, YAN - Minzu University Of China; GUO, FENGXIAN - Minzu University Of China; HUO, NAXIN - University Of California, Davis; ZHAN, LIN - Minzu University Of China; SUN, JIAQING - Minzu University Of China; ZUO, XIXI - Minzu University Of China; GUO, ZEGUANG - Minzu University Of China; Gu, Yong; WANG, YI - Southwest Forestry University; LIU, YUE - Minzu University Of China

Submitted to: Genetic Resources and Crop Evolution
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/23/2020
Publication Date: 8/6/2020
Citation: Yan, Q., Guo, F., Huo, N., Zhan, L., Sun, J., Zuo, Q., Guo, Z., Gu, Y.Q., Wang, Y., Liu, Y. 2020. Genotyping-by-sequencing to determine the genetic structure of a Tibetan medicinal plant Swertia mussotii franch. Genetic Resources and Crop Evolution. 68:469-484. https://doi.org/10.1007/s10722-020-00993-6.
DOI: https://doi.org/10.1007/s10722-020-00993-6

Interpretive Summary: The Gentianaceae family comprises approximately 90 genera, including the Swertia genus, which includes 170 species that are widespread throughout the world and commonly applied as herbal drugs to treat various ailments. However, little is known about the genetic structure of these important medicinal plants because of lack of genetics and genomics resources. Here, a genotyping-by-sequence technology was applied to study genomic variations of the medicinal plant, Swertia mussotii, across various geographical locations and potential association of the adaptive evolution with the phenotypic and chemical changes. Our study provides new insight into the evolutionary dynamics influencing the genetic structure and the location adaptation. The dataset generated in this work represents a useful genomic resource for future studies of S. mussotii to identify genes or molecular markers associated with valuable traits, such as those determining medicinal compounds, for crop improvement through breeding or biotechnological approaches.

Technical 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. Advances in next-generation sequencing techniques, such as genotyping-by-sequencing (GBS), have allowed for the rapid generation of genome-wide sequence data to gain insight into the evolutionary dynamics in'uencing the genetic structure and the local adaptation of plant species. Such studies on S. mussotii are still lacking. The objectives of this study are to (i) explore the adaptability of S. mussotii to different environments using GBS and (ii) evaluate the association of phenotypes and medicinal compounds with single nucleotide polymorphisms (SNPs). In this study, 72 samples of S. mussotii Franch and related species collected from Qinghai and Sichuan Provinces, China, were genotyped using GBS. GBS scored 4,095 SNPs with a minor-allele frequency (MAF) > 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 (GO) annotation results revealed that genetic differentiations often occurred in genes known or hypothesized to be involved in metabolic processes. The present results also revealed a correlation of the degree of genetic similarity with geographical distance. 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 adaptive evolution of S. mussotii species in heterogeneous environments plays an important role in inducing genetic differentiation among local populations. Analyses of the dynamics in'uencing the genetic structure and local adaptation of S. mussotii using GBS provide the first look into the potential associations of the adaptive evolution of this important medicinal plant with its phenotypic and chemical compound changes.