Population Genetic Analysis of Paris polyphylla var. yunnanensis Based on cpDNA Fragments

Dan Wang; Yu Huang; Lu Rui; Huihui Du; Junsheng Qi; Mingguo Ma; Nong Zhou

doi:10.3390/genes14091754

Population Genetic Analysis of Paris polyphylla var. yunnanensis Based on cpDNA Fragments

Genes (Basel). 2023 Sep 2;14(9):1754. doi: 10.3390/genes14091754.

Authors

Dan Wang¹, Yu Huang^{1

2}, Lu Rui¹, Huihui Du¹, Junsheng Qi¹, Mingguo Ma³, Nong Zhou¹

Affiliations

¹ The Chongqing Engineering Laboratory for Green Cultivation and Deep Processing of Three Gorges Reservoir Area's Medicinal Herbs, College of Food and Biology Engineering, Chongqing Three Gorges University, Chongqing 404120, China.
² College of Pharmacy, Dali University, Dali 671000, China.
³ Research Center of Biomass Clean Utilization, Beijing Key Laboratory of Lignocellulosic Chemistry, College of Materials Science and Technology, Beijing Forestry University, Beijing 100083, China.

Abstract

Paris polyphylla var. yunnanensis is a well-known medicinal plant that is mainly distributed in Southwest China; however, its genetic diversity and biodiversity processes are poorly understood. In this study, the sequences of cpDNA trnL-trnF fragments of 15 wild populations and 17 cultivated populations of P. polyphylla var. yunnanensis were amplified, sequenced, and aligned to study the population genetics of this species. Genetic diversity was analyzed based on nucleotide diversity, haplotype diversity, Watterson diversity, population-level diversity, and species-level genetic diversity. Genetic structure and genetic differentiation were explored using haplotype distribution maps and genetic distance matrices. A total of 15 haplotypes were identified in the 32 populations of P. polyphylla var. yunnanensis. Five unique haplotypes were identified from the fourteen haplotypes of the cultivated populations, while only one unique haplotype was identified from the ten haplotypes of the wild populations. The haplotype richness and genetic diversity of the cultivated populations were higher than those of the wild populations (H_T = 0.900 vs. 0.861). In addition, there were no statistically significant correlations between geographic distance and genetic distance in the cultivated populations (r = 0.16, p > 0.05), whereas there was a significant correlation between geographical distance and genetic structure in the wild populations (r = 0.32, p > 0.05), indicating that there was a geographical and genetic connection between the wild populations. There was only 2.5% genetic variation between the wild populations and cultivated populations, indicating no obvious genetic differentiation between the wild and cultivated populations. Overall, the genetic background of the cultivated populations was complex, and it was hypothesized that the unique haplotypes and higher diversity of the cultivated populations were caused by the mixed provenance of the cultivated populations.

Keywords: Paris polyphylla var. yunnanensis; cpDNA fragment; genetic distance; genetic diversity.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
Ascomycota*
Biodiversity
China
Coleoptera*
DNA, Chloroplast / genetics
Liliaceae* / genetics

Substances

DNA, Chloroplast

Grants and funding

This work was supported by the Chongqing Science and Technology Commission (cstc2018jcyjAX0267), and the Scientific and Technological Research Program of Chongqing Municipal Education Commission (KJQN202201205).