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Genetic structure of Polygonatum cyrtonema in Anhui province from eastern China

Citation

Li, Xiaohong; Shao, Jianwen (2020), Genetic structure of Polygonatum cyrtonema in Anhui province from eastern China, Dryad, Dataset, https://doi.org/10.5061/dryad.rn8pk0p63

Abstract

Polygonatum cyrtonema Hua, a rhizome-propagating herb endemic to China, is often used in many traditional Chinese medicines and foods. The hilly mountains in western and southern Anhui province is one of its main natural distribution and artificial cultivation areas. The genetic diversity and structure of P. cyrtonema germplasm resources in Anhui were assessed by 9 pairs of SSR primers. The results showed that the 13 sampled populations of P. cyrtonema possessed normal levels of genetic diversity and could be clustered into three genetic groups, i.e. group I (MC, FLS, BJS, HHGD, JHGS, JHHS), group II (YLC, HG, HGGS, HT), and group III (TTZ, YLP, TZS). The levels of genetic diversity of three groups were similar, but their distribution areas and morphological characters were remarkably different. Group I is confined to Tianmu (including Jiuhua) Mountains, Group II is distributed in Huangshan Mountains, and Group III is restricted in Dabie Mountains. In morphology, the leaf length:width ratio significantly differed among groups, and the peduncle length of group I was significantly shorter than that of the other two groups. In addition, the genetic differentiation among groups was closer to that of related species within the genus. Thus these three genetic groups of P. cyrtonema should be considered as independent units for conservation and breeding management in the Anhui region.

Methods

A total of 381 individuals were sampled from 17 natural populations, covering the main distribution areas of Polygonatum species in Anhui. Leaves collected were dried in silica gel in sealed polyethylene bags and genomic DNA was extracted using the modified CTAB method. 9 nuclear microsatellite markers were chosen to detect the genetic diversity and structure of P. cyrtonema  in Anhui.  The sequencing of successfully amplified products were performed using an ABI 3730 DNA Analyzer and typing was then performed using the GeneMarker software. In each population, we also measured the morphological characters.

For each microsatellite locus, the number of alleles (NA ), observed heterozygosity (HO ),expected heterozygosity (HE ), gene diversity (HS ) and GST (the proportion of the totalgenetic diversity that occurs among populations) were estimated using FSTAT1.2 . The polymorphic information content (PIC) of each primer wascalculated by Cervus. For each population, the observed and expected heterozygosity (HO and HE ), number of detected and effective alleles (NA and NE ) over loci were computed using POPGENE1.31 software. Allele richness (AR ) and Shannon′s information index (I) were calculated using the GenAlEx 6.0 software Finally, level of inbreeding (FIS ) of each population was calculatedusing FSTAT1.2. A consensus Neighbour-Joining tree was constructed based on pairwise estimates of Nei's genetic distance. A phylogeographic analysis was also performed by the NeighborNet method implemented in SplitsTree4 based on the uncorrected p-distance.  All individual's Euclidean distance matrix was subjected to a principal coordinate analysis (PCoA) using GenALEx 6.0. Bayesian clustering implemented in STRUCTURE version 2.3.1. was used to assign individuals to genetic clusters (K) and to estimate admixture proportions for each individual. AMOVA was conducted using the ARLEQUIN version 3.0 to quantify the partitioning of genetic variance among and within populations and groups. The patterns of spatial genetic structure described as isolation-by-distance (IBD) models were evaluated using a Mantel test in GenALEx 6.0. The FST values were calculated based on the allele frequency using GENETIX v4.05. Using SPSS 19.0 software, Kruskal-Wallis H Test were performed  to examine whether genetic diversity parameters differ between the investigated species and the genetic groups within P. cyrtonema, and used one-way ANOVA to test the significance of the differences of morphological characters.

Funding

National Project for Basic Work of Science and Technology of China, Award: No. 2015FY110200

Key Laboratory of Biotic Environment and Ecological Safety in Anhui Province