DOI: 10.5061/dryad.rn8pk0p63
title: Genetic structure of Polygonatum cyrtonema in Anhui province from eastern China

description: 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.
description: 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.<strong> </strong>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.