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Ejbio: Electronic Journal of Biology eJBio Electronic Journal of Biology, 2008, Vol. 4(4):134-141 Genetic Variation and Biodiversity of Paeonia lactiflora in China as Determined by Analysis of ISSR Using Phylogenetic Trees and Split Networks Siyan Cao1,2,*, Xubin Meng1,2, Yang Liu1,2, Chuan Shao1, Stefan Grünewald3, Chengxin Fu1, Ming Chen1 1College of Life Sciences, Zhejiang University, Hangzhou 310058, China; 2Chu Kochen Honors College, Zhejiang University, Hangzhou 310058, China; 3CAS-MPG Partner Institute for Computational Biology, Shanghai 200031, China; and Max-Planck- Institute for Mathematics in the Sciences, 04103 Leipzig, Germany. * Corresponding author. Tel: +86(0)571-88206649; Fax: +86(0)571-88206485; E-mail: [email protected] The most medicinally important ingredient is Abstract paeoniflorin, which has been shown to have a strong antispasmodic effect on mammalian Paeonia lactiflora, an important material of intestines. It also reduces blood pressure, reduces Traditional Chinese Medicine (TCM), is widely body temperature caused by fever and protects cultivated in China, but its population genetic against stress ulcers [1]. Recently, paeoniflorin was structure and phylogenetic relationship remain to be demonstrated to attenuate cognitive deficits and determined. In this paper, Inter-Simple Sequence brain damage induced by chronic cerebral Repeat (ISSR) markers were used to estimate the hypoperfusion [2]. genetic variation and biodiversity within and among 24 populations of Paeonia lactiflora in four different Traditionally, there are three main breeds of provinces across China. Nine UBC primers Paeonia lactiflora in China: Hang-paeonia from producing highly polymorphic DNA fragments were Dongyang and Pan’an (PA), Zhejiang Province; Bo- selected. Seventy-two discernible DNA fragments paeonia from Bozhou (BZ), Anhui Province; Chuan- were generated of which 71 (98.61%) were paeonia from Zhongjiang (ZJ), Sichuan Province polymorphic, indicating substantial genetic diversity (Figure 1). The three breeds of Chinese peony at species levels. The genetic diversity measured by formed several hundred years ago; their quality, for the percentage of polymorphic bands (PPB) at example, the content of paeoniflorin, is much higher population levels ranged from 2.78% to 63.89%. than any other breeds. The three breeds can be Both programs POPGENE32 and SplitsTree4 were cursorily distinguished by their morphological applied to analyze genetic distances among the features. However, the phylogenetic relationship populations, respectively. We constructed an between different populations is not very clear, unweighted pair-group method with arithmetic largely because of the wide cultivation as an means (UPGMA) dendrogram using POPGENE32, ornamental and for medicinal use [3]. In the past and a neighbor-joining (NJ) tree and a split network decade, several phylogenetic analyses on Paeonia by SplitsTree4. The differences between them were lactiflora and its close relatives have been reported expounded and compared. More complex [4-8]. However, most of them used DNA sequencing phylogenetic relationships among populations were or Random Amplification of Polymorphic DNA discovered and elucidated. Analyses based on the (RAPD) [9] markers with samples from a limited split network were more precise and comprehensive, number of populations. Additionally, the methods providing a series of novel conclusions, which may utilized to perform data analysis were conventional. help to standardize and optimize the growth of Inter-Simple Sequence Repeat (ISSR) [10] has the Paeonia lactiflora. advantage over RAPD for its high reproducibility, as well as the great power for detecting polymorphism. Keywords: Paeoniaceae; Paeonia lactiflora; ISSRs; Due to these strengths, ISSR becomes a powerful Split network; Phylogenetic relationship. approach for the assessment of genetic variation among related populations, especially for the 1. Introduction species in which no molecular genetic information was available. Paeonia lactiflora is mainly distributed in East Asia. The root of Chinese peony has been used for over In previous research, phylogenetic relationships 1,500 years in Traditional Chinese Medicine (TCM). were usually represented by using phylogenetic ISSN 1860-3122 - 134 - eJBio Electronic Journal of Biology, 2008, Vol. 4(4):134-141 tress, based on the model of evolution dominated products serve as important representative and by mutations and speciation events. However, cover the most range of the species distributed in under more complex models of phylogenesis, i.e. China (Table 1). Young leaf tissue was collected involving gene loss and duplication, or hybridization, from each sampled individual and dried in silica gel horizontal gene transfer or recombination, a single for subsequent DNA extraction (for two times). phylogenetic tree will not often be an appropriate Molecular experiments representation of the phylogenetic history or of the different incompatible phylogenetic signals, which Total genomic DNAs were extracted using the necessitates the use of a more realistic model [11]. modified CTAB method [13]. DNA was dissolved in The combined effect of sampling error and TE buffer, then electrophoresised in 1% agarose to systematic error makes phylogenetics an uncertain estimate DNA weight. ISSR Primers designed science, and network methods provide tools for according to sequences published by the University representing and quantifying this uncertainty [12]. of British Columbia, were synthesized by Sangon Here, we used a novel program SplitsTree4 (version Corp., Shanghai. In the preliminary study, primers 4.6, built 4 Aug 2006) [11], to provide a framework that produced polymorphic bands with strong signal for evolutionary analysis using both trees and and clear background were selected from all 100 networks. As the name of the program suggests, it primers to perform ISSR-PCR. To ensure the is based on the fundamental mathematical concept reliability and repeatability, we first optimized the of a “split”, that is a bipartition of the taxa set. The PCR reaction system. Orthogonal experimental program takes as input a set of taxa represented by design (Suppl. Table 1) was performed to establish characters (that is, aligned sequences), distances, highly repetitive, clear and stable experiment quartets, trees or splits and produces as output parameters including concentration of DNA template, trees or networks using a number of different Taq polymerase, Mg2+ and dNTP (No.5) for ISSR, methods. which laid the foundation for future studies of genetic diversity of the populations. PCRs of the same DNA extraction were replicated for three times; the final repeatability is around 90% once optimized. Nine selected UBC primers (Suppl. Table 2) generated 72 bands within 24 populations of Paeonia lactiflora corresponding to an average of 8 bands per primer. Phylogenetic analyses Statistical analyses of ISSR patterns were based on the assumptions that (i) ISSR fragments in Paeonia lactiflora behave as diploid, dominant markers with alleles being either present (amplified) or absent (non-amplified); (ii) co-migrating fragments represent putatively homologous loci; and (iii) most fragments are of nuclear origin and inherited bi- parentally [9,14]. The presence or absence of a homologous band was scored as 1 or 0, respectively. As for polymorphic sites, only stable differences during repetitive experiments were included for statistical analysis. We calculated the Figure 1. The sampling locations of three main breeds of genetic diversity parameters such as the percentage Paeonia lactiflora in China. The locations of the of polymorphic bands (PPB) at the species level, populations sampled in this study are shown. HZ: Heze, observed the number of alleles per locus (Na), the Shandong Province; BZ: Bozhou, Anhui Province; WH: effective number of alleles per locus (Ne), Nei’s Wuhu, Anhui Province; PA: Pan’an (located in East China, including XW: Xinwo and YT: Yangtou), Zhejiang gene diversities (h), and Shannon’s index (SI) with Province; ZJ: Zhongjiang, Sichuan Province. the assistance of POPGENE32 (Table 2). Based on the data above, the coefficient of genetic differentiation between populations (GST), Nei’s 2. Materials and Methods genetic distances (D) and genetic identity (I) were acquired. Plant materials In total, 259 individuals from 24 populations were collected from China’s four provinces, whose ISSN 1860-3122 - 135 - eJBio Electronic Journal of Biology, 2008, Vol. 4(4):134-141 Table 1. Locations of Paeonia lactiflora and the number of individuals sampled. Sample ID Code Breed Flower color Province Location size 1 P1 red 15 2 P2 dark red 14 3 P3 dark red 11 4 P4 red 9 5 P5 pink 5 Xinwo (XW) 6 P6 red 5 7 P7 pink 5 8 P8 red 12 9 P9 pink 7 10 P10 Hang-paeonia red 10 Zhejiang 11 P11 pink 6 12 P12 red 5 13 P13 pink 9 14 P14 pink 5 Yangtou (YT) 15 P15 red 8 16 P16 red 14 17 P17 red 3 18 P18 special 2 19 P19 pink 4 Chuan-paeonia 20 P20 pink 15 Sichuan Zhongjiang (ZJ) 21 P21 red 30 Anhui Wuhu (WH) 22 P22 red 20 Shandong Heze (HZ) 23 P23 white 25 24 P24 Bo-paeonia red 20 Anhui Bozhou (BZ) Total: 259 Table 2. Summary of genetic diversity estimated on the species level for Paeonia lactiflora. level Na Ne h SI PPB (%) Species mean 1.9861 1.5371 0.3189 0.4831 level 98.61 St. Dev 0.1179 0.3234 0.1497 0.1880 According to genetic distances among different applied to perform analyses for genetic distances, in Paeonia lactiflora populations, POPGENE32 was order to provide a framework for phylogenetic firstly used
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