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Genetic Diversity of Potamogeton Maackianus in the Yangtze River Wei Lia,*, Li-Qun Xiaa,B, Jian-Qiang Lia, Guang-Xi Wanga,C

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Genetic Diversity of Potamogeton Maackianus in the Yangtze River Wei Lia,*, Li-Qun Xiaa,B, Jian-Qiang Lia, Guang-Xi Wanga,C Aquatic Botany 80 (2004) 227–240 www.elsevier.com/locate/aquabot Genetic diversity of Potamogeton maackianus in the Yangtze River Wei Lia,*, Li-Qun Xiaa,b, Jian-Qiang Lia, Guang-Xi Wanga,c aLaboratory of Aquatic Plant Biology, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan 430074, Hubei, PR China bCollege of Fisheries, Zhanjiang Ocean University, Zhanjiang 524025, Guangdong, PR China cGraduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan Received 2 July 2003; received in revised form 8 March 2004; accepted 8 July 2004 Abstract The genetic diversity and genetic structure of Potamogeton maackianus A. Benn. in seven lakes of the middle reaches of the Yangtze River were studied using random amplified polymorphic DNA (RAPD). The gene flow and genetic relationships between populations were analyzed in combination with the geographic distribution and the river system of the lakes. A total of 112 bands were amplified and 59 bands (52.7%) were polymorphic. Each of the 86 individuals investigated exhibited a unique genotype. The Shannon index was used to measure genetic diversity, and the total genetic diversity was 0.414 and the mean genetic diversity of populations was 0.148. P. maackianus showed a relatively high level of genetic diversity. Analyses of molecular variance (AMOVA) revealed that 63.8% of the total genetic diversity existed among populations and 36.2% within them, which was consistent with the genetic structure computed by the Shannon index: among-population variation and within population variation accounted for 64.4 and 35.7%, respectively. The gene flow among populations was very limited, and genetic isolation among populations occurred even though they were connected through the Yangtze River. Cluster analysis divided the seven populations into two groups, and the genetic relationships among the populations had no obvious association with their geographic distribution, or the historical relations with the river system of the lakes where they occurred. Mantel tests revealed that distance was an important factor affecting the genetic structure in * Corresponding author. Tel.: +86 27 87510140; fax: +86 27 87510251. E-mail addresses: [email protected], [email protected] (W. Li). 0304-3770/$ – see front matter # 2004 Elsevier B.V. All rights reserved. doi:10.1016/j.aquabot.2004.07.003 228 W. Li et al. / Aquatic Botany 80 (2004) 227–240 populations. The development history of P. maackianus populations in Honghu Lake had an obvious effect on its genetic structure. # 2004 Elsevier B.V. All rights reserved. Keywords: Potamogeton maackianus A. Benn.; RAPD; Genetic diversity; Genetic structure; Gene flow; The Yangtze River 1. Introduction The middle-lower reaches of the Yangtze River is the largest floodplain in China. Thousands of shallow lakes exist in this enormous area and almost all are inter-connected via the river system. This connection accounts for the high similarities of macrophyte compositions in different lakes (Li, 1995; Li and Zheng, 1998). The genetic diversity of a macrophyte in such a habitat is the subject of the present paper. Allozyme methods have been widely used to analyze the genetic variation in aquatic plants. Many studies considered that macrophytes in general had relatively low levels of genetic variation, higher rates of fixation and lower levels of sexual recombination compared with terrestrial plants (Les, 1988; Laushman, 1993; Schlueter and Guttman, 1998). High levels of genetic diversity in aquatic plants have also been reported in some species (Harris et al., 1992; Lokker et al., 1994; Mader et al., 1998). Compared to the allozyme method, random amplified polymorphic DNA (RAPD) can detect more polymorphic loci, and can quantify the genetic diversity and genetic structure more accurately, especially when genetic variation is low (Furnier and Mustaphi, 1992; Esselman et al., 1999; Kerher et al., 2000; Comes and Abbott, 2000). Recently, RAPD has been applied in the studies of aquatic plants, e.g. population structure (Waycott, 1995, 1998; Angel, 2002); relationships among different accessions (Madeira et al., 1997) and evaluation of genetic variation of endangered species (San Mart´ın et al., 2003). Potamogeton maackianus A. Benn. (Potamogetonaceae) is widely distributed in East Asia and can be found in almost all kinds of freshwater habitat (Sun, 1992). It is one of the dominant species in many lakes of the middle-lower reaches of the Yangtze River, and also the main founder species of submerged vegetation of this area (Li, 1995). P. maackianus is wind-pollinated and self-compatible, but mainly reproduces vegetatively. The recruitment and expansion of its population depend mainly on the clonal growth of stolons. In this study, the genetic diversity of P. maackianus in lakes of the middle reaches of the Yangtze River was evaluated by RAPD with the following aims: (1) to determine the genetic variation level of the species: the recent rapid decline of P. maackianus in many lakes has been ascribed to its possible low genetic diversity; (2) to determine the genetic relationships among different populations in relation to their degree of connectivity. 2. Materials and method 2.1. Sample collection The river section from Yichang, Hubei to Hukou Jiangxi, about 938 km long, comprises the middle course of the Yangtze River with a catchment area about 680,000 km2. In the W. Li et al. / Aquatic Botany 80 (2004) 227–240 229 more than 30 lakes larger than 10 km2 investigated during June 1999–November 2000, six natural lakes, namely Changhu Lake (CL), Honghu Lake (HH), Xiliang Lake (XL), Niushan Lake (NS), Bao’an Lake (BA) and Chihu Lake (CH), together with a reservoir Mulan Lake (ML) had large populations of P. maackianus. In each lake, the geographical coordinates of sampling stations were pre-calculated with the aid of GIS. The actual sampling sites for P. maackianus depended on its distribution in the lakes. Each site was located using GPS. At each site, 10 random samplings were grabbed to get the plant materials. The material (mainly healthy leaves) was carefully washed and dried by placing it immediately in a plastic bag with desiccant. All the material collecting from one site was treated as one individual. Samples from one lake were treated as one population. In all, 86 individuals were collected in seven populations. The distances between the adjacent sample sites in a lake were 0.5–2 km. 2.2. DNA extraction The total genomic DNA was extracted with the modified CTAB method of (Rogers and Bendich, 1985), where 0.03–0.05 g dried plant tissue was ground in liquid nitrogen and incubated with 600 mLof2Â CTAB extraction buffer (2% CTAB, 100 mM Tris–HCl pH 8.0, 20 mM EDTA, 1.4 M NaCl, 0.1% b-mercaptoethanol) for 20–30 min at 56 8C, DNA was extracted with 500 mL of chloroform/isoamyl alcohol (24:1) two or three times and precipitated with 600 mL1Â CTAB precipitated buffer (1% CTAB, 50 mM Tris–HCl pH 8.0, 10 mM EDTA). The solution was centrifuged for 10 min at 3500 rpm.The DNA pellet was dissolved in 400 mL 1 M NaCl and re-precipitated with 800 mL ethanol at À20 8C overnight. After 2 min centrifugation at 13,000 rpm and a wash with 76% ethanol, the pellet was dried and resuspended in 100 mLTE(10mMTris and 1 mM EDTA). The quality of the isolated DNA was examined on a 0.8% agarose gel and the concentration was estimated by DNA/Protein Analyzer (Beckman DU530). 2.3. RAPD polymerase chain reaction (PCR) The RAPD technique has been criticized for its low reproducibility. However, the reproducibility of this method can be satisfactory if standard and strict experimental steps can be established and implemented (Zou et al., 2001), with special attention to: (a) shape of the temperature profile; (b) type of polymerase; and (c) Mg2+, Taq and DNA concentration (Hoelzel and Green, 1998). All the experiments in the present work were carried out on the same set of instruments. First, three samples from Honghu Lake were used to select primers and set up a RAPD procedure that can produce clear, stable and reproducible bands in at least three replicates. Primers and RAPD procedure were then evaluated on all samples from Honghu Lake and Niushan Lake with three replicates. Nineteen primers that produced clear and reproducible bands were selected from 60 primers (Operon kit A, B and R). The following procedure was strictly followed in the final experiment. DNA extracts were diluted to 10–20 ng/mL for use in the PCR reaction. The RAPD PCR was carried out in 20 mL reaction volumes consisting of 2.0 mLof10Â PCR reaction buffer 230 W. Li et al. / Aquatic Botany 80 (2004) 227–240 (TaKaRa Inc.), 0.125 mM of each dNTP, 0.25 mM of primer, 0.5 U of Taq DNA polymerase (TaKaRa) and 2 mL of template DNA. PCR reactions were carried out in a MJ Research PTC-100 thermocycler programmed for an initial denaturation step of 94 8C, followed by 40 cycles of 1 min at 94 8C, 1 min at 36 8C, 1.5 min at 72 8C. The reaction was completed with a final run at 72 8C for 6 min. A negative control reaction that had template DNA omitted was included with every run to check for contamination of stock chemicals. Amplification products were separated on 1.4% agarose gels in 1Â TAE buffer, stained with ethidium bromide and visualized and photographed under UV light (UVP GDS- 7600). The graphs were scored by two people, and their uncommon bands (less than 5%) were re-checked and discussed before making a final decision. 2.4. Data analysis RAPD bands were scored as present (1) or absent (0) for each DNA example (range of band sizes: 300–2000 bp), and treated as phenotypic data in the analysis.
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