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Genetic Diversity of Natural Cyclamen Alpinum Populations

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Genetic Diversity of Natural Cyclamen Alpinum Populations Turk J Biol 36 (2012) 413-422 © TÜBİTAK doi:10.3906/biy-1111-9 Genetic diversity of natural Cyclamen alpinum populations Belgin GÖÇMEN TAŞKIN1, Nilden VARDARELİ1, Ersin DOĞAÇ1, Ramazan MAMMADOV2, Vatan TAŞKIN1 1Department of Biology, Faculty of Science, Muğla University, Muğla - TURKEY 2Department of Biology, Faculty of Arts and Sciences, Pamukkale University, Denizli - TURKEY Received: 03.11.2011 ● Accepted: 27.02.2012 Abstract: Th e focus of this study was Cyclamen alpinum (formerly C. trochopteranthum). Habitat fragmentation, environmental degradation, and overharvesting of tubers have exerted pressure on native populations of this valuable ornamental species. Although the entire Cyclamen genus is in the Convention on International Trade in Endangered Species of Wild Fauna and Flora-Appendix II (CITES II), no species has yet been red-listed. Estimating the level and distribution of genetic variation in populations of rare and endemic species is important for conserving genetic diversity within a species in the context of well-developed conservation strategies. Currently, DNA markers are the most eff ective means used to infer genetic variation at the molecular level in conservation genetics. In this study, random amplifi ed polymorphic DNA (RAPD) analysis was employed to assess the genetic diversity within and among 6 natural C. alpinum populations in the south and southwest of Turkey. A total of 190 loci were determined by using 15 polymorphic primers. Total genetic variation (HT) was 0.27 ± 0.02. A high proportion of this variation, 0.16 ± 0.01 (59.26%), was due to within- population genetic variation (HS). Th e genetic diff erentiation coeffi cient (GST) was 0.41, and the level of gene fl ow (Nm) within a generation among the 6 populations studied was 0.73. As a result of these fi ndings, we propose in situ combined with ex situ conservation of all C. alpinum populations. In addition, our results support prior recommendations to add C. alpinum to the International Union for Conservation of Nature and Natural Resources (IUCN) Red List under the critically endangered (CR) category. Key words: Cyclamen alpinum, Cyclamen trochopteranthum, genetic diversity, RAPD Introduction normal physiological activity. Th e arrival of autumnal Th ere are more than 500 geophyte species growing precipitation and cooler temperatures induce an naturally in Turkey, and the bulbs of most of these important regrowth in this species. Aboveground species are exported (1,2). In general, they are parts of the plant die back, and drought is avoided propagated by vegetative means (3). However, the by means of a summer-dormant underground horticulturally important genus Cyclamen L. is a storage organ, the tuber. Regrowth occurs from tuberous perennial geophyte, and seeds are used in belowground perennating buds. Both the avoidance its propagation (4). Cyclamen species have a limited of summer drought and rapid regrowth in response dispersal capacity due to their primary dependence to environmental cues are enabled by the storage of on ants to transport their relatively few, large seeds nutrients in tubers (6). (5,6). Th ey show some form of summer dormancy in Cyclamen has been the focus of unusual response to a lack of moisture suffi cient to maintain taxonomic activity over the last 70 years. Nine 413 Genetic diversity of natural Cyclamen alpinum populations infrageneric classifi cations were proposed over that Th ese markers have been used to study genetic period for Cyclamen, a small genus with fewer than diversity in various plant species (10). However, 30 species (7). Th erefore, Cyclamen alpinum has a DNA marker systems are complex and there are basic confusing taxonomic history. It was fi rst described in diffi culties involved in using most of them, such as the last part of the 19th century and was known as restriction fragment length polymorphisms (RFLPs), Cyclamen alpinum Sprenger until it was redescribed simple sequence repeats (SSRs), and amplifi ed as Cyclamen trochopteranthum by Otto Schwarz in fragment length polymorphisms (AFLPs) (11). 1975. Today it is again known as C. alpinum (8). It Although AFLPs and SSRs are generally preferred is an ornamental species with attractive pink fl owers due to their informativeness, random amplifi ed and dark green leaves that are grey-green and cream- polymorphic DNAs (RAPDs) are still widely used; colored in the center. It is 1 of 10 Cyclamen species they are simple to perform, have low costs, and that grow naturally in Turkey. When it was described do not require DNA sequence information (12). as C. trochopteranthum, it was accepted as 1 of 6 Additionally, the RAPD system provides a more endemic species among the 10 Cyclamen species of arbitrary sample of the genome and can generate Turkey (1). However, under the name of C. alpinum, essentially unlimited numbers of loci for use in its endemism is controversial. It grows in the south genetic analysis (13). and southwestern parts of Turkey, especially in In this study, RAPD analysis was employed to Antalya, Muğla, Denizli, Burdur, and Isparta. In assess the genetic variability within and among 6 general, it is found at elevations of 350-1500 m under C. alpinum populations located in the southern Pinus brutia Ten. and Liquidambar orientalis Mill. and southwestern regions of Turkey at diff erent trees or under Laurus nobilis L. and Ceratonia siliqua elevations. Although there are several studies related L. shrubs, in partially shaded moist habitats with to its taxonomy (7), morphology, ecology, and soils rich in humus. However, some populations of cytology (14) as well as in vitro and in vivo seed this species can be found close to sea level in Dalyan germination (4), this is the fi rst report characterizing and Marmaris, and there are populations growing at the populations of this valuable yet taxonomically 1670 m on Sandras Mountain, as well (9). confusing and controversial ornamental species Because of the tremendous impact of humans using a DNA marker system. on their environment over the past 50 years (e.g., increase in agricultural and residential areas, tourism activities, and the construction of roads Materials and methods and dams), the natural growing areas of many plant Plant material species, including C. alpinum, have been destroyed. Four C. alpinum populations at elevations of 20, 30, Intense pasturing, collection of tubers for medicinal 40, and 50 m from Dalyan-Muğla, 1 population at 560 purposes, and exportation of the plants are additional m from Çukurköy-Denizli, and 1 population at 1100 human-created pressures on C. alpinum populations. m from Elmalı-Antalya were sampled and used in Th erefore, conservation is important for the the study (Figure 1). Populations sampled were from continued existence and evolution of this species. rarely found C. alpinum populations in Turkey, and A primary goal of conservation genetics is to they were located in a region that is very important estimate the level and distribution of genetic variation for tourism and agriculture. For this reason, some in the populations of rare and endemic species and of the populations screened in this study could only then create a plan to preserve genetic diversity within be minimally sampled. For example, Pop-4 and the species. Currently, DNA markers are the most Pop-6 were represented by only 3 and 6 individuals, eff ective means by which conservation genetics infers respectively (Figure 1). For the same reason, in the variation at the molecular level. Th ey are also eff ective Çukurköy-Denizli and Elmalı-Antalya populations tools that enable clarifi cation of taxonomic synonyms we obtained pieces of tuber tissues from individual and detection of the origin of species and cultivars. plants collected for another purpose and used them 414 B. GÖÇMEN TAŞKIN, N. VARDARELİ, E. DOĞAÇ, R. MAMMADOV, V. TAŞKIN 12345678910 42° A 40° B Denizli 38° Antalya C Muğla 01020 km 36° 26° 28° 30° 32° 34° 36° 38° 40° 42° 44° Figure 1. Locations of the 6 C. alpinum populations. Pop-1: Dalyan-Muğla (20 m), Pop-2: Dalyan-Muğla (30 m), Pop-3: Dalyan-Muğla (50 m), Pop-4: Dalyan-Muğla (40 m), Pop-5: Elmalı-Antalya (1100 m), Pop-6: Çukurköy-Denizli (560 m) in the analysis, while leaves from individual plants bromide) was added to 0.03 g of the fi nely powdered were used to analyze the remaining 4 populations tissue, vortexed very well, and incubated in a 65 °C from Dalyan-Muğla. water bath for 60 min by vortexing at the 20th, 40th, Individual plants in each population were and 60th minutes. Th is was followed by the addition collected using a transect method. Each transect of 500 μL chloroform and isoamyl alcohol (24:1). Th e consisted of a straight line. In each population, the samples were mixed well by inverting the tubes and length, numbers, and directions of transects were centrifuged for 10 min at 14,000 rpm. Next, the top determined depending on the size of the population aqueous layer was transferred to another tube. Th e and other characteristics of the location such as volume of the aqueous phase was estimated to be slope, topography, and uniformity. Depending on the approximately 300-350 μL, and 0.08 volumes of cold size of the population, 1 plant was sampled at every 7.5 M ammonium acetate and 0.54 volumes (using 10 to 30 m of a transect. Th e collected samples were the combined volume of aqueous phase and added stored at −20 °C in a freezer until the DNA extraction ammonium acetate) of cold isopropanol were added procedure. to precipitate the DNA. Aft er incubation at −20 °C for 30 min, the sample was centrifuged at 14,000 Genomic DNA isolation rpm for 4 min to pellet the DNA. Th e supernatant Genomic DNA was extracted from leaves and tubers was removed and 700 μL of cold 70% ethanol was using a protocol optimized according to the methods added to wash the pellet, followed by centrifugation of Doyle and Doyle (15), Cullings (16), and Sharma at 14,000 rpm for 3 min.
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