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Genetic Diversity and Population Structure of Endangered Neofinetia Falcata (Orchidaceae) in South Korea Based on Microsatellite Analysis

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Genetic Diversity and Population Structure of Endangered Neofinetia Falcata (Orchidaceae) in South Korea Based on Microsatellite Analysis Journal354 of Species Research 7(4):354-362, 2018JOURNAL OF SPECIES RESEARCH Vol. 7, No. 4 Genetic diversity and population structure of endangered Neofinetia falcata (Orchidaceae) in South Korea based on microsatellite analysis Jeong Eun Han1, Byoung-Hee Choi2,* and Myounghai Kwak3 1Biological and Genetic Resources Utilization Division, National Institute of Biological Resources, Republic of Korea 2Department of Biological Sciences, Inha University, Republic of Korea 3Plant resources Division, National Institute of Biological Resources, Republic of Korea *Correspondent: [email protected] Population genetic assessment is essential for the conservation and management of endangered and rare plants. Neofinetia falcata is endangered epiphyte orchid and protected by law in Korea. In Korea, this species is only found on islands in the South Sea of Korea (including Jeju-do) and the southern coast of the Korean Peninsula. We developed nine microsatellite makers to assess the genetic diversity and population genetic structure of three populations of N. falcata. The genetic diversity at the species level was low, which can be attributed to inbreeding or fragmentation into small, isolated populations. A recent bottleneck was detected in one population, likely due to overcollection. N. falcata exhibited moderated levels of differentiation among populations, with the three populations were divided into two clusters based on genetic structure. The genetic diversity and structure of N. falcata are affected by restricted gene flow by pollen or seeds due to isolation and geographic distance. Strategies for in situ and ex situ conservation of this species are been proposed based on the results of our study. Keywords: ‌conservation, genetic diversity, microsatellite markers, Neofinetia falcata, population genetic structure Ⓒ 2018 National Institute of Biological Resources DOI:10.12651/JSR.2018.7.4.354 INTRODUCTION tion (Segelbacher et al., 2003; Michael, 2016). In par- ticular, wild orchids are declining in numbers as a result Neofinetia falcata (Thunb.) Hu is an epiphytic orchid of over-collection, habitat destruction due to human that grows on tree trunks or rocks and is distributed in activities, and impact of climate change (Barman and Korea, Japan, and China (Dressler, 1993; Chen and Jef- Devadas, 2013; Michael, 2016; Tian et al., 2018; Xu et frey, 2009; Lee, 2011). This beautiful orchid contains a al., 2018). These factors induce genetic erosion from ge- pleasant fragrance and is a symbol of wealth and nobil- netic drift, inbreeding, decrease in populations size, and ity, which is why Japan began cultivating it in the 17th reduced gene flow within small and isolated populations century (Yoon and Chung, 2011; Duttke et al., 2012). Due (Murren, 2002; David and Richard, 2003; Honnay and to the popularity, it has been collected extensively and Jacquemyn, 2007; Hundera et al., 2013; Su et al., 2017). is now threatened with extinction. N. falcata is known Genetic variability in small populations is vulnerable to to be found at about 20 sites in Jeju-do and along the environmental changes due to inbreeding, isolation, and southern coast of the Korean Peninsula (Shin et al., 2009; bottleneck events, and this reduces the potential of small National Institute of Biological Resources, 2012). Cur- populations to respond to selective pressures (Spencer rently, this species has been classified as Critically En- et al., 2000; Su et al., 2017). Appropriate conservation dangered (CR) on the IUCN Red List (National Institute measures are needed of endangered to maintain genetic of Biological Resources, 2012) and protected by law diversity. For population genetics research, it is import- through the Ministry of Environment in Korea. ant to understand the level of population differentiation Endangered or rare plants, including orchids, have in order to properly conserve endangered or rare plants. undergone habitat loss, over-collection, and fragmenta- Microsatellites are codominant molecular markers that November 2018 Han et al. Genetic diversity and structure of endangered Neofinetia falcata 355 show a high level of polymorphism and contain repeat mation of wild this species have not been studied. For motifs of 1-6 nucleotides (Yun et al., 2011). They have this reason, we used next-generation sequencing (NGS) been effectively utilized as a tool for genetic assessment to develop microsatellites markers of N. falcata. We use of endangered or rare plants for conservation (Spencer these microsatellite markers to study the genetic struc- et al., 2000; Escudero et al., 2003; Sun et al., 2011). Re- ture, population differentiation, and gene flow between cently, the genetics of a wide range of endangered or rare natural populations. These data provide baseline genetic plants were evaluated using microsatellite markers (Hou information for conservation and management of this et al., 2012; Lavor et al., 2014; Miao et al., 2015; Kwak endangered species. et al., 2017; Su et al., 2017). N. falcata studies have primarily focused on the cul- ture of seeds or cells for horticultural value (Chung, MATERIALS AND METHODS ; 1980 1981; Ichihashi and Islam, 1999; Hahn and Paek, Plant materials and DNA extraction 2001; Mitsukuri et al., 2009; Han et al., 2010; 2013). As basic information for conservation, N. falcata is an ane- N. falcata is difficult to collect because it commonly mochorous plant that is pollinated by the long-tongued grows on steep cliffs and the number of natural popula- hawkmoth (genus Theretra) (Kiyohara et al., 2012; Shi- tions is small. We chose sampling sites based on inter- mizu, 2012; Suetsugu et al., 2015). The phylogeny of views with the national park official. Forty individuals Neofinetia and related genera has been extensively stud- of N. falcata were collected from Boksaeng Island (BS, ied, but there is a lack of research towards genetic diver- n =11), Geomun Island (GM, n=6) and Galgot Island sity using microsatellites (Duttke et al., 2012; Hidayat et (GG, n=23), located in the South Sea of Korea (Table al., 2012; Kim et al., 2014). 1; Fig 1). The leaves were dried on either silica gel or Understanding of genetic variation and population dif- frozen in liquid nitrogen. Genomic DNA was extracted ferentiation of N. falcata is essential for its conservation from the flesh of the leaves using the Wizard Genomic and restoration. However, the population genetic infor- DNA Purification Kit (Promega, USA). The quality and Fig. 1. Geographic distribution of N. falcata populations. Abbreviations are shown in Table 1. Pie charts represent assignment probability of belonging to each K=2 clusters identified by STRUCTURE based on microsatellite allele frequencies, with probability values normalized using CLUMPP. Table 1. Sample collection sites for populations. Population code No. individuals Location BS 11 Boksaeng Island, Wando-gun, Jeollanam-do Prov. GM 6 Geomun Island, Wando-gun, Jeollanam-do Prov. GG 23 Galgot Island, Geoje-si, Gyeongsangnam-do Prov. 356 JOURNAL OF SPECIES RESEARCH Vol. 7, No. 4 concentration of DNA were assessed using 0.7% aga- Data analysis rose gel electrophoresis and a spectrophotometer (Nano- The number of alleles (A), observed heterozygosity drop, USA). DNA was stored at 4°C until used for later (Ho), and expected hetrozygosity (He) for each locus laboratory work. were calculated using ARLEQUIN ver. 3.5.1.2 (Excof- fier and Lischer, 2010). Deviations from Hardy-Wein- Development of the microsatellite makers berg equilibrium (HWE) were tested using ARLEQUIN. DNA from one individual was used for NGS sequenc- Measures of the mean number of alleles per locus (Na), ing to screen for microsatellite fragments. Approximate- number of effective alleles per locus (Ne), Shannon’s ly 10 μg of genomic DNA was sequencing using the information index (I), and inbreeding coefficient (Fis) Roche 454 GS-FLX Titanium platform (454 Life Scienc- were performed with GenAlEx ver. 6.503 (Peakall and es, Branford, CT, USA) at the National Instrumentation Smouse, 2012). Allelic richness (Rs) and the number of Center for Environmental Management of Seoul Nation- private alleles (Ps) for a standard sample size were calcu- al University (NICEM). The sequence reads were assem- lated using a rarefaction approach in ADZE (Szpiech et bled using the Newbler software package (Roche Diag- al., 2008). The possible loss of genetic variation through nostics, 454 Life Science). The sequences were scanned the bottleneck effect was tested using the BOTTLE- for di- and trinucleotide repeats using the “SSR_finder. NECK ver. 1.2.02 (Piry et al., 1999). The Wilcoxon test pl” Perl program for the development of microsatellites was used to test the significance of heterozygote excess (Shanker et al., 2007). The repeats were sorted accord- under the infinite allele model (IAM), the stepwise mu- ing to the number of iterations, and primer pairs flanking tation (SMM), and two-phased models (TPM), as recom- each repeat were designed using Primer 3 to amplify mended by Piry et al. (1999). Population genetic struc- fragments containing repeats of more than four itera- ture was investigated using the STRUCTURE ver. 2.3.4 tions (Rozen and Skaletsky, 2000). The optimal primer (Pritchard et al., 2000). The assumed K number of pop- size was set at 22 bp (range 18-26 bp), the optimal an- ulations ranged from 1 to 20. Each run was performed nealing temperature was set at 58°C (range 55-59°C), using the admixture model and the burn-in period was and the product size was selected to be 130-270 bp, with set to 100,000 followed by 1,000,000 Markov chain the remaining parameters left at the default settings. Monte Carlo (MCMC) replicates, with 10 iterations per K to confirm stabilization of the summary statistics. The PCR and microsatellite genotyping most appropriate K was determined by calculating K following steps set forward by Evanno et al. (2005). Forty-eight designed primer pairs were tested for am- All K calculations were performed using the program△ plification using polymerase chain reaction (PCR) on STRUCTURE HARVESTER ver. 6.0 (Earl and von- two individuals.
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