Abstract
Lychnis wilfordii (Regel) Maxim. is a perennial plant designated as an endangered species by the Korean government because of rapid reduction in its population size. Thus, a population genetic study of this species is needed to establish the strategy for management and conservation based on scientific evidences. The goals of this study were to develop useful microsatellite markers for L. wilfordii and to understand current genetic status of L. wilfordii in Korean peninsula. Seventeen microsatellite markers were identified using next-generation sequencing and bioinformatic analysis and then analyzed genetic diversity in one hundred forty-five individuals from Korea (KI1, KI2, and KP), China (CX, CF) and Russia (RP). Analysis of molecular variance (AMOVA), principal coordinates analysis (PCoA) and STRUCTURE results consistently showed discontinuity among L. wilfordii populations. AMOVA showed that the percentage of variation among populations was 53%, which was higher than the variation within populations (19%). PCoA showed that the populations were divided into three genetic clusters, (1) Chinese (CX, CF), (2) Russian (RP) populations and Korean populations (KI1, KI2) excluding KP, and (3) the KP population. In particular, KP, the most southern population on the Korean peninsula, showed significantly lower observed and expected heterozygosity, number of effective alleles, and Shannon index (I) than those of KI1 and KI2. L. wilfordii showed high differentiation between populations with low genetic diversity within populations. Among Korean populations, KP is likely to be affected by genetic drift due to small population size, low genetic diversity and limited gene flow.
Similar content being viewed by others
References
Alcaide M, Serrano D, Negro JJ, Tella JL, Laaksonen T, Müller C (2008) Population fragmentation leads to isolation by distance but not genetic impoverishment in the philopatric Lesser Kestrel: a comparison with the widespread sympatric Eurasian Kestrel. Heredity 102:190–198
Caughley G, Gunn A (1996) Conservation biology in theory and practice. Blackwell, Oxford, p 459
Earl DA, von Holdt BM (2012) Structure harvester: a website and program for visualizing structure output and implementing the Evanno method. Conserv Genet Resour 4:359–361
Ellstrand NC, Elam DR (1993) Population genetic consequences of small population size: implication for plant conservations. Annu Rev Ecol Syst 24:217–242
Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14:2611–2620
Galeuchet DJ, Husi R, Perret C, Fischer M, Gauyschi B (2002) Characterization of microsatellite loci in Lychnis flos-cuculi (Caryophyllaceae). Mol Ecol Notes 2:491–492
Gomulkiewicz R, Holt RD (1995) When does evolution by natural selection prevent extinction? Evolution 49:201–207
Harvey PH, Pagel MD (1991) The comparative method in evolutionary biology. Oxford University Press, Oxford, pp 1–34
Hedrick PW, Gilpin ME (1997) Genetic effective size of a metapopulation. In: Hanski IA, Gilpin ME (eds) Metapopulation biology: ecology, genetics and evolution. Academic Press, California, pp 165–181
Hoffmann AA, Blows MW (1994) Species borders: ecological and evolutionary perspectives. Trends Ecol Evol 9:223–227
Hong SP (2007) Lychnis L. In: Park CW (ed) Flora of Korea. Academy Publishing Co., Seoul, pp 323–325
Jakobsson M, Rosenberg NA (2007) CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics 23:1801–1806
Kim ZS (2009) Developing sampling strategies for genetic conservation of endangered plant species. In: Proceedings of ‘international symposium on climate change and biodiversity conservation’, Korea National Arboretum, 25–26 May, pp 11–21
Kim ZS, Jo DG, Kim YH, Yoo KO, Cheon KS (2010) Genetic diversity and structure of Pulsatilla tongkangensis as inferred from ISSR markers. Korean J Plant Res 23:360–367
Lawton JH (1993) Range, population abundance and conservation. Trends Ecol Evol 8:409–413
Lesica P, Allendorf FW (1995) When are peripheral populations valuable for conservation? Conserv Biol 9:753–760
Liu S, Cantrell RG, McCarty JC, Stewart JMcD (2000) Simple sequence repeat based assessment of genetic diversity in cotton race stock accessions. Crop Sci 40:1459–1469
Lu D, Lidén M, Oxelman B (2001) Lychnis Linneaeus. In: Wu Z, Raven PH, Hong D (eds) Flora of China, vol 6. Science Press, Beijing, pp 100–102
McPhail JD (1993) Ecology and evolution of sympatric sticklebacks (Gasterosteus): origins of the species pairs. Can J Zool 71:515–523
Nei M, Maruyama T, Chakraborty R (1975) The bottleneck effect and genetic variability in populations. Evolution 29:1–10
Peakall R, Smouse PE (2012) GenAlEx6.5: genetic analysis in Excel. Population genetic software for teaching and research-an update. Bioinformatics 28:2537–2539
Powell W, Machray GC, Provan J (1996) Polymorphism revealed by simple sequence repeats. Trends Plant Sci 1:215–222
Raymond M, Rousset F (1995) GENEPOP, version 1.2. Population genetics software for exact tests and ecumenicism. J Hered 86:248–249
Rosenberg NA (2004) DISTRUCT: a program for the graphical display of population structure. Mol Ecol Notes 4:137–138
Takayama K, Lopez SP, Koenig C, Kohl G, Novak J, Stuessy TF (2011) A simple and cost-effective approach for microsatellite isolation in non-model plant species using small-scale 454 pyrosequencing. Taxon 60:1442–1449
Taylor EB, McPhail JD (2000) Historical contingency and ecological determinism interact to prime speciation in sticklebacks gasterosteus. Proc R Soc Lond B 267:2375–2384
Van Oosterhout C, Hutchinson WF, Wills DPM, Shipley P (2004) MICRO-CHECKER: software for identifying and correcting genotyping errors in microsatellite data. Mol Ecol Notes 4:535–538
Varshney RK, Graner A, Sorrells ME (2005) Genic microsatellite markers in plants: features and applications. Trends Biotechnol 23:48–55
Zalapa JE, Cuevas H, Zhu H, Steffan S, Senalik D, Zeldin E, McCown B, Harbut R, Simon P (2012) Using nest-generation sequencing approaches to isolate simple sequence repeat (SSR) loci in the plant science. Am J Bot 99:193–208
Acknowledgements
This work was supported by a grant from the National Institute of Biological Resources (NIBR), funded by the Ministry of Environment (MOE) of the Republic of Korea (NIBR201703101). The authors gratefully acknowledge the contributions of Jong-Soo Kang and Jaram Hong at the National Institute of Biological Resources, the late Dr. Kozhevnikov at the Institute of Biology and Soil Science of the Russian Academy of Sciences and Dr. Xian-chun Zhang at Institute of Botany, Chinese Academy of Sciences for sample collection.
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Kim, B., Nakamura, K., Tamura, S. et al. Genetic diversity and population structure of Lychnis wilfordii (Caryophyllaceae) with newly developed 17 microsatellite markers. Genes Genom 41, 381–387 (2019). https://doi.org/10.1007/s13258-018-0759-0
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s13258-018-0759-0