Abstract
Dendrobium officinale (Orchidaceae) is an endangered plant species with important medicinal value. To evaluate the effectiveness of ex situ collection of D. officinale genetic diversity, we developed 15 polymorphic trinucleotide microsatellite loci of D. officinale to examine the genetic diversity and structure of three D. officinale germplasm collections comprising 120 individuals from its germplasm collection base and their respective wild populations consisting of 62 individuals from three provinces in China. The three germplasm collections showed reductions in gene diversity and average number of alleles per locus, but an increase in average number of rare alleles (frequency ≤ 0.05) per locus in comparison to their wild populations. However, the differences in gene diversity between the germplasm collections and wild populations were not statistically significant. The analysis using STRUCTURE revealed evident differences in genetic composition between each germplasm collection and its wild population, probably because the D. officinale individuals with distinct genotypes in each wild population were unevenly selected for establishing its germplasm collection. For conservation management plans, we propose that D. officinale individuals with rare alleles need to be conserved with top priority, and those individuals with the most common alleles also should be concerned. The 15 new microsatellite loci may be used as a powerful tool for further evaluation and conservation of the genetic diversity of D. officinale germplasm resources.
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References
Caujapé-Castells, Pedrola-Monfort (2004) Designing ex-situ conservation strategies through the assessment of neutral genetic markers: application to the endangered Androcymbium gramineum. Conserv Genet 5:131–144
Ding G, Zhang DZ, Ding XY, Zhou Q, Zhang WC, Li XX (2008) Genetic variation and conservation of the endangered Chinese endemic herb Dendrobium officinale based on SRAP analysis. Plant Syst Evol 276:149–156
Ding G, Li X, Ding X, Qian L (2009) Genetic diversity across natural populations of Dendrobium officinale, the endangered medicinal herb endemic to China, revealed by ISSR and RAPD markers. Genetika 45:375–382
Doyle JJ, Doyle JL (1987) A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull 19:11–15
Ensslin A, Sandner TM, Matthies D (2011) Consequences of ex situ cultivation of plants: Genetic diversity, fitness and adaptation of the monocarpic Cynoglossum officinale L. in botanic gardens. Biol Conserv 144:272–278
Excoffier L, Laval G, Schneider S (2005) Arlequin (version 3.0): an integrated software package for population genetics data analysis. Evol Bioinform Online 1:47–50
Falush D, Stephens M, Pritchard JK (2003) Inference of population structure using multilocus genotype data: Linked loci and correlated allele frequencies. Genetics 164:1567–1587
Fan WJ, Luo YM, Li XX, Gu S, Xie ML, He J, Cai WT, Ding XY (2009) Development of microsatellite markers in Dendrobium fimbriatum Hook, an endangered Chinese endemic herb. Mol Ecol Resour 9:373–375
Farnsworth EJ, Klionsky S, Brumback WE, Havens K (2006) A set of simple decision matrices for prioritizing collection of rare plant species for ex situ conservation. Biol Conserv 128:1–12
Fu LK (1992) China plant red data book: rare and endangered plants, I. Science Press, Beijing
Gastier JM, Pulido JC, Sunden S, Brody T, Buetow KH, Murray JC, Weber JL, Hudson TJ, Sheffield VC, Duyk GM (1995) Survey of trinucleotide repeats in the human genome: assessment of their utility as genetic markers. Hum Mol Genet 4:1829–1836
Gomez OJ, Blair MW, Frankow-Lindberg BE, Gullberg U (2005) Comparative study of common bean (Phaseolus vulgaris L.) landraces conserved ex situ in genebanks and in situ by farmers. Genet Resour Crop Ev 52:371–380
Jiang M, Yang J, Zhang C, Liu B, Chan K, Cao H, Lu A (2010) Clinical studies with traditional Chinese medicine in the past decade and future research and development. Planta Med 76:2048–2064
Kalinowski ST (2005) HP-Rare 1.0: a computer program for performing rarefaction on measures of allelic richness. Mol Ecol Notes 5(1):187–189
Kalinowski ST, Taper ML, Marshall TC (2007) Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment. Mol Ecol 16:1099–1106
Lawson MJ, Zhang LQ (2006) Distinct patterns of SSR distribution in the Arabidopsis thaliana and rice genomes. Genome Biol 7:R14
Li YC, Korol AB, Fahima T, Beiles A, Nevo E (2002) Microsatellites: genomic distribution, putative functions and mutational mechanisms: a review. Mol Ecol 11:2453–2465
Li YC, Korol AB, Fahima T, Nevo E (2004) Microsatellites within genes: structure, function, and evolution. Mol Biol Evol 21:991–1007
Li X, Ding X, Chu B, Zhou Q, Ding G, Gu S (2008) Genetic diversity analysis and conservation of the endangered Chinese endemic herb Dendrobium officinale Kimura et Migo (Orchidaceae) based on AFLP. Genetica 133:159–166
Namoff S, Husby CE, Francisco-Ortega J, Noblick LR, Lewis CE, Griffith MP (2010) How well does a botanical garden collection of a rare palm capture the genetic variation in a wild population? Biol Conserv 143(5):1110–1117
Negri V, Tiranti B (2010) Effectiveness of in situ and ex situ conservation of crop diversity. What a Phaseolus vulgaris L. landrace case study can tell us. Genetica 138:985–998
Nybom H (2004) Comparison of different nuclear DNA markers for estimating intraspecific genetic diversity in plants. Mol Ecol 13:1143–1155
Raymond M, Rousset F (1995) GENEPOP (version 1.2): population genetics software for exact tests and ecumenicism. J Heredity 86:248–249
Rice EB, Smith ME, Mitchell SE, Kresovich S (2006) Conservation and change: a comparison of in situ and ex situ conservation of jala maize germplasm. Crop Sci 46:428–436
Rucińska A, Puchalski J (2011) Comparative molecular studies on the genetic diversity of an ex situ garden collection and its source population of the critically endangered polish endemic plant Cochlearia polonica E. Frohlich. Biodivers Conserv 20:401–413
Rychlik W (2007) OLIGO 7 primer analysis software. Methods Mol Biol 402:35–60
The State Pharmacopoeia Commission of P. R. China (2010) Pharmacopoeia of the People’s Republic of China 2010 (Set of 3, English edition). China Medical Science and Technology Press, Beijing
Vitalis R, Dawson K, Boursot P (2001) Interpretation of variation across marker loci as evidence of selection. Genetics 158:1811–1823
Wang S, Xie Y (2004) China species red list, vol 1. Higher Education Press, Beijing
Wright S (1978) Evolution and the genetics of populations: variability within and among natural populations, vol 4. University of Chicago Press, Chicago
Wu YQ, Si JP (2010) Present status and sustainable development of Dendrobium officinale industry. China J Chin Materia Medica 35:2033–2037
Xie ML, Hou BW, Han L, Ma YH, Ding XY (2010) Development of microsatellites of Dendrobium officinale and its application in purity identification of germplasm. Acta Pharmacol Sin 45:667–672
Xu SB, Tao YF, Yang ZQ, Chu JY (2002) A simple and rapid methods used for silver staining and gel preservation. Hereditas 24:335–336
Xu C, Zhan ZG, Liao SM (2008) Studies on agronomic characteristics, polysaccharide and cellulose contents of 8 kinds Dendrobium officinale from different distribution areas. J Zhejiang Univ (Science Edition) 35:576–579
Acknowledgments
We are grateful to Shu-Miaw Chaw for many helpful comments on previous drafts. This work was financed by the National Natural Science Foundation of China (no. 30870234) and the Natural Science Foundation of Jiangsu Province (no. BK2008431).
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Hou, B., Tian, M., Luo, J. et al. Genetic diversity assessment and ex situ conservation strategy of the endangered Dendrobium officinale (Orchidaceae) using new trinucleotide microsatellite markers. Plant Syst Evol 298, 1483–1491 (2012). https://doi.org/10.1007/s00606-012-0651-3
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DOI: https://doi.org/10.1007/s00606-012-0651-3