Abstract
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• The objective of this work is to estimate the level of genetic variation and pattern of genetic structure of isolated Picea balfouriana populations.
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• Nine SSR markers and six STS markers were assayed in ten natural populations of P. balfouriana, which is a regionally distributed conifer species in the southeast of the Qinghai-Tibet Plateau.
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• Expected heterozygosity ranged from 0.592 to 0.710 based on SSRs, and from 0.489 to 0.635 based on STS markers. The SSR and STS markers revealed that 11% and 12% of variation, respectively, was present among populations. However, the SSRs showed no deviation from the Hardy-Weinberg equilibrium (F IS = −0.030), unlike the STS markers (F IS = 0.249). In addition, assignment methods showed that individuals from the same sampling site usually cluster together.
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• Our results indicated that the distribution of genetic variation and population genetic structure of P. balfouriana may be attributed to habitat fragmentation and heterogeneous environments caused by the complex topographic environment in the Qinghai-Tibet Plateau. The population genetic information obtained in our study will benefit the development and utilization of appropriate conservation and breeding strategies for P. balfouriana.
Résumé
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• L’objectif de ce travail a été d’estimer le niveau de variation génétique et le modèle de la structure génétique de populations isolées de Picea balfouriana.
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• Neuf marqueurs SSR et six marqueurs STS ont été testés sur dix populations naturelles de P. balfouriana qui est un conifère distribué au niveau régional dans le sud-est du plateau Qinghai-Tibet.
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• L’hétérozygotie attendue allait de 0,592 à 0,710 sur la base des marqueurs SSR, et de 0,489 à 0,635 sur la base des marqueurs STS. Les marqueurs SSR et STS ont révélé que 11 % et 12 % de la variation, respectivement, étaient présentes parmi les populations. Toutefois, les marqueurs SSR ne montraient aucun écart par rapport à l’équilibre de Hardy-Weinberg (F I = −0,030) à la différence des marqueurs STS F I = 0,249).Les méthodes d’assignation bayésiennes ont montré que les individus d’un même site d’échantillonnage étaient habituellement groupés ensemble.
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• Nos résultats pourraient indiquer que la distribution de la variation génétique et la structure génétique de la population de Pinus balfouriana peuvent être attribuées à la fragmentation de l’habitat et à des environnements hétérogènes causés par un environnement topographique complexe dans le sud-est du plateau Qinghai-Tibet. L’information génétique obtenue sur la population dans notre étude sera bénéfique pour le développement et l’utilisation appropriés des stratégies de conservation et de sélection de Pinus balfouriana.
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References
Acheré V., Faivre R.P., Jeandroz S., Besnard G., Markussen T., Aragones A., Fladung M., Ritter E., and Favre J.M., 2004. A full saturated linkage map of Picea abies including AFLP, SSR, ESTP, 5S rDNA and morphological markers. Theor. Appl. Genet. 108: 1602–1613.
Allendorf F.W. and Leary R.F., 1986. Heterozygosity and fitness in natural populations of animals. Conservation Biology. In: Soule M.E. (Ed.), Sunderland, MA: Sinauer, the science of scarcity and diversity, pp. 57–76.
Bertorelle G. and Excoffier L., 1998. Inferring admixture proportions from molecular data. Mol. Biol. Evol. 15: 1298–1311.
Bouillé M. and Bousquet J., 2005. Trans-species shared polymorphisms at orthologous nuclear gene loci among distant species in the conifer Picea (Pinaceae): implications for the long-term maintenance of genetic diversity in trees. Am. J. Bot. 92: 63–73.
Brookfield J.F.Y., 1996. A simple new method for estimating null allele frequency from heterozygote deficiency. Mol. Ecol. 5: 453–455.
Collaborating Group for Vegetation of Sichuan, 1980. Vegetation of Sichuan. Sichuan People’s press, Chengdu, pp. 159–162 (in Chinese).
ECCAS (Editor Committee of the Chinese Academy of Sciences for Flora of China), 1978. Flora of China Vol. 7, science press, Beijing, pp. 153–155 (in Chinese).
Editorial Committee of the Sichuan Flora, 1983. Flora Sichuanica Vol. 2, Sichuan people’s press, Chengdu, pp. 77–79 (in Chinese).
Editorial Committee of Forest of China, 1999. Forest of China Vol. 2. China forestry publishing house, Beijing, pp. 731–743 (in Chinese).
Evanno G., Regnaut S., and Goudet J., 2005. Detecting the number of clusters of individuals using the software Structure: a simulation study. Mol. Ecol. 14: 2611–2620.
Excoffier L., Laval G., and 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., and Pritchard J.K., 2003. Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics 164: 1567–1587.
Gapare W.J., Aitken S.N., and Ritland C.E., 2005. Genetic diversity of core and peripheral Sitka spruce (Picea sitchensis (Bong.) Carr) populations: implications for conservation of widespread species. Biol. Conserv. 123: 113–123.
Ge X.J., Zhang Y.M., Hao G., and Chiang T.Y., 2005. Strong genetic differentiation of the East-Himalayan Megacodon stylophorus (Gentianaceae) detected by Inter-Simple Sequence Repeats (ISSR). Biodivers. Conserv. 14: 849–861.
Goudet J., 2001. FSTAT, A Program to Estimate and test gene diversities and fixation indices version 2.9.3. Available at: www.unil.ch/izea/softwares/fstat.html.
Guo S.W. and Thompson E.A., 1992. Performing the exact test of Hardy-Weinberg proportions for multiple alleles. Biometrics 48: 361–372.
Hochberg Y., 1988. A sharper Bonferroni procedure for multiple tests of significance. Biometrika 75: 800–802.
Li Y.C., Korol A.B., Fahima T., Beiles A., and Nevo E., 2002. Microsatellites: genomic distribution, putative functions, and mutational mechanisms: a review. Mol. Ecol. 11: 2453–2465.
Liu J.M., Wang L., Geng Y.P., Wang Q.B., Luo L.J., and Zhong Y., 2006. Genetic diversity and population structure of Lamiophlomis rotata (Lamiaceae), an endemic species of Qinghai-Tibet Plateau. Genetica 128: 385–394.
Liu Z.L., Fang J.Y., and Piao S.L., 2002. Geographical distribution of species in genera Abies, Picea and Larix in china. Acta Geogr. Sin. 57: 577–589.
Lu Z.X., Wang Y.H., Peng Y.H., Korpelainen H., and Li C.Y., 2005. Genetic diversity of Populus cathayana Rehd populations in southwestern China revealed by ISSR markers. Plant Sci. 170: 407–412.
Luo J.X., Wang Y.H., Korpelainen H., and Li C.Y., 2005. Allozyme variation in natural populations of Picea asperata. Silva Fenn. 39: 167–176.
Maghuly F., Pinsker W., Praznik W., and Fluch S., 2006. Genetic diversity in managed subpopulations of Norway spruce [Picea abies (L.) Karst.]. For. Ecol. Manage. 222: 266–271.
Mantel N., 1967. The detection of disease clustering and a generalized regression approach. Cancer Res. 27: 209–220.
Meloni M., Perini D., and Binelli G., 2007. The distribution of genetic variation in Norway spruce (Picea abies Karst.) populations in the western Alps. J. Biogeogr. 34: 929–938.
Myers N., Mittermeier R.A., Mittermeier C.G., da Fonseca G.A.B., and Kent J., 2000. Biodiversity hotspots for conservation priorities. Nature 403: 853–858.
Nei M., 1972. Genetic distance between populations. Am. Nat. 106: 283–292.
Olivier L., 2002. Populations 1.2.28. Available at: http://bioinformatics.org/~tryphon/populations/.
Oliveira E.J., Pádua J.G., Zucchi M.I., Vencovsky R., and Vieira M.L.C., 2006. Origin, evolution and genome distribution of microsatellites. Genet. Mol. Biol. 29: 294–307.
Ohsawa T., Saito Y., Sawada H., and Ide Y., 2008. Impact of altitude and topography on the genetic diversity of Quercus serrata populations in the Chichibu Mountains, central Japan. Flora 203: 187–196.
Page R.D.M., 1996. TREEVIEW: An application to display phylogenetic trees on personal computers. Comput. Appl. Biosci. 12: 357–358.
Panaud O., Chen X., and McCouch S.D., 1996. Development of microsatellite markers and characterization of sample sequence lengthen polymorphism (SSLP) in rice (Oryzastiva L.). Mol. Gen. Genet. 252: 597–607.
Peakall R. and Smouse P.E., 2006. GenAlEx 6: genetic analysis in Excel. Population genetic software for teaching and research. Mol. Ecol. Notes 6: 288–295.
Pelgas B., Beauseigle S., Acheré V., Jeandroz S., Bousquet J., and Isabel N., 2006. Comparative genome mapping among Picea glauca, P. mariana × P. rubens and P. abies, and correspondence with other Pinaceae. 113: 1371–1393.
Peng Y.H., Lu Z.X., Chen K., Luukanen O., Korpelainen H., and Li C.Y., 2005. Population genetic survey of Populus cathayana originating from Southeastern Qinghai-Tibetan plateau of China based on SSR markers. Silvae Genet. 54: 116–122.
Perry D.J. and Bousquet J., 1998a. Sequence-tagged-site (STS) markers of arbitrary genes: development, characterization and analysis of linkage in black spruce. Genetics 149: 1089–1098.
Perry D.J. and Bousquet J., 1998b. Sequence-tagged-site (STS) markers of arbitrary genes: the utility of black spruce-derived STS primers in other conifers. Theor. Appl. Genet. 97: 735–743.
Perry D.J. and Bousquet J., 2001. Genetic diversity and mating system of post-fire and post-harvest black spruce: an investigation using codominant sequence-tagged-site (STS) markers. Can. J. For. Res. 31: 32–40.
Pfeiffer A., Olivieri A.M., and Morgante M., 1997. Identification and characterization of microsatellites in Norway spruce (Picea abies K.). Genome 40: 411–419.
Pritchard J.K., Stephens M., and Donnelly P., 2000. Inference of population structure using multilocus genotype data. Genetics 155: 945–959.
Rajora O.P., Rahman M.H., Buchert G.P., and Dancik B.P., 2000. Microsatellite DNA analysis of genetic effects of harvesting in old-growth eastern white pine (Pinus strobes) Ontario, Canada. Mol. Ecol. 9: 339–348.
Raymond M. and Rousset F., 1995. GENEPOP (version 1.2): population genetics software for exact tests and ecumenicism. J. Hered. 86: 248–249.
Rice W.R., 1989. Analyzing tables of statistical tests. Evolution 43: 223–225.
Scotti I., Magni F., Paglia G.P., and Morgante M., 2002a. Trinucleotide microsatellites in Norway spruce (Picea abies): their features and the development of molecular markers. Theor. Appl. Genet. 106: 40–50.
Scotti I., Paglia G.P., Magni F., and Morgante M., 2002b. Efficient development of dinucleotide microsatellite markers in Norway spruce (Picea abies Karst.) through dot-blot selection. Theor. Appl. Genet. 104: 1035–1041.
Scotti I., Paglia G.P., Magni F., and Morgante M., 2006. Population genetics of Norway spruce (Picea abies Karst.) at regional scale: sensitivity of different microsatellite motif classes in detecting differentian. Ann. For. Sci. 63: 485–491.
Selkoe K.A. and Toonen R.J., 2006. Microsatellites for ecologists: a practical guide to using and evaluating microsatellite markers. Ecol. Lett. 9: 615–629.
Szmidt A.Z. and Wang X.R., 1993. Molecular systematics and genetic differentiation of Pinus sylvestris (L.) and P. densiflora (Sieb. et Zucc.). Theor. Appl. Genet. 86: 159–165.
Thomas B.R., Macdonald S.E., Hicks M., Adams D.L., and Hodgetts R.B., 1999. Effects of reforestation methods on genetic diversity of lodgepole pine: an assessment using microsatellite and randomly amplified polymorphic DNA markers. Theor. Appl. Genet. 98: 793–801.
Wang Y.H., Korpelainen H., and Li C.Y., 2006. Microsatellite polymorphism in the edaphic spruce, Picea asperata, originating from the mountains of China. Silva Fenn. 40: 561–575.
Weir B.S. and Cockerham C.C., 1984. Estimating F-statistics for the analysis of population structure. Evolution 38: 1358–1370.
Wright S., 1969. Evolution and genetics of populations. Vol. 2, The theory of gene frequencies, Chicago, University of Chicago Press.
Xia T., Meng L., Mao K., Tian B., Miehe G., and Liu J., 2008. Genetic variation in the Qinghai-Tibetan plateau endemic and endangered conifer Cupressus gigantea, detected using RAPD and ISSR markers. Silvae Genet. 57: 85–92.
Ying T.S., 1989. Areography of the gynmosperms of China (1) — distribution of the Pinaceae of China. Acta Phytotaxonomica Sinica 27: 27–38.
Yuan R.J., Wang B.R., and Yang S.H., 2007. Comparative study on Picea and Abies in Hengduan mountainous areas. Journal of West China Forestry Science 36: 16–21.
Zhang Q., Chiang T.Y., George M., Liu J.Q., and Abbott R.J., 2005. Phylogeography of the Qinghai-Tibetan Plateau endemic Juniperus przewalskii (Cupressaceae) inferred from chloroplast DNA sequence variation. Mol. Ecol. 14: 3513–3524.
Zhang X.L., Yuan Y.M., and Ge X.J., 2007. Genetic structure and differentiation of Gentiana atuntsiensis. In: W.W. Smith and G.S.T.N. Ho (Eds), (Gentianaceae) as revealed by ISSR markers. Bot. J. Linn. Soc. 154: 225–232.
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Lu, Z., Wang, Y., Zhang, X. et al. Genetic variation of isolated Picea balfouriana populations from the southeast of the Qinghai-Tibet Plateau. Ann. For. Sci. 66, 607 (2009). https://doi.org/10.1051/forest/2009052
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DOI: https://doi.org/10.1051/forest/2009052