1. bookVolume 69 (2020): Issue 1 (January 2020)
Journal Details
First Published
22 Feb 2016
Publication timeframe
1 time per year
Open Access

Chloroplast microsatellites reveal genetic diversity and population structure in natural populations of Himalayan Cedar (Cedrus deodara (Roxb.) G. Don) in India

Published Online: 24 Aug 2020
Volume & Issue: Volume 69 (2020) - Issue 1 (January 2020)
Page range: 86 - 93
Journal Details
First Published
22 Feb 2016
Publication timeframe
1 time per year

Himalayan cedar (Cedrus deodara) is one of the most important temperate timber species of Western Himalayas and is considered to be among the endangered conifer species in the region. Knowledge of genetic diversity and population structure will help guide gene conservation strategies for this species. Ten polymorphic chloroplast microsatellites (cpSSR) were used to study genetic diversity and population structure in twenty one natural populations of C. deodara throughout its entire distribution range in Western Himalayas. When alleles at each of the 10 loci were jointly analysed, 254 different haplotypes were identified among 1050 individuals. The cpSSRs indicate that C. deodara forests maintain a moderately high level of genetic diversity (mean h = 0.79 ). AMOVA analysis showed that most of the diversity in C. deodara occurs within populations. Bayesian analysis for population structure (BAPS) revealed spatial structuration of the variation (22 % of the total variation) and substructuring captured nineteen genetic clusters in the entire divisions of the populations. Most of the populations were clustered independently with minor admixtures. The distribution of genetic diversity and sub-structuring of C. deodara may be due to restricted gene flow due to geographic isolation, genetic drift, and natural selection. These findings indicated existence of genetically distinct and different high diversity and low diversity clusters, which are potential groups of populations that require attention for their conservation and management. The results are interpreted in context of future conservation plans for C. deodara.


Al-Rabab’Ah MA and Williams CG (2002) Population dynamics of Pinus taeda L. based on nuclear microsatellites. Forest Ecology and Management, 163: 263-271. https://doi.org/10.1016/s0378-1127(01)00584-910.1016/S0378-1127(01)00584-9Search in Google Scholar

Batar A, Watanabe T and Kumar A (2017) Assessment of Land-Use/Land-Cover Change and Forest Fragmentation in the Garhwal Himalayan Region of India. Environments, 4(2). https://doi.org/10.3390/environments402003410.3390/environments4020034Search in Google Scholar

Cato SA and Richardson TE (1996) Inter- and Intra-specific polymorphism at chloroplast SSR loci and the inheritance of plastids in Pinus radiate D. Don. Theoretical and Applied Genetics, 93(4):587-592. https://doi.org/10.1007/s00122005031910.1007/BF0041795224162352Search in Google Scholar

Chauhan P (2011) Molecular genetic analysis of Chir pine (Pinus roxburghii Sarg. ) through microsatellite markers. Ph.D thesis submitted to Forest Research Institute, Deemed University, Dehradun, India.Search in Google Scholar

Clark CM, Wentworth TR and O’Malley DM (2000) Genetic discontinuity revealed by chloroplast microsatellites in eastern North American Abies (Pinaceae). American Journal of Botany, 87: 774-782. https://doi.org/10.2307/265688510.2307/2656885Search in Google Scholar

Corander J, Cheng L, Marttinen P, Siren J and Tang J (2013) BAPS: Bayesian analysis of population structure manual v. 6.0. Accessed 9 August 2018. http://www.helsinki.fi/bsg/software/BAPS/Search in Google Scholar

Corander J, Waldmann P and Sillanpaa MJ (2003) Bayesian analysis of genetic differentiation between populations. Genetics, 163, 367–374.10.1093/genetics/163.1.367146242912586722Search in Google Scholar

Corander J, Waldmann P, Marttinen P and Sillanpaa MJ (2004) BAPS 2: enhanced possibilities for the analysis of genetic population structure. Bioinformatics, 20: 2363-2369. https://doi.org/10.1093/bioinformatics/bth25010.1093/bioinformatics/bth25015073024Search in Google Scholar

Dagher-Kharrat MBD, Mariette S, Lefevre F, Fady B, March GG, Plomion C and Sovoure A (2006) Geographical diversity and genetic relationships among Cedrus species estimated by AFLP. Tree Genetics and Genomics, 3(3): 275-285. https://doi.org/10.1007/s11295-006-0065-x10.1007/s11295-006-0065-xSearch in Google Scholar

Debazac EF (1964) Manuel des conifères. ENGREF, NancySearch in Google Scholar

Doyle JJ and Doyle JL (1990) Isolation of plant DNA from fresh tissue. Focus, 12: 13-15.Search in Google Scholar

Dumolin-Lapégue S, Demesure B., Corre LEV., Fineschi S, Petit RJ (1997) Phylo-geographic structure of white oaks throughout the European continent. Genetics, 146: 1475–1487.10.1093/genetics/146.4.147512080909258689Search in Google Scholar

Echt C, Vernol DEL., Anzidei M and Vendramin GG (1998) Chloroplast microsatellites reveal population genetic diversity in red pine, Pinus resinosa Ait. Molecular Ecology.7: 307-316. https://doi.org/10.1046/j.1365-294x.1998.00350.x10.1046/j.1365-294X.1998.00350.xSearch in Google Scholar

Eliades N-G, Gailing O, Leinemann L, Fady B and Finkeldey R (2011) High genetic diversity and significant population structure in Cedrus brevifolia Henry, a narrow endemic Mediterranean tree from Cyprus. Plant Systematics and Evolution, 294: 185-198. https://doi.org/10.1007/s00606-011-0453-z10.1007/s00606-011-0453-zSearch in Google Scholar

Eliades N-G and Eliades DG (2009) HAPLOTYPE ANALYSIS: Software for analysis of haplotype data. Distributed by the authors.Forest Genetics and Tree Breeding, Georg-August University Goettingen, Germany. URLSearch in Google Scholar

Excoffier L, Laval G and Schneider S (2005) ARLEQUIN ver. 3.0: An integrated software package for population genetics data analysis. Evolutionary Bioinformatics Online, 1: 47-50. https://doi.org/10.1177/11769343050010000310.1177/117693430500100003Search in Google Scholar

Ginwal HS, Chauhan P, Barthwal S, Sharma A and Sharma R (2011) Cross-Species Amplification and Characterization of Pinus Chloroplast Microsatellite Markers in Cedrus deodara Roxb. Silvae Genetica, 60 (2): 65-69. https://doi.org/10.1515/sg-2011-000910.1515/sg-2011-0009Search in Google Scholar

Gomez A, Gonzalez-Martinez SC, Collada C, Climent J and Gil I (2003) Complex population genetic structure in the endemic Canary Island pine revealed using chloroplast microsatellite markers. Theoretical and Applied Genetics, 107: 1123–1131. https://doi.org/10.1007/s00122-003-1320-210.1007/s00122-003-1320-214523525Search in Google Scholar

Goudet J (2002) FSTAT: A program to estimate and test gene diversities and fixation indices. Version http://www.unil.ch/izea/softwares/fstat.html Grivet D and Petit RJ (2002) Phylogeography of the common ivy (Hedera sp.) in Europe: genetic differentiation through space and time. Molecular Ecology, 11: 1351–1362. https://doi.org/10.1046/j.1365-294x.2002.01522.x10.1046/j.1365-294X.2002.01522.xSearch in Google Scholar

Hamrick JL, Godt MJW and S. L. Sherman-Broyles SL (1992) Factors influencing levels of genetic diversity in woody plant species. New Forests, 6: 95–124. https://doi.org/10.1007/bf0012064110.1007/BF00120641Search in Google Scholar

Hansen OK, Kjaer ED and Vendramin GG (2005) Chloroplast microsatellite variation in Abies nordmanniana and simulation of causes for low differentiation among populations. Tree Genetics and Genomes, 1: 116–123. https://doi.org/10.1007/s11295-005-0016-y10.1007/s11295-005-0016-ySearch in Google Scholar

Heuertz M, FINESCHI S and Anzidei M (2004) Chloroplast DNA variation and postglacial recolonisation of common ash (Fraxinus excelsior L.) in Europe. Molecular Ecology, 13: 3423–3438. https://doi.org/10.1111/j.1365-294x.2004.02333.x10.1111/j.1365-294X.2004.02333.x15488002Search in Google Scholar

Khasa DP, Jaramillo-Correa JP, Jaquish B and Bosquet J (2006) Contrasting micro-satellite variation between subalpine larch and western larch, two closely related species with different distribution patterns. Molecular Ecology, 15:3907–3918. https://doi.org/10.1111/j.1365-294x.2006.03066.x10.1111/j.1365-294X.2006.03066.x17054492Search in Google Scholar

Konzen E (2014) Towards conservation strategies for forest tree endangered species: the meaning of population genetic statistics. Advances in Forestry Science, 1 (1): 45-51.Search in Google Scholar

Ledig FT and Conkle MR (1983) Gene diversity and genetic structure in a narrow endemic torrey pine (Pinus torreyana Parry ex. Carr). Evolution, 37: 79-85. https://doi.org/10.1111/j.1558-5646.1983.tb05515.x10.1111/j.1558-5646.1983.tb05515.x28568032Search in Google Scholar

Lee SL, Wickneswari R, Mahani MC and Zakri AH (2000) Genetic diversity of a tropical tree species, Shorea leprosula Miq. (Dipterocarpaceae), in Malaysia: Implications for conservation of genetic resources and tree improvement. Biotropica, 32: 213-224. https://doi.org/10.1111/j.1744-7429.2000.tb00464.x10.1111/j.1744-7429.2000.tb00464.xSearch in Google Scholar

Maheshwari P and Biswas C (1970) Cedrus. Botanical Monograph No.5 Series. Council of Scientific and Industrial Research, New Delhi.Search in Google Scholar

McDermott JM and McDonald BA (1993) Gene flow in plant pathosystems. Annual Review Phytopathology, 31: 353-373. https://doi.org/10.1146/annurev.py.31.090193.00203310.1146/annurev.py.31.090193.002033Search in Google Scholar

Mehes M, Nkongolo KK and Michael P (2009) Assessing genetic diversity and structure of fragmented populations of eastern white pine (Pinus strobus) and western white pine (Pinus monticola) for conservation management. Journal of Plant Ecology, 2(3): 143-151. https://doi.org/10.1093/jpe/rtp01610.1093/jpe/rtp016Search in Google Scholar

Mehta JP, Shreshthamani and Bhatt VP (2015) Regeneration potential and distribution pattern of tree species along altitudinal gradient in Central Himalaya. International Journal of Scientific and Research Publications, 5 (5): 1-6.Search in Google Scholar

Morgante M, Felice N and Vendramin GG (1998) Analysis of hypervariable chloroplast microsatellites in Pinus halepensis reveals a dramatic genetic bottleneck. In A. Karp, P. G. Isaac, and D. S. Ingram [eds.], Molecular tools for screening biodiversity, 407–412. Chapman and Hall, London, UK. https://doi.org/10.1007/978-94-009-0019-6_7310.1007/978-94-009-0019-6_73Search in Google Scholar

Neale DB and SEDEROFF RR (1989) Paternal inheritance of chloroplast DNA and maternal inheritance of mitochondrial DNA in loblolly pine. Theoretical and Applied Genetics, 77: 212-216. https://doi.org/10.1007/bf0026618910.1007/BF0026618924232531Search in Google Scholar

Nei M (1987) Molecular Evolutionary Genetics. Columbia University Press, New York.10.7312/nei-92038Search in Google Scholar

Nybom H and Bartish IV (2000) Effects of life history traits and sampling strategies on genetic diversity estimates obtained with RAPD markers in plants. Perspectives in Plant Ecology, Evolution and Systematics, 3: 93–114. https://doi.org/10.1078/1433-8319-0000610.1078/1433-8319-00006Search in Google Scholar

Palmé A and Vendramin GG (2002) Chloroplast DNA variation, postglacial recolonization and hybridization in hazel, Corylus avellana. Molecular Ecology, 11, 1769–1779. https://doi.org/10.1046/j.1365-294x.2002.01581.x10.1046/j.1365-294X.2002.01581.xSearch in Google Scholar

Parducci L, Szmidt AE, Madaghiele A, Anziei M and Vendramin GG (2001) Genetic variation at chloroplast microsatellites (cpSSRs) in Abies nebrodensis (Lojac.) Mattei and three neighboring Abies species. Theoretical and Applied Genetics, 102: 733–740. https://doi.org/10.1007/s00122005170410.1007/s001220051704Search in Google Scholar

Pons A (1998) L’histoire du genre Cedrusd’aprés les donnéespaléobotaniquesdisponibles. For Méditerr,14: 236–242Search in Google Scholar

Reddy CS, Sreelekshmi S, Jha CS and Dadhwal VK (2013) National assessment of forest fragmentation in India: Landscape indices as measures of the effects of fragmentation and forest cover change. Ecological Engineering, 60, 453e464. http://dx.doi.org/10.1016/j.ecoleng.2013.09.06410.1016/j.ecoleng.2013.09.064Search in Google Scholar

Ribeiro MM, Plomion C, Petit R, Vendramin GG and Szmidt AE (2001) Variation in chloroplast single-sequence repeats in Portuguese maritime pine (Pinus pinaster Ait. ). Theoretical and Applied Genetics, 102: 97–103. https://doi.org/10.1007/s00122005162310.1007/s001220051623Search in Google Scholar

Richards CM, Antolin MF, Reilley A, Poole J and Walters C (2007) Capturing genetic diversity of wild populations for ex situ conservation: Texas wild rice (Zizania texana) as a model. Genetic Resources and Crop Evolution, 54(4): 837–848. https://doi.org/10.1007/s10722-006-9167-410.1007/s10722-006-9167-4Search in Google Scholar

Schoettle AW, Goodrich BA, Hipkins V, Richards C and Kray J (2012) Geographic patterns of genetic variation and population structure in Pinus aristata, Rocky Mountain bristlecone pine. Canadian Journal of Forest Research, 42: 23–37. https://doi.org/10.1139/x11-15210.1139/x11-152Search in Google Scholar

Sharma R and Bhondge S (2016) Unpredictable Reproductive Behavior of Cedrus deodara (Roxb.) G. Don. Journal of Forest and Environmental Science, 32: 113-119. https://doi.org/10.7747/jfes.2016.32.2.11310.7747/JFES.2016.32.2.113Search in Google Scholar

Sharma S and Roy PS (2007) Forest fragmentation in the Himalaya: A Central Himalayan case study. Int. J. Sustain. Dev. World Ecol. 14, 201–210. https://doi.org/10.1080/1350450070946972010.1080/13504500709469720Search in Google Scholar

Sinclair WT, Moncur JD and Ennos RA (1997) Multiple origins for Scots pine (Pinus sylvestris L. ) in Scotland: evidence from mitochondrial DNA variation. Heredity, 80: 233-240. https://doi.org/10.1046/j.1365-2540.1998.00287.x10.1046/j.1365-2540.1998.00287.xSearch in Google Scholar

Szmidt AE (1982) Genetic variation in isolated populations of stone pine (Pinus cembra). SilvaeFennica, 16: 196–200.Search in Google Scholar

Terrab A, Paun O, Talavera S, Tremetsberger K, Arista M, Stuessy TF (2006) Genetic diversity and populations of Moroccan Atlas Cedar (Cedrus atlantica; Pinaceae) determined with cpSSR markers. American Journal of Botany, 93(9): 1274-1280. https://doi.org/10.3732/ajb.93.9.127410.3732/ajb.93.9.127421642191Search in Google Scholar

Tewari DN (1994) A monograph on deodar (Cedrus deodara (Roxb.) G. Don). International Book Distributors, Dehra Dun, India, pp. 3, 14.Search in Google Scholar

Tiwari OP, Rana YS, Krishan RAM, Sharma CM and Bhandari BS (2018) Regeneration dynamics, population structure, and forest composition in some ridge forests of the Western Himalaya, India. Forest Science and Technology, 14: 2, 66-75.https://doi.org/10.1080/21580103.2018.144751710.1080/21580103.2018.1447517Search in Google Scholar

Troup RS (1921) The Silviculture of Indian Trees. Vol. III. Clarendon Press, Oxford. https://doi.org/10.5962/bhl.title.2436310.5962/bhl.title.24363Search in Google Scholar

Vendramin GG, Anzidei M, Madaghiele M and Bucci G (1998) Distribution of genetic diversity in Pinus pinaster Ait. as revealed by chloroplast microsatellites. Theoretical and Applied Genetics, 97: 456–463. https://doi.org/10.1007/s00122005091710.1007/s001220050917Search in Google Scholar

Vendramin GG and Ziegenhagen B (1997) Characterization and inheritance of polymorphic plastid microsatellites in Abies. Genome, 40: 857-864. https://doi.org/10.1139/g97-81110.1139/g97-8119449797Search in Google Scholar

Vendramin GG, Degen B, Petit RJ, Anzidie M, Madaghiele A and Ziegenhagen B (1999) High level of variation at Abies alba chloroplast microsatellite loci in Europe. Molecular Ecology, 8: 1117-1126. https://doi.org/10.1046/j.1365-294x.1999.00666.x10.1046/j.1365-294x.1999.00666.x10447853Search in Google Scholar

Vendramin GG, Lellilr Rossi P and Morgante M (1996) A set of primers for the amplification of 20 chloroplast microsatellites in Pinaceae. Molecular Ecology, 5: 595–598. https://doi.org/10.1046/j.1365-294x.1996.00111.x10.1046/j.1365-294X.1996.00111.xSearch in Google Scholar

Vidakovic M (1991) Conifers. In: Brekalo B (Ed) Morphology and variation. Graficki Zavod, Hrvatske, pp 129–136.Search in Google Scholar

Watano Y, Imazu M and Shimizu T (1996) Spatial distribution of cpDNA and mtDNA haplotypes in a hybrid zone between Pinus pumila and P. parviflora var. Pentaphylla (Pinaceae). Journal of Plant Research, 109: 403-408. https://doi.org/10.1007/bf0234455510.1007/BF02344555Search in Google Scholar

Wright S (1978) Evolution and the Genetics of Population, Variability Within and Among Natural Populations. The University of Chicago Press, Chicago.Search in Google Scholar

Wu JW, Krutovskii KV and Strauss SH (1998) Abundant mitochondrial genome diversity, population differentiation and convergent evolution in pines. Genetics, 150: 1605–1614.10.1093/genetics/150.4.160514604219832536Search in Google Scholar

Yeh FC, Yang RC and Boyle TBJ (1999) PopGene Version 1.31: Microsoft windows based Freeware for Population Genetic Analysis. University of Albert, Edmonton. http://www.ualberta.ca/fyeh/Search in Google Scholar

Ziegenhagen B, Scholz F, Madaghiele A and Vendramin GG (1998) Chloroplast microsatellites as markers for paternity analysis in Abies alba. Canadian Journal of Forestry Research, 28: 317-321. https://doi.org/10.1139/x97-21310.1139/x97-213Search in Google Scholar

Recommended articles from Trend MD

Plan your remote conference with Sciendo