OJGen  Vol.3 No.2 , June 2013
Transferability and application of microsatellites (SSRs) from Juniperus communis L. to Juniperus procera Hochst. Ex endl.
ABSTRACT

Transferability of five nuclear microsatellite markers (Jc-16, Jc-31, Jc-32, Jc-35 and Jc-37) that were originally developed for J. communis was tested to J. procera. Jc-31 & Jc-37 showed successful amplifications and polymorphism in J. procera. Jc-35 which had been reported as polymorphic in J. communis was monomorphic in J. procera while the primer pair for Jc-32 failed to record any amplification. The remaining one primer pair (Jc-16) showed double loci ampli-fication in both J. procera and the control J. communis suggesting further examination of the primer pair and its binding sites. Genetic variation of six Ethiopian J. procera populations: Chilimo, Goba, Menagesha-Suba, Wef-Washa, Yabelo and Ziquala was assessed based on the two polymorphic loci (Jc-31 & Jc-37) in 20 - 24 individuals of each population. From these two loci, a total of 41 alleles could be retrieved. Two populations that are located south east of the Great Rift Valley together harboured 75% of private alleles signifying their deviant geo-ecological zones and suggesting special consideration for conservation. Chilimo, which is at the western margin of Juniper habitat in Ethiopian central highlands scored the highest fixation (FIS = 0.584) entailing lower immigrant genes and hence higher inbreeding. The AMOVA revealed that 97% of the variation resided within the population while still among population variation was significant (p < 0.05).


Cite this paper
Sertse, D. , Gailing, O. , Eliades, N. and Finkeldey, R. (2013) Transferability and application of microsatellites (SSRs) from Juniperus communis L. to Juniperus procera Hochst. Ex endl.. Open Journal of Genetics, 3, 115-126. doi: 10.4236/ojgen.2013.32015.
References
[1]   [1] Keiper, F.J., Hayden, M.J., Park, R.F. and Wellings, C.R. (2003) Molecular genetic variability of Australian isolates of five cereal rust pathogens. Mycological Research, 107, 545-556. doi:10.1017/S0953756203007809

[2]   Stefenon, V.M., Gailing, O. and Finkeldey, R. (2008) The role of gene flow in shaping genetic structures of the subtropical conifer species Araucaria angustifolia. Plant Biology, 10, 356-364. doi:10.1111/j.1438-8677.2008.00048.x

[3]   Finkeldey, R. and Hattemer, H.H. (2007) Tropical forest genetics. Springer-Verlag, Berlin, Heidelberg, 315 pp. doi:10.1007/978-3-540-37398-8

[4]   Dow, B.D. and Ashley, M.V. (1996) Microsatellite analysis of seed dispersal and parentage of saplings in bur oak, Quercus macrocarpa. Molecular Ecology, 5, 120-132. doi:10.1111/j.1365-294X.1996.tb00357.x

[5]   Streiff, R., Labbe, T., Bacilieri, R., Steinkellner, H., Glossl, J. and Kremer, A. (1998) With in population genetics structure in Quercus rubor L. and Quercus petaea (Matt.) Liebl. Assessed with izozymes and microsatellites. Molecular Ecology, 7, 317-328. doi:10.1046/j.1365-294X.1998.00360.x

[6]   Collevatti, R.G., Grattapaglia, D. and Hay, J.D. (2001) Population genetic structure of the endangered tropical tree species Caryocar brasiliense, based on variability at microsatellite loci. Molecular Ecology, 10, 349-356.

[7]   Mottura, M.C., Finkeldey, R., Verga, A.R. and Gailing, O. (2005) Development and characterization of microsatellite markers for Prosopis chilensis and Prosopis flexuosa and cross-species amplification. Plant Molecular Biology Reporter, 22, 251-258. doi:10.1007/BF02773135

[8]   Pandey, M. (2005) Development of microsatellites in sycamore maple (Acer pseudoplatanus L.) and their application in population genetics. Ph.D. Dissertation, Institute of Forest Genetics and Forest Tree Breeding, Georg-August University of Gottingen, Gottingen.

[9]   Pohjonen, V. and Pukkala, T. (1992) Juniperus procera Hocht. ex Endl. in Ethiopian forestry. Forest Ecology and Management, 49, 75-85. doi:10.1016/0378-1127(92)90161-2

[10]   Negash, L. (1995) Indigenous trees of Ethiopia: Biology, uses and propagation techniques. SLU Rprocentralen, Umea, 285 pp.

[11]   Adams, R.P. (2004) Juniperus of the world: The genus Juniperus. Trafford Publishing, Victoria BC, Canada, 275 pp.

[12]   Kerfoot, O. (1975) Origin and speciation of the Cupressaceae in Sub-Sahara Africa. Boissiera, 24, 145-150.

[13]   Adams, R.P., Demeke, T. and Abulfatih, H.A. (1993) RAPD DNA Fingerprints and terpenoids: Clues to past migrations of Juniperus in Arabia and east Africa. Theoretical and Applied Genetics, 87, 22-26. doi:10.1007/BF00223738

[14]   Berube, Y., Ritland, C. and Ritland, K. (2003) Isolation, characterization, and cross-species utility of microsatellites in yellow cedar (Chamaecyparis nootkatensis). Genome, 46, 353-361. doi:10.1139/g03-014

[15]   Nakao, Y., Itwata, H., Mutsumota, A., Tsumura, Y. and Tomaru, N. (2001) Highly polymorphic microsatellite markers in chmaecyparis obtusa. Canadian Journal of Forest Research, 31, 2248-2251. doi:10.1139/x01-145

[16]   Mlangeni, E.T. (2005) Genetic diversity and population structure in the East African Pencil Cedar, Juniperus procera (Cupressaceae). M.Sc. Thesis, University of Oslo, Oslo.

[17]   Michalczyk, I.M., Sebastiani, F., Buonamici, A., Cremer, E., Mengel, C., Ziegenhagen, B. and Vendramin, G.G. (2006) Characterization of highly polymorphic nuclear microsatellite loci in Juniperus communis L. Molecular Ecology Notes, 6, 346-348. doi:10.1111/j.1471-8286.2005.01227.x

[18]   Zhang, Q., Yang, Y.Z., Wu, G.L., Zhang, D.Y. and Liu, J.Q. (2008) Isolation and characterization of microsatellite DNA primers in Juniperus przewalskii Kom (Cupressaceae). Conservation Genetics, 9, 767-769. doi:10.1007/s10592-007-9387-y

[19]   Opgenoorth, L. (2009) Identification and characterization of microsatellite marker in the tetraploid Juniperus tibetica Kom. using next generation sequencing. Conservation Genetic Resources, 1, 253-255. doi:10.1007/s12686-009-9062-3

[20]   Bekele, A.T. (2007) Useful trees and shrubs for Ethiopia: Identification, propagation and management for agricultural and pastoral community. World Agroforestry Center, Nairobi, 559 pp.

[21]   Garzulia, M. (2006) Threatened, endangered and vulnerable tree species: A comparison between FRA 2005 and the IUCN red list. Working Paper 108/E, FAO, Forestry Department, Rome, Italy.

[22]   Borghesio, L., Giannetti, F., Ndang’ang’a, K. and Shimelis, A. (2004) The present conservation status of Juniperus forests in the South Ethiopian Endemic Bird Area. African Journal of Ecology, 42, 137-143. doi:10.1111/j.1365-2028.2004.00511.x

[23]   IUCN (2009) Juniperus procera: Red list of threatened species. Conifer Specialist Group Report, 1998.

[24]   Nei, M. (1978) Estimation of Average heterozygosity and genetic distance from a small number of individuals. Genetics, 89, 583-590.

[25]   Yeh, F., Yang, R.C. and Boyle, T. (2000) POPGEN (version 1.32), microsoft windows-based freeware for population genetic analysis. http://www.ualberta.ca/~fyeh/pr01.htm

[26]   Rohlf, F.J. (1998) NTSYSpc. Numerical taxonomy and multivariate analysis system. Version 2.0, User Guide: Exeter Software, Setauket, New York, 31 pp.

[27]   Farjon, A. (2005) A monograph of Cupressaceae and Sciadopitys. Royal Botanic Gardens, Kew, 648 pp.

[28]   Michalczyk, I.M. (2008) Application of DNA marker systems to test for genetic imprints of habitat fragmentation in Juniperus communis L. on different spatial and temporal scales. Ph.D. Dissertation, Department of Conservation Biology, Philipps-University of Marburg, Marburg.

[29]   Primmer, C.R., Raudsepp, T., Chowdhary, B.P., Moller, A.P. and Ellegren, H. (1997) Low frequency of microsatellites in the avian genome. Genome Research, 7, 471-482.

[30]   Hancock, J.M. (1999) Microsatellites and other simple sequences: Genomic context and mutational mechanism, In: Goldstein, D.B. and Schlotterer, C., Eds., Microsatellites: Evolution and applications, Oxford University Press, New York, 1-9.

[31]   Garner, T.W.J. (2002) Genome size and microsatellites: The effect of nuclear size on amplification potential. Genome, 45, 212-215. doi:10.1139/g01-113

[32]   Fischer, D. and Bachman, K. (1998) Microsatellite enrichment in organisms with large genomes (Allium cepa L.). BioTechniques, 24, 796-802.

[33]   Elsik, C.G. and Williams, C.G. (2001) Low-copy microsatellite recovery from a conifer genome. Theoretical and Applied Genetics, 13, 1189-1195. doi:10.1007/s001220100725

[34]   Bogunic, F., Muratovic, E., Brown, S.C. and Siljak-Yakovlev, S. (2003) Genome size and base composition of five Pinus species from the Balkan region. Plant Cell Reports, 22, 59-63. doi:10.1007/s00299-003-0653-2

[35]   Fisher, P.J., Richardson, T.E. and Gardner, R.C. (1998) Characteristics of single- and multi-copy microsatellites from Pinus radiate. Theoretical and Applied Genetics, 96, 969-979. doi:10.1007/s001220050828

[36]   Billington, H.L. (1992) Effect of population size on genetic variation in a dioecious conifer. Conservation Biology, 5, 115-119. doi:10.1111/j.1523-1739.1991.tb00394.x

[37]   Hamrick, J.L., Godt, M.J.W. and Sherman-Broyles, S.L. (1992) Factors influencing levels of genetic diversity in woody plant species. New Forests, 6, 95-124. doi:10.1007/BF00120641

[38]   Hamrick, J.L. and Godt, M.J.W. (1996) Effects of life history traits on genetic diversity in plant species. Transaction of the Royal Society of London Series B, 351, 1291-1298. doi:10.1098/rstb.1996.0112

[39]   Weidema, I.R., Magnussen, L.S. and Philipp, M. (2000) Gene flow and mode of pollination in a dry-grassland species, Filipendula vulgaris (Rosaceae). Heredity, 84, 311-320. doi:10.1046/j.1365-2540.2000.00669.x

[40]   Gerard, J., Oostermeijer, B. and de Knegt, B. (2004) Genetic population structure of the wind-pollinated, dioecious shrub Juniperus communis in fragmented Dutch heathlands. Plant Species Biology, 19, 175-184. doi:10.1111/j.1442-1984.2004.00113.x

[41]   White, T.L., Adams, W.T. and Neale, D.B. (2007) Forest genetics. Oxford University Press, Oxford. doi:10.1079/9781845932855.0000

[42]   Demissew, S. (1988) The floristic composition of the Menagesha state forest and the need to conserve such forests in Ethiopia. Mountain Research and Development, 8, 243-247. doi:10.2307/3673454

[43]   Eshetu, Z. (2002) Historical C3–C4 vegetation pattern on forested mountain slopes: Its implication for ecological rehabilitation of degraded highlands of Ethiopia by afforestation. Journal of Tropical Ecology, 18, 743-758. doi:10.1017/S0266467402002481

[44]   Sertse, D., Gailing, O., Eliades, E.G. and Finkeldey, R. (2011) Anthropogenic and natural causes influencing genetic structure of Juniperus procera. Hochst. ex. Endl. in the Ethiopian highlands. Genetic Resource and Crop Evolution, 58, 849-859. doi:10.1007/s10722-010-9623-z

[45]   Lee, S.L., Tani, N., Ng, K.K.S. and Tsumura, Y. (2004) Characterization of 15 polymorphic microsatellite loci in an endangered tropical tree Hopea bilitonensis (Dipterocarpaceae) in Peninsular Malaysia. Molecular Ecology Notes, 4, 147-149. doi:10.1111/j.1471-8286.2004.00593.x

[46]   Sanderson, M.J. and Hufford, L. (1996) Homoplasy: The recurrence of similarity in evolution. Academic Press, San Diego.

[47]   Donoghue, M.J. and Ree, R.H. (2000) Homoplasy and developmental constraints: A model and example from plants. American Zoologist, 40, 759-769. doi:10.1668/0003-1569(2000)040[0759:HADCAM]2.0.CO;2

[48]   Malcolm, J. and Evangelista, P.H. (2005) The range and status of Mountain Nyala: Case study in Bale Mountains, Ethiopia, 42 pp. www.ethiopianwolf.org/publications

[49]   Umer, M., Lamb, H.F., Bonnefill, R., Le′zin, A.M., Tierceline, J.J., Gibert, E., Cazet, J.P. and Watrin, J. (2007) Late pleistocene and holocene vegetation history of the Bale Mountains, Ethiopia. Quaternary Science Reviews, 26, 2229-2246. doi:10.1016/j.quascirev.2007.05.004

[50]   Allendorf, F.W. (1986) Genetic drift and the loss of alleles versus heterozygosity. Zoo Biology, 5, 181-190. doi:10.1002/zoo.1430050212

[51]   Knapp, E.E. and Connors, P.G. (1999) Genetic consequences of a single-founder population bottleneck in Trifolium amoenum (Fabaceae). American Journal of Botany, 86, 124-130. doi:10.2307/2656961

[52]   Keller, L.F., Jeffery, K.J., Arcese, P., Beaumont, M.A., Hochachka, W.M., Smith, J.N.M. and Bruford, M.W. (2001) Immigration and the ephemerality of a natural population bottleneck: Evidence from molecular markers. Proceedings: Biological Sciences, 268, 1387-1394. doi:10.1098/rspb.2001.1607

[53]   Wright, S. (1931) Evolution in Mendelian populations. Genetics, 16, 97-159.

[54]   Wright, S. (1951) The genetical structure of populations. Annals of Eugenics, 15, 323-354.

[55]   Suter, M., Schneller, J.J. and Vogel, J.C. (2000) Investigations into the genetic variation, population structure, and breeding systems of the fern Asplenium trichomanes subsp. Quadrivalens. International Journal of Plant Science, 161, 233-244. doi:10.1086/314258

[56]   Franceschinelli, E.V., Jacobi, C.M., Drummond, G.M. and Resende, M.F.S. (2006) The genetic diversity of two Brazilian Vellozia (Velloziaceae) with different patterns of spatial distribution and pollination biology. Annals of Botany, 97, 585-592. doi:10.1093/aob/mcl007

[57]   Collevatti, R.G., Leite, K.C.E., de Miranda, G.H.B. and Rodrigues, F.H.G. (2007) Evidence of high inbreeding in a population of the endangered giant anteater, Myrmecophaga tridactyla (Myrmecophagidae), from Emas National Park. Genetics and Molecular Biology, 30, 112-120. doi:10.1590/S1415-47572007000100020

[58]   Bekele, T. (1994) Phytosociology and ecology of a humid afromontane forest on the central plateau of Ethiopia. Journal of Vegetation Science, 5, 87-98. doi:10.2307/3235642

[59]   Kingdon, J. (1990) Island Africa: The evolution of Africa’s rare animals and plants. Princeton University Press, Princeton.

[60]   Hillman, J.C. (1988) The Bale Mountains National Park area, southeast Ethiopia, and its management. Mountain Research and Development, 8, 253-258. doi:10.2307/3673456

[61]   Mamo, N., Mihretu, M., Fekadu, M., Tigabu, M. and Teketay, D. (2006) Variation in seed and germination characteristics among Juniperus procera populations in Ethiopia. Forest Ecology and Management, 225, 320-327. doi:10.1016/j.foreco.2006.01.026

[62]   Tigabu, M., Fjellstrom, J., Odén, P.C. and Teketay, D. (2007) Germination of Juniperus procera seeds in response to stratification and smoke treatments, and detection of insect-damaged seeds with VIS + NIR spectroscopy. New Forests, 33, 155-169. doi:10.1007/s11056-006-9020-9

[63]   Wodemariam, T.G. (1998) Diversity of woody plants and avi fauna in a dry afromontane forest: On the central platue of Ethiopia. Master of Science Thesis, Swedish University of Agricultural Science, Skinnskatteberg.

[64]   Shumi, G. (2009) The structure and regeneration status of trees and shub species of Chilimo forest-ecological sustainability indicators for participatory forest management (PFM) in Oromia Ethiopia. Master of Science Thesis, University of Dresden, Dresden.

 
 
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