Identification of gene pools used in restoration and conservation by chloroplast microsatellite markers in Iberian pine species

  • Enrique Hernández-Tecles ETSIA, University of Castilla-La Mancha. Dept. Plant Prod and Agric Technol. Campus Universitario s/n. 02071 Albacete
  • Jorge de las Heras ETSIA, University of Castilla-La Mancha. Dept. Plant Prod and Agric Technol. Campus Universitario s/n. 02071 Albacete
  • Zaida Lorenzo INIA-CIFOR, Dept. Ecol and Genet. Ctra. de la Coruña km. 7,5, 28040 Madrid
  • Miguel Navascués INRA, UMR CBGP Centre de Biologie pour la Gestion des Populations. 755 avenue du campus Agropolis. CS30016. 34988 Montferrier-sur-Lez Cedex
  • Ricardo Alia INIA-CIFOR, Dept. Ecol and Genet. Ctra. de la Coruña km. 7,5, 28040 Madrid. Sustainable Forest Management Research Institute, UVA-INIA. Avda Madrid 57, 34004 Palencia.
Keywords: genetic distance, region of provenance, fingerprinting


Aim of study: To contribute to the characterization of the origin of material used in afforestation, restoration or conservation activities by using Cp-SSR markers.

Area of study: We used information from the natural range of Iberian pines, from Spain.

Materials and methods: We used Iberian pines as an example to undertook gene pool characterization based on a wide Iberian sample of 97 populations from five Pinus species (Pinus halepensis, Pinus pinaster, Pinus nigra, Pinus sylvestris and Pinus uncinata). Haplotypes from each analyzed tree (derived from nine chloroplast microsatellites markers in P. halepensis and six in the rest of the species) were obtained. Based on this information we subdivided each species in regions (considering both genetic structure and its application in afforestation, restoration and conservation programs) and tested the assignation of populations to the different groups based on the genetic distance among samples.

Main results: The rate of successful identification of populations among the different species was very high (> 94 %) for P. nigra, P. sylvestris and P. uncinata, high (81 %) for P. pinaster, and low (< 65 %) for P. halepensis.

Research highlights: Chloroplast DNA markers from extensive population datasets can be used to assign the origin of the forest reproductive material in some pine species.


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Alfaro RI, Fady B, Vendramin GG, Dawson IK, Fleming RA, Sáenz-Romero C, Lindig-Cisneros RA, Murdock, T et al., 2014. The role of forest genetic resources in responding to biotic and abiotic factors in the context of anthropogenic climate change. For Ecol Manage 333: 76-87.

Alía R, Garcia del Barrio JM, Iglesias S, 2009a. Regiones de procedencia de especies forstales de España. Parques Nacionales, Madrid. 361 p.

Alía R, Alba N, Chambel MR, Barba D, Iglesias S, 2009b. Genetic quality of forest reproductive materials in Land restoration programmes. In Innovative approaches in forest restoration; Vallejo VR, Bautista S, Aaronson J (eds), pp: 89-103. CEAM, Valencia.

Anonymous, 2007. Pan-European Recommendations for Afforestation and Reforestation in the context of the UNFCCC. Warsaw, Poland.

Aragonés A, Barrena I, Espinel S, Herrán A, Ritter E, 1997. Origin of Basque populations of radiata pine inferred from RAPD data. Ann Sci For 54 (8): 697-703.

Aravanopoulos FA, 2011. Genetic monitoring in natural perennial plant populations. Botany 89: 75-81.

Bautista S, Aronson J, Vallejo VR, 2009. Land restoration to combat desertification. Innovative approaches, quality control and project evaluation. CEAM, Valencia.

Breed MF, Stead MG, Ottewell KM, Gardner MG, Lowe AJ, 2012. Which provenance and where ? Seed sourcing strategies for revegetation in a changing environment. Conserv Genet 14 (1): 1-10.

Bucci G, Vendramin GG, 2000. Delineation of genetic zones in the European Norway spruce natural range: preliminary evidence. Mol Ecol 9 (7): 923-34.

Bucci G, González-Martínez SC, Le Provost G, Plomion C, Ribeiro MM, Sebastiani F, Alía R, Vendramin GG, 2007. Range-wide phylogeography and gene zones in Pinus pinaster Ait. revealed by chloroplast microsatellite markers. Mol Ecol 16(10):2137-53.

Bucharova A, Michalski S, Hermann JM, Heveling K, Durka W, Hölzel N, Kollmann J, Bossdorf O, 2016. Genetic differentiation and regional adaptation among seed origins used for grassland restoration: Lessons from a multispecies transplant experiment. J Appl Ecol 54: 127-136.

Corander J, Waldmann P, Sillanpää MJ, 2003. Bayesian analysis of genetic differentiation between populations. Genetics 163 (1): 367-374.

Dawson KJ, Belkhir K, 2001. A Bayesian approach to the identification of panmictic populations and the assignment of individuals. Genet Res 78(1):59-77.

Degen B, Holtken A, Rogge M. 2010. Use of DNA-Fingerprints to control the origin of forest reproductive material. Silvae Genetica 59 (6): 268-273.

Deguilloux MF, Pemonge MH, Petit RJ, Eguillouxa MD, Emongea MP, Etitb RJP, 2004. DNA-based control of oak wood geographic origin in the context of the cooperage industry. Ann For Sci 61: 97-104.

Dupanloup I, Scheneider S, Excoffier L, 2002. A simulated annealing approach to define the genetic structure of populations. Mol Ecol 11: 2571-2581.

Earl DA, vonHoldt BM, 2012. STRUCTURE HARVESTER: A website and program for visualizing STRUCTURE output and implementing the Evanno method. Conserv Genet Resour 4(2):359-361.

Evanno G, Regnaut S, Goudet J, 2005. Detecting the number of clusters of individuals using the software STRUCTURE: A simulation study. Mol Ecol 14 (8): 2611-2620.

Falush D, Stephens M, Pritchard JK, 2003. Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics 164 (4): 1567-1587.

Fidler F, Burgman MA, Cumming G, Buttrose R, Thomason N, 2006. Impact of criticism of null-hypothesis significance testing on statistical reporting practices in conservation biology. Conserv Biol 20 (5): 1539-1544.

Fussi B, Westergren M, Aravanopoulos F, Baier R, Kavaliauskas D, Finzgar D, Alizoti P, Bozic G, et al., 2016, Forest genetic monitoring: an overview of concepts and definitions. Environ Monit Assess 188 (8): 493.

García del Barrio JM, Auñon FJ, Sánchez de Ron D, Alía R, 2013. Assessing regional species pools for restoration programs in Spain. New Forests 44 (4): 559-576.

Gil LA, Diaz-Fernandez P, Jiménez P, Roldan M, Alía R, Agúndez D, Miguel J, Martín S, et al., 1996. Las regiones de procedencia de Pinus halepensis Mill. en España. ICONA, Madrid.

Gómez A, Vendramin GG, González-Martínez SC, Alía R, 2005. Genetic diversity and differentiation of two Mediterranean pines (Pinus halepensis Mill. and Pinus pinaster Ait.) along a latitudinal cline using chloroplast microsatellite markers. Divers Distrib 11 (3): 257-263.

González-Martínez SC, Mariette S, Ribeiro MM, Burban C, Raffin A, Chambel MR, Ribeiro CAM, Aguiar A, et al., 2004. Genetic resources in maritime pine (Pinus pinaster Aiton): molecular and quantitative measures of genetic variation and differentiation among maternal lineages. For Ecol Manage 197 (1-3): 103-115.

Graudal L, Aravanopoulos FA, Bennadji Z, Changtragoon S, Fady B, Kjær ED, Loo J, Ramamonjisoa L, et al., 2014. Global to local genetic diversity indicators of evolutionary potential in tree species within and outside forests. For Ecol Manage 333: 35-51.

Grivet D, Sebastiani F, González-Martínez SC, Vendramin GG, 2009. Patterns of polymorphism resulting from long-range colonization in the Mediterranean conifer Aleppo pine. The New Phytologist 184 (4): 1016-28.

Grivet D, Climent J, Zabal-Aguirre M, Neale DB, Vendramin GG, González-Martínez SC, 2013. Adaptive evolution of Mediterranean pines. Mol Phylog Evol 68 (3): 555-566.

Hamann A, Koshy MP, Namkoong G, Ying CC, 2000. Genotype-environment interactions in Alnus rubra : developing seed zones and seed-transfer guidelines with spatial statistics and GIS. For Ecol Manage 136: 107-119.

Heuertz M, Teufel J, González-Martínez SC, Soto A, Fady B, Alía R, Vendramin GG, 2009. Geography determines genetic relationships between species of mountain pine Pinus mugo complex in western Europe. J Biogeogr 37 (3): 541-556.

Holmes PM, Richardson DM, 1999. Protocols for restoration based on recruitment dynamics, community structure, and ecosystem function: Perspectives from South African fynbos. Restor Ecol 7 (3): 215-230.

Hong L, Leong S, Kit K, Ng S, Faridah Q, Faridah-Hanum I, 2010. Forensic DNA profiling of tropical timber species in Peninsular Malaysia. For Ecol Manage 259 (8): 1436-1446.

Honjo M, Ueno S, Tsumura Y, Handa T, Washitani I, Ohsawa R, 2008. Conservation genetics. V. 9. Kluwer Academic Publishers.

Isbell F, Calcagno V, Hector A, Connolly J, Harpole WS, Reich PB, Scherer-Lorenzen M, Schmid B, et al., 2011. High plant diversity is needed to maintain ecosystem services. Nature 477 (7363): 199-202.

Jaramillo-Correa JP, Verdú M, González-Martínez SC, 2010. The contribution of recombination to heterozygosity differs among plant evolutionary lineages and life-forms. BMC Evol Biol 10: 22.

Jimenez P, Díaz-Fernández PM, Iglesias S, Prada A, García-del-Barrio JM, Alba N, Alía R, 2009. National strategy for the conservation and sustainable use of forest genetic resources: a framework for coordinating Central and Autonomous Regional Government activities in Spain. Inv Agrar: Sist Rec For 18 (1): 13-19.

Jones TA, 2003. The restoration gene pool concept: Beyond the native versus non-native debate. Restor Ecol 11 (3): 281-290.

Jones TA, Monaco TA, 2009. A role for assisted evolution in designing native plant materials for domesticated landscapes. Frontiers Ecol Environ 7 (10): 541-547.

Konnert M, Fady B, Wolter F, Ducci F, Bozzano M, Maaten T, Kowalczyk J, 2015. Use and transfer of forest reproductive material Use and transfer of forest reproductive material in Europe in the context. European Forest Genetic Resources Programme (EUFORGEN), Bioversity International, Rome, Italy.

Koskela J, Lefèvre F, Schueler S, Kraigher H, Olrik DC, Hubert J, Longauer R, Bozzano M, et al., 2013. Translating conservation genetics into management : Pan-European minimum requirements for dynamic conservation units of forest tree genetic diversity. Biol Conserv 157: 39-49.

Langlet O, 1971. Two hundred years genecology. Taxon 20 (5-6): 653-721.

Leimu R, Fischer M, 2008. A meta-analysis of local adaptation in plants. PLoS ONE 3 (12): 1-8.

Manly BFJ, 1997. Randomization, Bootstrap and Monte Carlo Methods in Biology, 2nd ed. Chapman & Hall, NY.

Mckay JK, Christian CE, Harrison S, Rice KJ. 2005. How local is local? A review of practical and conceptual issues in the genetics of restoration. Restor Ecol 13 (3): 432-440.

Montero G, 1997. L'attività di rimboschimento in Spagna negli ultimi 50 anni. Legno, Cellulosa, Carta 4: 35-42.

Morgante M, Pfeiffer A, Costacurta A, Olivieri AM, 1996. Molecular tools for population and ecological genetics in coniferous trees. Phyton 36: 133-142.

Moritz C, 1994. Defining evolutionarily-significant-units for conservation. Trends Ecol Evol 9: 373-375.

Moritz C, 1999. Conservation units and traslocations: stategies for conserving evolutionary processes. Hereditas 130 (3):217-228.

Nanson A, 2001. The New OECD Scheme for the Certification of Forest Reproductive Materials. Silvae Genetica 50 (5-6): 181-187.

Partel M, Szava-Kovats R, Zobel M, Pärtel M, 2011. Dark diversity: shedding light on absent species. Trends Ecol Evol 26 (3): 124-128.

Pritchard JK, Stephens M, Donnelly P, 2000. Inference of population structure using multilocus genotype data. Genetics 155 (2): 945-959.

Ribeiro MM, Le-Provost G, Gerber S, Vendramin GG, Anzidei M, Decroocq S, Marpeau A, Mariette S. et al., 2002. Origin identification of maritime pine stands in France using chloroplast simple-sequence repeats. Ann Forest Sci 59 (1): 53-62.

Robledo-Arnuncio JJ, Navascués M, González-Martínez SC, Gil LA, 2009. Estimating gametic introgression rates in a risk assessment context: A case study with Scots pine relicts. Heredity 103 (5): 385-393.

Sgrò CM, Lowe AJ, Hoffmann AA, 2011. Building evolutionary resilience for conserving biodiversity under climate change. Evol Appl 4 (2): 326-337.

Soranzo N, Alía R, Provan J, Powell W, 2000. Patterns of variation at a mitochondrial sequence-tagged- site locus provides new insights into the postglacial history of European Pinus sylvestris populations. Mol Ecol 9 (9): 1205-1211.

Soto A, Robledo-Arnuncio JJ, González-Martínez SC, Smouse PE, Alía R, 2010. Climatic niche and neutral genetic diversity of the six Iberian pine species : a retrospective and prospective view. Mol Ecol 19 (7): 1396-1409.

Steinitz O, Robledo-Arnuncio JJ, Nathan R, 2012. Effects of forest plantations on the genetic composition of conspecific native Aleppo pine populations. Mol Ecol 21 (2): 300-313.

Sutherland WJ, Armstrong-Brown S, Armsworth PR, Tom B, Brickland J, Campbell CD, Chamberlain DE, Cooke AI, et al., 2006. The identification of 100 ecological questions of high policy relevance in the UK. J Appl Ecol 43 (4): 617-627.

Thomson JR, Moilanen AJ, Vesk PA, Bennett AF, Nally RM, 2009. Where and when to revegetate: a quantitative method for scheduling landscape reconstruction. Ecol Appl 19 (4): 817-828.

Tigabu M, Oden PC, Lindgren D, 2005. Identification of seed sources and parents of Pinus sylvestris L. using visible-near infrared reflectance spectra and multivariate analysis. Trees-Structure and Function 19: 468-476.

Tnah LH, Lee SL, Ng KKS, Tani N, Bhassu S, Othman RY, 2009. Geographical traceability of an important tropical timber (Neobalanocarpus heimii) inferred from chloroplast DNA. For Ecol Manage 258 (9): 1918-1923.

Unger GM, Vendramin GG, Robledo-Arnuncio JJ, 2014. Estimating exotic gene flow into native pine stands: zygotic vs. gametic components. Mol Ecol 23 (22): 5435-5447.

Valbuena-Carabaña M, de Heredia UL, Fuentes-Utrilla P, González-Doncel I, Gil L, 2009. Historical and recent changes in the Spanish forests: A socio-economic process. Rev Palaeobot Palynol 162 (3): 492-506.

Vander-Mijnsbruggea K, Bischoff A, Smith B, 2010. A question of origin : Where and how to collect seed for ecological restoration. Basic Appl Ecol 11: 300-311.

Van Andel J, 1998. Intraspecific variability in the context of ecological restoration projects. Persp Plant Ecol Evol Syst 1 (2): 221-237.

Vendramin GG, Anzidei M, Madaghiele A, Bucci G, 1998. Distribution of genetic diversity in Pinus pinaster Ait. as revealed by chloroplast microsatellites. Theor Appl Genet 97 (3): 456-463.

Whitham TG, Bailey JK, Schweitzer JA, Shuster SM, Bangert RK, Leroy CJ, Lonsdorf EV, Allan GJ, et al, 2006. A framework for community and ecosystem genetics: from genes to ecosystems. Nat Rev Genet 7 (7): 510-523.

Zobel M, van der Maarel E, Cecilia D, 1998. Species pool: the concept, its determination and significance for community restoration. Appl Veget Sci 1 (1): 56-66.

How to Cite
Hernández-Tecles, E., de las Heras, J., Lorenzo, Z., Navascués, M., & Alia, R. (2017). Identification of gene pools used in restoration and conservation by chloroplast microsatellite markers in Iberian pine species. Forest Systems, 26(2), e05S.