International Journal of Innovative Approaches in Agricultural Research
Abbreviation: IJIAAR | ISSN (Online): 2602-4772 | DOI: 10.29329/ijiaar

Review article    |    Open Access
International Journal of Innovative Approaches in Agricultural Research 2023, Vol. 7(3) 356-370

Microsatellite Markers: The Efficient Method for the Determination of Pollen Contamination in Conifer Seed Orchards

Behiye Banu Bilgen & Nuray Kaya

pp. 356 - 370   |  DOI: https://doi.org/10.29329/ijiaar.2023.602.10

Published online: September 30, 2023  |   Number of Views: 47  |  Number of Download: 141

Download PDF

Abstract

Seed orchards are specialized forest plantations of genetically superior candidate parents selected to produce genetically superior seeds and/or seedlings. Pollen contamination is one of the most important factors affecting the yield, adaptation, and genetic quality of seeds produced from seed orchards in forest tree breeding programs. Potential pollen from forests surrounding the seed orchard is a major concern in tree breeding because it contributes to the loss in genetic gains expected from seed orchard crops. Microsatellite markers are among the most effective markers that are frequently used for creating genetic maps of many species, determining genetic diversity, identifying genetic diseases, population genetic studies, linkage analysis, fingerprint analysis, genotyping, and parental identification. In this study, a bibliometric analysis was performed to quantitatively and qualitatively evaluate the articles published in the last 25 years on seed orchards and pollen contamination. Searching the Web of Science (WOS) with the criteria of “forest trees” and “seed orchards” revealed that 820 articles were published in the last 25 years. It is seen that 77 of these articles are related to pollen contamination. Canada, China, Japan, Sweden, and the USA have been the top contributors to research on pollen contamination in seed orchards of forest trees in the last 25 years, respectively. According to the data obtained, it has been shown that the genetic contamination level of forest tree species in seed orchards is generally between 5% and 90%. It has been determined that microsatellite markers are more widely used in recent years to determine the degree of pollen migration and genetic contamination. It was concluded that studies on pollen contamination were carried out in only two Turkish red pine orchards in Türkiye, which has a total of 189 seed orchards, the majority of which belong to conifers, and that similar studies should be planned in other seed orchards.

Keywords: Bibliometric analysis, Pollen contamination, Seed Orchards, Simple Sequence Repeats

How to Cite this Article

APA 6th edition
Bilgen, B.B. & Kaya, N. (2023). Microsatellite Markers: The Efficient Method for the Determination of Pollen Contamination in Conifer Seed Orchards . International Journal of Innovative Approaches in Agricultural Research, 7(3), 356-370. doi: 10.29329/ijiaar.2023.602.10

Harvard
Bilgen, B. and Kaya, N. (2023). Microsatellite Markers: The Efficient Method for the Determination of Pollen Contamination in Conifer Seed Orchards . International Journal of Innovative Approaches in Agricultural Research, 7(3), pp. 356-370.

Chicago 16th edition
Bilgen, Behiye Banu and Nuray Kaya (2023). "Microsatellite Markers: The Efficient Method for the Determination of Pollen Contamination in Conifer Seed Orchards ". International Journal of Innovative Approaches in Agricultural Research 7 (3):356-370. doi:10.29329/ijiaar.2023.602.10.
References
  1. Adams, W.T., & Birkes, D.S. (1989). Mating patterns in seed orchards. In: Proceedings of 20th Southern Forest tree Improvement Conference, June 26-30, 1989, Charleston, South Carolina. [Google Scholar]
  2. Austerlitz, F., Dick, C.W., Dutech, C., Klein, E.K., Oddou-Muratorio, S., Smouse, P.E., & Sork, V.L. (2004). Using genetic markers to estimate the polen dispersal curve. Molecular Ecology, 13: 937-954. [Google Scholar]
  3. Balloux, F., & Lugon-Moulin, N. (2002). The estimation of population differentiation with microsatellite markers. Molecular Ecology, 11: 155-165. [Google Scholar]
  4. Bandelj, D., Jakse, J., & Javornik, B. (2004). Amplification of fluorescent-labelled microsatellite markers in olives by a novel, economic method. Acta agriculturae Slovenica, 83(2): 323-329. [Google Scholar]
  5. Bilgen, B.B., & Kaya, N. (2014). Chloroplast DNA variation and pollen contamination in a Pinus brutia Ten. clonal seed orchard: implication for progeny performance in plantations. Turkish Journal of Agriculture and Forestry, 38: 540-549. [Google Scholar]
  6. Bilgen, B.B., & Kaya, N. (2016). Use of nSSR markers for determination of clonal identity and genetic structure in a Pinus brutia Ten. clonal seed orchard. Fresenius Environmental Bulletin, 25(9): 3687-3693. [Google Scholar]
  7. Bilir, N., Kang, K.S., Zang, D., & Lindgren, D. (2004). Fertility variation and status number between a base population and a seed orchard of Pinus brutia. Silvae Genetica, 53: 161-163. [Google Scholar]
  8. Bradshaw, A.D. (1972). Some of the evolutionary conseqences of being a Plant. In: M. Dobzhansky K. Hecht and W.C. Stere (Eds.). Evolutionary Biology. Appl. Century Crofts, 25-47, New York. [Google Scholar]
  9. Buiteveld, J., Bakker, E.G., Bovenschen, J., & de Vries, S.M.G. (2001). Paternity analysis in a seed orchard of Quercus robur L. and estimation of the amount of background pollination using microsatellite markers. Forest Genetics, 8 (4): 331-337. [Google Scholar]
  10. Chen, X., Sun, X., Dong, L., & Zhang, S. (2018). Mating patterns and pollen dispersal in a Japanese larch (Larix kaempferi) clonal seed orchard: a case study. Sci. China Life Sci. 61: 1011-1023. https://doi.org/10.1007/s11427-018-9305-7 [Google Scholar] [Crossref] 
  11. D’Amico, I., Juan, C.V., Beatriz, O.S., Ewens, M., & Bessega, C. (2019). Pollen contamination and mating patterns in a Prosopis alba clonal orchard: impact on seed orchards establishment. iForest, 12: 330-337. https://doi.org/10.3832/ifor2936-012 [Google Scholar] [Crossref] 
  12. Di-Giovanni, F., & Kevan, P.G. (1991). Factors affecting pollen dynamics and its importance to pollen contamination: a review. Canadian Journal of Forest Research, 21: 1155-1170. [Google Scholar]
  13. Dzialuk, A., Muchewicz, E., Boratynski, A., Montserrat, J.M., Boratynska, K., & Burczyk, J. (2009). Genetic variation of Pinus uncinata (Pinaceae) in the Pyrenees determined with cpSSR markers. Plant Systematics and Evolution, 277: 197-205. [Google Scholar]
  14. El-Kassaby, Y.A., Rudin, D., & Yazdani, R. (1989). Levels of outcrossing and contamination in two Pinus sylvestris L. seed orchards in Northern Sweden. Scandinavian Journal of Forest Research, 4: 41-49. [Google Scholar]
  15. Ennos, R.A. (1994). Estimating the relative rates of pollen and seed migration among plant populations. Heredity, 72: 250-259. [Google Scholar]
  16. Ertekin, M. (2012). Genetic diversity of seed orchard crops, The molecular basis of plant genetic diversity, Prof. Mahmut Caliskan (Ed.), ISBN: 978-953-51-0157-4, InTech, http://www.intechopen.com/books/the-molecular-basis-of-plant-genetic-diversity/genetic-diversity-of-seedorchard-crops. [Google Scholar]
  17. Feng, F.J., Suı, X., Chen, M.M., Zhao, D., Han, S.J., & Li, M.H. (2010). Mode of pollen spread in clonal seed orchard of Pinus koraiensis. Journal of Biophysical Chemistry, 1(1): 33-39. [Google Scholar]
  18. Feilberg, L., & Soegaard, B. (1975). Historical review of seed orchards, in. Seed orchards, Forestry Commission Bulletin, No.54, pp. 1-8, London, England. [Google Scholar]
  19. Fernandes, L., Rocheta, M., Cordeiro, J., Pereira, S., Gerber, S., Oliveira, M.M., & Ribeiro, M.M. (2008). Genetic variation, mating patterns and gene flow in a Pinus pinaster Aiton clonal seed orchard. Annals of Forest Science, 65: 706p1-10. [Google Scholar]
  20. Funda, T., & El-Kassaby, Y.A. (2012). Seed orchard genetics. CAB Reviews, 7: 13. [Google Scholar]
  21. Gonzaga, J.M.S., Manoel, R.O., Sousa, A.C.B., Souza, A.P., Moraes, M.L.T., Freitas, M.L.M., & Sebbenn, A.M. (2016). Pollen contamination and nonrandom mating in a Eucalyptus camaldulensis Dehnh seedling seed orchard. Silvae Genetica, 65: 1-11. https://doi.org/10.1515/sg-2016-0001 [Google Scholar] [Crossref] 
  22. Greenwood, M.S., & Rucker, T. (1985). Estimating pollen contamination in Loblolly pine seed orchards by pollen trapping. Proc. 18th Southern Forest Tree Improv. Conf., May 21-23, 1985. [Google Scholar]
  23. Hamann, A., El-Kassaby, Y.A., Koshy, M.P., & Namkoong, G. (1998). Multivariate analysis of allozymic and quantitative trait variation in Alnus rubra: geographic patterns and evolutionary implications. Canadian Journal of Forest Research, 28: 1557-1565. [Google Scholar]
  24. Heywood, V.H., & Iriondo, J.M. (2003). Plant conservation: old problems, new perspectives. Biological Conservation, 113: 321-335. [Google Scholar]
  25. Işik, K. (1999a). Orman ağacı türlerimizde lokal ırkların önemi ve genetik kirlenme sorunları. Çevre Sorunları, Biyolojik Çeşitlilik ve Orman Gen Kaynaklarımız, TEMA Vakfı, İstanbul. 25: 137-150. [Google Scholar]
  26. Işik, K. (1999b). Bitki gen kaynaklarımız niçin korunmalı ve planlanmalıdır? Çevre Sorunları, Biyolojik Çeşitlilik ve Orman Gen Kaynaklarımız, TEMA Vakfı, İstanbul. 25: 151-160. [Google Scholar]
  27. Kang, K.S., Lindgren, D., & Mullin, T.J. (2001a). Prediction of genetic gain and gene diversity in seed orchard crops under alternative management strategies. Theoretical and Applied Genetics, 103: 1099-1107. [Google Scholar]
  28. Kang, K.S., Harju, A.M., Lindgren, D., Nikkanen, T., Almqvist, C., & Suh, G.U. (2001b). Variation in effective number of clones in seed orchards. New Forests, 21: 17-33. [Google Scholar]
  29. Kang, K.S., Lindgren, D., & Mullin, T.J. (2004). Fertility variation, genetic relatedness, and their impacts on gene diversity of seeds from a seed orchard of Pinus thunbergii. Silvae Genetica, 53(5-6): 202-206. [Google Scholar]
  30. Kaya, N. 2005. Orman ağaçlarında eşleşme şekilleri. Süleyman Demirel Üniversitesi, Orman Fakültesi Dergisi, 2: 125-137. [Google Scholar]
  31. Kaya, N., Isik, K., & Adams, W.T. (2006). Mating system and pollen contamination in a Pinus brutia seed orchard. New For 31: 409-416. [Google Scholar]
  32. Kaya, Z., Skaggs, A., & Neale, D.B. (2008). Genetic differentiation of Abies equi-trojani (Asch.& Sint. ex Boiss) Mattf. populations from Kazdağı, Turkey and the genetic relationship between Turkish Firs belonging to the Abies nordmanniana Spach complex. Turkish Journal Botany, 32:1-10. [Google Scholar]
  33. Kess, T., & El-Kassaby, Y.A. (2015). Estimates of pollen contamination and selfing in a coastal Douglas-fir seed orchard. Scandinavian Journal of Forest Research, 30(4): 266-275. https://doi.org/10.1080/02827581.2015.1012112 [Google Scholar] [Crossref] 
  34. Kocaman, B., Toy, S., & Maraklı, S. (2020). Application of different molecular markers in biotechnology. International Journal of Science Letters, 2(2): 98-113. [Google Scholar]
  35. Kurt, Y., González-Martínez, S.C., Alía, R., & Isik, K. (2012). Genetic differentiation in Pinus brutia Ten. using molecular markers and quantitative traits: the role of altitude. Annals of Forest Science, 69: 345-351. https://doi.org/10.1007/s13595-011-0169-9 [Google Scholar] [Crossref] 
  36. Li, Y.C., Korol, A.B., Fahima, T., Beiles, A., & Nevo, E. (2002). Microsatellites: genomic distribution, putative functions and mutational mechanisms: a review. Molecular Ecology, 11: 2453-2465. [Google Scholar]
  37. Lowe, W.J., & Wheeler, N.C. (1993). Pollen contamination in seed orchards. In: D.L. Bramlett, G.R. Askew, T.D. Blush, F.E. Bridgwater and J.B. Jett (eds). Advances in Pollen Management. pp.49-54. USDA Agric. Handb. 698. Washington, DC. [Google Scholar]
  38. Myers, E.R., Chung, M.Y., & Chung, M.G. (2007). Genetic diversity and spatial genetic structure of Pinus strobus (Pinaceae) across an island landscape inferred from allozyme and cpDNA markers. Plant Systematics and Evolution, 264: 15-30. [Google Scholar]
  39. Navascues, M., Vaxevanidou, Z, Gonzalez-Martinez, S.C., Climent, J., Gil, L., & Emerson, B.C. (2006). Chloroplast microsatellites reveal colonization and metapopulation dynamics in the Canary Island pine. Molecular Ecology, 15: 2691-2698. [Google Scholar]
  40. Naydenov, K.D., Tremblay, F.M., Bergeron, Y., Alexandrov, A., & Fenton, N. (2005a). Dissimilar patterns of Pinus heldreichii Christ. populations in Bulgaria revealed by chloroplast microsatellites and terpenes analysis. Biochemical Systematics and Ecology, 33: 133-148. [Google Scholar]
  41. Naydenov, K.D., Tremblay, F.M., Alexandrov, A., & Fenton, N.J. (2005b). Structure of Pinus sylvestris L. populations in Bulgaria revealed by chloroplast microsatellites and terpenes analysis: Provenance tests. Biochemical Systematics and Ecology, 33: 1226-1245. [Google Scholar]
  42. Naydenov, K.D., Tremblay, F.M., Fenton, N.J., & Alexandrov, A. (2006). Structure of Pinus nigra Arn. populations in Bulgaria revealed by chloroplast microsatellites and terpenes analysis: Provenance tests. Biochemical Systematics and Ecology, 34: 562-574. [Google Scholar]
  43. OATIAM. (2023). General Directorate of Forestry. Forest Tree Seeds and Tree Breeding Research Directorate. http://www.ortohum.gov.tr/ [Google Scholar]
  44. Ohsawa, T., & Ide, Y. (2008). Global patterns of genetic variation in plant species along vertical and horizontal gradients on mountains. Global Ecology and Biogeography, 17: 152-163. [Google Scholar]
  45. Oliveira, E.J., Padua, J.G., Zucchi, M.I., Vencovsky, R., & Carneiro-Vieria, M.L. (2006). Origin, evolution and genome distribution of microsatellites. Genetics and Molecular Biology, 29(2): 294-307. [Google Scholar]
  46. Pakkanen, A., Nikkanen, T., & Pulkkinen, P. (2000). Annual Variation in Pollen Contamination and Outcrossing in a Picea abies Seed Orchard. Scandinavian Journal of Forest Research, 15: 399-404. [Google Scholar]
  47. Plomion, C., Leprovost, G., Pot, D., Vendramin, G., Gerber, S., Decroocq, S., Brach, J., Raffin, A., & Pastuszka, P. (2001). Pollen contamination in a maritime pine polycross seed orchard and certification of improved seeds using chloroplast microsatellites. Canadian Journal of Forest Research, 31: 1816-1825. [Google Scholar]
  48. Pupin, S., Sebbenn, A.M., Cambuim, J., da Silva, A.M., Zaruma, D.U.G., Silva, P.H.M., Rosse, L.N., Souza, I.C.G., Marino, C.L., & Moraes, M.L.T. (2019). Effects of pollen contamination and non-random mating on inbreeding and outbreeding depression in a seedling seed orchard of Eucalyptus urophylla. Forest Ecology and Management, 437: 272-281. https://doi.org/10.1016/j.foreco.2019.01.050. [Google Scholar] [Crossref] 
  49. Ribeiro, M.M., Mariette, S., Vendramin, G.G., Szmidt, A.E., Plomion, C., & Kremer, A. (2002). Comparison of genetic diversity estimates within and among populations of maritime pine using chloroplast simple-sequence repeat and amplified fragment length polymorphism data. Molecular Ecology, 11: 869-877. [Google Scholar]
  50. Semagn, K., Bjornstad, A., & Ndjiondjop, M.N. (2006). An overview of molecular marker methods for plants. African Journal of Biotechnology, 5(25): 2540-2568. [Google Scholar]
  51. Sheller, M., Ciocîrlan, E., Mikhaylov, P., Kulakov, S., Kulakova, N., Ibe, A., Sukhikh, T., & Curtu, A.L. (2021). Chloroplast DNA diversity in populations of P. sylvestris L. From Middle Siberia and the Romanian Carpathians. Forests, 12: 1757. https://doi.org/10.3390/f12121757 [Google Scholar] [Crossref] 
  52. Slavov, G.T., Howe, G.T., Yakovlev, I., Edwards, K.J., Krutovskii, K.V., Tuskan, G.A., Carlson, J.E., Strauss, S.H., & Adams, W.T. (2004). Highly variable SSR markers in Douglas-fir: Mendelian inheritance and map locations. Theoretical and Applied Genetics, 108: 873-880. [Google Scholar]
  53. Slavov, G.T., Howe, G.T., & Adams, W.T. (2005). Pollen contamination and mating patterns in a Douglas-fir seed orchard as measured by simple sequence repeat markers. Canadian Journal of Forest Research, 35(7): 1592-1603. [Google Scholar]
  54. Sonstebo, J.H., Tollefsrud, M.M., Myking, T., Steffenrem, A., Nilsen, A.E., Edvardsen, O.M., Johnskas, O.R., & El-Kassaby, Y.A. (2018). Genetic diversity of Norway spruce (Picea abies (L.) Karst.) seed orchard crops: Effects of number of parents, seed year, and pollen contamination. Forest Ecology and Management, 411: 132-141. https://doi.org/10.1016/j.foreco.2018.01.009. [Google Scholar] [Crossref] 
  55. Sniezko, R.A. (1981). Genetic and economic consequences of pollen contamination in seed orchards. In: Proceedings, 16th Southern Forest Tree Improvement Conference; 1981 May 27-28: Blacksburg, VA. Blacksburg: Virginia Polytechnic Institute: 225-233. [Google Scholar]
  56. Soto, A., Robledo-Arnuncio, J.J., Gonzalez-Martinez, S.C., Smouse, P.E., & Alia, R. (2010). Climatic niche and neutral genetic diversity of the six Iberian pine species: a retrospective and prospective view. Molecular Ecology, 19: 1396-1409. [Google Scholar]
  57. Stoehr, M.U., & Newton, C.H. (2002). Evaluation of mating dynamics in a lodgepole pine seed orchard using chloroplast DNA markers. Canadian Journal of Forest Research, 32: 469-476. [Google Scholar]
  58. Sütcü, T., Bilgen, B.B., & Tuna, M. (2022). Analysis of genetic diversity among Onobrychis accessions with high agronomic performance by simple sequence repeat (SSR) markers. Molecular Biology Reports, 49: 5659-5668. https://doi.org/10.1007/s11033-022-07584-x [Google Scholar] [Crossref] 
  59. Terrab, A., Paun, O., Talavera, S., Tremetsberger, K., Arısta, M., & Stuessy, T.F. (2006). Genetic diversity and population structure in natural populations of Moroccan Atlas cedar (Cedrus atlantica; Pinaceae) determined with cpSSR markers. American Journal of Botany, 93(9): 1274-1280. [Google Scholar]
  60. Torimaru, T., Wang, X.R., Fries, A., Andersson, B., & Lindgren, D. (2009). Evaluation of pollen contamination in an advanced scots pine seed orchard. Silvae Genetica, 58(5-6): 262-269. [Google Scholar]
  61. Tunçtaner, K. (2007). Orman genetiği ve ağaç ıslahı, Türkiye Ormancılar Derneği, Eğitim Dizisi: 4, 364 s. [Google Scholar]
  62. Urbaniak, L., Wojnicka-Poltorak, A., Celinski, K., Lesiczka, P., Pawlaczyk, E., & Aucina, A. (2019). Genetic resources of relict populations of Pinus sylvestris (L.) in Western Carpathians assessed by chloroplast microsatellites. Biologia, 74: 1077-1086. https://doi.org/10.2478/s11756-019-00255-6 [Google Scholar] [Crossref] 
  63. Varshney, R.K., Graner, A., & Sorrels, M.E. (2005). Genic microsatellite markers in plants: features and applications. Trends in Biotechnology, 23: 48-55. [Google Scholar]
  64. Vendramin, G.G., Lelli, L., Rossi, P., & Morgante, M. (1996). A set of primers for the amplification of 20 chloroplast microsatellites in Pinaceae. Molecular Ecology, 5: 595-598. [Google Scholar]
  65. Vieira, M.L.C., Santini, L., Diniz, A.L., & Munhoz, C.F. (2016). Microsatellite markers: what they mean and why they are so useful. Genet Mol Biol., 39: 312-328. [Google Scholar]
  66. Wheeler, N., & Jech, K. (1986). Pollen contamination in a mature, Douglas-fir seed orchard. Proc. IUFRO Conf. Breeding, Theory, Progeny testing of seed orchards. Oct. 13-17, 1986. Williamsburg, VA. [Google Scholar]
  67. Yang, H., Zhang, R., & Zhou, Z. (2017). Pollen dispersal, mating patterns and pollen contamination in an insect-pollinated seed orchard of Schima superba Gardn. et Champ. New Forests, 48: 431-444. https://doi.org/10.1007/s11056-017-9568-6 [Google Scholar] [Crossref] 
  68. Zhuowen, Z. (2002). Pollen dispersal and its spatial distribution in seed orchards of Cunninghamia lanceolata (LAMB.) Hook. Silvae Genetica, 51(5-6): 237-241. [Google Scholar]
  69. Zobel, B.J., & Talbert, J. (1984). Applied forest tree improvement. John Wiley and Sons, Inc. New York, 505 p. [Google Scholar]
Meta
Vol. 7 (3)
Download
Metric
History
Related

Volume 7 Issue 3

September 2023

All Articles
Copyright © 2012 - 2024 International Journal of Innovative Approaches in Agricultural Research.
Pen Academic Publishing is a trademark of THDSoft.
This work is licensed under a Creative Commons Attribution 4.0 International License. CC BY-NC-ND
Electronic Journal Management System. This software was developed in Türkiye. ejournal.gen.tr
Pen Academic Publishing General Publication Policy: