J. For. Sci., 2024, 70(1):1-13 | DOI: 10.17221/95/2023-JFS

Genetic diversity and phylogenetic analysis of Robinia pseudoacacia L. populations using ISSR markers, ITS1 and trnL-F intergenic spacer sequencesOriginal Paper

Mehmet Emin Uras ORCID...1, Ertugrul Filiz ORCID...2, Ugur Sen ORCID...3, Ibrahim Ilker Ozyigit ORCID...3
1 Department of Molecular Biology and Genetics, Faculty of Science and Arts, Haliç University, Istanbul, Türkiye
2 Department of Crop and Animal Production, Çilimli Vocational School, Düzce University, Düzce, Türkiye
3 Department of Biology, Faculty of Science, Marmara University, Istanbul, Türkiye

Robinia pseudoacacia L. is a deciduous tree planted almost all around the world for a wide variety of uses such as ornamental in urban ecosystems and forest trees in afforestation. This study aims to evaluate the genetic diversity and phylogenetic relations of R. pseudoacacia using some selected populations in Istanbul and Kocaeli cities. For this aim, molecular marker-assisted and DNA sequence-based analyses were performed. According to the results, nine of 15 inter simple sequence repeats (ISSR) primers gave clear and distinguishable bands with a total of 100 loci. The percentage of polymorphic loci (PPL) was calculated as 100% for multi-populations and ranged from 46% to 76% for single populations. Nei's gene diversity value was calculated between 0.165 and 0.251. The lowest and highest PPL were found in populations of Barbaros Boulevard and Dilovası District, respectively. Population structure analysis showed seven different genetic structures for five populations. Internal transcribed spacer 1 region (ITS1) and trnL-F intergenic spacer region were used to examine the phylogenetic relationships of R. pseudoacacia, and both regions showed a high discriminative power at the family level. Based on the findings, R. pseudoacacia, as a forest tree residing in the urban ecosystem, may face the risk of population decline in the upcoming years due to its moderate/low genetic diversity and susceptibility to environmental pressures.

Keywords: DNA barcoding; forest tree; molecular marker; molecular phylogeny; urban population

Received: August 21, 2023; Revised: October 16, 2023; Accepted: October 27, 2023; Prepublished online: January 23, 2024; Published: January 30, 2024  Show citation

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Emin Uras M, Filiz E, Sen U, Ilker Ozyigit I. Genetic diversity and phylogenetic analysis of Robinia pseudoacacia L. populations using ISSR markers, ITS1 and trnL-F intergenic spacer sequences. J. For. Sci.. 2024;70(1):1-13. doi: 10.17221/95/2023-JFS.
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    References

    1. Bingol D., Ay Ü., Bozbaº S.K., Uzgören N. (2013): Chemometric evaluation of the heavy metals distribution in waters from the Dilovasi region in Kocaeli, Turkey. Marine Pollution Bulletin, 68: 134-139. Go to original source... Go to PubMed...
    2. Bingol D., Bozbaº S.K., Ümit A.Y., Uzgören N. (2018): Chemometric evaluation of the heavy metal contents in surface soils from the Dilovasi region (Kocaeli/Turkey). Cumhuriyet Science Journal, 39: 23-33. Go to original source...
    3. Cierjacks A., Kowarik I., Joshi J., Hempe S., Ristow M., Lippe M., Weber E. (2013): Biological flora of the British Isles: Robinia pseudoacacia. Journal of Ecology, 101: 1623-1640. Go to original source...
    4. Doyle J. (1991): DNA protocols for plants. In: Hewitt G.M., Johnston A.W.B., Young J.P.W. (eds): Molecular Techniques in Taxonomy. NATO ASI Series, Vol. 57. Berlin, Springer: 412. Go to original source...
    5. Earl D.A., VonHoldt B.M. (2012): STRUCTURE HARVESTER: A website and program for visualizing STRUCTURE output and implementing the Evanno method. Conservation of Genetic Resources, 4: 359-361. Go to original source...
    6. Ebert A.W., Engels J.M.M. (2020): Plant biodiversity and genetic resources matter! Plants, 9: 1706. Go to original source... Go to PubMed...
    7. Evanno G., Regnaut S., Goudet J. (2005): Detecting the number of clusters of individuals using the software STRUCTURE: A simulation study. Molecular Ecology, 14: 2611-2620. Go to original source... Go to PubMed...
    8. Filiz E., Birbilener S., Ozyigit I.I., Kulac S., Sakinoglu Oruc F.C. (2015): Assessment of genetic variations of silver lime (Tilia tomentosa Moench.) by RAPD markers in urban and forest ecosystems. Biotechnology & Biotechnological Equipment, 29: 631-636. Go to original source...
    9. Filiz E., Uras M.E., Ozyigit I.I., Sen U., Gungor H. (2018): Genetic diversity and phylogenetic analyses of Turkish rice varieties revealed by ISSR markers and chloroplast trnl-F region. Fresenius Environmental Bulletin, 27: 8351-8358.
    10. Govindaraj M., Vetriventhan M., Srinivasan M. (2015): Importance of genetic diversity assessment in crop plants and its recent advances: An overview of its analytical perspectives. Genetic Resources International, 2015: 1-15. Go to original source... Go to PubMed...
    11. Guo Q., Wang J.X., Su L.Z., Lv W., Sun Y.H., Li Y. (2017): Development and evaluation of a novel set of EST-SSR markers based on transcriptome sequences of black locust (Robinia pseudoacacia L.). Genes, 8: 177. Go to original source... Go to PubMed...
    12. Guo Q., Li X., Yang S., Yang Z., Sun Y., Zhang J., Cao S., Dong L., Uddin S., Li Y. (2018): Evaluation of the genetic diversity and differentiation of black locust (Robinia pseudoacacia L.) based on genomic and expressed sequence tag-simple sequence repeats. International Journal of Molecular Sciences, 19: 2492. Go to original source... Go to PubMed...
    13. Guo Q., Cao S., Dong L., Li X., Zhang J., Zhang Y., Zhang Z., Sun Y., Long C., Fan Y., Han C., Han P., Liu X., Li Y. (2022a): Genetic diversity and population structure of Robinia pseudoacacia from six improved variety bases in China as revealed by simple sequence repeat markers. Journal of Forestry Research, 33: 611-621. Go to original source...
    14. Guo Q., Liu J., Li J., Cao S., Zhang Z., Zhang J., Zhang Y., Deng Y., Niu D., Su L., Li X., Dong L., Sun Y., Li Y. (2022b): Genetic diversity and core collection extraction of Robinia pseudoacacia L. germplasm resources based on phenotype, physiology, and genotyping markers. Industrial Crops and Products, 178: 114627. Go to original source...
    15. Hall T.A. (1999): BioEdit: A user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series, 41: 95-98.
    16. Hocaoglu-Ozyigit A., Ucar B., Altay V., Ozyigit I.I. (2022): Genetic diversity and phylogenetic analyses of Turkish cotton (Gossypium hirsutum L.) lines using ISSR markers and chloroplast trnL-F regions. Journal of Natual Fibers, 5: 1-14. Go to original source...
    17. Ingvarsson P.K., Dahlberg H. (2019): The effects of clonal forestry on genetic diversity in wild and domesticated stands of forest trees. Scandinavian Journal of Forest Research, 34: 370-379. Go to original source...
    18. Ivanovych Y.I., Udovychenko K.M., Bublyk M.O., Volkov R.A. (2017): ISSR-PCR fingerprinting of Ukrainian sweet cherry (Prunus avium L.) cultivars. Cytology and Genetics, 51: 40-47. Go to original source...
    19. Kumar S., Stecher G., Li M., Knyaz C., Tamura K. (2018): MEGA X: Molecular evolutionary genetics analysis across computing platforms. Molecular Biology Evolution, 35: 1547-1549. Go to original source... Go to PubMed...
    20. Larkin M.A., Blackshields G., Brown N.P., Chenna R., McGettigan P.A., McWilliam H., Valentin F., Wallace I.M., Wilm A., Lopez R., Thompson J.D., Gibson T.J., Higgins D.G. (2007) ClustalW and ClustalX version 2.0. Bioinformatics, 23: 2947-2948. Go to original source... Go to PubMed...
    21. Letunic I., Bork P. (2016): Interactive tree of life (iTOL) v3: An online tool for the display and annotation of phylogenetic and other trees. Nucleic Acids Research, 44: W242-W245. Go to original source... Go to PubMed...
    22. Li X., Yang Y., Henry R.J., Rossetto M., Wang Y., Chen S. (2015): Plant DNA barcoding: From gene to genome. Biological Reviews, 90: 157-166. Go to original source... Go to PubMed...
    23. Moser A., Rötzer T., Pauleit S., Pretzsch H. (2016): The urban environment can modify drought stress of small-leaved lime (Tilia cordata Mill.) and black locust (Robinia pseudoacacia L.). Forests, 7: 71. Go to original source...
    24. Nadeem M.A., Nawaz M.A., Shahid M.Q., Doğan Y., Comertpay G., Yildiz M., Hatipoğlu R., Ahmad F., Alsaleh A., Labhane N., Özkan H., Chung G., Baloch F.S. (2018): DNA molecular markers in plant breeding: Current status and recent advancements in genomic selection and genome editing. Biotechnology & Biotechnological Equipment, 32: 261-285. Go to original source...
    25. Nagaoka T., Ogihara Y. (1997): Applicability of inter-simple sequence repeat polymorphisms in wheat for use as DNA markers in comparison to RFLP and RAPD markers. Theoretical and Applied Genetics, 94: 597-602. Go to original source...
    26. Nasim N., Sandeep I.S., Sahoo A., Das S., Panda M.K., Acharya L., RamaRao V.V., Sanghamitra N., Mohanty S. (2020): Population genetic structure and diversity analysis in economically important Pandanus odorifer (Forssk.) Kuntze accessions employing ISSR and SSR markers. Industrial Crops and Products, 143: 111894. Go to original source...
    27. Neale D.B., Wheeler N.C. (2019): Neutral genetic variation. In: The Conifers: Genomes, Variation and Evolution. Cham, Springer: 181-224. Go to original source...
    28. Nei M. (1987): Genetic distance and molecular phylogeny. In: Ryman N., Utter F.M. (eds): Population Genetics and Fishery Management. Seattle, University of Washington Press: 193-223.
    29. Pritchard J.K., Stephens M., Donnelly P. (2000): Inference of population structure using multilocus genotype data. Genetics, 155: 945-959. Go to original source... Go to PubMed...
    30. Shaygan N., Etminan A., Hervan I.M., Azizinezhad R., Mohammadi R. (2021): The study of genetic diversity in a minicore collection of durum wheat genotypes using agromorphological traits and molecular markers. Cereal Research Communications, 49: 141-147. Go to original source...
    31. Shneyer V.S., Rodionov A.V. (2019): Plant DNA barcodes. Biology Bulletin Reviews, 9: 295-300. Go to original source...
    32. Sitzia T., Cierjacks A., de Rigo D., Caudullo G. (2016): Robinia pseudoacacia in Europe: Distribution, habitat, usage and threats. In: San-Miguel-Ayanz J., de Rigo D., Caudullo G., Houston Durrant T., Mauri A. (eds): European Atlas of Forest Tree Species. Luxembourg, Publications Office of the EU: 166-167.
    33. Sun F., Yang M.S., Zhang J., Gu J.T. (2009): ISSR analysis of genetic diversity of Robinia pseudoacacia populations. Journal of Plant Genetic Resources, 10: 91-96.
    34. Taberlet P., Gielly L., Pautou G., Bouvet J. (1991): Universal primers for amplification of three non-coding regions of chloroplast DNA. Plant Molecular Biology, 17: 1105-1109. Go to original source... Go to PubMed...
    35. Tamura K., Stecher G., Peterson D., Filipski A., Kumar S. (2013): MEGA6: Molecular evolutionary genetics analysis version 6.0. Molecular Biology and Evolution, 30: 2725-2729. Go to original source... Go to PubMed...
    36. Wang J., Abbas M., Wen Y., Niu D., Wang L., Sun Y., Li Y. (2018): Selection and validation of reference genes for quantitative gene expression analyses in black locust (Robinia pseudoacacia L.) using real-time quantitative PCR. PLoS ONE, 13: e0193076. Go to original source... Go to PubMed...
    37. White T.J., Bruns T., Lee S., Taylor J.W. (1990): Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis M.A., Gelfand D.H., Sninsky J.J., White T.J. (eds): PCR Protocols: A Guide to Methods and Applications. New York, Academic Press: 315-322. Go to original source...
    38. Yang X., Zhang K., Wang J., Jia H., Ma L., Li Y., Duan J. (2020): Assessment of genetic diversity and chemical composition among seven black locust populations from Northern China. Biochemical Systematics and Ecology, 90: 104010. Go to original source...
    39. Yeh F.C., Boyle T.J.B. (1997): Population genetic analysis of co-dominant and dominant markers and quantitative traits. Belgian Journal of Botany, 129: 157.

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