Skip to main navigation menu Skip to main content Skip to site footer
ACI Avances en Ciencias e Ingenierías

SECTION B: LIFE SCIENCES

Vol. 13 No. 2 (2021)

Heterologous microsatellite markers assay in Rubus niveus for the study of its genetic diversity in the Galapagos Islands

DOI
https://doi.org/10.18272/aci.v13i2.2293
Submitted
May 14, 2021
Published
2021-11-05

Abstract

Rubus niveus is a species that originated in Asia. This plant has spread over several continents due to its anthropogenic uses and biological characteristics. It presents high adaptability which has allowed it to establish in new environments and invade them, as is the case of the Galapagos Islands, Ecuador. Since it arrived in the archipelago, R. niveus has displaced native plants. Existing control methods have so far been ineffective. Understanding this plant's genetic diversity using molecular markers could explain its invasive success and aid in developing efficient control strategies. Therefore, in this study, we carried out a preliminary analysis of the transferability of heterologous microsatellite markers for the study of genetic diversity of R. niveus in the Galapagos Islands. For this purpose, we collected and analyzed 68 samples from different locations within Santa Cruz, San Cristobal, Isabel, and Floreana islands and 10 samples from Continental Ecuador. We chose 15 microsatellite markers for this study, all of which amplified successfully, demonstrating transferability from one species to another. However, all 15 loci were monomorphic in every amplified sample from the Galapagos Islands and Continental Ecuador, therefore, we were unable to determine the genetic diversity of R. niveus in our samples. Our research with microsatellite markers and similar studies with species in the Rubus genus found monomorphic loci. Therefore, we suggest that a better strategy would be to sequence R. niveus' genome and explore other molecular markers such as Single Nucleotide Polymorphisms to determine genetic diversity levels of this species.

viewed = 991 times

References

  1. Quinton St., J. M., Fay, M. F., Ingrouille, M., & Faull, J. (2011). Characterisation of Rubus niveus: A prerequisite to its biological control in oceanic islands. Biocontrol Science and Technology, 21 (6), 733-752. doi: https://doi.org/10.1080/09583157.2011.570429
  2. Caidan, R., Cairang, L., & Yourui, S. (2013). Simultaneous analysis of fatty acids in Rubus niveus Thunb. Fruits by HPLC- MS/MS. Asian Journal of Chemistry, 25(4), 1866-1870. doi: https://doi.org/10.14233/ajchem.2013.13204
  3. Centre for Agricultural Bioscience International. (2019). Rubus niveus (Mysore raspberry). Recuperado de https://web.archive.org/web/20210506091150/https://www.cabi.org/isc/datasheet/107939
  4. Global Invasive Species Database. (2021). Species profile: Rubus niveus. Recuperado de http://www.iucngisd.org/gisd/species.php?sc=1232
  5. BIISC. (2013). Family: Rubus glaucus Mysore Raspberry Rubus niveus Thimbleberry Rubus rosifolius Koster’s Curse Clidemia hirta Glory Bush Tibouchina herbacea Lasiandra Tibouchina urvilleana. Article. Recuperado de: https://web.archive.org/web/20210514222533/http://www.hear.org/operationmiconia/BIISC_ WEEDS_01-15.pdf
  6. Starr, F., Starr, K., & Loope, L. (2003). Rubus niveus f. a Hill or mysore raspberry Rosaceae. Recuperado de http://www.hear.org/PIER/pdf/pohreports/rubus_niveus_f_a.pdf
  7. Renteria, J. L., Gardener, M. R., Panetta, F. D., & Crawley, M. J. (2012). Management of the Invasive Hill Raspberry (Rubus niveus) on Santiago Island, Galapagos: Eradication or Indefinite Control? Invasive Plant Science and Management, 5(1), 37-46. doi: https://doi.org/10.1614/ipsm-d-11-00043.1
  8. Rentería, J. L., Gardener, M. R., Panetta, F. D., Atkinson, R., & Crawley, M. J. (2012). Possible Impacts of the Invasive Plant Rubus niveus on the Native Vegetation of the Scalesia Forest in the Galapagos Islands. PLoS ONE, 7(10), 1-9. doi: https://doi.org/10.1371/journal.pone.0048106
  9. Malanson, G., & Walsh, S. (2013). A Geographical Approach to Optimization of Response to Invasive Species. En S. Walsh & C. Mena (Eds.), Social and Ecological Interactions in the Galapagos Islands (pp.199-215). Springer Science+Business Media, LLC 2013
  10. Moity, N & Rivas, G. (2018). Ecosistemas. En P. Araujo, H. Arnal, B. Delgado, P. Díaz, A. Izurieta, G. Jiménez-Uzcátegui, J. R. Marín, N. Moity, J. Ramírez, M. Schuiteman (Eds.), Atlas de Galápagos, Ecuador: Especies Nativas e Invasoras (pp. 36). Quito: Fundación Charles Darwin y WWF-Ecuador.
  11. Lawesson, J., & Ortiz, L. (1994). Plantas introducidas en las Islas Galápagos. En A. Carrasco & H. Valdebenito (Eds.), Investigación Botánica y Manejo en Galápagos: Memorias (Versión en Español) Taller sobre Investigación Botánica y Manejo en Galápagos Abril 11-18 de 1987 (pp. 224-235). Quito: USAID.
  12. Jäger, H., Buchholz, S., Cimadom, A., Tebbich, S., Rodriguez, J., Barrera, D., . Causton, C. E. (2017). Restoration of the blackberry-invaded Scalesia forest: Impacts on the vegetation, invertebrates, and birds. Galapagos Report 2015-2016, 142-148.
  13. Ministerio del Ambiente. (2009). Términos de referencia para la prestación de servicios para realizar monitoreo, delimitación y control de mora (Rubus niveus) en la isla Santiago y la isla Floreana. Santa Cruz, Ecuador.
  14. Lawson, L. J., Estoup, A., Evans, D. M.,Thomas, C. E., Lombaert, E., Facon, B., .. Roy, H. E. (2011). Ecological genetics of invasive alien species. BioControl, 56(4), 409-428. doi: https://doi.org/10.1007/s10526-011-9386-2
  15. Sakai, A. K., Allendorf, F. W., Holt, J. S., Lodge, D. M., Molofsky, J., With, K. A., ... Weller, S. G. (2001). The Population Biology of Invasive Species. Annual Review of Ecology and Systematics, 32(1), 305-332. doi: https://doi.org/10.1146/annurev.ecolsys.32.081501.114037
  16. Prentis, P. J., Sigg, D. P., Raghu, S., Dhileepan, K., Pavasovic, A., & Lowe, A. J. (2009). Understanding invasion history: Genetic structure and diversity of two globally invasive plants and implications for their management. Diversity and Distributions, 15(5), 822-830. doi: https://doi.org/10.1111/j.1472-4642.2009.00592.x
  17. Graham, J., Squire, G. R., Marshall, B., & Harrison, R. E. (2003). Spatially dependent genetic diversity within and between colonies of wild raspberry Rubus idaeus detected using RAPD markers. Molecular Ecology, 6(11), 1001-1008. doi: https://doi.org/10.1046/j.1365-294X.1997.00272.x
  18. Garrido, P., Morillo, E., & Vásquez-Castillo, W. (2020). Genetic diversity of the Andean blackberry (Rubus glaucus Benth.) in Ecuador assessed by AFLP markers. Plant Genetic Resources: Characterisation and Utilisation, 18(4), 1-8. doi: https://doi.org/10.1017/S1479262120000283
  19. Miyashita, T., Kunitake, H., Yotsukura, N., & Hoshino, Y. (2015). Assessment of genetic relationships among cultivated and wild Rubus accessions using AFLP markers. Scientia Horticulturae, 193, 165-173. doi: https://doi.org/10.1016/j.scienta.2015.07.004
  20. Marulanda, M. L., López, A. M., & Aguilar, S. B. (2007). Genetic diversity of wild and cultivated Rubus species in Colombia using AFLP and SSR markers. Crop Breeding and Applied Biotechnology, 7, 242-252.
  21. Graham, J., & McNicol, R. J. (1995). An examination of the ability of RAPD markers to determine the relationships within and between Rubus species. Theoretical and Applied Genetics, 90(7-8), 1128-1132. doi: https://doi.org/10.1007/BF00222932
  22. Debnath, S. C. (2007). Inter-simple sequence repeat (ISSR)-PCR analysis to assess genetic diversity in a collection of wild cloudberry (Rubus chamaemorus L.) clones. Journal of Horticultural Science and Biotechnology, 82(5), 727-732. doi: https://doi.org/10.1080/14620316.2007.11512297
  23. Lee, G. A., Song, J. Y., Choi, H. R., Chung, J. W., Jeon, Y. A., Lee, J. R., ... Lee, M. C. (2015). Novel microsatellite markers acquired from Rubus coreanus miq. and cross-amplification in other Rubus species. Molecules, 20(4), 6432-6442. doi: https://doi.org/10.3390/molecules20046432
  24. Dossett, M., Bassil, N. V., Lewers, K. S., & Finn, C. E. (2012). Genetic diversity in wild and cultivated black raspberry (Rubus occidentalis L.) evaluated by simple sequence repeat markers. Genetic Resources and Crop Evolution, 59(8), 1849-1865. doi: https://doi.org/10.1007/s10722-012-9808-8
  25. Marulanda, M., López, A. M., & Uribe, M. (2012). Molecular characterization of the Andean blackberry, Rubus glaucus, using SSR markers. Genetics and molecular research: GMR, 11(1), 322-331. doi: https://doi.org/10.4238/2012. February.10.3
  26. Innis, A. F., Forseth, I. N., Whigham, D. F., & McCormick, M. K. (2011). Genetic diversity in the invasive Rubus phoenicolasius as compared to the native Rubus argutus using inter-simple sequence repeat (ISSR) markers. Biological Invasions, 13(8), 1735-1738. doi: https://doi.org/10.1007/s10530-011-0012-0
  27. Yang, J., Pak, J.-H., Maki, M., & Kim, S.-C. (2019). Multiple origins and the population genetic structure of Rubus takesimensis (Rosaceae) on Ulleung Island: Implications for the genetic consequences of anagenetic speciation. PLoS ONE, 14(9), e0222707. doi: https://doi.org/10.1371/journal.pone.0222707
  28. Amsellem, L., Dutech, C., & Billotte, N. (2001). Isolation and characterization of polymorphic microsatellite loci in Rubus alceifolius Poir. (Rosaceae), an invasive weed in la Réunion island. Molecular Ecology Notes, 1(1-2), 33-35. doi: https://doi.org/10.1046/j.1471-8278.2000.00013.x
  29. Lee, K. J., Lee, G.-A., Kang, H.-K., Lee, J.-R., Raveendar, S., Shin, M.-J., ... Ma, K.-H. (2016). Genetic Diversity and Population Structure of Rubus Accessions Using Simple Sequence Repeat Markers. Plant Breeding and Biotechnology, 4(3), 345-351. doi: https://doi.org/10.9787/pbb.2016.4.3.345
  30. Marulanda, M., López, A., & Uribe, M. (2012). Genetic Diversity and Transferability of Rubus Microsatellite Markers to South American Rubus Species. The Molecular Basis of Plant Genetic Diversity, 151-164. doi: https://doi.org/10.5772/32838
  31. Murray, M. & Thompson, W. (1980). Rapid isolation of high molecular weight plant DNA. Nucleic Acids Research, 8(19), 4321-4326. doi: https://doi.org/10.1093/nar/8.19.4321
  32. Castillo, N. R. F., Reed, B. M., Graham, J., Fernández-Fernández, F., & Bassil, N. V. (2010). Microsatellite markers for raspberry and blackberry. Journal of the American Society for Horticultural Science, 135(3), 271-278. doi: https://doi.org/10.21273/jashs.135.3.271
  33. Graham, J., Smith, K., MacKenzie, K., Jorgenson, L., Hackett, C., & Powell, W. (2004). The construction of a genetic linkage map of red raspberry (Rubus idaeus subsp. idaeus) based on AFLPs, genomic-SSR and EST-SSR markers. Theoretical and Applied Genetics, 109(4), 740-749. doi: https://doi.org/10.1007/s00122-004-1687-8
  34. Blacket, M. J., Robin, C., Good, R. T., Lee, S. F., & Miller, A. D. (2012). Universal primers for fluorescent labelling of PCR fragments-an efficient and cost-effective approach to genotyping by fluorescence. Molecular Ecology Resources, 12(3), 456-463. doi: https://doi.org/10.1111/j.1755-0998.2011.03104.x
  35. Matlock, B. (2015). Assessment of Nucleic Acid Purity. Recuperado de: https://assets.thermofisher.com/TFS-Assets/CAD/Product-Bulletins/TN52646-E-0215M-NucleicAcid.pdf
  36. Thermo Fisher Scientific Inc. (2009). NanoDrop 2000 / 2000c Spectrophotometer V1.0 User Manual, 97. Recuperado de: https://assets.thermofisher.com/TFS-Assets/CAD/manuals/NanoDrop-2000-User-Manual-EN.pdf
  37. Álvarez, M. (2016). Evaluación de la variabilidad genética en cinco especies de mora (Rubus spp) mediante marcadores microsatélites SSR (Tesis de pregrado). Universidad San Francisco de Quito USFQ, Quito. Recuperado de http://repositorio.usfq.edu.ec/bitstream/23000/5695/1/126382.pdf
  38. Meng, R., & Finn, C. (2002). Determining ploidy level and nuclear DNA content in Rubus by flow cytometry. Journal of the American Society for Horticultural Science, 127(5), 767-775. doi: https://doi.Org/10.21273/jashs.127.5.767
  39. Thompson, M. M. (1995). Chromosome numbers of Rubus species at the national clonal germplasm repository. HortScience, 30(7), 1447-1452. doi: https://doi.org/10.21273/hortsci.30.7.1447
  40. Dossett, M., Bassil, N. V., & Finn, C. E. (2012). High resolution melting detects sequence polymorphism in Rubus occidentalis monomorphic microsatellite markers. Acta Horticulturae, 926, 91-96. doi: https://doi.org/10.17660/actahortic.2012.926.11
  41. Foster, T. M., Bassil, N. V., Dossett, M., Leigh Worthington, M., & Graham, J. (2019). Genetic and genomic resources for Rubus breeding: a roadmap for the future. Horticulture Research, 6(1). doi: https://doi.org/10.1038/s41438-019- 0199-2
  42. Vieira, M. L. C., Santini, L., Diniz, A. L., & Munhoz, C. de F. (2016). Microsatellite markers: What they mean and why they are so useful. Genetics and Molecular Biology, 39(3), 312-328. doi: https://doi.org/10.1590/1678-4685-GMB-2016-0027
  43. Aranguren-Méndez, J. A., Román-Bravo, R., Isea, W., Villasmil, Y., & Jordana, J. (2005). Los microsatélites (STR's), marcadores moleculares de ADN por excelencia para programas de conservación: una revisión Microsatellites (STR’s), ADN Molecular Markers for Excellency for conservation programs: A review. Arch. Latinoam. Prod. Anim., 13(11), 30-42.
  44. Tautz, D., & Schlötterer, C. (1994). Simple sequences. Current Opinion in Genetics and Development, 4(6), 832-837. doi: https://doi.org/10.1016/0959-437X(94)90067-1
  45. Palais, R., & Wittwer, C. T. (2009). Chapter 13 Mathematical Algorithms for High-Resolution DNA Melting Analysis. En M. Johnson, & L. Brand (Eds.), Methods in Enzymology (pp. 323-332). Vol. 454. Elsevier Inc. doi: https://doi.org/10.1016/S0076-6879(08)03813-5
  46. Ng, P. C., & Kirkness, E. F. (2010). Whole Genome Sequencing. Genetic Variation, 215-226. doi: https://doi.org/10.1007/978-1-60327-367-1_12
  47. Ward, J. A., Bhangoo, J., Fernández-Fernández, F., Moore, P., Swanson, J. D., Viola, R., ... Sargent, D. J. (2013). Saturated linkage map construction in Rubus idaeus using genotyping by sequencing and genome-independent imputation. BMC Genomics, 14(1), 1-14. doi: https://doi.org/10.1186/1471-2164-14-2
  48. Ryu, J., Kim, W. J., Im, J., Kim, S. H., Lee, K. S., Jo, H. J., ... Ha, B. K. (2018). Genotyping-by-sequencing based single nucleotide polymorphisms enabled Kompetitive Allele Specific PCR marker development in mutant Rubus genotypes. Electronic Journal ofBiotechnology, 35, 57-62. doi: https://doi.org/10.1016/j.ejbt.2018.08.001
  49. Escobedo López, D., & Núñez Colín, C. (2015). Variabilidad genética de una población segregante de mora mexicana (Morus celtidifolia Kunth) determinada por marcadores ISSR. Acta Agrícola y Pecuaria, 1(3), 93-98.
  50. Amsellem, L., Noyer, J. L., Bourgeois, T. L. E., & Hossaert-Mckey, M. (2000). Comparison of genetic diversity of the invasive weed Rubus alceifolius Poir. (Rosaceae) in its native range and in areas of introduction, using amplified fragment length polymorphism (AFLP) markers. Molecular Ecology, 9(4), 443-455. doi: https://doi.org/10.1046/j.1365-294X.2000.00876.x
  51. Le Bourgeois, T., Baret, S., & de Chenon, R. D. (2011). Biological Control of Rubus alceifolius (Rosaceae) in La Réunion Island (Indian Ocean): From Investigations on the Plant to the Release of the Biological Control Agent Cibdela janthina (Argidae). En Y. Wu, T. Johnson, S. Sing, S. Raghu, G. Wheeler, P. Pratt, K. Warner, T. Center, J. Goolsby, & R. Reardon (Eds.), Proceedings of the XIII International Symposium on Biological Control of Weeds: Session 4 Target and Agent Selection (pp. 153-160), Waikoloa, Hawái, Estados Unidos: U.S. Forest Service.