Skip to main content
Log in

Genetic Analysis of Turkey Common Bean (Phaseolus vulgaris L.) Genotypes by Simple Sequence Repeats Markers

  • PLANT GENETICS
  • Published:
Russian Journal of Genetics Aims and scope Submit manuscript

Abstract

Common bean (Phaseolus vulgaris L.), besides being an agricultural product that can be consumed as fresh vegetable, is a significant legume widely being planted in both Turkey and world. Because of having different usage areas, it is being considered as a valuable plant for human nutrition, trade and in many respects. In this study, we aimed at genetically characterization of the local and registered common bean genotypes and population structure of genotype groups belong to these common bean genotypes in Turkey. For this purpose, total 102 common bean genotypes including 93 local genotypes from 8 provinces, 7 cultivars and 2 reference cultivars were analyzed by 13 fluorescent SSR markers. As the result of the study, it was determined that the total SSR allele number was 192 and the average allele number was 14.8. While it was found that there were no synonymous genotypes, the highest heterozygosity rate was determined in three loci. Factorial correspondence analysis partially demonstrated substructure among common bean genotype groups. Structure analysis showed the same results as the Nm values and the Fst values. In the study, it was observed that SSR markers could be easily used in the molecular studies of common bean germplasm. The obtained results will be able to be used at the conservation, utilization of local common bean genetic resources and at the marker assisted selection studyings.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Fig. 1.
Fig. 2.
Fig. 3.
Fig. 4.

Similar content being viewed by others

REFERENCES

  1. Diaz-Camino, C., Annamalai, P., Sanchez, F., et al., An effective virus-based gene silencing method for functional genomics studies in common bean, Plant Methods, 2011, vol. 7, no. 1, pp. 1—11. https://doi.org/10.1186/1746-4811-7-16

    Article  CAS  Google Scholar 

  2. Broughton, W.J., Hernandez, G., Blair, M., et al., Beans (Phaseolus spp.)—model food legumes, Plant and Soil, 2003, vol. 252, no. 1, pp. 55—128. https://doi.org/10.1023/A:1024146710611

    Article  CAS  Google Scholar 

  3. Bozoglu, H. and Sozen, O., A sample for biodiversity in Turkey: common bean (Phaseolus vulgaris L.) landraces from Artvin, Afr. J. Biotechnol., 2011, vol. 10, no. 36, pp. 13789—13796. https://doi.org/10.5897/AJB11.942

    Article  Google Scholar 

  4. Türkiye İstatistik Kurumu (Tuik), Bitkisel Üretim İstatistikleri, 2016. http://www.tuik.gov.tr/PreTabloArama.do.

  5. Food and Agriculture Organization of the United Nations (FAO), FAOSTAT data, 2014. http://www.fao.org/faostat/en/#data.

  6. Akdağ, C. and Düzdemir, O., Türkiye kuru fasulye (Phaseolus vulgaris L.) gen kaynaklarının karakterizasyonu: 1. Bazı morfolojik ve fenolojik özellikleri, Gaziosmanpaşa Üniv. Ziraat Fak. Dergisi, 2001, vol. 18, no. 1, pp. 95—100.

    Google Scholar 

  7. Ammar, M.H., Alghamdi, S.S., Migdadi, H.M., et al., Assessment of genetic diversity among faba bean genotypes using agro-morphological and molecular markers, Saudi J. Biol. Sci., 2015, vol. 22, no. 3, pp. 340—350. https://doi.org/10.1016/j.sjbs.2015.02.005

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Jose, F.C., Mohammed, M.M.S., Thomas, G., et al., Genetic diversity and conservation of common bean (Phaseolus vulgaris L., Fabaceae) landraces in Nilgiris, Curr. Sci., 2009, vol. 97, no. 2, pp. 227—235.

    CAS  Google Scholar 

  9. Gill-Langarica, H.R., Muruaga-Martinez, J.S., Vargas-Vazquez, M.L.P., et al., Genetic diversity analysis of common beans based on molecular markers, Genet. Mol. Biol., 2011, vol. 34, no. 4, pp. 595—605. https://doi.org/10.1590/S1415-47572011005000056

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Powell, W., Morgante, M., Andre, C., et al., The comparison of RFLP, RAPD, AFLP and SSR (microsatellite) markers for germplasm analysis, Mol. Breed., 1996, vol. 2, no. 3, pp. 225—238. https://doi.org/10.1007/BF00564200

    Article  CAS  Google Scholar 

  11. Sarıkamış, G., Yaşar, F., Bakır, M., et al., Genetic characterization of green bean (Phaseolus vulgaris L.) genotypes from eastern Turkey, Genet. Mol. Res., 2009, vol. 8, no. 3, pp. 880—887. https://doi.org/10.4238/vol8-3gmr605

    Article  PubMed  Google Scholar 

  12. Ince, A.G. and Karaca, M., Genetic variation in common bean landraces efficiently revealed by Td-DAMD-PCR markers, Plant Omics, 2011, vol. 4, no. 4, pp. 220—227.

    CAS  Google Scholar 

  13. Khaidizar, M.I., Haliloglu, K., Elkoca, E., et al., Genetic diversity of common bean (Phaseolus vulgaris L.) landraces grown in Northeast Anatolia of Turkey assessed with simple sequence repeat markers, Turk. J. Field Crops, 2012, vol. 17, no. 2, pp. 145—150.

    Google Scholar 

  14. Ulukapı, K. and Onus, A.N., Molecular characterization of some selected landrace green bean (Phaseolus vulgaris L.) genotypes, J. Agric. Sci., 2012, vol. 18, no. 4, pp. 277—286.

    Google Scholar 

  15. Yu, K., Park, S.J., Poysa, V., and Gepts, P., Integration of simple sequence repeat (SSR) markers into a molecular linkage map of common bean (Phaseolus vulgaris L.), J. Hered., 2001, vol. 91, no. 6, pp. 429—434.

    Article  Google Scholar 

  16. Blair, M.W., Giraldo, M.C., Buendia, H.F., et al., Microsatellite marker diversity in common bean (Phaseolus vulgaris L.), Theor. Appl. Genet., 2006, vol. 113, no. 1, pp. 100—109. https://doi.org/10.1007/s00122-006-0276-4

    Article  CAS  PubMed  Google Scholar 

  17. Maras, M., Susnik, S., Meglic, V., and Sustar-Vozlic, J., Characterization and genetic diversity changes in the Slovenian common bean, Cesnjevec landrace, Acta Biol. Cracov Bot., 2006, vol. 48, no. 2, pp. 39—47.

    Google Scholar 

  18. Lefort, F., Lally, M., Thompson, D., and Douglas, G.C., Morphological traits, microsatellite fingerprinting and genetic relatedness of a stand of elite oaks (Q. robur L.) at Tullynally, Ireland, Silvae Genet., 1998, vol. 47, no. 5—6, pp. 257—262.

    Google Scholar 

  19. Gaitan-Solis, E., Duque, M.C., Edwards, K.J., and Tohme, J., Microsatellite repeats in common bean (Phaseolus vulgaris), Crop Sci., 2002, vol. 42, no. 6, pp. 2128—2136. https://doi.org/10.2135/cropsci2002.2128

    Article  CAS  Google Scholar 

  20. Loridon, K., McPhee, K., Morin, J., et al., Microsatellite marker polymorphism and mapping in pea (Pisum sativum L.), Theor. Appl. Genet., 2005, vol. 111, no. 6, pp. 1022—1031. https://doi.org/10.1007/s00122-005-0014-3

    Article  CAS  PubMed  Google Scholar 

  21. Wagner, H.W. and Sefc, K.M., IDENTITY 1.0, Vienna: Centre for Applied Genetics, University of Agricultural Sciences, 1999.

    Google Scholar 

  22. Paetkau, D., Calvert, W., Stirling, I., and Strobeck, C., Microsatellite analysis of population structure in Canadian polar bears, Mol. Ecol., 1995, vol. 4, no. 3, pp. 347—354.

    Article  CAS  PubMed  Google Scholar 

  23. Minch, E., Ruiz-Linares, A., Goldstein, D., et al., Microsat (version 1.4d): A Computer Program for Calculating Various Statistics on Microsatellite Allele Data, Stanford, California: University of Stanford, 1995. http://hpgl.stanford.edu/projects/microsat/.

    Google Scholar 

  24. Bowcock., A.M., Ruiz-Linares, A., Tomfohrde, J., et al., High resolution of human evolutionary tress with polymorphic microsatellites, Nature, 1994, vol. 368, no. 6470, pp. 455—457. https://doi.org/10.1038/368455a0

    Article  CAS  PubMed  Google Scholar 

  25. Rohlf, F.J., NTSYS-pc: Numerical Taxonomy and Multivariate Analysis: Version 2.02, Setauket: Exeter Software, 1998.

    Google Scholar 

  26. Sneath, P.H.A. and Sokal, R.R., Numerical Taxonomy: The Principles and Practice of Numerical Classification, San Francisco, 1973.

    Google Scholar 

  27. Belkhir, K., Borsa, P., Goudet, J., et al., GENETIX, logiciel sous WindowsTM pour la genetique des populations, Laboratoire Genome Populations, 1996–1998, Montpellier: CNRS UPR 9060, Universite de Montpellier II. Free program distributed by the authors over the internet. http://ci.nii.ac.jp/naid/10027575711/.

  28. Excoffier, L., Laval, G., and Schneider, S., Arlequin (version 3.0): an integrated software package for population genetics data analysis, Evol. Bioinf. Online, 2005, vol. 1, pp. 47—50.

    Article  CAS  Google Scholar 

  29. Rohlf, F.J., NTSYS-pc: Numerical Taxonomy System, Version 2.1, Setauket: Exeter, 2002.

  30. Pritchard, J.K., Stephens, M., and Donnelly, P., Inference of population structure using multilocus genotype data, Genetics, 2000, vol. 155, no. 2, pp. 945—959.

    CAS  PubMed  PubMed Central  Google Scholar 

  31. Falush, D., Stephens, M., and Pritchard, J.K., Inference of population structure: extensions to linked loci and correlated allele frequencies, Genetics, 2003, vol. 164, no. 4, pp. 1567—1587.

    CAS  PubMed  PubMed Central  Google Scholar 

  32. Corander, J., Marttinen, P., Sir’en, J., and Tang, J., Enhanced Bayesian modelling in BAPS software for learning genetic structures of populations, BMC Bioinformatics, 2008, vol. 9, no. 539, pp. 1—14. https://doi.org/10.1186/1471-2105-9-539

    Article  CAS  Google Scholar 

  33. Nei, M., Genetic distance between populations, Am. Nat., 1972, vol. 106, no. 949, pp. 283—292.

    Article  Google Scholar 

  34. Martinez, L.F.G., Evaluación de la diversidad genética en una colección de germoplasma de frijol común (Phaseolus vulgaris L.) de Ruanda (Africa), Ciencias Sci. (Biol.) Dissertation, Bogota: Pontificia Universidad Javeriana, 2008. https://repository.javeriana.edu.co/handle/10554/8743.

    Google Scholar 

  35. Blair, M.W., Gonzalez, L.F., Kimani, P.M., and Butare, L., Genetic diversity, inter-gene pool introgression and nutritional quality of common beans (Phaseolus vulgaris L.) from Central Africa, Theor. Appl. Genet., 2010, vol. 121, no. 2, pp. 237—248. https://doi.org/10.1007/s00122-010-1305-x

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Blair, M.W., Diaz, J.M., Hidalgo, R., and Diaz, L.M., Microsatellite characterization of Andean races of common bean (Phaseolus vulgaris L.), Theor. Appl. Genet., 2007, vol. 116, no. 1, pp. 29—43. https://doi.org/10.1007/s00122-007-0644-8

    Article  CAS  PubMed  Google Scholar 

  37. Blair, M.W., Soler, A., and Cortes, A.J., Diversification and population structure in common beans (Phaseolus vulgaris L.), PLoS One, 2012, vol. 7, no. 11. https://doi.org/10.1371/journal.pone.0049488

  38. Diaz, L.M. and Blair, M.W., Race structure within the Mesoamerican gene pool of common bean (Phaseolus vulgaris L.) as determined by microsatellite markers, Theor. Appl. Genet., 2006, vol. 114, no. 4, pp. 143—154. https://doi.org/10.1007/s00122-006-0417-9

    Article  CAS  PubMed  Google Scholar 

  39. Burle, M.L., Fonseca, J.R., Kami, J.A., and Gepts, P., Microsatellite diversity and genetic structure among common bean (Phaseolus vulgaris L.) landraces in Brazil, a secondary center of diversity, Theor. Appl. Genet., 2010, vol. 121, no. 5, pp. 801—813. https://doi.org/10.1007/s00122-010-1350-5

    Article  PubMed  PubMed Central  Google Scholar 

  40. Shabib, J.M., Shehata, A.I., Al-Hazzani, A.A., and Al-Rumaih, M., Assessment the genetic diversity of common bean Phaseolus vulgaris collection by microsatellite SSR markers, Afr. J. Agric. Res., 2013, vol. 8, no. 40, pp. 5032—5046. https://doi.org/10.5897/AJAR12.1013

    Article  CAS  Google Scholar 

  41. Cabral, P.D.S., Soares, T.C.B., Lima, A.B.P., et al., Genetic diversity in local and commercial dry bean (Phaseolus vulgaris L.) genotypes based on microsatellite markers, Genet. Mol. Res., 2011, vol. 10, no. 1, pp. 140—149. https://doi.org/10.4238/vol10-1gmr993

    Article  CAS  PubMed  Google Scholar 

  42. Ceylan, A., Öcal, N., and Akbulut, M., Genetic diversity among the Turkish common bean cultivars (Phaseolus vulgaris L.) as assessed by SRAP, POGP and cpSSR markers, Biochem. Syst. Ecol., 2014, vol. 54, pp. 219—229. https://doi.org/10.1016/j.bse.2014.01.014

    Article  CAS  Google Scholar 

  43. Okii, D., Tukamuhabwa, P., Kami, J., et al., The genetic diversity and population structure of common bean (Phaseolus vulgaris L.) germplasm in Uganda, Afr. J. Biotechnol., 2014, vol. 13, no. 29, pp. 2935—2949. https://doi.org/10.5897/AJB2014.13916

    Article  Google Scholar 

  44. Asfaw, A., Blair, M.W., and Almekinders, C., Genetic diversity and population structure of common bean (Phaseolus vulgaris L.) landraces from the East African Highlands, Theor. Appl. Genet., 2009, vol. 120, no. 1, pp. 1—12. https://doi.org/10.1007/s00122-009-1154-7

    Article  PubMed  Google Scholar 

  45. Madakbaş, S.Y., Sarıkamış, G., Başak, H., et al., Genetic characterization of green bean (Phaseolus vulgaris L.) accessions from Turkey with SCAR and SSR markers, Biochem. Genet., 2016, vol. 54, no. 4, pp. 495—505. https://doi.org/10.1007/s10528-016-9737-x

    Article  CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Ö. Bilir.

Additional information

The article is published in the original.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Bilir, Ö., Özmen, C.Y., Özcan, S. et al. Genetic Analysis of Turkey Common Bean (Phaseolus vulgaris L.) Genotypes by Simple Sequence Repeats Markers. Russ J Genet 55, 61–70 (2019). https://doi.org/10.1134/S1022795419010034

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1134/S1022795419010034

Keywords:

Navigation