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Research Article

volume 42 issue 1 (february 2019) : 18-24,   Doi: 10.18805/LR-423

Exploring the genetic diversity and population structure of Turkish common bean germplasm by the iPBS-retrotransposons markers

M
Muhammet Fatih Aydin
F
Faheem Shehzad Baloch
1Department of Field Crops, Faculty of Agricultural and Natural Science, Abant Ýzzet Baysal University, 14030, Bolu, Turkey.

  • Submitted24-04-2018|

  • Accepted04-07-2018|

  • First Online 16-10-2018|

  • doi 10.18805/LR-423

Cite article:- Aydin Fatih Muhammet, Baloch Shehzad Faheem (2018). Exploring the genetic diversity and population structure of Turkish common bean germplasm by the iPBS-retrotransposons markers. Legume Research. 42(1): 18-24. doi: 10.18805/LR-423.

ABSTRACT

Present study was aimed to investigate the genetic diversity and population structure of Turkish common bean germplasm. A total of 96 bean genotypes were characterized with iPBS-retrotansposons that yielded a mean polymorphism information contents of 0.8. Mean gene diversity and Shannon information index were 0.14 and 0.25, respectively. Neighbor joining analysis divided the bean genotypes into two main group (A and B) according to their geographical regions, growth habits and seed size. Bingol-l7, Sivas-14 and Hakkari-11 genotypes were found very distinct and can be used as candidate parents for the bean breeding. The higher efficiency and reproducibility of iPBS-retrotransposons was witnessed in common bean as compared to earlier studies using the same marker system. Results of this study will boost up the investigators for genotyping the larger germplasm of common bean with minimum laboratory infrastructure in developing and least developed countries.

REFERENCES

  1. Andeden, E.E., Baloch, F.S., Derya, M., Kilian, B., Özkan, H. (2013). iPBS-Retrotransposons-based genetic diversity and relationship among wild annual Cicer species. J. Plant Biochem. Biot., 22:453-466.
  2. Angioi, S.A., Rau, D., Attene, G., Nanni, L., Bellucci, E., Logozzo, G., Negri, V., Zeuli, P.S., Papa, R. (2010). Beans in Europe: origin and structure of the European landraces of Phaseolus vulgaris L. Theor. Appl. Genet., 121:829-843.
  3. Baloch F.S., Alsaleh, A., Andeden, E.E., Hatipoglur, R., Nachit, M., Ozkan, H. (2016). High levels of segregation distortion in the molecular linkage map of bread wheat representing the West Asia and North Africa region. Turk. J. Agric. For., 40: 352-64.
  4. Baloch, F.S., Alsaleh, A., de Miera, L.E., Hatipoðlu, R., Çiftçi, V., Karaköy, T., Yýldýz, M. Özkan, H. (2015a). DNA based iPBS-    retrotransposon markers for investigating the population structure of pea (Pisum sativum L.) germplasm from Turkey. Biochem. Syst. Ecol., 61:244-52.
  5. Baloch, F.S., Derya, M., Andeden, E.E., Alsaleh, A., Cömertpay, G., Kilian, B., Özkan, H. (2015b). Inter-primer binding site retrotransposon and inter-simple sequence repeat diversity among wild Lens species. Biochem. Syst. Ecol., 58:162-168.
  6. Baloch F.S., Alsaleh, A., Shahid M.Q., Çiftçi, V., de Miera L.E., Aasim, M., Nadeem, M.A., et al. (2017). A whole genome DArTseq and SNP analysis for genetic diversity assessment in durum wheat from central Fertile Crescent. Plos one, e0167821. doi.org/    10.1371/journal.pone.0167821
  7. Bitocchi, E., Bellucci, E., Giardini, A., Rau, D., Rodriguez, M., Biagetti, E., Santilocchi, R., et al. (2013). Molecular analysis of the parallel domestication of the common bean (Phaseolus vulgaris L.) in Mesoamerica and the Andes. New Phytologist., 197:300-13.
  8. Bozoðlu, H. and Sozen, O. (2011). A sample for biodiversity in Turkey: Common bean (Phaseolus vulgaris L.) landraces from Artvin. Afr. J. Biotechnol., 63:13789-13796.
  9. Ceylan, A., Ocal, N. Akbulut, M. (2014). Genetic diversity among the Turkish common bean cultivars (Phaseolus vulgaris L.) as assessed by SRAP, POGP and cpSSR markers. Biochem. Syst. Ecol., 54: 219-29.
  10. Devi, J., Sharma, A., Singh, Y., Katoch, V., Sharma, K. C. (2015). Genetic variability and character association studies in French bean (Phaseolus vulgaris L.) under North-Western Himalayas. Legume Res, 38: 149-156.
  11. Doyle, J. J., Doyle, J. L. (1990). Isolation of plant DNA from fresh leaf tissue. Focus, 12:13–15
  12. Erdinç, C., Turkmen, O., Dasgan, H.Y., Sensoy, S. (2017). Phenotypic and molecular genetic diversity among some Turkish bean genotypes. J. Anim. Plant Sci., 27:1963-1973.
  13. Evanno, G., Regnaut, S. Goudet, J. (2005). Detecting the number of clusters of individuals using the software structure: A simulation study. Mol. Ecol., 14: 2611-20.
  14. FAO. (2013). FAOSTAT. Food and Agriculture Organization of the United Nations.
  15. Gioia, T., Logozzo, G., Attene, G., Bellucci, E., Benedettelli, S., Negri, V., Papa, R., Zeuli, P.S. (2013). Evidence for introduction bottleneck and extensive inter-gene pool (Mesoamerica x Andes) hybridization in the European common bean (Phaseolus vulgaris L.) germplasm. PLoS One, 18: e75974.
  16. Hinze, L.L., Fang, D.D., Gore, M.A., Scheffler, B.E., John, Z.Y., Frelichowski, J., Percy, R.G. (2015). Molecular characterization of the Gossypium diversity reference set of the US National Cotton Germplasm Collection. Theor. Appl. Genet., 128: 313-27.
  17. Immaculee, N., Uma, M. S., Hegde, N., Nagaraja, T. E., and Somashekahar, Y. M. (2015). Microsatellite DNA marker aided diversity analysis in frenchbean (Phaseolus vulgaris L.). Legume Res, 38 :16-23.
  18. Jaccard, P. (1987). Nouvelles recherces sur la distribution florale. Bulletin de la Société Vaudoise des Sciences Naturelles, 44: 103-107.
  19. Kalendar, R., Antonius, K., Smýkal, P., Schulman, A.H. (2010). iPBS: a universal method for DNA fingerprinting and retrotransposon isolation. Theor. Appl. Genet., 121: 1419-1430.
  20. Khaidizar, M.I., Haliloglu, K., Elkoca, E., Aydin, M., Kantar, F. (2012). Genetic diversity of commonbean (Phaseolus vulgaris L.) landraces grown in North East Anatolia of Turkey assessed with simple sequence repeat markers. Turk. J. Field Crops., 17: 145-150.
  21. Lima, M.S., Carneiro, J.E., Carneiro, P.C., Pereira, C.S., Vieira, R.F., Cecon, P.R. (2012). Characterization of genetic variability among common bean genotypes by morphological descriptors. Crop Breed. Appl. Biot., 12: 76-84.
  22. Madakbaþ, S.Y., Sarýkamýþ, G., Baþak, H., Karadavut, U., Özmen, C.Y., Daþçý, M.G., Çayan, S. (2016). Genetic characterization of green bean (Phaseolus vulgaris L.) accessions from Turkey with SCAR and SSR markers. Biochem. Genet., 54: 495-505.
  23. Mall, N. and Chawla, H. S. (2015). Suitability of SSR marker for establishing distinctiveness in french bean varieties (Phaseolus vulgaris L.). Legume Res, 37:353-358.
  24. Nadeem, M.A., Nawaz, M.A., Shahid, M.Q., Doðan, Y., Comertpay, G., Yýldýz, M., et al (2017). DNA molecular markers in plant breeding: current status and recent advancements in genomic selection and genome editing. Biotechnol. Biotechnol. Equip., 32: 261-285
  25. Nemli, S., Kaya, H.B., Tanyolac, B. (2014). Genetic assessment of common bean (Phaseolus vulgaris L.) accessions by peroxidase gene based markers. J. Sci. Food Agric., 94:1672-1680.
  26. Nemli, S., Kianoosh, T., Tanyolac, M.B. (2015). Genetic diversity and population structure of common bean (Phaseolus vulgaris L.) accessions through retrotransposon-based interprimer binding sites (iPBSs) markers. Turk. J. Agric. For., 39:940-948.
  27. Razvi, S. M., Khan, M. N., Bhat, M. A., Ahmad, M., Ganaie, S. A., Sheikh, F. A., et al.. (2018). Morphological variability and phylogenetic analysis in common bean (Phaseolus vulgaris L.). Legume Res., 41:208-212
  28. Sarýkamýþ, G., Yaºar, F., Bakýr, M., Kazan, K., Ergül, A. (2009). Genetic characterization of green bean (Phaseolus vulgaris L.) genotypes from eastern Turkey. Genet. Mol. Res., 8:880-887.
  29. Schmutz, J., McClean, P.E., Mamidi, S., Wu, G.A., Cannon, S.B., Grimwood, J., Jenkins, J., et al Shu, S., Song, Q., Chavarro, C., Torres-Torres, M. (2014). A reference genome for common bean and genome-wide analysis of dual domestications. Nat. Genet., 46: 707-713.
  30. Singh, S.P., Gepts, P., Debouck, D.G. (1991). Races of common bean (Phaseolus vulgaris L. Fabaceae). Econ. Bot., 45: 379-396.
  31. Yaldiz, G., Çamlica, M., Nadeem, M.A., Nawaz, M.A., Baloch, F.S. (2018). Genetic diversity assessment in Nicotiana tabacum L. with iPBS-retrotransposons. Turk. J. Agric. For., 42.
  32. Yeh, F. C., Yang, R., Boyle, T. J., Ye, Z., and Xiyan, J. M. (2000). PopGene32, Microsoft Windows-based freeware for population genetic analysis, version 1.32. Molecular Biology and Biotechnology Centre, University of Alberta, Edmonton, Alberta, Canada. 
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    Research Article

    volume 42 issue 1 (february 2019) : 18-24,   Doi: 10.18805/LR-423

    Exploring the genetic diversity and population structure of Turkish common bean germplasm by the iPBS-retrotransposons markers

    M
    Muhammet Fatih Aydin
    F
    Faheem Shehzad Baloch
    1Department of Field Crops, Faculty of Agricultural and Natural Science, Abant Ýzzet Baysal University, 14030, Bolu, Turkey.

    • Submitted24-04-2018|

    • Accepted04-07-2018|

    • First Online 16-10-2018|

    • doi 10.18805/LR-423

    Cite article:- Aydin Fatih Muhammet, Baloch Shehzad Faheem (2018). Exploring the genetic diversity and population structure of Turkish common bean germplasm by the iPBS-retrotransposons markers. Legume Research. 42(1): 18-24. doi: 10.18805/LR-423.

    ABSTRACT

    Present study was aimed to investigate the genetic diversity and population structure of Turkish common bean germplasm. A total of 96 bean genotypes were characterized with iPBS-retrotansposons that yielded a mean polymorphism information contents of 0.8. Mean gene diversity and Shannon information index were 0.14 and 0.25, respectively. Neighbor joining analysis divided the bean genotypes into two main group (A and B) according to their geographical regions, growth habits and seed size. Bingol-l7, Sivas-14 and Hakkari-11 genotypes were found very distinct and can be used as candidate parents for the bean breeding. The higher efficiency and reproducibility of iPBS-retrotransposons was witnessed in common bean as compared to earlier studies using the same marker system. Results of this study will boost up the investigators for genotyping the larger germplasm of common bean with minimum laboratory infrastructure in developing and least developed countries.

    REFERENCES

    1. Andeden, E.E., Baloch, F.S., Derya, M., Kilian, B., Özkan, H. (2013). iPBS-Retrotransposons-based genetic diversity and relationship among wild annual Cicer species. J. Plant Biochem. Biot., 22:453-466.
    2. Angioi, S.A., Rau, D., Attene, G., Nanni, L., Bellucci, E., Logozzo, G., Negri, V., Zeuli, P.S., Papa, R. (2010). Beans in Europe: origin and structure of the European landraces of Phaseolus vulgaris L. Theor. Appl. Genet., 121:829-843.
    3. Baloch F.S., Alsaleh, A., Andeden, E.E., Hatipoglur, R., Nachit, M., Ozkan, H. (2016). High levels of segregation distortion in the molecular linkage map of bread wheat representing the West Asia and North Africa region. Turk. J. Agric. For., 40: 352-64.
    4. Baloch, F.S., Alsaleh, A., de Miera, L.E., Hatipoðlu, R., Çiftçi, V., Karaköy, T., Yýldýz, M. Özkan, H. (2015a). DNA based iPBS-    retrotransposon markers for investigating the population structure of pea (Pisum sativum L.) germplasm from Turkey. Biochem. Syst. Ecol., 61:244-52.
    5. Baloch, F.S., Derya, M., Andeden, E.E., Alsaleh, A., Cömertpay, G., Kilian, B., Özkan, H. (2015b). Inter-primer binding site retrotransposon and inter-simple sequence repeat diversity among wild Lens species. Biochem. Syst. Ecol., 58:162-168.
    6. Baloch F.S., Alsaleh, A., Shahid M.Q., Çiftçi, V., de Miera L.E., Aasim, M., Nadeem, M.A., et al. (2017). A whole genome DArTseq and SNP analysis for genetic diversity assessment in durum wheat from central Fertile Crescent. Plos one, e0167821. doi.org/    10.1371/journal.pone.0167821
    7. Bitocchi, E., Bellucci, E., Giardini, A., Rau, D., Rodriguez, M., Biagetti, E., Santilocchi, R., et al. (2013). Molecular analysis of the parallel domestication of the common bean (Phaseolus vulgaris L.) in Mesoamerica and the Andes. New Phytologist., 197:300-13.
    8. Bozoðlu, H. and Sozen, O. (2011). A sample for biodiversity in Turkey: Common bean (Phaseolus vulgaris L.) landraces from Artvin. Afr. J. Biotechnol., 63:13789-13796.
    9. Ceylan, A., Ocal, N. Akbulut, M. (2014). Genetic diversity among the Turkish common bean cultivars (Phaseolus vulgaris L.) as assessed by SRAP, POGP and cpSSR markers. Biochem. Syst. Ecol., 54: 219-29.
    10. Devi, J., Sharma, A., Singh, Y., Katoch, V., Sharma, K. C. (2015). Genetic variability and character association studies in French bean (Phaseolus vulgaris L.) under North-Western Himalayas. Legume Res, 38: 149-156.
    11. Doyle, J. J., Doyle, J. L. (1990). Isolation of plant DNA from fresh leaf tissue. Focus, 12:13–15
    12. Erdinç, C., Turkmen, O., Dasgan, H.Y., Sensoy, S. (2017). Phenotypic and molecular genetic diversity among some Turkish bean genotypes. J. Anim. Plant Sci., 27:1963-1973.
    13. Evanno, G., Regnaut, S. Goudet, J. (2005). Detecting the number of clusters of individuals using the software structure: A simulation study. Mol. Ecol., 14: 2611-20.
    14. FAO. (2013). FAOSTAT. Food and Agriculture Organization of the United Nations.
    15. Gioia, T., Logozzo, G., Attene, G., Bellucci, E., Benedettelli, S., Negri, V., Papa, R., Zeuli, P.S. (2013). Evidence for introduction bottleneck and extensive inter-gene pool (Mesoamerica x Andes) hybridization in the European common bean (Phaseolus vulgaris L.) germplasm. PLoS One, 18: e75974.
    16. Hinze, L.L., Fang, D.D., Gore, M.A., Scheffler, B.E., John, Z.Y., Frelichowski, J., Percy, R.G. (2015). Molecular characterization of the Gossypium diversity reference set of the US National Cotton Germplasm Collection. Theor. Appl. Genet., 128: 313-27.
    17. Immaculee, N., Uma, M. S., Hegde, N., Nagaraja, T. E., and Somashekahar, Y. M. (2015). Microsatellite DNA marker aided diversity analysis in frenchbean (Phaseolus vulgaris L.). Legume Res, 38 :16-23.
    18. Jaccard, P. (1987). Nouvelles recherces sur la distribution florale. Bulletin de la Société Vaudoise des Sciences Naturelles, 44: 103-107.
    19. Kalendar, R., Antonius, K., Smýkal, P., Schulman, A.H. (2010). iPBS: a universal method for DNA fingerprinting and retrotransposon isolation. Theor. Appl. Genet., 121: 1419-1430.
    20. Khaidizar, M.I., Haliloglu, K., Elkoca, E., Aydin, M., Kantar, F. (2012). Genetic diversity of commonbean (Phaseolus vulgaris L.) landraces grown in North East Anatolia of Turkey assessed with simple sequence repeat markers. Turk. J. Field Crops., 17: 145-150.
    21. Lima, M.S., Carneiro, J.E., Carneiro, P.C., Pereira, C.S., Vieira, R.F., Cecon, P.R. (2012). Characterization of genetic variability among common bean genotypes by morphological descriptors. Crop Breed. Appl. Biot., 12: 76-84.
    22. Madakbaþ, S.Y., Sarýkamýþ, G., Baþak, H., Karadavut, U., Özmen, C.Y., Daþçý, M.G., Çayan, S. (2016). Genetic characterization of green bean (Phaseolus vulgaris L.) accessions from Turkey with SCAR and SSR markers. Biochem. Genet., 54: 495-505.
    23. Mall, N. and Chawla, H. S. (2015). Suitability of SSR marker for establishing distinctiveness in french bean varieties (Phaseolus vulgaris L.). Legume Res, 37:353-358.
    24. Nadeem, M.A., Nawaz, M.A., Shahid, M.Q., Doðan, Y., Comertpay, G., Yýldýz, M., et al (2017). DNA molecular markers in plant breeding: current status and recent advancements in genomic selection and genome editing. Biotechnol. Biotechnol. Equip., 32: 261-285
    25. Nemli, S., Kaya, H.B., Tanyolac, B. (2014). Genetic assessment of common bean (Phaseolus vulgaris L.) accessions by peroxidase gene based markers. J. Sci. Food Agric., 94:1672-1680.
    26. Nemli, S., Kianoosh, T., Tanyolac, M.B. (2015). Genetic diversity and population structure of common bean (Phaseolus vulgaris L.) accessions through retrotransposon-based interprimer binding sites (iPBSs) markers. Turk. J. Agric. For., 39:940-948.
    27. Razvi, S. M., Khan, M. N., Bhat, M. A., Ahmad, M., Ganaie, S. A., Sheikh, F. A., et al.. (2018). Morphological variability and phylogenetic analysis in common bean (Phaseolus vulgaris L.). Legume Res., 41:208-212
    28. Sarýkamýþ, G., Yaºar, F., Bakýr, M., Kazan, K., Ergül, A. (2009). Genetic characterization of green bean (Phaseolus vulgaris L.) genotypes from eastern Turkey. Genet. Mol. Res., 8:880-887.
    29. Schmutz, J., McClean, P.E., Mamidi, S., Wu, G.A., Cannon, S.B., Grimwood, J., Jenkins, J., et al Shu, S., Song, Q., Chavarro, C., Torres-Torres, M. (2014). A reference genome for common bean and genome-wide analysis of dual domestications. Nat. Genet., 46: 707-713.
    30. Singh, S.P., Gepts, P., Debouck, D.G. (1991). Races of common bean (Phaseolus vulgaris L. Fabaceae). Econ. Bot., 45: 379-396.
    31. Yaldiz, G., Çamlica, M., Nadeem, M.A., Nawaz, M.A., Baloch, F.S. (2018). Genetic diversity assessment in Nicotiana tabacum L. with iPBS-retrotransposons. Turk. J. Agric. For., 42.
    32. Yeh, F. C., Yang, R., Boyle, T. J., Ye, Z., and Xiyan, J. M. (2000). PopGene32, Microsoft Windows-based freeware for population genetic analysis, version 1.32. Molecular Biology and Biotechnology Centre, University of Alberta, Edmonton, Alberta, Canada. 
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