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Research Article

volume 51 issue 6 (december 2017) : 580-585,   Doi: 10.18805/IJARe.A-286

Genetic divergence analysis among barley genotypes using inter-retrotransposon amplified polymorphism markers (IRAP)

A
A. Elframawy
R
R. EL-Bakatoushi
1Biology and Geology Sciences Department, Faculty of Education, University of Alexandria, Egypt
Cite article:- Elframawy A., EL-Bakatoushi R. (2017). Genetic divergence analysis among barley genotypes using inter-retrotransposon amplified polymorphism markers (IRAP). Indian Journal of Agricultural Research. 51(6): 580-585. doi: 10.18805/IJARe.A-286.

ABSTRACT

The genetic diversity among 14 barley accessions was evaluated using seven designed primers based on long terminal repeat (LTR) retrotransposons derived from the barley genome. LTR primers amplified 96 bands of < 100- 1500 bp, of which 84 were polymorphic. The number of polymorphic fragments ranged from 5 (LTR, LTR1 and LTR6150) to 18 (Sukkula) with an average of 9.33.  The highest marker index (MI) was observed with the primer Nikita (3.93) and the lowest with the primer LTR2 (1.05), with an average MI of 2.28 per primer. The insertion patterns of retrotransposones have interesting implications for genome organization in Hordeum. The Shannon diversity index with markers obtained on the accessions level was 0.45. Barely accessions are clustered according to their pedigree and caryopsis character (hulled or naked caryopsis). This study demonstrates the efficiency of IRAP markers as a genetic tool for selection of suitable accessions for breeding programs.

REFERENCES

  1. Abdellaoui, R., Kadri, K., Naceur M’barek, B. and Bettaib ben Kaab, L. (2010). Genetic Diversity In Some Tunisian Barley Landraces Based on RAPD Markers. Pakistan Journal of Botany, 42: 3 775-82.
  2. Alavi-kia, S.S., Mohammadi, S.A., Aharizad S. and Moghaddam, M. (2008). Analysis of genetic diversity and phylogenetic relationships in Crocus genus of Iran using inter-retrotransposon amplified polymorphism. Biotechnology and Biotechnological Equipments, 22: 795–800. 
  3. Belghouti, A. (2007). Caracte´risation morphologique et mole´culaire de quelques ge´notypes d’orge, Me´moire de Maste‘re de l’Ecole Supe´rieure d’Agriculture du Kef (Tunisie).
  4. Ben naceur, A., Chaabane, R., El-Faleh, M., Abdelly, C., Ramla, D., Nada, A., Sakr, M. and Ben naceur, M. (2012). Genetic diversity analysis of North Africa’s barley using SSR markers. Journal of Genetic Engineering and Biotechnology, 10: 13–22.
  5. Bengtsson, B.O. (1992). Barley genetics. Trends in Genetics, 8: 3–5. 
  6. Chand, N., Vishwakarma, S.R., Verma, O.P. and Kumar, M. (2008). Worth of genetic parameters to sort out new elite barley lines over heterogeneous environments. Barley Genetics Newsletter, 38: 10-13. 
  7. Du, Y.P., He, H.B., Wang, Z.X., LI, S., Wei, C., Yuan, X.N., Cui, Q. and Jia G.X. (2014). Molecular phylogeny and genetic variation in the genus Lilium native China based on the internal transcribed spacer sequences of nuclear ribosomal DNA. Journal of Plant Research, 127:249–263.
  8. Eshghi, R. and Akhundova E. (2009). Genetic diversity of the monomeric prolamins and hordein in hulless barley genotypes and their relation with agronomical traits. African journal of Biotechnology, 8: 1819-1826.
  9. Fan, F., Cui, B., Zhang, T., Ding, g. and Wen, X. (2014). LTR-retrotransposon activation, IRAP marker development and its potential in genetic diversity assessment of mason pine (Pinus massoniana). Tree Genetics and Genome, 10:213–222. 
  10. Finnegan, D.J. (1989). Eukaryotic transposable elements and genome evolution. Trends in Genetics, 5: 103–1077. Ghaffariyan, S., Mohammadi, S.A., Aharizad, S. (2011). Patterns of population diversity in lemon balm (Melissa officinalis L.) as revealed by IRAP markers. Journal of Plant Physiology and Breeding, 1: 39–51.
  11. Kalendar, R., Grob, T., Regina, M., Suoniemi, A. and Schulman, A.H. (1999). IRAP and REMAP: two new retrotransposon-based DNA fingerprinting techniques. Theoretical and Applied Genetics, 98: 704–711.
  12. Kalendar, R., Flavell, A.J., Ellis, T.H.N., Sjakste, T., Moisy C. and Schulman, A.H. (2011). Analysis of plant diversity with retrotransposon-based molecular markers. Heredity, 106:520–530
  13. Kanbar, A. and Kondo, K. (2011). Efficiency of ISSR and RAPD Dominant Markers in Assessing Genetic Diversity among Japanese and Syrian Cultivars of Barley (H. Vulgare L.). Research journal of agriculture and biological sciences, 7: 4-10. 
  14. Macas, J., Neumann, P. and Navra´Tilova´ A. (2007). Repetitive DNA in the pea (Pisum sativum L.) genome: comprehensive characterization using 454 sequencing and comparison to soybean and Medicago truncatula. BMC Genome, 8: 427. 
  15. Manninen, I. and Schulman, A.H. (1993). BARE-1, a copia-like retroelement in barley (Hordeum vulgare L.). Plant Molecular Biology, 22: 829-846. 
  16. Rohlf, F.J. (2002). NTSYS-pc: Numerical Taxonomy System ver.2.1. Exeter Publishing Ltd., Setauket, New York.
  17. Roldan-Ruiz, I., Dendauw, J., Vanbockstaele, E., Depicker, A. and De Loose, M. (2000). AFLP markers reveal high polymorphic rates in ryegrasses (Lolium spp.). Molecular Breeding, 6:125–134.
  18. Russell, J.R., Fuller, J.D., Macaulay, M., Hatz, B.G., Jahoor, A., Powell, W. and Waugh, R. (1997). Direct comparison of levels of genetic variation among barley accessions detected by RFLPs, AFLPs, SSRs and RAPDs. Theoretical and Applied Genetics, 95: 714–722.
  19. Smy‘kal, P. (2006). Development of an efficient retrotransposon based fingerprinting method for rapid pea variety identification. Journal of Applied Genetics, 47: 221–230. 
  20. Sneath, P.H.A. and Sokal, R.R. (1973). Numerical Taxonomy. Freeman, San Francisco. pp. 573.
  21. Suoniemi, A., Narvanto, A. and Schulman, A. (1996). The BARE-1 retrotransposon is transcribed in barley from an LTR promoter active in transient assays. Plant Molecular Boilogy, 3: 295-306.
  22. Taketa, S., Kikuchi, S., Awayama, T., Yamamoto, S., Ichii, M. and Kawasaki, S. (2004). Monophyletic origin of naked barley inferred from molecular analyses of a marker closely linked to the naked caryopsis gene (nud). Theoretical and Applied Genetics, 108: 1236-1242.
  23. Varshney, R.K., Beier, U., Khlestkina, E., Kota, R., Korzun, V., Röder, M., Graner, A. and Börner, A. (2007). Single nucleotide polymorphisms in rye: discovery, frequency and applications for genome mapping and diversity studies. Theoretical and Applied Genetics, 114:1105-1116.
  24. Vicient, C.M., Kalendar, R. and Schulman, A.H. (2001). Envelope-class retrovirus-like elements are widespread, transcribed and spliced, and insertionally polymorphic in plants. Genome Research, 11: 2041-2049.
  25. Vukich, M., Schulman, A.H., Giordani, T., Natali, L., Kalendar, R. and Cavallini, A. (2009). Genetic variability in sunflower (Helianthus annus L.) and in the Helianthus genus as assessed by retrotransposon based molecular markers. Theoretical and Applied Genetics, 119:1027-1038.
  26. Yeh, F.C., Yang, R.C. and Boyle, T. (1999). POPGENE. Microsoft Windows Based Freeware for Population Genetic Analysis. Release 1.31. University of Alberta, Edmonton.
  27. Zhang, Q., Yang, G.P., Dai, X. and Sun, J.Z. (1994). A comparative analysis of genetic polymorphism in wild and cultivated barley from tibet using isozyme and ribosomal DNA markers. Genome, 37: 631-638.
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Indian Journal of Agricultural Research
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    Research Article

    volume 51 issue 6 (december 2017) : 580-585,   Doi: 10.18805/IJARe.A-286

    Genetic divergence analysis among barley genotypes using inter-retrotransposon amplified polymorphism markers (IRAP)

    A
    A. Elframawy
    R
    R. EL-Bakatoushi
    1Biology and Geology Sciences Department, Faculty of Education, University of Alexandria, Egypt
    Cite article:- Elframawy A., EL-Bakatoushi R. (2017). Genetic divergence analysis among barley genotypes using inter-retrotransposon amplified polymorphism markers (IRAP). Indian Journal of Agricultural Research. 51(6): 580-585. doi: 10.18805/IJARe.A-286.

    ABSTRACT

    The genetic diversity among 14 barley accessions was evaluated using seven designed primers based on long terminal repeat (LTR) retrotransposons derived from the barley genome. LTR primers amplified 96 bands of < 100- 1500 bp, of which 84 were polymorphic. The number of polymorphic fragments ranged from 5 (LTR, LTR1 and LTR6150) to 18 (Sukkula) with an average of 9.33.  The highest marker index (MI) was observed with the primer Nikita (3.93) and the lowest with the primer LTR2 (1.05), with an average MI of 2.28 per primer. The insertion patterns of retrotransposones have interesting implications for genome organization in Hordeum. The Shannon diversity index with markers obtained on the accessions level was 0.45. Barely accessions are clustered according to their pedigree and caryopsis character (hulled or naked caryopsis). This study demonstrates the efficiency of IRAP markers as a genetic tool for selection of suitable accessions for breeding programs.

    REFERENCES

    1. Abdellaoui, R., Kadri, K., Naceur M’barek, B. and Bettaib ben Kaab, L. (2010). Genetic Diversity In Some Tunisian Barley Landraces Based on RAPD Markers. Pakistan Journal of Botany, 42: 3 775-82.
    2. Alavi-kia, S.S., Mohammadi, S.A., Aharizad S. and Moghaddam, M. (2008). Analysis of genetic diversity and phylogenetic relationships in Crocus genus of Iran using inter-retrotransposon amplified polymorphism. Biotechnology and Biotechnological Equipments, 22: 795–800. 
    3. Belghouti, A. (2007). Caracte´risation morphologique et mole´culaire de quelques ge´notypes d’orge, Me´moire de Maste‘re de l’Ecole Supe´rieure d’Agriculture du Kef (Tunisie).
    4. Ben naceur, A., Chaabane, R., El-Faleh, M., Abdelly, C., Ramla, D., Nada, A., Sakr, M. and Ben naceur, M. (2012). Genetic diversity analysis of North Africa’s barley using SSR markers. Journal of Genetic Engineering and Biotechnology, 10: 13–22.
    5. Bengtsson, B.O. (1992). Barley genetics. Trends in Genetics, 8: 3–5. 
    6. Chand, N., Vishwakarma, S.R., Verma, O.P. and Kumar, M. (2008). Worth of genetic parameters to sort out new elite barley lines over heterogeneous environments. Barley Genetics Newsletter, 38: 10-13. 
    7. Du, Y.P., He, H.B., Wang, Z.X., LI, S., Wei, C., Yuan, X.N., Cui, Q. and Jia G.X. (2014). Molecular phylogeny and genetic variation in the genus Lilium native China based on the internal transcribed spacer sequences of nuclear ribosomal DNA. Journal of Plant Research, 127:249–263.
    8. Eshghi, R. and Akhundova E. (2009). Genetic diversity of the monomeric prolamins and hordein in hulless barley genotypes and their relation with agronomical traits. African journal of Biotechnology, 8: 1819-1826.
    9. Fan, F., Cui, B., Zhang, T., Ding, g. and Wen, X. (2014). LTR-retrotransposon activation, IRAP marker development and its potential in genetic diversity assessment of mason pine (Pinus massoniana). Tree Genetics and Genome, 10:213–222. 
    10. Finnegan, D.J. (1989). Eukaryotic transposable elements and genome evolution. Trends in Genetics, 5: 103–1077. Ghaffariyan, S., Mohammadi, S.A., Aharizad, S. (2011). Patterns of population diversity in lemon balm (Melissa officinalis L.) as revealed by IRAP markers. Journal of Plant Physiology and Breeding, 1: 39–51.
    11. Kalendar, R., Grob, T., Regina, M., Suoniemi, A. and Schulman, A.H. (1999). IRAP and REMAP: two new retrotransposon-based DNA fingerprinting techniques. Theoretical and Applied Genetics, 98: 704–711.
    12. Kalendar, R., Flavell, A.J., Ellis, T.H.N., Sjakste, T., Moisy C. and Schulman, A.H. (2011). Analysis of plant diversity with retrotransposon-based molecular markers. Heredity, 106:520–530
    13. Kanbar, A. and Kondo, K. (2011). Efficiency of ISSR and RAPD Dominant Markers in Assessing Genetic Diversity among Japanese and Syrian Cultivars of Barley (H. Vulgare L.). Research journal of agriculture and biological sciences, 7: 4-10. 
    14. Macas, J., Neumann, P. and Navra´Tilova´ A. (2007). Repetitive DNA in the pea (Pisum sativum L.) genome: comprehensive characterization using 454 sequencing and comparison to soybean and Medicago truncatula. BMC Genome, 8: 427. 
    15. Manninen, I. and Schulman, A.H. (1993). BARE-1, a copia-like retroelement in barley (Hordeum vulgare L.). Plant Molecular Biology, 22: 829-846. 
    16. Rohlf, F.J. (2002). NTSYS-pc: Numerical Taxonomy System ver.2.1. Exeter Publishing Ltd., Setauket, New York.
    17. Roldan-Ruiz, I., Dendauw, J., Vanbockstaele, E., Depicker, A. and De Loose, M. (2000). AFLP markers reveal high polymorphic rates in ryegrasses (Lolium spp.). Molecular Breeding, 6:125–134.
    18. Russell, J.R., Fuller, J.D., Macaulay, M., Hatz, B.G., Jahoor, A., Powell, W. and Waugh, R. (1997). Direct comparison of levels of genetic variation among barley accessions detected by RFLPs, AFLPs, SSRs and RAPDs. Theoretical and Applied Genetics, 95: 714–722.
    19. Smy‘kal, P. (2006). Development of an efficient retrotransposon based fingerprinting method for rapid pea variety identification. Journal of Applied Genetics, 47: 221–230. 
    20. Sneath, P.H.A. and Sokal, R.R. (1973). Numerical Taxonomy. Freeman, San Francisco. pp. 573.
    21. Suoniemi, A., Narvanto, A. and Schulman, A. (1996). The BARE-1 retrotransposon is transcribed in barley from an LTR promoter active in transient assays. Plant Molecular Boilogy, 3: 295-306.
    22. Taketa, S., Kikuchi, S., Awayama, T., Yamamoto, S., Ichii, M. and Kawasaki, S. (2004). Monophyletic origin of naked barley inferred from molecular analyses of a marker closely linked to the naked caryopsis gene (nud). Theoretical and Applied Genetics, 108: 1236-1242.
    23. Varshney, R.K., Beier, U., Khlestkina, E., Kota, R., Korzun, V., Röder, M., Graner, A. and Börner, A. (2007). Single nucleotide polymorphisms in rye: discovery, frequency and applications for genome mapping and diversity studies. Theoretical and Applied Genetics, 114:1105-1116.
    24. Vicient, C.M., Kalendar, R. and Schulman, A.H. (2001). Envelope-class retrovirus-like elements are widespread, transcribed and spliced, and insertionally polymorphic in plants. Genome Research, 11: 2041-2049.
    25. Vukich, M., Schulman, A.H., Giordani, T., Natali, L., Kalendar, R. and Cavallini, A. (2009). Genetic variability in sunflower (Helianthus annus L.) and in the Helianthus genus as assessed by retrotransposon based molecular markers. Theoretical and Applied Genetics, 119:1027-1038.
    26. Yeh, F.C., Yang, R.C. and Boyle, T. (1999). POPGENE. Microsoft Windows Based Freeware for Population Genetic Analysis. Release 1.31. University of Alberta, Edmonton.
    27. Zhang, Q., Yang, G.P., Dai, X. and Sun, J.Z. (1994). A comparative analysis of genetic polymorphism in wild and cultivated barley from tibet using isozyme and ribosomal DNA markers. Genome, 37: 631-638.
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