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Research Article

volume 41 issue 6 (december 2018) : 822-827,   Doi: 10.18805/LR-401

Investigation of IRAP transposon-based molecular markers for analysis of genetic diversity in pea germplasm

S
Sajjad Ahmad
R
Rajvinder Kaur
M
Mark Lefsrud
J
Jaswinder Singh
1Macdonald Campus, McGill University, Ste Anne de Bellevue, Quebec H9X3V9

  • Submitted25-12-2017|

  • Accepted24-03-2018|

  • First Online 20-08-2018|

  • doi 10.18805/LR-401

Cite article:- Ahmad Sajjad, Kaur Rajvinder, Lefsrud Mark, Singh Jaswinder (2018). Investigation of IRAP transposon-based molecular markers for analysis of genetic diversity in pea germplasm. Legume Research. 41(6): 822-827. doi: 10.18805/LR-401.

ABSTRACT

Retrotransposons diversity has been extensively studied in monocots, but it is not well documented in dicot species. Transposition activity of transposons creates DNA polymorphism and their abundant presence in genomes is making transposons a promising marker system for varietal identification and fingerprinting. In this study, four transposon-based markers (two DNA- and two RNA-transposons)  were employed to evaluate the effectiveness of Inter-Retrotransposon Amplified Polymorphism (IRAP) transposon system in assessing genetic diversity in pea germplasm accessions. A total of 28 alleles were detected across the 35 pea accessions with number of alleles per locus ranged from 5 (Mutator) to 9 (Cyclops). RNA transposons produced a higher number of polymorphic alleles (Ogre: 8, Cyclops: 9) than DNA transposon markers (Mutator: 5, MITE: 6). Overall mean PIC value and D values for these transposon markers were 0.810 and 0.817 respectively. Genetic similarity values ranged from 0.143 to 0.823 with a mean similarity value of 0.403. Cluster analysis classified pea genotypes into six major groups that were somewhat consistent with their geographical origins. The molecular analyses differentiated all the 35 accessions and generated higher PIC and D values that can be useful for MAS-based breeding programs in pea.

REFERENCES

  1. hmad, S., Singh, M., Lamb-Palmer, N. D., Lefsrud, M., Singh, J. (2012). Assessment of genetic diversity in 35 Pisum sativum accessions using microsatellite markers. Canadian Journal of Plant Science, 92:1075-1081.
  2. Ahmad, S., Lamb-Palmer, N. D., Kaur, S., Lefsrud, M., Singh, J. (2015). Genetic diversity and population structure of Pisum sativum accessions for marker-trait association. The Crop Journal 3: 238-245.
  3. Bennetzen, J.L. (2000). Transposable element contributions to plant gene and genome evolution. Plant Molecular Biology, 42:251-269.
  4. Campbell, B.C., LeMare, S., Piperidis, G., Godwin, I. D. (2011). IRAP, a retrotransposon-based marker system for the detection of somaclonal variation in barley. Molecular Breeding, 72:193-206.
  5. Cardinal, M.J., Kaur, R., Singh, J. (2016). Genetic transformation of Hordeum vulgare ssp. spontaneum for the development of a transposon-based insertional mutagenesis system. Molecular Biotechnology 58: 672-683.
  6. Jing, R.C., Vershinin, A., Grzebyta, J., Shaw, P., Smykal, P., Marshall, D., Ambrose, M.J., Ellis, T.H.N., Flavell, A.J. (2010). The genetic diversity and evolution of field pea (Pisum) studied by high throughput retrotransposon based insertion polymorphism (RBIP) marker analysis. BMC Evolutionary Biology, 10:44.
  7. Jiang, N., Bao, Z., Zhang, X., Hirochika, H., Eddy, S. R., McCouch, S. R., Wessler, S. R. (2003). An active DNA transposon family in rice. Nature, 421:163-167.
  8. Kalendar, R. and Schulman, A. (2006). IRAP and REMAP for retrotransposon based genotyping and fingerprinting, Nature Protocols, 1: 2478–2484.
  9. Khadapanahi, E., Lefsrud, M., Orsat, V., Singh, J., Warkentin, T. (2012). Study of pea accessions for development of an oilseed pea. Energies, 5: 3788-3802.
  10. Kumar, A. and Hirochika, H. (2001). Applications of retrotransposons as genetic tools in plant biology. Trends in Plant Science 6:127-134.
  11. Macas, J., Neumann, P., Pozarkova, D. (2003). Zaba: a novel miniature transposable element present in genomes of legume plants. Molecular Genetics and Genomics, 269:624-631.
  12. Macas, J., Koblizkova, A., Neumann, P. (2005). Characterization of Stowaway MITEs in pea (Pisum sativum L.) and identification of their potential master elements. Genome, 48:831-839.
  13. Macas, J., Neumann, P., Navratilova, A. (2007). Repetitive DNA in the pea (Pisum sativum L.) genome: comprehensive characterization using 454 sequencing and comparison to soybean and Medicago truncatula. BMC Genomics, 8:427.
  14. McClintock, B. (1941). The stability of broken ends of chromosomes in Zea mays. Genetics, 26: 234-282.
  15. Munoz-Lopez, M., Garcia-Perez, J.L. (2010). DNA Transposons: Nature and Applications in Genomics. Current Genomics, 11:115-128.
  16. Pearce, S.R., Knox, M., Ellis, T.H.N., Flavell, A.J. and Kumar, A., (2000). Pea Ty1-copia group retrotransposons: transpositional activity and use as markers to study genetic diversity in Pisum. Molecular and General Genetics, 263:898-907.
  17. Randhawa, H., Singh, J. , Lemaux, P.G., Gill, K.S. (2009). Mapping barley Ds insertions using wheat deletion lines reveals high insertion frequencies in gene-rich regions with high to moderate recombination rates Genome, 52: 566–575
  18. Singh, S., Singh, J. (2017). Sequence-based genetic mapping of Ds-tagged insertions to characterize malting-related traits in barley. The Crop Journal, 5:11-20.
  19. Singh, S., Nandha, P. S., Singh, J. (2017). Transposon-based genetic diversity assessment in wild and cultivated barley. The Crop Journal, 5: 296-304.
  20. Singh, S., Tan, H-Q., Singh, J. (2012). Mutagenesis of barley malting quality QTLs with Ds transposons. Functional & Integrative Genomics, 12:131-141.
  21. Smykal, P. (2006). Development of an efficient retrotransposon-based fingerprinting method for rapid pea variety identification. Journal of Applied Genetics, 47:221-230.
  22. Tessier, C., David, J., This, P., Boursiquot, J. M. Charrier, A. (1999). Optimization of the choice of molecular markers for varietal identification in Vitis vinifera L. Theoretical and Applied Genetics, 98:171-177.
  23. Zhang, S., Gu, Y., Singh, J., Coleman-Derr, D., Brar, D. S., Jiang N., Lemaux, P. G (2007). New insights into Oryza genome evolution: High gene collinearity and differential reterotransposon amplification. Plant Molecular Biology, 64: 589-600. 
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    Research Article

    volume 41 issue 6 (december 2018) : 822-827,   Doi: 10.18805/LR-401

    Investigation of IRAP transposon-based molecular markers for analysis of genetic diversity in pea germplasm

    S
    Sajjad Ahmad
    R
    Rajvinder Kaur
    M
    Mark Lefsrud
    J
    Jaswinder Singh
    1Macdonald Campus, McGill University, Ste Anne de Bellevue, Quebec H9X3V9

    • Submitted25-12-2017|

    • Accepted24-03-2018|

    • First Online 20-08-2018|

    • doi 10.18805/LR-401

    Cite article:- Ahmad Sajjad, Kaur Rajvinder, Lefsrud Mark, Singh Jaswinder (2018). Investigation of IRAP transposon-based molecular markers for analysis of genetic diversity in pea germplasm. Legume Research. 41(6): 822-827. doi: 10.18805/LR-401.

    ABSTRACT

    Retrotransposons diversity has been extensively studied in monocots, but it is not well documented in dicot species. Transposition activity of transposons creates DNA polymorphism and their abundant presence in genomes is making transposons a promising marker system for varietal identification and fingerprinting. In this study, four transposon-based markers (two DNA- and two RNA-transposons)  were employed to evaluate the effectiveness of Inter-Retrotransposon Amplified Polymorphism (IRAP) transposon system in assessing genetic diversity in pea germplasm accessions. A total of 28 alleles were detected across the 35 pea accessions with number of alleles per locus ranged from 5 (Mutator) to 9 (Cyclops). RNA transposons produced a higher number of polymorphic alleles (Ogre: 8, Cyclops: 9) than DNA transposon markers (Mutator: 5, MITE: 6). Overall mean PIC value and D values for these transposon markers were 0.810 and 0.817 respectively. Genetic similarity values ranged from 0.143 to 0.823 with a mean similarity value of 0.403. Cluster analysis classified pea genotypes into six major groups that were somewhat consistent with their geographical origins. The molecular analyses differentiated all the 35 accessions and generated higher PIC and D values that can be useful for MAS-based breeding programs in pea.

    REFERENCES

    1. hmad, S., Singh, M., Lamb-Palmer, N. D., Lefsrud, M., Singh, J. (2012). Assessment of genetic diversity in 35 Pisum sativum accessions using microsatellite markers. Canadian Journal of Plant Science, 92:1075-1081.
    2. Ahmad, S., Lamb-Palmer, N. D., Kaur, S., Lefsrud, M., Singh, J. (2015). Genetic diversity and population structure of Pisum sativum accessions for marker-trait association. The Crop Journal 3: 238-245.
    3. Bennetzen, J.L. (2000). Transposable element contributions to plant gene and genome evolution. Plant Molecular Biology, 42:251-269.
    4. Campbell, B.C., LeMare, S., Piperidis, G., Godwin, I. D. (2011). IRAP, a retrotransposon-based marker system for the detection of somaclonal variation in barley. Molecular Breeding, 72:193-206.
    5. Cardinal, M.J., Kaur, R., Singh, J. (2016). Genetic transformation of Hordeum vulgare ssp. spontaneum for the development of a transposon-based insertional mutagenesis system. Molecular Biotechnology 58: 672-683.
    6. Jing, R.C., Vershinin, A., Grzebyta, J., Shaw, P., Smykal, P., Marshall, D., Ambrose, M.J., Ellis, T.H.N., Flavell, A.J. (2010). The genetic diversity and evolution of field pea (Pisum) studied by high throughput retrotransposon based insertion polymorphism (RBIP) marker analysis. BMC Evolutionary Biology, 10:44.
    7. Jiang, N., Bao, Z., Zhang, X., Hirochika, H., Eddy, S. R., McCouch, S. R., Wessler, S. R. (2003). An active DNA transposon family in rice. Nature, 421:163-167.
    8. Kalendar, R. and Schulman, A. (2006). IRAP and REMAP for retrotransposon based genotyping and fingerprinting, Nature Protocols, 1: 2478–2484.
    9. Khadapanahi, E., Lefsrud, M., Orsat, V., Singh, J., Warkentin, T. (2012). Study of pea accessions for development of an oilseed pea. Energies, 5: 3788-3802.
    10. Kumar, A. and Hirochika, H. (2001). Applications of retrotransposons as genetic tools in plant biology. Trends in Plant Science 6:127-134.
    11. Macas, J., Neumann, P., Pozarkova, D. (2003). Zaba: a novel miniature transposable element present in genomes of legume plants. Molecular Genetics and Genomics, 269:624-631.
    12. Macas, J., Koblizkova, A., Neumann, P. (2005). Characterization of Stowaway MITEs in pea (Pisum sativum L.) and identification of their potential master elements. Genome, 48:831-839.
    13. Macas, J., Neumann, P., Navratilova, A. (2007). Repetitive DNA in the pea (Pisum sativum L.) genome: comprehensive characterization using 454 sequencing and comparison to soybean and Medicago truncatula. BMC Genomics, 8:427.
    14. McClintock, B. (1941). The stability of broken ends of chromosomes in Zea mays. Genetics, 26: 234-282.
    15. Munoz-Lopez, M., Garcia-Perez, J.L. (2010). DNA Transposons: Nature and Applications in Genomics. Current Genomics, 11:115-128.
    16. Pearce, S.R., Knox, M., Ellis, T.H.N., Flavell, A.J. and Kumar, A., (2000). Pea Ty1-copia group retrotransposons: transpositional activity and use as markers to study genetic diversity in Pisum. Molecular and General Genetics, 263:898-907.
    17. Randhawa, H., Singh, J. , Lemaux, P.G., Gill, K.S. (2009). Mapping barley Ds insertions using wheat deletion lines reveals high insertion frequencies in gene-rich regions with high to moderate recombination rates Genome, 52: 566–575
    18. Singh, S., Singh, J. (2017). Sequence-based genetic mapping of Ds-tagged insertions to characterize malting-related traits in barley. The Crop Journal, 5:11-20.
    19. Singh, S., Nandha, P. S., Singh, J. (2017). Transposon-based genetic diversity assessment in wild and cultivated barley. The Crop Journal, 5: 296-304.
    20. Singh, S., Tan, H-Q., Singh, J. (2012). Mutagenesis of barley malting quality QTLs with Ds transposons. Functional & Integrative Genomics, 12:131-141.
    21. Smykal, P. (2006). Development of an efficient retrotransposon-based fingerprinting method for rapid pea variety identification. Journal of Applied Genetics, 47:221-230.
    22. Tessier, C., David, J., This, P., Boursiquot, J. M. Charrier, A. (1999). Optimization of the choice of molecular markers for varietal identification in Vitis vinifera L. Theoretical and Applied Genetics, 98:171-177.
    23. Zhang, S., Gu, Y., Singh, J., Coleman-Derr, D., Brar, D. S., Jiang N., Lemaux, P. G (2007). New insights into Oryza genome evolution: High gene collinearity and differential reterotransposon amplification. Plant Molecular Biology, 64: 589-600. 
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