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Research Article

volume 53 issue 3 (june 2019) : 284-290,   Doi: 10.18805/IJARe.A-5182

Variations in the trnHpsbA region of Mucuna pruriens L. (DC.) varieties of India: an insight on intraspecific diversity 

K
K.V. Rashmi
N
N. Sathyanarayana
S
S.M. Vidya
1Department of Biotechnology, Sir M Visvesvaraya Institute of Technology, Hunasamaranahalli, Bangalore-562 157, Karnataka, India.
Cite article:- Rashmi K.V., Sathyanarayana N., Vidya S.M. (2019). Variations in the trnHpsbA region of Mucuna pruriens L. (DC.) varieties of India: an insight on intraspecific diversity. Indian Journal of Agricultural Research. 53(3): 284-290. doi: 10.18805/IJARe.A-5182.

ABSTRACT

Mucuna pruriens is a nutritionally and pharmaceutically important underutilized legume belonging to genus Mucuna of Leguminosae family. Extensive intraspecific diversity and adverse morphological features among the members have led to taxonomical confusions in the species. A total of 12 Mucuna pruriens accessions including its two botanical varieties, var. pruriens and var. utilis with six accessions each were analyzed to characterize the intraspecific diversity among them using the three barcode markers viz. ITS2, matK and trnHpsbA.  Extensive intraspecific sequence diversity was observed in the trnHpsbA region, where as ITS2 and matK exhibited significant conserved regions. Such intraspecific sequence diversity is a limitation in adapting trnHpsbA as barcode as it may lead to misinterpretations, but in the present study an attempt has been made to extrapolate this diversity to explain within the species variations among Mucuna pruriens genotypes. Intraspecific sequence variations exhibited by trnHpsbA sequences were 83% in correlation with morphological features. The between groups mean distance of var. pruriens and var. utilis was found to be 0.346. Results of this study will complement with the existing molecular, morphological, ytological and biochemical markers towards Velvet bean improvement programs.

REFERENCES

  1. Bieniek, W., Mizianty, M., Szklarczyk, M., (2015). Sequence variation at the three chloroplast loci (matK, rbcL, trnH-psbA) in the Triticeae tribe (Poaceae): comments on the relationships and utility in DNA barcoding of selected species. Plant Syst. Evol. 301: 1275–1286. 
  2. Burkill, I.H., (1966). A dictionary of the economic products of the Malay Peninsula. A Dictionary of the Economic Products of the Malay Peninsula., 2(2nd edition).
  3. CBOL Plant Working Group,. (2009). A DNA barcode for land plants. Proc. Natl. Acad. Sci. U. S. A. 106: 12794–7. 
  4. Dassanayake, M.D., Fosberg, F.R., (1980). A Revised Handbook to the Flora of Ceylon-Complete Set. Taylor &and Francis US.
  5. Doyle, J. J., Doyle, L. J., (1990). Isolation of DNA from plant tissue. Focus. 12: 13-15.
  6. Edgar, R.C., (2004). MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32(5): 1792-1797.
  7. Ehlers, B.K., Damgaard, C.F., Laroche, F., (2016). Intraspecific genetic variation and species coexistence in plant communities. Biol. Lett. 12: 20150853.
  8. Hughes, A.R., Inouye, B.D., Johnson, M.T., Underwood, N. and Vellend, M., (2008). Ecological consequences of genetic diversity. Ecol. Lett. 11(6): 609-623.
  9. Jaheer, M., Chopra, R., Kunder, K. R., Bhat, D., Rashmi, K. V., Sathyanarayana, N., (2015). Cytogenetic and ITS-psbA-trnH Sequence Analysis for Phylogenetic Inference in Mucuna sp. of India. Trop. Plant Biol. 8(3-4): 108–116. 
  10. Jiang, G.F., Hinsinger, D.D., Strijk, J.S., (2016) Comparison of intraspecific, interspecific and intergeneric chloroplast diversity in Cycads. Sci Rep., 6:31473.
  11. Jorge, M.A., Eilittä, M., Proud, F.J., Maasdorp, V., Beksissa, H., Sarial, K. and Hanson, J., (2007). Mucuna species: recent advances in application of biotechnology. Fruit, Vegetable and Cereal Science and Biotechnology, Global Science Books, 1: 80-94.
  12. Kress, W.J., Erickson, D.L., (2008). DNA barcodes: genes, genomics, and bioinformatics. Proc. Natl. Acad. Sci. U. S. A. 105: 2761–    2762. 
  13. Larkin, M.A., Blackshields, G., Brown, N.P., Chenna, R., McGettigan, P.A., McWilliam, H., Valentin, F., Wallace, I.M., Wilm, A., Lopez, R. and Thompson, J.D.,et al (2007). Clustal W and Clustal X version 2.0. Bioinformatics,, 23(21): 2947-2948.
  14. Leelambika, M., Mahesh, S., Jaheer, M., Sathyanarayana, N., (2010). Comparative evaluation of genetic diversity among Indian Mucuna species using morphometric, biochemical and molecular approaches. World J. Agric. Sci. 6(5): 568–578.
  15. Leelambika, M., Sathyanarayana, N., (2011). Genetic characterization of Indian Mucuna (Leguminoceae) species using morphometric and random amplification of polymorphic DNA (RAPD) approaches. Plant Biosyst. 145: 786–797. 
  16. Li, Q., Xu, J., Han, L., Gao, C., Lu, J., Du, G., Sun, X., (2017) Evaluation of ITS2 for intraspecific identification of Paeonia lactiflora cultivars. Biotechnol Rep. 15:101-106
  17. Lieu, C.A., Kunselman, A.R., Manyam, B.V., Venkiteswaran, K., Subramanian, T., (2010). A water extract of Mucuna pruriens provides long-term amelioration of parkinsonism with reduced risk for dyskinesias. Parkinsonism Relat. Disord. 16(7): 458-65.
  18. Liu, J., Provan, J., Gao, L.M., Li, D.Z., (2012). Sampling strategy and potential utility of indels for DNA barcoding of closely related plant species: a case study in Taxus. Int J Mol Sci. 13(7): 8740-8751.
  19. Mahesh, S., Sathyanarayana, N., (2015). Intra-specific variability for salinity tolerance in Indian Mucuna pruriens L. (DC.) germplasm. J. Crop Sci. Biotechnol. 18: 181–194. 
  20. Padmesh, P., Reji, J. V, Dhar, M.J., Seeni, S., (2006). Estimation of genetic diversity in varieties of Mucuna pruriens using RAPD. Chem. Anal. 50: 367–372.
  21. Patil, R.R., Pawar, K.D., Rane, M.R., Yadav, S.R., Bapat, V.A., Jadhav, J.P., (2016) Assessment of genetic diversity in Mucuna species of India using randomly amplified polymorphic DNA and inter simple sequence repeat markers. Physiol Mol Biol Plants.    22(2):207-217.
  22. Patil, S., Nadukeri, S., Shetty, G. R., Bindu, K. H., &and Ganapathi, M. (2018). Evaluation of cowhage (Mucuna pruriens L.) genotypes for growth and flowering characters in arecanut plantation under hill zone of Karnataka. Legume Research: An International Journal, 41(1).48-52.
  23. Razvi, S. M., Khan, M. N., Bhat, M. A., Ahmad, M., Ganaie, S. A., Sheikh, F. A., Najeeb, S., Parry, F. A. (2018). Morphological variability and phylogenetic analysis in common bean (Phaseolus vulgaris L.). Legume Research: An International Journal, 41(2):208-212.
  24. Sasidharan, N., (2004). Biodiversity documentation for Kerala. Part 6. Flowering plants. KFRI handbook 17.
  25. Sathiyanarayanan, L. and Arulmozhi, S., (2007). Mucuna pruriens Linn.-A comprehensive review. Pharmacogn.Rev. 1(1): 157.
  26. Sathyanarayana, N., Leelambika, M., Mahesh, S., Jaheer, M., (2011). AFLP assessment of genetic diversity among Indian Mucuna accessions. Physiol. Mol. Biol. Plants. 17: 171–180. 
  27. Singh, N., Meena, B., Pal, A.K., Roy, R.K., Tewari, S.K., Tamta, S. and Rana, T.S., (2017). Nucleotide diversity and phylogenetic relationships among Gladiolus cultivars and related taxa of family Iridaceae. J. Genet. 96: 135–145. 
  28. Tamura, K., Stecher, G., Peterson, D., Filipski, A. and Kumar, S., (2013). MEGA6: molecular evolutionary genetics analysis version 6.0. Mol.Biol.Evol. 30(12): 2725-2729.
  29. Technelysium, P., (2015). Chromas lite 2.01.
  30. Thakur, B., Sharma, S., Sharma, I., Sharma, P., and Zargar, S. M. (2018). Diversity analysis of pea genotypes using RAPD markers.    Legume Research: An International Journal, 41(2): 196-201.
  31. UNDP, (2015). Sustainable Development Goals. Undp 24. https://doi.org/10.1017/CBO9781107415324.004.
  32. Vir, O., &and Singh, A. K. (2015). Moth bean [Vigna aconitifolia (Jacq.) Marechal] germplasm: Evaluation for genetic variability and inter characters relationship in hot arid climate of western Rajasthan, India. Legume Research-An International Journal, 38(6): 748-752.
  33. Whitlock, B.A., Hale, A.M. and Groff, P.A., (2010). Intraspecific inversions pose a challenge for the trnH-psbA plant DNA barcode. PloS One, 5(7): e11533.
  34. Wilmot Dear, C. M., (1987). A revision of Mucuna (Leguminosae-Phaseolae) in the Indian Subcontinent and Burma. Kew Bull. 42(1):23-46.
  35. Wilmot-Dear, C.M., (1984). A revision of Mucuna (Leguminosae-Phaseoleae) in China and Japan. Kew Bull. 23-ii. 
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Indian Journal of Agricultural Research
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    Research Article

    volume 53 issue 3 (june 2019) : 284-290,   Doi: 10.18805/IJARe.A-5182

    Variations in the trnHpsbA region of Mucuna pruriens L. (DC.) varieties of India: an insight on intraspecific diversity 

    K
    K.V. Rashmi
    N
    N. Sathyanarayana
    S
    S.M. Vidya
    1Department of Biotechnology, Sir M Visvesvaraya Institute of Technology, Hunasamaranahalli, Bangalore-562 157, Karnataka, India.
    Cite article:- Rashmi K.V., Sathyanarayana N., Vidya S.M. (2019). Variations in the trnHpsbA region of Mucuna pruriens L. (DC.) varieties of India: an insight on intraspecific diversity. Indian Journal of Agricultural Research. 53(3): 284-290. doi: 10.18805/IJARe.A-5182.

    ABSTRACT

    Mucuna pruriens is a nutritionally and pharmaceutically important underutilized legume belonging to genus Mucuna of Leguminosae family. Extensive intraspecific diversity and adverse morphological features among the members have led to taxonomical confusions in the species. A total of 12 Mucuna pruriens accessions including its two botanical varieties, var. pruriens and var. utilis with six accessions each were analyzed to characterize the intraspecific diversity among them using the three barcode markers viz. ITS2, matK and trnHpsbA.  Extensive intraspecific sequence diversity was observed in the trnHpsbA region, where as ITS2 and matK exhibited significant conserved regions. Such intraspecific sequence diversity is a limitation in adapting trnHpsbA as barcode as it may lead to misinterpretations, but in the present study an attempt has been made to extrapolate this diversity to explain within the species variations among Mucuna pruriens genotypes. Intraspecific sequence variations exhibited by trnHpsbA sequences were 83% in correlation with morphological features. The between groups mean distance of var. pruriens and var. utilis was found to be 0.346. Results of this study will complement with the existing molecular, morphological, ytological and biochemical markers towards Velvet bean improvement programs.

    REFERENCES

    1. Bieniek, W., Mizianty, M., Szklarczyk, M., (2015). Sequence variation at the three chloroplast loci (matK, rbcL, trnH-psbA) in the Triticeae tribe (Poaceae): comments on the relationships and utility in DNA barcoding of selected species. Plant Syst. Evol. 301: 1275–1286. 
    2. Burkill, I.H., (1966). A dictionary of the economic products of the Malay Peninsula. A Dictionary of the Economic Products of the Malay Peninsula., 2(2nd edition).
    3. CBOL Plant Working Group,. (2009). A DNA barcode for land plants. Proc. Natl. Acad. Sci. U. S. A. 106: 12794–7. 
    4. Dassanayake, M.D., Fosberg, F.R., (1980). A Revised Handbook to the Flora of Ceylon-Complete Set. Taylor &and Francis US.
    5. Doyle, J. J., Doyle, L. J., (1990). Isolation of DNA from plant tissue. Focus. 12: 13-15.
    6. Edgar, R.C., (2004). MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32(5): 1792-1797.
    7. Ehlers, B.K., Damgaard, C.F., Laroche, F., (2016). Intraspecific genetic variation and species coexistence in plant communities. Biol. Lett. 12: 20150853.
    8. Hughes, A.R., Inouye, B.D., Johnson, M.T., Underwood, N. and Vellend, M., (2008). Ecological consequences of genetic diversity. Ecol. Lett. 11(6): 609-623.
    9. Jaheer, M., Chopra, R., Kunder, K. R., Bhat, D., Rashmi, K. V., Sathyanarayana, N., (2015). Cytogenetic and ITS-psbA-trnH Sequence Analysis for Phylogenetic Inference in Mucuna sp. of India. Trop. Plant Biol. 8(3-4): 108–116. 
    10. Jiang, G.F., Hinsinger, D.D., Strijk, J.S., (2016) Comparison of intraspecific, interspecific and intergeneric chloroplast diversity in Cycads. Sci Rep., 6:31473.
    11. Jorge, M.A., Eilittä, M., Proud, F.J., Maasdorp, V., Beksissa, H., Sarial, K. and Hanson, J., (2007). Mucuna species: recent advances in application of biotechnology. Fruit, Vegetable and Cereal Science and Biotechnology, Global Science Books, 1: 80-94.
    12. Kress, W.J., Erickson, D.L., (2008). DNA barcodes: genes, genomics, and bioinformatics. Proc. Natl. Acad. Sci. U. S. A. 105: 2761–    2762. 
    13. Larkin, M.A., Blackshields, G., Brown, N.P., Chenna, R., McGettigan, P.A., McWilliam, H., Valentin, F., Wallace, I.M., Wilm, A., Lopez, R. and Thompson, J.D.,et al (2007). Clustal W and Clustal X version 2.0. Bioinformatics,, 23(21): 2947-2948.
    14. Leelambika, M., Mahesh, S., Jaheer, M., Sathyanarayana, N., (2010). Comparative evaluation of genetic diversity among Indian Mucuna species using morphometric, biochemical and molecular approaches. World J. Agric. Sci. 6(5): 568–578.
    15. Leelambika, M., Sathyanarayana, N., (2011). Genetic characterization of Indian Mucuna (Leguminoceae) species using morphometric and random amplification of polymorphic DNA (RAPD) approaches. Plant Biosyst. 145: 786–797. 
    16. Li, Q., Xu, J., Han, L., Gao, C., Lu, J., Du, G., Sun, X., (2017) Evaluation of ITS2 for intraspecific identification of Paeonia lactiflora cultivars. Biotechnol Rep. 15:101-106
    17. Lieu, C.A., Kunselman, A.R., Manyam, B.V., Venkiteswaran, K., Subramanian, T., (2010). A water extract of Mucuna pruriens provides long-term amelioration of parkinsonism with reduced risk for dyskinesias. Parkinsonism Relat. Disord. 16(7): 458-65.
    18. Liu, J., Provan, J., Gao, L.M., Li, D.Z., (2012). Sampling strategy and potential utility of indels for DNA barcoding of closely related plant species: a case study in Taxus. Int J Mol Sci. 13(7): 8740-8751.
    19. Mahesh, S., Sathyanarayana, N., (2015). Intra-specific variability for salinity tolerance in Indian Mucuna pruriens L. (DC.) germplasm. J. Crop Sci. Biotechnol. 18: 181–194. 
    20. Padmesh, P., Reji, J. V, Dhar, M.J., Seeni, S., (2006). Estimation of genetic diversity in varieties of Mucuna pruriens using RAPD. Chem. Anal. 50: 367–372.
    21. Patil, R.R., Pawar, K.D., Rane, M.R., Yadav, S.R., Bapat, V.A., Jadhav, J.P., (2016) Assessment of genetic diversity in Mucuna species of India using randomly amplified polymorphic DNA and inter simple sequence repeat markers. Physiol Mol Biol Plants.    22(2):207-217.
    22. Patil, S., Nadukeri, S., Shetty, G. R., Bindu, K. H., &and Ganapathi, M. (2018). Evaluation of cowhage (Mucuna pruriens L.) genotypes for growth and flowering characters in arecanut plantation under hill zone of Karnataka. Legume Research: An International Journal, 41(1).48-52.
    23. Razvi, S. M., Khan, M. N., Bhat, M. A., Ahmad, M., Ganaie, S. A., Sheikh, F. A., Najeeb, S., Parry, F. A. (2018). Morphological variability and phylogenetic analysis in common bean (Phaseolus vulgaris L.). Legume Research: An International Journal, 41(2):208-212.
    24. Sasidharan, N., (2004). Biodiversity documentation for Kerala. Part 6. Flowering plants. KFRI handbook 17.
    25. Sathiyanarayanan, L. and Arulmozhi, S., (2007). Mucuna pruriens Linn.-A comprehensive review. Pharmacogn.Rev. 1(1): 157.
    26. Sathyanarayana, N., Leelambika, M., Mahesh, S., Jaheer, M., (2011). AFLP assessment of genetic diversity among Indian Mucuna accessions. Physiol. Mol. Biol. Plants. 17: 171–180. 
    27. Singh, N., Meena, B., Pal, A.K., Roy, R.K., Tewari, S.K., Tamta, S. and Rana, T.S., (2017). Nucleotide diversity and phylogenetic relationships among Gladiolus cultivars and related taxa of family Iridaceae. J. Genet. 96: 135–145. 
    28. Tamura, K., Stecher, G., Peterson, D., Filipski, A. and Kumar, S., (2013). MEGA6: molecular evolutionary genetics analysis version 6.0. Mol.Biol.Evol. 30(12): 2725-2729.
    29. Technelysium, P., (2015). Chromas lite 2.01.
    30. Thakur, B., Sharma, S., Sharma, I., Sharma, P., and Zargar, S. M. (2018). Diversity analysis of pea genotypes using RAPD markers.    Legume Research: An International Journal, 41(2): 196-201.
    31. UNDP, (2015). Sustainable Development Goals. Undp 24. https://doi.org/10.1017/CBO9781107415324.004.
    32. Vir, O., &and Singh, A. K. (2015). Moth bean [Vigna aconitifolia (Jacq.) Marechal] germplasm: Evaluation for genetic variability and inter characters relationship in hot arid climate of western Rajasthan, India. Legume Research-An International Journal, 38(6): 748-752.
    33. Whitlock, B.A., Hale, A.M. and Groff, P.A., (2010). Intraspecific inversions pose a challenge for the trnH-psbA plant DNA barcode. PloS One, 5(7): e11533.
    34. Wilmot Dear, C. M., (1987). A revision of Mucuna (Leguminosae-Phaseolae) in the Indian Subcontinent and Burma. Kew Bull. 42(1):23-46.
    35. Wilmot-Dear, C.M., (1984). A revision of Mucuna (Leguminosae-Phaseoleae) in China and Japan. Kew Bull. 23-ii. 
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