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Current IssueEditorial BoardOnline First ArticlesArchive

Research Article

volume 39 issue 3 (september 2019) : 228-231,   Doi: 10.18805/ag.D-4768

Comparison of Methods for Genomic Deoxyribonucleic Acid (DNA) Extraction Suitable for Whole-Genome Genotyping in Traditional Varieties of Rice

B
B. Priyadharshini
M
M. Vignesh
M
M. Prakash
R
R. Anandan
1<div style="text-align: justify;">Department of Genetics and Plant Breeding, Faculty of Agriculture,&nbsp;Annamalai University, Annamalai nagar, Tamilnadu, India.</div>
Cite article:- Priyadharshini B., Vignesh M., Prakash M., Anandan R. (2019). Comparison of Methods for Genomic Deoxyribonucleic Acid (DNA) Extraction Suitable for Whole-Genome Genotyping in Traditional Varieties of Rice. Agricultural Science Digest. 39(3): 228-231. doi: 10.18805/ag.D-4768.

ABSTRACT

The utilization and conservation traditional rice genotypes have attracted global attention. Optimization of DNA isolation protocol for genetic characterization of plants is a necessary and primary step. Over the recent years, next generation sequencing and microarray technologies have revolutionized scientific research, with their applications to high-throughput analysis of biological systems. Isolation of high quantities of pure, intact, double stranded, highly concentrated DNA is prerequisite for successful and reliable large-scale genotyping analysis. Therefore, standardization of DNA isolation is a basic requirement. Here we employed three methods of DNA isolation namely, Dellaporta, Hi-purA and modified CTAB techniques for isolation of genomic DNA from 25 indigenous rice genotypes. From the results, it was found that genomic DNA isolated by modified CTAB method to be the most appropriate for extracting high quality and maximum quantity DNA suitable for genotyping.  The quality and quantity of the differentially extracted DNA was subsequently assessed by spectrophotometric measurements and gel electrophoresis.

REFERENCES

  1. Ahmadikhah, A. (2009). A rapid mini-prep DNA extraction method in rice (Oryza sativa). Afr. J. Biotechnol., 8(2): 323–328.
  2. Aliyu, R. E., Wasiu A A, Dangora D B, Ademola J O, Adamu A K. (2013). Comparative study of genomic DNA extraction protocols in rice species. Int. J. Adv. Res. Technol., 2(2): 1–3.
  3. Brush, S.B. (1995). In situ conservation of landraces in centers of crop diversity. Crop Sci., 35(2):346–354.
  4. Channarayappa. (2007). Molecular Biotechnology, Principles and Practices. 1st Edn., University
  5. Doyle, J.J. and Doyle, J.J. (1990). Isolation of plant DNA from fresh tissue.  Focus, 12: 13-15.
  6. Duan, Y. B., Zhao F L, Chen H D, Li H, Ni D H, Wei P C, Sheng W, Teng J T, Zhang A M, Xue, J P. (2015). A simplified genomic DNA extraction protocol for pre-germination genotyping in rice. Genet Mol Res., 14(2): 6369–6375.
  7. Fouladvand, A., Yari H, Emami A, Khosravi H R M, Pourmehdi S. (2013). Optimization of a rapid DNA extraction protocol in rice focusing on age of plant and EDTA concentration. J Med Bioengin, 2(3): 218–223.
  8. Guin, G. (1966). Extraction of nucleic acids from lyophilized plant material: Plant Physiol., 41: 689-695.
  9. Hoisington, D., Khairallah, M., Reeves, T., Ribaut J.M., Skovmand, B., Taba, S., Warburton, M. (1999). Plant genetic resources: what can they contribute toward increased crop productivity?. Proc. Natl. Acad. Sci.,96 (11):5937–5943.
  10. Mandel, J.R., Dechaine, J.M., Marek, L.F., Burke, J.M. (2011). Genetic diversity and population structure in cultivated sunflower and a comparison to its wild progenitor, Helianthus annuus L. Theor. Appl. Genet., 123(5):693–704.
  11. Nieman, R.H. and Poulsen,L.L. (1963). Spectrophotometric estimation of nucleic acid of plant leaves. Plant Physiol., 38: 31-35.
  12. Stephen L, Dellaporta, Jonathan Wood, James B, Hicks.(1983). A plant DNA minipreparation: Version II. Dellaporta DNA Extraction Citation: Plant Mol. Biol. Rep., 1(4): 19-21.
  13. Suman, P.S. and   Khanuja. (1999). Rapid Isolation of DNA from Dry and Fresh Samples of Plants Producing Large Amounts of Secondary Metabolites and Essential Oils. Plant Mol. Biol. Rep, 17: 1–7.
  14. Tan, S.C. and Yiap, B.C. (2009). DNA, RNA and protein extraction: The past and the present. J. Biomed. Biotechnol., 10-10.
  15. Varma, A., Padh, H., Shrivastava, N. (2007). Plant genomic DNA isolation: An art or a science. Biotechnol. J., 2: 386-392.
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    Research Article

    volume 39 issue 3 (september 2019) : 228-231,   Doi: 10.18805/ag.D-4768

    Comparison of Methods for Genomic Deoxyribonucleic Acid (DNA) Extraction Suitable for Whole-Genome Genotyping in Traditional Varieties of Rice

    B
    B. Priyadharshini
    M
    M. Vignesh
    M
    M. Prakash
    R
    R. Anandan
    1<div style="text-align: justify;">Department of Genetics and Plant Breeding, Faculty of Agriculture,&nbsp;Annamalai University, Annamalai nagar, Tamilnadu, India.</div>
    Cite article:- Priyadharshini B., Vignesh M., Prakash M., Anandan R. (2019). Comparison of Methods for Genomic Deoxyribonucleic Acid (DNA) Extraction Suitable for Whole-Genome Genotyping in Traditional Varieties of Rice. Agricultural Science Digest. 39(3): 228-231. doi: 10.18805/ag.D-4768.

    ABSTRACT

    The utilization and conservation traditional rice genotypes have attracted global attention. Optimization of DNA isolation protocol for genetic characterization of plants is a necessary and primary step. Over the recent years, next generation sequencing and microarray technologies have revolutionized scientific research, with their applications to high-throughput analysis of biological systems. Isolation of high quantities of pure, intact, double stranded, highly concentrated DNA is prerequisite for successful and reliable large-scale genotyping analysis. Therefore, standardization of DNA isolation is a basic requirement. Here we employed three methods of DNA isolation namely, Dellaporta, Hi-purA and modified CTAB techniques for isolation of genomic DNA from 25 indigenous rice genotypes. From the results, it was found that genomic DNA isolated by modified CTAB method to be the most appropriate for extracting high quality and maximum quantity DNA suitable for genotyping.  The quality and quantity of the differentially extracted DNA was subsequently assessed by spectrophotometric measurements and gel electrophoresis.

    REFERENCES

    1. Ahmadikhah, A. (2009). A rapid mini-prep DNA extraction method in rice (Oryza sativa). Afr. J. Biotechnol., 8(2): 323–328.
    2. Aliyu, R. E., Wasiu A A, Dangora D B, Ademola J O, Adamu A K. (2013). Comparative study of genomic DNA extraction protocols in rice species. Int. J. Adv. Res. Technol., 2(2): 1–3.
    3. Brush, S.B. (1995). In situ conservation of landraces in centers of crop diversity. Crop Sci., 35(2):346–354.
    4. Channarayappa. (2007). Molecular Biotechnology, Principles and Practices. 1st Edn., University
    5. Doyle, J.J. and Doyle, J.J. (1990). Isolation of plant DNA from fresh tissue.  Focus, 12: 13-15.
    6. Duan, Y. B., Zhao F L, Chen H D, Li H, Ni D H, Wei P C, Sheng W, Teng J T, Zhang A M, Xue, J P. (2015). A simplified genomic DNA extraction protocol for pre-germination genotyping in rice. Genet Mol Res., 14(2): 6369–6375.
    7. Fouladvand, A., Yari H, Emami A, Khosravi H R M, Pourmehdi S. (2013). Optimization of a rapid DNA extraction protocol in rice focusing on age of plant and EDTA concentration. J Med Bioengin, 2(3): 218–223.
    8. Guin, G. (1966). Extraction of nucleic acids from lyophilized plant material: Plant Physiol., 41: 689-695.
    9. Hoisington, D., Khairallah, M., Reeves, T., Ribaut J.M., Skovmand, B., Taba, S., Warburton, M. (1999). Plant genetic resources: what can they contribute toward increased crop productivity?. Proc. Natl. Acad. Sci.,96 (11):5937–5943.
    10. Mandel, J.R., Dechaine, J.M., Marek, L.F., Burke, J.M. (2011). Genetic diversity and population structure in cultivated sunflower and a comparison to its wild progenitor, Helianthus annuus L. Theor. Appl. Genet., 123(5):693–704.
    11. Nieman, R.H. and Poulsen,L.L. (1963). Spectrophotometric estimation of nucleic acid of plant leaves. Plant Physiol., 38: 31-35.
    12. Stephen L, Dellaporta, Jonathan Wood, James B, Hicks.(1983). A plant DNA minipreparation: Version II. Dellaporta DNA Extraction Citation: Plant Mol. Biol. Rep., 1(4): 19-21.
    13. Suman, P.S. and   Khanuja. (1999). Rapid Isolation of DNA from Dry and Fresh Samples of Plants Producing Large Amounts of Secondary Metabolites and Essential Oils. Plant Mol. Biol. Rep, 17: 1–7.
    14. Tan, S.C. and Yiap, B.C. (2009). DNA, RNA and protein extraction: The past and the present. J. Biomed. Biotechnol., 10-10.
    15. Varma, A., Padh, H., Shrivastava, N. (2007). Plant genomic DNA isolation: An art or a science. Biotechnol. J., 2: 386-392.
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