Banner
Current IssueEditorial BoardOnline First ArticlesArchive
Current IssueEditorial BoardOnline First ArticlesArchive

Research Article

volume 52 issue 2 (april 2018) : 167-171,   Doi: 10.18805/IJARe.A-4793

Molecular characterization and phylogenetic analysis of NBS-LRR genes in wild relatives of eggplant (Solanum melongena L.)

S
Sona S Dev
P
P. Poornima
A
Akhil Venu
1Department of Biotechnology, St Peter’s College, Kolenchery, Kochi-682 311, Kerala, India.
Cite article:- Dev S Sona, Poornima P., Venu Akhil (2018). Molecular characterization and phylogenetic analysis of NBS-LRR genes in wild relatives of eggplant (Solanum melongena L.). Indian Journal of Agricultural Research. 52(2): 167-171. doi: 10.18805/IJARe.A-4793.

ABSTRACT

Eggplantor brinjal (Solanum melongena L.), is highly susceptible to various soil-borne diseases.  The extensive use of chemical fungicides to combat these diseases can be minimized by identification of resistance gene analogs (RGAs) in wild species of cultivated plants.In the present study, degenerate PCR primers for the conserved regions ofnucleotide binding site-leucine rich repeat (NBS-LRR) were used to amplify RGAs from wild relatives of eggplant (Black nightshade (Solanum nigrum), Indian nightshade (Solanumviolaceum)and Solanu mincanum) which showed resistance to the bacterial wilt pathogen, Ralstonia solanacearumin the preliminary investigation. The amino acid sequence of the amplicons when compared to each other and to the amino acid sequences of known RGAs deposited in Gen Bank revealed significant sequence similarity. The phylogenetic analysis indicated that they belonged to the toll interleukin-1 receptors (TIR)-NBS-LRR type R-genes. Multiple sequence alignment with other known R genes showed significant homology with P-loop, Kinase 2 and GLPL domains of NBS-LRR class genes. There has been no report on R genes from these wild eggplants and hence the diversity analysis of these novel RGAs can lead to the identification of other novel R genes within the germplasm of different brinjal plants as well as other species of Solanum.

REFERENCES

  1. Bikandi, J., San Millán, R., Rementeria, A., Garaizar, J. (2004). In silico analysis of complete bacterial genomes: PCR, AFLP-PCR and endonuclease restriction. Bioinformatics, 20:798–799. 
  2. Chandrashekara, K.N., Prasannakumar, M.K.., Deepa, M., Vani, A., Khan, A.N.A. (2012). Prevalence of races and biotypes of Ralstonia solanacearum in India. Journal of Plant Protection Research, 52 (1): 53–58.
  3. Daunay, M.C., Lester, R.N., Laterrot, H. (1991). The use of wild species for the genetic improvement of brinjal eggplant (Solanum melongena) and tomato (Lycopersicone sculentum). In: “Solanaceae III: taxonomy, chemistry, evolution” (J.C. Hawkes, R.N. Lester, M. Nee, N. Estrada, eds.). Royal Botanic Gardens Kew and LinneanSoc, London, 389–413 pp
  4. Deng, Z., Huang, S., Ling, P., Chen, C., Yu, C., Weber, C. A., Moore, G. A., Gmiter, F. G. (2000). Cloning and characterization of NBS–    LRR class resistance gene candidate sequences in citrus. Theor Appl Genet, 101: 814–822
  5. Deslandes, L., Jocelyne, O., Frederic, T., Judith, H., Dong, X. F., Peter, B. E., Jim, B., Yves M.(2002). Resistance to Ralstonia solanacearum in Arabidopsis thaliana is conferred by the recessive RRS1-R gene, a member of a novel family of resistance genes. PNAS,99(4): 2404–2409.
  6. Noir, S., Combes, M.C., Anthony, F., Lashermes, P. (2001). Origin, diversity and evolution of NBS-type disease-resistance homologues in coffee trees (Coffea L.). Molecular Genetics and Genomics,265: 654–662.
  7. Reddy, A.C.,Venkat, S., Singh, T.H., Aswath, C., Reddy, M.K., Reddy, D.C. (2015). Isolation, characterization and evolution of NBS-    LRR encoding disease-resistance gene analogs in eggplant against bacterial wilt.Eur J Plant Pathol, 10658-10693
  8. Sekhwal, M. K.., Li, P., Lam, I., Wang, X., Cloutier, S and Frank, M. (2015). Disease Resistance Gene Analogs (RGAs) in Plants. Int. J. Mol. Sci.,16: 19248-19290, 
  9. Tamura, K., Stecher, G., Peterson, D., Filipski, A., Kumar, S. (2013). MEGA6: molecular evolutionary genetics analysis version 6.0. Molecular Biology and Evolution,30: 2725– 2729.
  10. Thompson, J. D., Gibson, T. J., Plewniak, F., Jeanmougin, F., Higgins, D. G. (1997). The CLUSTAL-X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Research, 25: 4876– 4882.
  11. Timothy, L. B and Charles E. (1994). Fitting a mixture model by expectation maximization to discover motifs in biopolymers. In Proceedings of the Second International Conference on “Intelligent Systems for Molecular Biology”, AAAI Press, Menlo Park, California, 28–36 pp.
  12. Totad, A. S., Fakrudin, B., Kuruvinashetti, M. S. (2005). Isolation and characterization of resistance gene analogs (RGAs) from sorghum (Sorghum bicolor L. Moench). Euphytica,143: 179–188.
  13. Wei, C., Chen ,J., Kuang, H. (2016). Dramatic number variation of R genes in Solanaceae species accounted for by a few R gene subfamilies. PLoS ONE,11(2): e0148708. 
  14. Zhuang, Y., Zhou, X., Wang, S. (2012). Genetic diversity of NBS-LRR class-resistance gene analogs in cultivated and wild eggplants. Plant Systematics and Evolution,298: 1399–1406. http:// www.ncbi.nlm.nih.gov
Published In
Indian Journal of Agricultural Research
Article Metrics
Metrics Icon
0
Views
0
Citations
Reviewed By
Share Article
Download Article
In this Article
    Contact us
    Follow us

    Research Article

    volume 52 issue 2 (april 2018) : 167-171,   Doi: 10.18805/IJARe.A-4793

    Molecular characterization and phylogenetic analysis of NBS-LRR genes in wild relatives of eggplant (Solanum melongena L.)

    S
    Sona S Dev
    P
    P. Poornima
    A
    Akhil Venu
    1Department of Biotechnology, St Peter’s College, Kolenchery, Kochi-682 311, Kerala, India.
    Cite article:- Dev S Sona, Poornima P., Venu Akhil (2018). Molecular characterization and phylogenetic analysis of NBS-LRR genes in wild relatives of eggplant (Solanum melongena L.). Indian Journal of Agricultural Research. 52(2): 167-171. doi: 10.18805/IJARe.A-4793.

    ABSTRACT

    Eggplantor brinjal (Solanum melongena L.), is highly susceptible to various soil-borne diseases.  The extensive use of chemical fungicides to combat these diseases can be minimized by identification of resistance gene analogs (RGAs) in wild species of cultivated plants.In the present study, degenerate PCR primers for the conserved regions ofnucleotide binding site-leucine rich repeat (NBS-LRR) were used to amplify RGAs from wild relatives of eggplant (Black nightshade (Solanum nigrum), Indian nightshade (Solanumviolaceum)and Solanu mincanum) which showed resistance to the bacterial wilt pathogen, Ralstonia solanacearumin the preliminary investigation. The amino acid sequence of the amplicons when compared to each other and to the amino acid sequences of known RGAs deposited in Gen Bank revealed significant sequence similarity. The phylogenetic analysis indicated that they belonged to the toll interleukin-1 receptors (TIR)-NBS-LRR type R-genes. Multiple sequence alignment with other known R genes showed significant homology with P-loop, Kinase 2 and GLPL domains of NBS-LRR class genes. There has been no report on R genes from these wild eggplants and hence the diversity analysis of these novel RGAs can lead to the identification of other novel R genes within the germplasm of different brinjal plants as well as other species of Solanum.

    REFERENCES

    1. Bikandi, J., San Millán, R., Rementeria, A., Garaizar, J. (2004). In silico analysis of complete bacterial genomes: PCR, AFLP-PCR and endonuclease restriction. Bioinformatics, 20:798–799. 
    2. Chandrashekara, K.N., Prasannakumar, M.K.., Deepa, M., Vani, A., Khan, A.N.A. (2012). Prevalence of races and biotypes of Ralstonia solanacearum in India. Journal of Plant Protection Research, 52 (1): 53–58.
    3. Daunay, M.C., Lester, R.N., Laterrot, H. (1991). The use of wild species for the genetic improvement of brinjal eggplant (Solanum melongena) and tomato (Lycopersicone sculentum). In: “Solanaceae III: taxonomy, chemistry, evolution” (J.C. Hawkes, R.N. Lester, M. Nee, N. Estrada, eds.). Royal Botanic Gardens Kew and LinneanSoc, London, 389–413 pp
    4. Deng, Z., Huang, S., Ling, P., Chen, C., Yu, C., Weber, C. A., Moore, G. A., Gmiter, F. G. (2000). Cloning and characterization of NBS–    LRR class resistance gene candidate sequences in citrus. Theor Appl Genet, 101: 814–822
    5. Deslandes, L., Jocelyne, O., Frederic, T., Judith, H., Dong, X. F., Peter, B. E., Jim, B., Yves M.(2002). Resistance to Ralstonia solanacearum in Arabidopsis thaliana is conferred by the recessive RRS1-R gene, a member of a novel family of resistance genes. PNAS,99(4): 2404–2409.
    6. Noir, S., Combes, M.C., Anthony, F., Lashermes, P. (2001). Origin, diversity and evolution of NBS-type disease-resistance homologues in coffee trees (Coffea L.). Molecular Genetics and Genomics,265: 654–662.
    7. Reddy, A.C.,Venkat, S., Singh, T.H., Aswath, C., Reddy, M.K., Reddy, D.C. (2015). Isolation, characterization and evolution of NBS-    LRR encoding disease-resistance gene analogs in eggplant against bacterial wilt.Eur J Plant Pathol, 10658-10693
    8. Sekhwal, M. K.., Li, P., Lam, I., Wang, X., Cloutier, S and Frank, M. (2015). Disease Resistance Gene Analogs (RGAs) in Plants. Int. J. Mol. Sci.,16: 19248-19290, 
    9. Tamura, K., Stecher, G., Peterson, D., Filipski, A., Kumar, S. (2013). MEGA6: molecular evolutionary genetics analysis version 6.0. Molecular Biology and Evolution,30: 2725– 2729.
    10. Thompson, J. D., Gibson, T. J., Plewniak, F., Jeanmougin, F., Higgins, D. G. (1997). The CLUSTAL-X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Research, 25: 4876– 4882.
    11. Timothy, L. B and Charles E. (1994). Fitting a mixture model by expectation maximization to discover motifs in biopolymers. In Proceedings of the Second International Conference on “Intelligent Systems for Molecular Biology”, AAAI Press, Menlo Park, California, 28–36 pp.
    12. Totad, A. S., Fakrudin, B., Kuruvinashetti, M. S. (2005). Isolation and characterization of resistance gene analogs (RGAs) from sorghum (Sorghum bicolor L. Moench). Euphytica,143: 179–188.
    13. Wei, C., Chen ,J., Kuang, H. (2016). Dramatic number variation of R genes in Solanaceae species accounted for by a few R gene subfamilies. PLoS ONE,11(2): e0148708. 
    14. Zhuang, Y., Zhou, X., Wang, S. (2012). Genetic diversity of NBS-LRR class-resistance gene analogs in cultivated and wild eggplants. Plant Systematics and Evolution,298: 1399–1406. http:// www.ncbi.nlm.nih.gov
    In this Article
      Contact us
      Follow us
      Published In
      Indian Journal of Agricultural Research

      Editorial Board

      View all (0)