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Research Article

volume 42 issue 6 (december 2019) : 856-861,   Doi: 10.18805/LR-461

Computational assessment of polymorphism with linkage disequilibrium and hotspots of recombination in pathogenic genes of Fusarium oxysporum f. sp. lycopersici

S
Supriya Dixit
M
Mukesh Srivastava
P
Pramod Katara
1Biocontrol Lab, Department of Plant Pathology, Chandra Shekhar Azad University of Agriculture and Technology, Kanpur-208 002, Uttar Pradesh, India.

  • Submitted27-10-2018|

  • Accepted12-01-2019|

  • First Online 13-03-2019|

  • doi 10.18805/LR-461

Cite article:- Dixit Supriya, Srivastava Mukesh, Katara Pramod (2019). Computational assessment of polymorphism with linkage disequilibrium and hotspots of recombination in pathogenic genes of Fusarium oxysporum f. sp. lycopersici. Legume Research. 42(6): 856-861. doi: 10.18805/LR-461.

ABSTRACT

Linkage disequilibrium and recombination rate analysis are the major aspects to study association between nucleotide variations. Species of Fusarium oxysporum includes extensive group of soil and plant pathogens which causes vascular wilt and root diseases to wide range of agricultural crops. Further F. oxysporum is divided into more than 120 formea species (f.sp.) depending upon their hosts. Among all formea species, Fusarium oxysporum f. sp. lycopersici (Fol) is well known pathogen which infects tomato plants and leads towards a destructive disease i.e. “Fusarium wilt”. Our study is focused to analyse association based linkage disequilibrium pattern and recombination rate in five genes of interest for causing pathogenicity in both, plants as well as humans. The fmk1 gene has the highest average nucleotide diversity (ð) value (0.66) and lowest was found in fpr1 (0.54) whereas calculation of average number of nucleotide variation per site showed that gene fpr1 (765) to be highly variating gene and fmk1 (121) to be lowest variating gene. Further, LD analysis all polymorphic sites were considered except those sites which were segregating for three or four nucleotides. LD was calculated in terms of ZnS and variations indicate the success of linkage study and minimum number of recombination event identified in terms of Rm. Through observation it is concluded that the low nucleotide diversity was there, due to the presence of high number of repeated variable nucleotides in sequence because the current estimated LD suggests that it does not extend beyond a few hundreds of base pair.

REFERENCES

  1. Alabid, T., Kordofani, A. A. Y, Atalla, B., Altayb, H. N., Fadla, A. A., Osman, M. M., Salih, M. A., Elamin, B. K. (2016). In Silico analysis of Single nucleotide polymorphisms (SNPs) in HumanVCAM-1 gene. J Bioinform, Genomics, Proteomics, 1(1): 1004.
  2. Beckstrom-Sternberg, S. M., Auerbach, R. K., Godbole, S., Pearson, J. V., et al. (2007). Complete genomic characterization of a pathogenic A.II strain of Francisella tularensis subspecies tularensis. PLoS One., 2(9): e947.
  3. Beisswanger, S., Stephan, W., Lorenzo, D. D. (2006). Evidence for a Selective Sweep in the wapl Region of Drosophila melanogaster. Genetics, 172(1): 265–274.
  4. Blair, M. W., Cortés, A. J., Farmer, A. D., Huang, W., Ambachew, D., et al. (2018). Uneven recombination rate and linkage disequilibrium across a reference SNP map for common bean (Phaseolus vulgaris L.). PLoS One., 13(3): e0189597.
  5. Boualem, B., Sofiane, B., Abdelhamid, G., Benzohra, I. E., M’hamed, B., Mohamed, B., Omar, K. (2018). Effects of different levels of saline water on infection of tomato by Botrytis cinerea, the causal agent of gray mold. Indian J. Agric. Res., 52(5): 530-535.
  6. Fu, Y. X. and Li, W. H. (1993). Statistical tests of neutrality of mutations. Genetics, 133(3): 693–709.
  7. Gaut, B. S. and Clegg, M. (1993). Molecular evolution of the Adh 1 locus in the genus Zea. Proceedings of the National Academy of Sciences of the United States of America., 90: 5095-9. 10.1073/pnas.90.11.5095.
  8. Hall, T. A. (1999). BioEdit: a user-friendly biological sequence alignment editor and analysis program for windows 95/98/NT. Nucl Acids Symp Ser., 41: 95-98.
  9. Hudson, R. R., Kreitman, M., Aguade, M. (1987). A test of neutral molecular evolution based on nucleotide data. Genetics, 116(1): 153-159.
  10. Hughes, A. L., Friedman, R., Rivailler, P., French, J. O. (2008). Synonymous and nonsynonymous polymorphisms versus divergences in bacterial genomes. Mol Biol Evol., 25(10): 2199-209.
  11. Jhanavi, R. D., Patil, B. H., Justin, P., Hadimani, H. P. R., Mulla, R. W. S., Sarvamangala, C. (2018). Genetic variability, heritability and genetic advance studies in french bean (Phaseolus vulgaris L.) genotypes. Indian J. Agric. Res., 52(2): 162-166.
  12. Konstantin, V. K. and David, B. N. (2005). Nucleotide Diversity and Linkage Disequilibrium in Cold Hardiness and Wood Quality Related Candidate Genes in Douglas-fir. Genetics, 171(4): 2029-2041.
  13. Larkin, M. A., Blackshields, G., Brown, N. P., Chenna, R., McGettigan, P. A., McWilliam, H., et al. (2007). Clustal W and Clustal X version 2.0. Bioinformatics, 23(21): 2947–8. 
  14. Ortoneda, M., Guarro, J., Madrid, M. P., Caracuel, Z., Roncero, M. I., Mayayo, E., Di Pietro A. (2004). Fusarium oxysporum as a multihost model for the genetic dissection of fungal virulence in plants and mammals. Infect. Immun., 72(3): 1760–1766.
  15. Rozas, J., Sa´nchez-DelBarrio, J. C., Messeguer, X., Rozas, R. (2003). DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics, 19(18): 2496–7.
  16. Smith, M. S., Yuan, Y., Doust, N. A., Bennetzen L. J. (2012). Haplotype Analysis and Linkage Disequilibrium at Five Loci in Eragrostis tef. G3 (Bethesda), 2(3): 407-19.
  17. Suharyanto and Shiraishi, S. (2011). Nucleotide diversities and genetic relationship in the three Japanese pine species; Pinus thunbergii, Pinus densiflora, and Pinus luchuensis. Diversity, 3(1): 121–135.
  18. Szklarczyk, D., Morris, J. H., Cook, H., Kuhn, M., Wyder, S., Simonovic, M., et al. (2017). The STRING database in 2017: quality-    controlled protein-protein association networks, made broadly accessible. Nucleic Acids Res., 45(D1):D362-D368.
  19. Tajima, F. (1989). Statistical Method for Testing the Neutral Mutation Hypothesis by DNA Polymorphism. Genetics, 123(3): 585–595.
  20. Wang, Y., Shahid, Q. M., Huang, H., Wang Y. (2015). Nucleotide diversity patterns of three divergent soybean populations: evidences for population-dependent linkage disequilibrium and taxonomic status of Glycine gracilis. Ecology and Evolution, 5(18): 3969–3978.
  21. Wu, X., Wang, B., Wu, X., Lu, Z., Li, G., Xu, P. (2018). SNP marker-based genetic mapping of rust resistance gene in the vegetable cowpea landrace ZN016. Legume Research, 41(2): 222-225.
  22. Zhao, L., Zhang, X., Tao, X., Wang, W., Li M. (2012). Preliminary analysis of the mitochondrial genome evolutionary pattern in primates. Dongwuxue Yanjiu, 33(E3-4): E47-56.
  23. Zhu, Y. L., Song, Q. J., Hyten, D. L., Van Tassell, C. P., Matukumalli, L. K., Grimm, D. R., et al. (2003). Single-nucleotide polymorphisms in soybean. Genetics, 163(3):1123–1134. 
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    Research Article

    volume 42 issue 6 (december 2019) : 856-861,   Doi: 10.18805/LR-461

    Computational assessment of polymorphism with linkage disequilibrium and hotspots of recombination in pathogenic genes of Fusarium oxysporum f. sp. lycopersici

    S
    Supriya Dixit
    M
    Mukesh Srivastava
    P
    Pramod Katara
    1Biocontrol Lab, Department of Plant Pathology, Chandra Shekhar Azad University of Agriculture and Technology, Kanpur-208 002, Uttar Pradesh, India.

    • Submitted27-10-2018|

    • Accepted12-01-2019|

    • First Online 13-03-2019|

    • doi 10.18805/LR-461

    Cite article:- Dixit Supriya, Srivastava Mukesh, Katara Pramod (2019). Computational assessment of polymorphism with linkage disequilibrium and hotspots of recombination in pathogenic genes of Fusarium oxysporum f. sp. lycopersici. Legume Research. 42(6): 856-861. doi: 10.18805/LR-461.

    ABSTRACT

    Linkage disequilibrium and recombination rate analysis are the major aspects to study association between nucleotide variations. Species of Fusarium oxysporum includes extensive group of soil and plant pathogens which causes vascular wilt and root diseases to wide range of agricultural crops. Further F. oxysporum is divided into more than 120 formea species (f.sp.) depending upon their hosts. Among all formea species, Fusarium oxysporum f. sp. lycopersici (Fol) is well known pathogen which infects tomato plants and leads towards a destructive disease i.e. “Fusarium wilt”. Our study is focused to analyse association based linkage disequilibrium pattern and recombination rate in five genes of interest for causing pathogenicity in both, plants as well as humans. The fmk1 gene has the highest average nucleotide diversity (ð) value (0.66) and lowest was found in fpr1 (0.54) whereas calculation of average number of nucleotide variation per site showed that gene fpr1 (765) to be highly variating gene and fmk1 (121) to be lowest variating gene. Further, LD analysis all polymorphic sites were considered except those sites which were segregating for three or four nucleotides. LD was calculated in terms of ZnS and variations indicate the success of linkage study and minimum number of recombination event identified in terms of Rm. Through observation it is concluded that the low nucleotide diversity was there, due to the presence of high number of repeated variable nucleotides in sequence because the current estimated LD suggests that it does not extend beyond a few hundreds of base pair.

    REFERENCES

    1. Alabid, T., Kordofani, A. A. Y, Atalla, B., Altayb, H. N., Fadla, A. A., Osman, M. M., Salih, M. A., Elamin, B. K. (2016). In Silico analysis of Single nucleotide polymorphisms (SNPs) in HumanVCAM-1 gene. J Bioinform, Genomics, Proteomics, 1(1): 1004.
    2. Beckstrom-Sternberg, S. M., Auerbach, R. K., Godbole, S., Pearson, J. V., et al. (2007). Complete genomic characterization of a pathogenic A.II strain of Francisella tularensis subspecies tularensis. PLoS One., 2(9): e947.
    3. Beisswanger, S., Stephan, W., Lorenzo, D. D. (2006). Evidence for a Selective Sweep in the wapl Region of Drosophila melanogaster. Genetics, 172(1): 265–274.
    4. Blair, M. W., Cortés, A. J., Farmer, A. D., Huang, W., Ambachew, D., et al. (2018). Uneven recombination rate and linkage disequilibrium across a reference SNP map for common bean (Phaseolus vulgaris L.). PLoS One., 13(3): e0189597.
    5. Boualem, B., Sofiane, B., Abdelhamid, G., Benzohra, I. E., M’hamed, B., Mohamed, B., Omar, K. (2018). Effects of different levels of saline water on infection of tomato by Botrytis cinerea, the causal agent of gray mold. Indian J. Agric. Res., 52(5): 530-535.
    6. Fu, Y. X. and Li, W. H. (1993). Statistical tests of neutrality of mutations. Genetics, 133(3): 693–709.
    7. Gaut, B. S. and Clegg, M. (1993). Molecular evolution of the Adh 1 locus in the genus Zea. Proceedings of the National Academy of Sciences of the United States of America., 90: 5095-9. 10.1073/pnas.90.11.5095.
    8. Hall, T. A. (1999). BioEdit: a user-friendly biological sequence alignment editor and analysis program for windows 95/98/NT. Nucl Acids Symp Ser., 41: 95-98.
    9. Hudson, R. R., Kreitman, M., Aguade, M. (1987). A test of neutral molecular evolution based on nucleotide data. Genetics, 116(1): 153-159.
    10. Hughes, A. L., Friedman, R., Rivailler, P., French, J. O. (2008). Synonymous and nonsynonymous polymorphisms versus divergences in bacterial genomes. Mol Biol Evol., 25(10): 2199-209.
    11. Jhanavi, R. D., Patil, B. H., Justin, P., Hadimani, H. P. R., Mulla, R. W. S., Sarvamangala, C. (2018). Genetic variability, heritability and genetic advance studies in french bean (Phaseolus vulgaris L.) genotypes. Indian J. Agric. Res., 52(2): 162-166.
    12. Konstantin, V. K. and David, B. N. (2005). Nucleotide Diversity and Linkage Disequilibrium in Cold Hardiness and Wood Quality Related Candidate Genes in Douglas-fir. Genetics, 171(4): 2029-2041.
    13. Larkin, M. A., Blackshields, G., Brown, N. P., Chenna, R., McGettigan, P. A., McWilliam, H., et al. (2007). Clustal W and Clustal X version 2.0. Bioinformatics, 23(21): 2947–8. 
    14. Ortoneda, M., Guarro, J., Madrid, M. P., Caracuel, Z., Roncero, M. I., Mayayo, E., Di Pietro A. (2004). Fusarium oxysporum as a multihost model for the genetic dissection of fungal virulence in plants and mammals. Infect. Immun., 72(3): 1760–1766.
    15. Rozas, J., Sa´nchez-DelBarrio, J. C., Messeguer, X., Rozas, R. (2003). DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics, 19(18): 2496–7.
    16. Smith, M. S., Yuan, Y., Doust, N. A., Bennetzen L. J. (2012). Haplotype Analysis and Linkage Disequilibrium at Five Loci in Eragrostis tef. G3 (Bethesda), 2(3): 407-19.
    17. Suharyanto and Shiraishi, S. (2011). Nucleotide diversities and genetic relationship in the three Japanese pine species; Pinus thunbergii, Pinus densiflora, and Pinus luchuensis. Diversity, 3(1): 121–135.
    18. Szklarczyk, D., Morris, J. H., Cook, H., Kuhn, M., Wyder, S., Simonovic, M., et al. (2017). The STRING database in 2017: quality-    controlled protein-protein association networks, made broadly accessible. Nucleic Acids Res., 45(D1):D362-D368.
    19. Tajima, F. (1989). Statistical Method for Testing the Neutral Mutation Hypothesis by DNA Polymorphism. Genetics, 123(3): 585–595.
    20. Wang, Y., Shahid, Q. M., Huang, H., Wang Y. (2015). Nucleotide diversity patterns of three divergent soybean populations: evidences for population-dependent linkage disequilibrium and taxonomic status of Glycine gracilis. Ecology and Evolution, 5(18): 3969–3978.
    21. Wu, X., Wang, B., Wu, X., Lu, Z., Li, G., Xu, P. (2018). SNP marker-based genetic mapping of rust resistance gene in the vegetable cowpea landrace ZN016. Legume Research, 41(2): 222-225.
    22. Zhao, L., Zhang, X., Tao, X., Wang, W., Li M. (2012). Preliminary analysis of the mitochondrial genome evolutionary pattern in primates. Dongwuxue Yanjiu, 33(E3-4): E47-56.
    23. Zhu, Y. L., Song, Q. J., Hyten, D. L., Van Tassell, C. P., Matukumalli, L. K., Grimm, D. R., et al. (2003). Single-nucleotide polymorphisms in soybean. Genetics, 163(3):1123–1134. 
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