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Current IssueEditorial BoardOnline First ArticlesArchive

Research Article

volume 54 issue 12 (december 2020) : 1459-1464,   Doi: 10.18805/ijar.B-1065

Genetic Variability and Structure of Three Tunisian Ovine Breeds Based on Microsatellite Polymorphism

Z
Z. Khaldi
S
S. Souid
B
B. Rekik
B
B. Haddad
1Regional Center for Research in Oasian Agriculture, Degueche, 2260 Tunisia.
Cite article:- Khaldi Z., Souid S., Rekik B., Haddad B. (2019). Genetic Variability and Structure of Three Tunisian Ovine Breeds Based on Microsatellite Polymorphism. Indian Journal of Animal Research. 54(12): 1459-1464. doi: 10.18805/ijar.B-1065.

ABSTRACT

Genetic diversity of native ovine Barbarine (BR=80) and Queue Fine de l’Ouest (QF=150) breeds as well as the exotic D’man (DM=70) breed were investigated using a panel of ten microsatellite markers. The markers used were all polymorphic and exhibited high levels of polymorphism. The total number of observed alleles across all breeds was 83. The allelic frequency distribution was heterogeneous and tests of genotype frequencies for deviation from HWE revealed significant departure from HWE of all populations for the TGLA48 and MCM527 loci. The mean expected and observed heterozygosity for the BR, QF and DM populations varied from 0.69 to 0.74 and 0.58 to 0.67, respectively. The average Polymorphism information content (PIC) was 0.683, 0.699, 0.697 and 0.657 for BR, QFG, QFT and DM, respectively. The mean F (ST) was 0.149 and indicated that most (85.1%) of total genetic variation raised from differences among individuals and only 14.9% came from differences among breeds. Per pair estimator of F(ST) indicated a low to moderate differentiation between BR and QF but a relatively high (F(ST) > 0.15) differentiation between Tunisian native (BR and QF) and DM breeds. Genetic distance and factorial analyses showed that genetic distances observed between BR-DM and between QF-DM were larger than those found between BR-QF breeds. 

REFERENCES

  1. Amareswarai, P., Gnana Prakash, M., Ekambaram, B., Mahendar, M., Hari Krishna, C.H. (2018). Molecular genetic studies on Nellore and Deccani sheep using microsatellite Markers. Indian Journal of Animal Research. 52: 805-810.
  2. Arora, R. and Bhatia, S. (2004). Genetic structure of Muzzafarnagri sheep based on microsatellite analysis. Small Ruminant Research. 54: 227-230.
  3. Barker, J.S.F., Tan, S.G., Moore, S.S., Mukherjee, T.K., Matheson, J.L., Selvaraj, O.S. (2001). Genetic variation within and relationships among populations of Asian goats. Journal of Animal Breeding and Genetics. 118: 213-233.
  4. Belkhir, K., Goudet, J., Chikhi, L. (2000). Genetix (Ver. 4.01) logiciel sous windowsTM pour la génétique des populations. Laboratoire Génome et Population, Université Montpellier II, Montpellier, France.
  5. Benbouza, H., Jean-Marie, J., Jean-Pierre, B., Guy, M. (2006). Optimization of a reliable, fast, cheap and sensitive silver staining method to detect SSR markers in polyacrylamide gels. Biotechnology Agronomy Society and Environment. 10:77-81.
  6. Ben Sassi-Zaidy, Y., Maretto, F., Charfi-Cheikrouha, F., Cassandro, M. (2014). Genetic diversity, structure and breed relationships in Tunisian sheep. Small Ruminant Research. 119: 52-56. 
  7. Calvo, J.H., Bouzada, J.A., Jurado, J.J., Serrano, M. (2006). Genetic substructure of the Spanish Manchega sheep breed. SmallRuminant Research. 64: 116-125.
  8. Cavalli-Sforza, L.L. and Edwards, A.W.F. (1967). Phylogenetic analysis: models and estimation procedures. Evolution. 21: 550-570.
  9. Dalvit, C., De Marchi, M., Dal Zotto, R., Zanetti, E., Meuwissen, T.,Cassandro, M. (2008). Genetic characterization of the Burlina cattle breed using microsatellite molecular markers. Journal of Animal Breeding and Genetics. 125: 137-144.
  10. Das, H., Turan, I., Demir, S. (2015). Genetic characterization of the Akkaraman, Morkaraman and Karayaka sheep through microsatellite variation. Indian Journal of Animal Research. 49: 173-179.
  11. De Araujo, A.M., Guimaraes, S.E.F., Machado, T.M.M., Lopes, P.S., Pereira, C.S., et al. (2006). Genetic diversity between herds of Alpine and Saanen dairy goats and the naturalized Brazilian Moxoto breed. Genetics and Molecular Biology. 29: 67-74.
  12. El Nahas, S.M., Hassan, A.A., AbouMossallam, A.A., Mahfouz, E.R., Bibars, M.A.,Oraby, H.A.S., Hondt, H.A. (2008). Analysis of genetic variation in different sheep breeds using microsatellites. African Journal of Biotechnology. 7:1060-1068.
  13. Felsenstein, J. (1993). PHYLIP-Phylogeny Inference Package (version 3.5c). Department of Genetics. University of Washington, Seattle.
  14. Goudet, J. (1995). FSTAT (version1.2): a computer program to calculate F-statistics. Heredity. 86: 485-486.
  15. Jun, Y.B., You, B.Y., Yu Qin, W., Xiao, H.Z., You, Z.P. (2015). Polymorphism analysis of three Chinese indigenous sheep breeds by microsatellite markers. Indian Journal of Animal Reseach. 49: 585-590. 
  16. Kalinwski, S.T. (2002). How many alleles per locus should be used to estimate genetic distances. Heredity. 88:62-65.
  17. Kavitha, S.T., Subramanian, A., Sivaselvam, S.N., Thiagarajan, R., Balasubramanian, S. (2015). Genetic characterisation of Tiruchy Black sheep of Tamil Nadu using microsatellite markers. Indian Journal of Animal Research. 49: 320-324. 
  18. Kumar, S., Gupta, T., Kumar, N., Dikshit, K., Navani, N., Jain, P., Nagarajan, M. (2006). Genetic variation and relationships among eight Indian riverine buffalo breeds. Molecular Ecology. 15: 593-600.
  19. Laval, G., Iannuccelli, N., Legault, C., Milan, D., Groenen, M.A.M., Giuffra, E., et al. (2000). Genetic diversity of eleven European pig breeds. Genetic Selection Evolution. 32:187-203.
  20. Louis, E.J. and Dempster, E.R. (1987). An exact test for Hardy-Weinberg and multiple alleles. Biometrics. 43: 805-811.
  21. Mukesh, M., Sodhi, M., Bhatia, S., Mishra, B.P. (2004). Genetic diversity of Indian native cattle breeds as analyzed with 20 microsatellites. Journal of Animal Breeding and Genetics. 121: 416-424.
  22. Nei, M. (1978). Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics. 89: 583-590.
  23. Park, S.D.E. (2001). Trypanotolerance in West African cattle and the population genetic effects of selection. Ph.D. Thesis. Trinity College, University of Dublin, Ireland.
  24. Pemberton, J.M., Slate, J., Bancroft, D.R., Barret, J.A. (1995). Non amplifying alleles at microsatellite loci: A caution for parentage and population studies. Molecular Ecology. 4: 249-52.
  25. Raymond, M. and Rousse, F. (1995). GENEPOP (version 1.2) population genetics software for exact tests and ecumenicism. Heredity. 86: 248-24.
  26. Saitbekova, N., Gaillard, C., Obexer-Ruff, G., Dolf, G. (1999). Genetic diversity in Swiss goat breeds based on microsatellite analysis. Animal Genetics. 30: 36-41.
  27. Sarson, M. (1972). L’élevage du mouton de la race Barbarine au centre de Ouesslattia, Tunisie centrale. Document technique INRAT. pp.55.
  28. Sodhi, M., Mukesh, M., Arora, R., Tantia, M.S., Bhatia, S. (2003). Genetic structure of Garole-a unique Indian microsheep assessed using microsatellite markers. Indian Journal of Dairy Science. 56: 167-173.
  29. Sodhi, S., Mukesh, M.,Bathia, S. (2006). Characterizing Nali and Chokla sheep differentiation with microsatellite markers. Small Ruminant Research. 65: 185-192.
  30. Weir, B.S. and Cockerham, C.C. (1984). Estimating F-statistics for the analysis of population structure. Evolution. 38: 1358-1370.
  31. Yeh, F.C., Yang, R.C., Boyle, T.B.J., Ye, Z.H., Mao, J.X. (1999). POPGENE (Version 1.32): the User-friendly Shareware for Population Genetic Analysis. Molecular Biology and Biotechnology Centre, University of Alberta, Canada. 
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    Research Article

    volume 54 issue 12 (december 2020) : 1459-1464,   Doi: 10.18805/ijar.B-1065

    Genetic Variability and Structure of Three Tunisian Ovine Breeds Based on Microsatellite Polymorphism

    Z
    Z. Khaldi
    S
    S. Souid
    B
    B. Rekik
    B
    B. Haddad
    1Regional Center for Research in Oasian Agriculture, Degueche, 2260 Tunisia.
    Cite article:- Khaldi Z., Souid S., Rekik B., Haddad B. (2019). Genetic Variability and Structure of Three Tunisian Ovine Breeds Based on Microsatellite Polymorphism. Indian Journal of Animal Research. 54(12): 1459-1464. doi: 10.18805/ijar.B-1065.

    ABSTRACT

    Genetic diversity of native ovine Barbarine (BR=80) and Queue Fine de l’Ouest (QF=150) breeds as well as the exotic D’man (DM=70) breed were investigated using a panel of ten microsatellite markers. The markers used were all polymorphic and exhibited high levels of polymorphism. The total number of observed alleles across all breeds was 83. The allelic frequency distribution was heterogeneous and tests of genotype frequencies for deviation from HWE revealed significant departure from HWE of all populations for the TGLA48 and MCM527 loci. The mean expected and observed heterozygosity for the BR, QF and DM populations varied from 0.69 to 0.74 and 0.58 to 0.67, respectively. The average Polymorphism information content (PIC) was 0.683, 0.699, 0.697 and 0.657 for BR, QFG, QFT and DM, respectively. The mean F (ST) was 0.149 and indicated that most (85.1%) of total genetic variation raised from differences among individuals and only 14.9% came from differences among breeds. Per pair estimator of F(ST) indicated a low to moderate differentiation between BR and QF but a relatively high (F(ST) > 0.15) differentiation between Tunisian native (BR and QF) and DM breeds. Genetic distance and factorial analyses showed that genetic distances observed between BR-DM and between QF-DM were larger than those found between BR-QF breeds. 

    REFERENCES

    1. Amareswarai, P., Gnana Prakash, M., Ekambaram, B., Mahendar, M., Hari Krishna, C.H. (2018). Molecular genetic studies on Nellore and Deccani sheep using microsatellite Markers. Indian Journal of Animal Research. 52: 805-810.
    2. Arora, R. and Bhatia, S. (2004). Genetic structure of Muzzafarnagri sheep based on microsatellite analysis. Small Ruminant Research. 54: 227-230.
    3. Barker, J.S.F., Tan, S.G., Moore, S.S., Mukherjee, T.K., Matheson, J.L., Selvaraj, O.S. (2001). Genetic variation within and relationships among populations of Asian goats. Journal of Animal Breeding and Genetics. 118: 213-233.
    4. Belkhir, K., Goudet, J., Chikhi, L. (2000). Genetix (Ver. 4.01) logiciel sous windowsTM pour la génétique des populations. Laboratoire Génome et Population, Université Montpellier II, Montpellier, France.
    5. Benbouza, H., Jean-Marie, J., Jean-Pierre, B., Guy, M. (2006). Optimization of a reliable, fast, cheap and sensitive silver staining method to detect SSR markers in polyacrylamide gels. Biotechnology Agronomy Society and Environment. 10:77-81.
    6. Ben Sassi-Zaidy, Y., Maretto, F., Charfi-Cheikrouha, F., Cassandro, M. (2014). Genetic diversity, structure and breed relationships in Tunisian sheep. Small Ruminant Research. 119: 52-56. 
    7. Calvo, J.H., Bouzada, J.A., Jurado, J.J., Serrano, M. (2006). Genetic substructure of the Spanish Manchega sheep breed. SmallRuminant Research. 64: 116-125.
    8. Cavalli-Sforza, L.L. and Edwards, A.W.F. (1967). Phylogenetic analysis: models and estimation procedures. Evolution. 21: 550-570.
    9. Dalvit, C., De Marchi, M., Dal Zotto, R., Zanetti, E., Meuwissen, T.,Cassandro, M. (2008). Genetic characterization of the Burlina cattle breed using microsatellite molecular markers. Journal of Animal Breeding and Genetics. 125: 137-144.
    10. Das, H., Turan, I., Demir, S. (2015). Genetic characterization of the Akkaraman, Morkaraman and Karayaka sheep through microsatellite variation. Indian Journal of Animal Research. 49: 173-179.
    11. De Araujo, A.M., Guimaraes, S.E.F., Machado, T.M.M., Lopes, P.S., Pereira, C.S., et al. (2006). Genetic diversity between herds of Alpine and Saanen dairy goats and the naturalized Brazilian Moxoto breed. Genetics and Molecular Biology. 29: 67-74.
    12. El Nahas, S.M., Hassan, A.A., AbouMossallam, A.A., Mahfouz, E.R., Bibars, M.A.,Oraby, H.A.S., Hondt, H.A. (2008). Analysis of genetic variation in different sheep breeds using microsatellites. African Journal of Biotechnology. 7:1060-1068.
    13. Felsenstein, J. (1993). PHYLIP-Phylogeny Inference Package (version 3.5c). Department of Genetics. University of Washington, Seattle.
    14. Goudet, J. (1995). FSTAT (version1.2): a computer program to calculate F-statistics. Heredity. 86: 485-486.
    15. Jun, Y.B., You, B.Y., Yu Qin, W., Xiao, H.Z., You, Z.P. (2015). Polymorphism analysis of three Chinese indigenous sheep breeds by microsatellite markers. Indian Journal of Animal Reseach. 49: 585-590. 
    16. Kalinwski, S.T. (2002). How many alleles per locus should be used to estimate genetic distances. Heredity. 88:62-65.
    17. Kavitha, S.T., Subramanian, A., Sivaselvam, S.N., Thiagarajan, R., Balasubramanian, S. (2015). Genetic characterisation of Tiruchy Black sheep of Tamil Nadu using microsatellite markers. Indian Journal of Animal Research. 49: 320-324. 
    18. Kumar, S., Gupta, T., Kumar, N., Dikshit, K., Navani, N., Jain, P., Nagarajan, M. (2006). Genetic variation and relationships among eight Indian riverine buffalo breeds. Molecular Ecology. 15: 593-600.
    19. Laval, G., Iannuccelli, N., Legault, C., Milan, D., Groenen, M.A.M., Giuffra, E., et al. (2000). Genetic diversity of eleven European pig breeds. Genetic Selection Evolution. 32:187-203.
    20. Louis, E.J. and Dempster, E.R. (1987). An exact test for Hardy-Weinberg and multiple alleles. Biometrics. 43: 805-811.
    21. Mukesh, M., Sodhi, M., Bhatia, S., Mishra, B.P. (2004). Genetic diversity of Indian native cattle breeds as analyzed with 20 microsatellites. Journal of Animal Breeding and Genetics. 121: 416-424.
    22. Nei, M. (1978). Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics. 89: 583-590.
    23. Park, S.D.E. (2001). Trypanotolerance in West African cattle and the population genetic effects of selection. Ph.D. Thesis. Trinity College, University of Dublin, Ireland.
    24. Pemberton, J.M., Slate, J., Bancroft, D.R., Barret, J.A. (1995). Non amplifying alleles at microsatellite loci: A caution for parentage and population studies. Molecular Ecology. 4: 249-52.
    25. Raymond, M. and Rousse, F. (1995). GENEPOP (version 1.2) population genetics software for exact tests and ecumenicism. Heredity. 86: 248-24.
    26. Saitbekova, N., Gaillard, C., Obexer-Ruff, G., Dolf, G. (1999). Genetic diversity in Swiss goat breeds based on microsatellite analysis. Animal Genetics. 30: 36-41.
    27. Sarson, M. (1972). L’élevage du mouton de la race Barbarine au centre de Ouesslattia, Tunisie centrale. Document technique INRAT. pp.55.
    28. Sodhi, M., Mukesh, M., Arora, R., Tantia, M.S., Bhatia, S. (2003). Genetic structure of Garole-a unique Indian microsheep assessed using microsatellite markers. Indian Journal of Dairy Science. 56: 167-173.
    29. Sodhi, S., Mukesh, M.,Bathia, S. (2006). Characterizing Nali and Chokla sheep differentiation with microsatellite markers. Small Ruminant Research. 65: 185-192.
    30. Weir, B.S. and Cockerham, C.C. (1984). Estimating F-statistics for the analysis of population structure. Evolution. 38: 1358-1370.
    31. Yeh, F.C., Yang, R.C., Boyle, T.B.J., Ye, Z.H., Mao, J.X. (1999). POPGENE (Version 1.32): the User-friendly Shareware for Population Genetic Analysis. Molecular Biology and Biotechnology Centre, University of Alberta, Canada. 
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