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Research Article

volume 52 issue 6 (june 2018) : 805-810,   Doi: 10.18805/ijar.B-3300

Molecular genetic studies on Nellore and Deccani sheep using microsatellite markers

P
P. Amareswari
M
M. Gnana Prakash
B
B. Ekambaram
M
M. Mahendar
C
Ch. Hari Krishna
1College of Veterinary Science, Sri P.V. Narasimha Rao Telangana Veterinary University for Veterinary, Animal and Fisheries Sciences, Hyderabad-500 030, Telangana, India.
Cite article:- Amareswari P., Prakash Gnana M., Ekambaram B., Mahendar M., Krishna Hari Ch. (2017). Molecular genetic studies on Nellore and Deccani sheep using microsatellite markers. Indian Journal of Animal Research. 52(6): 805-810. doi: 10.18805/ijar.B-3300.

ABSTRACT

The study was undertaken to understand the genetic architecture of Deccani and Nellore sheep breeds and to assess the genetic distance between the breeds. Allele diversity, genetic variability and population structure in the two breeds were estimated using 30 microsatellite markers. A total of 100 sheep, 50 each from Deccani and Nellore breeds were genotyped. The total number of alleles observed was 254 and 260 in Deccani and Nellore, respectively. The mean expected heterozygosity among the breeds ranged from 0.79 (Deccani) to 0.80 (Nellore) whereas the mean observed heterozygosity levels ranged from 0.77 in Deccani to 0.78 in Nellore sheep. The overall mean inbreeding coefficient was 0.029 in Deccani and 0.031 in Nellore sheep and of the 30 loci studied, 14 loci in Deccani and 16 loci in Nellore sheep showed negative inbreeding coefficient indicating the presence of outbreeding. However, eight loci (BM1314, BM6506, BM8125, ILSTS28, MAF70, MCM140, OarCB226 and OarFCB128) showed positive, mild to moderate inbreeding ranging from 0.007 to 0.25 in Deccani and 0.066 to 0.37 in Nellore sheep studied.  The FIS values ranged from -0.372 to 0.74, FST values ranged from 0.001 to 0.172 and FIT values ranged from -0.370 to 0.728 between the Deccani and Nellore sheep breeds studied. The PIC values ranged from 0.498 to 0.886 with a mean of 0.773 in Deccani and from 0.574 to 0.894 with a mean of 0.777 in Nellore breed. The information generated from the present study will be valuable for setting conservation priority of these two breeds.

REFERENCES

  1. Ahmed, Z., Babar, M. E., Hussain, T., Nadeem. A., Awan, F. I., Wajid, A., Shah, S. A. and Ali, M. M. (2014). Genetic diversity analysis of Kail sheep by using microsatellite markers. J. Anim. Plant Sci. 24:1329-1333.
  2. Arora, R. and Bhatia, S. (2004). Genetic structure of Muzzafarnagri sheep based on microsatellite analysis. Small Rumin. Res. 54: 227-230.
  3. Arora, R. and Bhatia, S. (2006). Genetic diversity of Magra sheep from India using microsatellite analysis. Asian – Aust. J. Anim. Sci.19: 938-942.
  4. Arora, R. and Bhatia, S. (2008). Microsatellite variation and genetic relationship among Rajasthani sheep: Relevance for conservation. Livest. Res. Rur. Dev.20: 12.
  5. Arora, R., Bhatia, S. and Jain, S. (2010). Morphological and genetic characterization of Ganjam sheep. Anim. Genet. Res.46: 1-9.
  6. Barker, J. S. F. 1994. A global protocol for determining genetic distances among domestic livestock breeds. Proc. 5th world cong. Genet. Livest. Prod.21: 501-508. 
  7. Chen, R. J., Yang, Z. P., Ji, D. J., Qu, D.Y., Li, Y. L., Mao, Y. J. and Huang, D. L. (2009). Analysis of genetic polymorphism in six meat sheep breeds and genetic distances between them. Czech. J. Anim. Sci.54: 461-467.
  8. Diez-Tascon, C. R., Little John, P., Almedia, A. R. and Crawford, A. M. (2000). Genetic variation within the Merino sheep breed: Analysis of closely related populations using microsatellites. Anim. Genet. 31: 243-251.
  9. FAOSTAT (2012). Food and Agriculture Organization of the United Nations. [http://faostat.fao.org].
  10. Farid, A., O’Reilly, E., Dollard, C. and Kelsey, Jr. C. R. (2000). Genetic analysis of ten sheep breeds using microsatellite markers. Canad. J Anim. Sci. 80: 9-17.
  11. Girish, H., Sivaselvam, S. N., Karthikeyan, S. M. K. and Saravanan, R. (2007). Molecular characterisation of Nilagiri sheep of south India based on microsatellites. Asian – Aust. J. Anim. Sci.20: 633-637.
  12. Hoda, A., Dobi, P. and Hyka, G. (2009). Genetic diversity and distances of Albanian local sheep breeds using microsatellite markers. Livest. Res. Rur. Dev.21:93.
  13. Jyotsana, B., Jakhesara, S., Prakash, V., Rank, D. N. and Vataliya, P. H. (2010). Genetic features of Patanwadi Marwari and Dumba sheep breeds (India) inferred by microsatellite markers. Small Rumin. Res. 93: 57-60.
  14. Kumar S, Tamura K and Nei M. (2004). Mega 3: Integrated software for molecular evolutionary genetics analysis and sequence alignment. Briefings in Bioinformatics.5: 150–163.
  15. Kumarasamy, P., Prema, S., Ganapathi, P., Karthickeyan, S. M. K. and Kanakaraj, P.(2009). Molecular characterization of Coimbatore breed of sheep in South India. ICFAI Univ J Genet Evol.2: 56-65.
  16. Nanekarani, S., Amirinia, C., Amirmozafari, N., Torshizi, R. V. and Gharahdaghi, A. A. (2010). Genetic variation among pelt sheep population using microsatellite markers. Af. J. Biotechnol.9: 7437-7445.
  17. Ozerov, M. Y., Marzanov, N. S., Tapio, M., Burabaev, A. A., Marzanova, L. K., Amerkhanov, K. A. and Kantanenen, J. (2008). Genetic features of Kazakh sheep breeds according to microsatellites. Russ. Agri. Sci.34: 45–48.
  18. Park, S. D. E.(2001). The Excel microsatellite toolkit V 31 Animal Genomics Laboratory University College, Dublin, Ireland. 
  19. Peakall, R. and Smouse, P. E.(2006). GENALEX 6: genetic analysis in Excel Population genetic software for teaching and research. Molecular Ecology Notes.6: 288-295.
  20. Pramod, S., Kumarasamy, P., Chandra, A. R. M., Sridevi, P. and Rahmathullah, P. S. (2009). Molecular characterization of Vembur sheep of South India based on microsatellites. Indian J. Sci. Technol. 2: 55-58.
  21. Prema, S., Sivaselvam, S. N. and Karthickeyan, S. M. K.(2008a). Evaluation of genetic diversity in Mecheri sheep of Tamil Nadu using microsatellite markers. Indian J. Biotechnol.7: 401-403.
  22. Prema, S., Sivaselvam, S. N. and Karthickeyan, S. M. K. (2008b). A note on genetic analysis in Madras Red sheep of India using microsatellite markers. Livst. Res. Rur. Deve. 20: 181.
  23. Radha, P., Sivaselvam, S. N., Kumaraswamy, P. and Kumanan, K. (2011). Genetic diversity and bottleneck analysis of Kilakarsal sheep by microsatellite markers. Indian J. Biotechnol.10: 52-55.
  24. Rodrigo de la, B., Héctor, U., Etel, L., Fermín San, P. and Arranz, J. (2010). Genetic structure and diversity of four Chilean sheep breeds. Chil. J. Agri. Res.70: 646-651.
  25. Saitbekova-Stahlberger, N., Schlapfer, J., Dolf, G. and Gaillord, C. (2001). Genetic relationships in Swiss sheep breeds based on microsatellite analysis. J. Anim. Breed. Genet. 118: 379-387. 
  26. Sambrook, J., Fritsch, E. F. and Maniatis, T.(1989). Molecular Cloning: A Laboratory Manual. Vol 3. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York.
  27. Takezaki, N. and Nei, M. (1996). Genetic distances and reconstruction of phylogenetic trees from microsatellite DNA. Genet. 144: 389-399. 
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    Research Article

    volume 52 issue 6 (june 2018) : 805-810,   Doi: 10.18805/ijar.B-3300

    Molecular genetic studies on Nellore and Deccani sheep using microsatellite markers

    P
    P. Amareswari
    M
    M. Gnana Prakash
    B
    B. Ekambaram
    M
    M. Mahendar
    C
    Ch. Hari Krishna
    1College of Veterinary Science, Sri P.V. Narasimha Rao Telangana Veterinary University for Veterinary, Animal and Fisheries Sciences, Hyderabad-500 030, Telangana, India.
    Cite article:- Amareswari P., Prakash Gnana M., Ekambaram B., Mahendar M., Krishna Hari Ch. (2017). Molecular genetic studies on Nellore and Deccani sheep using microsatellite markers. Indian Journal of Animal Research. 52(6): 805-810. doi: 10.18805/ijar.B-3300.

    ABSTRACT

    The study was undertaken to understand the genetic architecture of Deccani and Nellore sheep breeds and to assess the genetic distance between the breeds. Allele diversity, genetic variability and population structure in the two breeds were estimated using 30 microsatellite markers. A total of 100 sheep, 50 each from Deccani and Nellore breeds were genotyped. The total number of alleles observed was 254 and 260 in Deccani and Nellore, respectively. The mean expected heterozygosity among the breeds ranged from 0.79 (Deccani) to 0.80 (Nellore) whereas the mean observed heterozygosity levels ranged from 0.77 in Deccani to 0.78 in Nellore sheep. The overall mean inbreeding coefficient was 0.029 in Deccani and 0.031 in Nellore sheep and of the 30 loci studied, 14 loci in Deccani and 16 loci in Nellore sheep showed negative inbreeding coefficient indicating the presence of outbreeding. However, eight loci (BM1314, BM6506, BM8125, ILSTS28, MAF70, MCM140, OarCB226 and OarFCB128) showed positive, mild to moderate inbreeding ranging from 0.007 to 0.25 in Deccani and 0.066 to 0.37 in Nellore sheep studied.  The FIS values ranged from -0.372 to 0.74, FST values ranged from 0.001 to 0.172 and FIT values ranged from -0.370 to 0.728 between the Deccani and Nellore sheep breeds studied. The PIC values ranged from 0.498 to 0.886 with a mean of 0.773 in Deccani and from 0.574 to 0.894 with a mean of 0.777 in Nellore breed. The information generated from the present study will be valuable for setting conservation priority of these two breeds.

    REFERENCES

    1. Ahmed, Z., Babar, M. E., Hussain, T., Nadeem. A., Awan, F. I., Wajid, A., Shah, S. A. and Ali, M. M. (2014). Genetic diversity analysis of Kail sheep by using microsatellite markers. J. Anim. Plant Sci. 24:1329-1333.
    2. Arora, R. and Bhatia, S. (2004). Genetic structure of Muzzafarnagri sheep based on microsatellite analysis. Small Rumin. Res. 54: 227-230.
    3. Arora, R. and Bhatia, S. (2006). Genetic diversity of Magra sheep from India using microsatellite analysis. Asian – Aust. J. Anim. Sci.19: 938-942.
    4. Arora, R. and Bhatia, S. (2008). Microsatellite variation and genetic relationship among Rajasthani sheep: Relevance for conservation. Livest. Res. Rur. Dev.20: 12.
    5. Arora, R., Bhatia, S. and Jain, S. (2010). Morphological and genetic characterization of Ganjam sheep. Anim. Genet. Res.46: 1-9.
    6. Barker, J. S. F. 1994. A global protocol for determining genetic distances among domestic livestock breeds. Proc. 5th world cong. Genet. Livest. Prod.21: 501-508. 
    7. Chen, R. J., Yang, Z. P., Ji, D. J., Qu, D.Y., Li, Y. L., Mao, Y. J. and Huang, D. L. (2009). Analysis of genetic polymorphism in six meat sheep breeds and genetic distances between them. Czech. J. Anim. Sci.54: 461-467.
    8. Diez-Tascon, C. R., Little John, P., Almedia, A. R. and Crawford, A. M. (2000). Genetic variation within the Merino sheep breed: Analysis of closely related populations using microsatellites. Anim. Genet. 31: 243-251.
    9. FAOSTAT (2012). Food and Agriculture Organization of the United Nations. [http://faostat.fao.org].
    10. Farid, A., O’Reilly, E., Dollard, C. and Kelsey, Jr. C. R. (2000). Genetic analysis of ten sheep breeds using microsatellite markers. Canad. J Anim. Sci. 80: 9-17.
    11. Girish, H., Sivaselvam, S. N., Karthikeyan, S. M. K. and Saravanan, R. (2007). Molecular characterisation of Nilagiri sheep of south India based on microsatellites. Asian – Aust. J. Anim. Sci.20: 633-637.
    12. Hoda, A., Dobi, P. and Hyka, G. (2009). Genetic diversity and distances of Albanian local sheep breeds using microsatellite markers. Livest. Res. Rur. Dev.21:93.
    13. Jyotsana, B., Jakhesara, S., Prakash, V., Rank, D. N. and Vataliya, P. H. (2010). Genetic features of Patanwadi Marwari and Dumba sheep breeds (India) inferred by microsatellite markers. Small Rumin. Res. 93: 57-60.
    14. Kumar S, Tamura K and Nei M. (2004). Mega 3: Integrated software for molecular evolutionary genetics analysis and sequence alignment. Briefings in Bioinformatics.5: 150–163.
    15. Kumarasamy, P., Prema, S., Ganapathi, P., Karthickeyan, S. M. K. and Kanakaraj, P.(2009). Molecular characterization of Coimbatore breed of sheep in South India. ICFAI Univ J Genet Evol.2: 56-65.
    16. Nanekarani, S., Amirinia, C., Amirmozafari, N., Torshizi, R. V. and Gharahdaghi, A. A. (2010). Genetic variation among pelt sheep population using microsatellite markers. Af. J. Biotechnol.9: 7437-7445.
    17. Ozerov, M. Y., Marzanov, N. S., Tapio, M., Burabaev, A. A., Marzanova, L. K., Amerkhanov, K. A. and Kantanenen, J. (2008). Genetic features of Kazakh sheep breeds according to microsatellites. Russ. Agri. Sci.34: 45–48.
    18. Park, S. D. E.(2001). The Excel microsatellite toolkit V 31 Animal Genomics Laboratory University College, Dublin, Ireland. 
    19. Peakall, R. and Smouse, P. E.(2006). GENALEX 6: genetic analysis in Excel Population genetic software for teaching and research. Molecular Ecology Notes.6: 288-295.
    20. Pramod, S., Kumarasamy, P., Chandra, A. R. M., Sridevi, P. and Rahmathullah, P. S. (2009). Molecular characterization of Vembur sheep of South India based on microsatellites. Indian J. Sci. Technol. 2: 55-58.
    21. Prema, S., Sivaselvam, S. N. and Karthickeyan, S. M. K.(2008a). Evaluation of genetic diversity in Mecheri sheep of Tamil Nadu using microsatellite markers. Indian J. Biotechnol.7: 401-403.
    22. Prema, S., Sivaselvam, S. N. and Karthickeyan, S. M. K. (2008b). A note on genetic analysis in Madras Red sheep of India using microsatellite markers. Livst. Res. Rur. Deve. 20: 181.
    23. Radha, P., Sivaselvam, S. N., Kumaraswamy, P. and Kumanan, K. (2011). Genetic diversity and bottleneck analysis of Kilakarsal sheep by microsatellite markers. Indian J. Biotechnol.10: 52-55.
    24. Rodrigo de la, B., Héctor, U., Etel, L., Fermín San, P. and Arranz, J. (2010). Genetic structure and diversity of four Chilean sheep breeds. Chil. J. Agri. Res.70: 646-651.
    25. Saitbekova-Stahlberger, N., Schlapfer, J., Dolf, G. and Gaillord, C. (2001). Genetic relationships in Swiss sheep breeds based on microsatellite analysis. J. Anim. Breed. Genet. 118: 379-387. 
    26. Sambrook, J., Fritsch, E. F. and Maniatis, T.(1989). Molecular Cloning: A Laboratory Manual. Vol 3. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York.
    27. Takezaki, N. and Nei, M. (1996). Genetic distances and reconstruction of phylogenetic trees from microsatellite DNA. Genet. 144: 389-399. 
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