Loading...

​Elucidation of Genetic Divergence among Cattle Breeds of Tamil Nadu in Mitochondrial Genome

DOI: 10.18805/IJAR.B-4974    | Article Id: B-4974 | Page : 1448-1453
Citation :- ​Elucidation of Genetic Divergence among Cattle Breeds of Tamil Nadu in Mitochondrial Genome.Indian Journal of Animal Research.2022.(56):1448-1453
S. Vani, D. Balasubramanyam, S.M.K. Karthickeyan, M. Parthiban, P.S.L. Sesh vanireddy12786@gmail.com
Address : Department of Animal Genetics and Breeding, Madras Veterinary College, Tamil Nadu Veterinary and Animal Sciences University, Chennai-600 007, Tamil Nadu, India.
Submitted Date : 1-07-2022
Accepted Date : 31-08-2022

Abstract

Background: The present study was carried out for genetic characterization and assessment of evolutionary status of native cattle breeds of Tamil Nadu, India.
Methods: Complete mitochondrial genome sequence of 15 pooled samples belonging to five cattle breeds of Tamil Nadu was carried out for the first time using Illumina platform. These mitogenomes were utilized in the present investigation to study the mitochondrial diversity. using suitable statistical tools. 
Result: The sequences encompassed 16,338 to 16,340 nucleotides with 273 variants. Low degree of genetic divergence and polymorphism was observed in the population. Higher rate of migrants (11.77) between populations caused increase in gene flow. FST value of -0.04435 revealed low level of genetic differentiation between cattle breeds of Tamil Nadu. A significant negative Tajima’s D (P<0.05) for all the Bos indicus cattle indicates operation of purifying selection and population expansion among the genetic groups under study. Maximum likelihood reconstruction using complete mitochondrial sequences of the present study combined with previously reported sequences of Nellore cattle and eight Bos taurus cattle breeds illustrated close genetic relationship among the Bos indicus cattle under study with a clear demarcation from the Bos taurus cattle indicating higher genetic divergence between the two lineages. This finding was also supported by multi-dimensional scaling. Analysis of molecular variance revealed no differentiation between cattle breeds of Tamil Nadu.

Keywords

Bos indicus cattle Genetic divergence Mitogenome Phylogeny Whole genome sequencing

References

  1. Barani, A., Rahumathulla, P.S., Rajendran, R., Kumarasamy, P., Ganapathi, P., Radha, P. (2015). Molecular characterization of Pulikulam cattle using microsatellite markers. Indian Journal of Animal Research. 49(1): 36-39.
  2. Chung, H. (2013). Phylogenetic analysis and characterization of mitochondrial DNA for Korean native cattle. Open Journal of Genetics. 3(1): 12-23.
  3. Fu, Y. (1997). Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics. 147: 915-925.
  4. Fu, Y.X. and Li, W.H. (1993). Statistical tests of neutrality of mutations. Genetics. 133: 693-709. 
  5. Gautier, M., Foucaud, J. Gharbi, K. Cezard, T. Galan, M. Loiseau, A. Thomson, M. Pudlo, P., Kerdelhue, C., Estoup, A. (2013). Estimation of population allele frequencies from next- generation sequencing data: Pool versus individual based genotyping. Molecular Ecology. 22(14): 3766-3779.
  6. Hudson, R.R., Boos, D.D., Kalpan, N.L. (1992). A statistical test for detecting population subdivision. Molecular Biology and Evolution. 9: 138-151. 
  7. Hudson, R.R. (2000). A new statistic for detecting genetic differentiation. Genetics.155: 2011-2014. 
  8. Jakaria, J., Musyaddad, T., Rahayu, S., Muladno, M., Sumantri, C. (2019). Diversity of D-loop mitochondrial DNA (mtDNA) sequence in Bali and Sumba Ongole cattle breeds. Journal of the Indonesian Tropical Animal Agriculture. 44(4): 335-345. 
  9. Jeevan, C. (2022). Prediction of semen production potential using conventional and machine learning approaches. Thesis submitted to Tamil Nadu Veterinary and Animal Sciences University.
  10. Kumar, S., Stecher, G., Li, M., Knyaz, C., Tamura, K. (2018). MEGA X: Molecular evolutionary genetics analysis across computing platforms. Molecular Biology and Evolution. 35: 1547-1549.
  11. Loftus, R.T., MacHugh, D.E. Bradley, D.G., Sharp, P.M., Cunningham, P. (1994). Evidence for two independent domestications of cattle. Proceedings of the National Academy of Sciences. 91(7): 2757-2761.
  12. Lynch, M. and Crease, T.J. (1990). The analysis of population survey data on DNA sequence variation. Molecular Biology and Evolution. 7: 377-394. 
  13. Nei, M. (1987). Molecular Evolutionary Genetics. Columbia University. Press, New York. 
  14. Parameswari, S., Cauveri, D., Karthickeyan, S.M.K., Arunachalam, K., Kumarasamy, P. (2019). Cytogenetic Characterisation of Alambadi breed of cattle in Tamil Nadu. Indian Veterinary Journal. 96(5): 49-52.
  15. Petretto, E., Dettori, M.L., Pazzola, M., Manca, F., Amills, M., Vacca, G.M. (2022). Mitochondrial DNA diversity of the Sardinian local cattle stock. Scientific Reports. 12(1): 1-7. 
  16. Pramod, R.K., Velayutham, D., Sajesh, P.K., Beena, P.S., Zachariah, A., Zachariah. A., Chandramohan, B., et al. (2018). The complete mitochondrial genome of Indian cattle (Bos indicus). Mitochondrial DNA B: Resources. 3(1): 207-208. 
  17. Posada, D. and Crandall, K.A. (1998). Model test: Testing the model of DNA substitution. Bioinformatics. 14: 817-818.
  18. Rozas, J., Ferrer-Mata, A., Sanchez-DelBarrio, J.C., Guirao-Rico, S., Librado, P., Ramos-Onsins, S.E., Sanchez-Gracia, A. (2017). DnaSP 6: DNA sequence polymorphism analysis of large data sets. Molecular Biology and Evolution. 34(12): 3299-3302.
  19. Sambrook, J. (1989). Isolation of DNA from mammalian cells: Protocol I. Molecular cloning. A Laboratory Manual. Pp. 916-919.
  20. Sharma, R., Kishore, A., Mukesh, M., Ahlawat, S., Maitra, A., Pandey, A.K., Tantia, M.S. (2015). Genetic diversity and relationship of Indian cattle inferred from microsatellite and mitochondrial DNA markers. BMC Genetics. 16(1): 1-12.
  21. Tajima, F. (1983). Evolutionary relationship of DNA sequences in finite populations. Genetics. 105: 437-460. 
  22. Tajima, F. (1989). Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics. 123: 585- 595.

Global Footprints