Genome-wide Single Nucleotide Polymorphism Analyses Reveal Genetic Diversity and Structure of Wild and Domestic Cattle in Bangladesh

  • Uzzaman, Md. Rasel (Brain Korea 21 Center for Bio-Resource Development, Department of Animal Science, Chungbuk National University) ;
  • Edea, Zewdu (Brain Korea 21 Center for Bio-Resource Development, Department of Animal Science, Chungbuk National University) ;
  • Bhuiyan, Md. Shamsul Alam (Department of Animal Breeding and Genetics, Bangladesh Agricultural University) ;
  • Walker, Jeremy (GeneSeek, Neogen Corporation) ;
  • Bhuiyan, A.K.F.H. (Department of Animal Breeding and Genetics, Bangladesh Agricultural University) ;
  • Kim, Kwan-Suk (Brain Korea 21 Center for Bio-Resource Development, Department of Animal Science, Chungbuk National University)
  • Received : 2014.03.03
  • Accepted : 2014.06.09
  • Published : 2014.10.01


In spite of variation in coat color, size, and production traits among indigenous Bangladeshi cattle populations, genetic differences among most of the populations have not been investigated or exploited. In this study, we used a high-density bovine single nucleotide polymorphism (SNP) 80K Bead Chip derived from Bos indicus breeds to assess genetic diversity and population structure of 2 Bangladeshi zebu cattle populations (red Chittagong, n = 28 and non-descript deshi, n = 28) and a semi-domesticated population (gayal, n = 17). Overall, 95% and 58% of the total SNPs (69,804) showed polymorphisms in the zebu and gayal populations, respectively. Similarly, the average minor allele frequency value was as high 0.29 in zebu and as low as 0.09 in gayal. The mean expected heterozygosity varied from $0.42{\pm}0.14$ in zebu to $0.148{\pm}0.14$ in gayal with significant heterozygosity deficiency of 0.06 ($F_{IS}$) in the latter. Coancestry estimations revealed that the two zebu populations are weakly differentiated, with over 99% of the total genetic variation retained within populations and less than 1% accounted for between populations. Conversely, strong genetic differentiation ($F_{ST}=0.33$) was observed between zebu and gayal populations. Results of population structure and principal component analyses suggest that gayal is distinct from Bos indicus and that the two zebu populations were weakly structured. This study provides basic information about the genetic diversity and structure of Bangladeshi cattle and the semi-domesticated gayal population that can be used for future appraisal of breed utilization and management strategies.


Bangladesh;Genome-wide Single Nucleotide Polymorphism Analyses;Gayal;Domestic Cattle


  1. Dadi, H., J. J. Kim, D. Yoon, and K. S. Kim. 2012. Evaluation of single nucleotide polymorphisms (SNPs) genotyped by the illumina bovine SNP50K in cattle focusing on Hanwoo breed. Asian Australas. J. Anim. Sci. 25:28-32.
  2. Dalvit, C., M. De Marchi, R. Dal Zotto, E. Zanetti, T. Meuwissen, and M. Cassandro. 2008. Genetic characterization of the Burlina cattle breed using microsatellites markers. J. Anim. Breed. Genet. 125:137-144.
  3. DNA Genotek Inc. 2012. Performa-gene.Livestock (PG-100). Available at: PG100.html Accessed April 8, 2012.
  4. Edea, Z., H. Dadi, S. W. Kim, T. Dessie, and K.-S. Kim. 2012. Comparison of SNP variation and distribution in indigenous Ethiopian and Korean Cattle (Hanwoo) populations. Genomics Inform. 10:200-205.
  5. Tanaka, K., T. Takizawa, T. Dorji, T. Amano, H, Mannen, Y. Maeda, Y. Yamamoto, and T. Namikawa. 2011. Polymorphisms in the bovine hemoglobin-beta gene provide evidence for gene-flow between wild species of Bos (Bibos) and domestic cattle in Southeast Asia. Anim. Sci. J. 82:36-45.
  6. Vignal, A., D. Milan, M. SanCristobal, and A. Eggen. 2002. A review on SNP and other types of molecular markers and their use in animal genetics. Genet. Sel. Evol. 34:275-306.
  7. Weir, B. 1996. Genetic Data Analysis II. Sinauer Associates, Sunderland, MA, USA.
  8. Karim, Z., K. S. Huque, G. Hussain, Z. Ali, and M. Hossain. 2010. Growth and development potential of livestock and fisheries in Bangladesh. Bangladesh Food Security Investment Forum. May 26-27, 2010; Dhaka, Bangladesh.
  9. Lin, B. Z., S. Sasazaki, and H. Mannen. 2010. Genetic diversity and structure in Bos taurus and Bos indicus populations analyzed by SNP markers. Anim. Sci. J. 81:281-289.
  10. Liu, K. and S. V. Muse. 2005. PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics 21:2128-2129.
  11. McKay, S., R. Schnabel, B. Murdoch, L. Matukumalli, J. Aerts, W. Coppieters, D. Crews, E. Neto, C. Gill, and C. Gao. 2008. An assessment of population structure in eight breeds of cattle using a whole genome SNP panel. BMC Genetics 9:37.
  12. Payne, W. J. A. 1970. Cattle production in the tropics. Vol. I. Breeds and Breeding. Longman Group Ltd., London, UK.
  13. Pritchard, J. K., M. Stephens, and P. Donnelly. 2000. Inference of population structure using multilocus genotype data. Genetics 155:945-959.
  14. Reynolds, J., B. S. Weir, and C. C. Cockerham. 1983. Estimation of the coancestry coefficient: basis for a short-term genetic distance. Genetics 105:767-779.
  15. Baker, F. 2004. Selected indicators of food and agriculture development in asia-pacific region 1993-2003. FAO Regional Office for Asia and the Pacific, Bangkok, Thailand.
  16. Bhuiyan, A., M. Hossain, and G. Deb. 2007a. Indigenous cattle genetic resources of Bangladesh and a way forward to their development. Bangladesh J. Prog. Sci. Tech. 5:105-112.
  17. Bhuiyan, M. S. A., A. K. F. H. Bhuiyan, D. H. Yoon, J. T. Jeon, C. S. Park, and J. H. Lee. 2007b. Mitochondrial DNA diversity and origin of Red Chittagong cattle. Asian Australas. J. Anim. Sci. 20:1478-1484.
  18. Edea, Z., H. Dadi, S.-W. Kim, T. Dessie, T. Lee, H. Kim, J.-J. Kim, and K.-S. Kim. 2013. Genetic diversity, population structure and relationships in indigenous cattle populations of Ethiopia and Korean Hanwoo breeds using SNP markers. Front. Genet. 4:35.
  19. Giasuddin, M., K. S. Huque, and J. Alam. 2003. Reproductive potentials of gayal (Bos frontalis) under semi-intensive management. Asian Australas. J. Anim. Sci. 16:331-334.
  20. Golden Helix, I. 2012. SNP & Variation Suite Manual, Version 7.6.9. Available at: Accessed April 10, 2012.

Cited by

  1. Genetic diversity and relationship of Indian cattle inferred from microsatellite and mitochondrial DNA markers vol.16, pp.1, 2015,
  2. Prioritization for conservation of Iranian native cattle breeds based on genome-wide SNP data vol.17, pp.1, 2016,
  3. Evaluation of Bovine High-Density SNP Genotyping Array in Indigenous Dairy Cattle Breeds pp.1532-2378, 2017,
  4. Genetic diversity and divergence among Korean cattle breeds assessed using a BovineHD single-nucleotide polymorphism chip vol.31, pp.11, 2018,
  5. High-density Genotyping reveals Genomic Characterization, Population Structure and Genetic Diversity of Indian Mithun (Bos frontalis) vol.8, pp.1, 2018,