Determination of Genetic Diversity Using 15 Simple Sequence Repeats Markers in Long Term Selected Japanese Quail Lines

  • Karabag, Kemal (Department of Agricultural Biotechnology, Faculty of Agriculture, Akdeniz University) ;
  • Balcioglu, Murat Soner (Department of Animal Science, Faculty of Agriculture, Akdeniz University) ;
  • Karli, Taki (Department of Animal Science, Faculty of Agriculture, Akdeniz University) ;
  • Alkan, Sezai (Department of Animal Science, Faculty of Agriculture, Ordu University)
  • Received : 2015.11.19
  • Accepted : 2016.04.02
  • Published : 2016.12.01


Japanese quail is still used as a model for poultry research because of their usefulness as laying, meat, and laboratory animals. Microsatellite markers are the most widely used molecular markers, due to their relative ease of scoring and high levels of polymorphism. The objective of the research was to determine genetic diversity and population genetic structures of selected Japanese quail lines (high body weight 1 [HBW1], HBW2, low body weight [LBW], and layer [L]) throughout 15th generations and an unselected control (C). A total of 69 individuals from five quail lines were genotyped by fifteen microsatellite markers. When analyzed profiles of the markers the observed ($H_o$) and expected ($H_e$) heterozygosity ranged from 0.04 (GUJ0027) to 0.64 (GUJ0087) and 0.21 (GUJ0027) to 0.84 (GUJ0037), respectively. Also, $H_o$ and $H_e$ were separated from 0.30 (L and LBW) to 0.33 (C and HBW2) and from 0.52 (HBW2) to 0.58 (L and LBW), respectively. The mean polymorphic information content (PIC) ranged from 0.46 (HBW2) to 0.52 (L). Approximately half of the markers were informative ($PIC{\geq}0.50$). Genetic distances were calculated from 0.09 (HBW1 and HBW2) to 0.33 (C and L). Phylogenetic dendrogram showed that the quail lines were clearly defined by the microsatellite markers used here. Bayesian model-based clustering supported the results from the phylogenetic tree. These results reflect that the set of studied markers can be used effectively to capture the magnitude of genetic variability in selected Japanese quail lines. Also, to identify markers and alleles which are specific to the divergence lines, further generations of selection are required.


Simple Sequence Repeats;Selection;Breeding;Genetic Diversity;Quail


Supported by : Akdeniz University, TUBITAK (The Scientific and Technological Research Council of Turkey)


  1. Abdelkrim, J., B. C. Robertson, J. A. L. Stanton, and N. J. Gemmell. 2009. Fast, cost-effective development of species-specific microsatellite markers by genomic sequencing. Biotechniques 46:185-192.
  2. Ahmad, A., I. Zahoor, M. Akram, M. E. Babar, and A. Basheer. 2014. Evaluation of genetic diversity within and between the quail breeds in Pakistan. Sci. Int. 26:1175-1179.
  3. Alkan, S., T. Karsli, K. Karabag, A. Galic, and M. S. Balcioglu. 2013. The effects of thermal manipulation during early and late embryogenesis on hatchability, hatching weight and body weight in Japanese quails (Coturnix coturnix japonica). Arc. Tierz. 56:789-796.
  4. Amirinia, C., H. Emrani, M. A. R. Arbabe, R. V. Torshizi, and A. N. Javaremi. 2007. Evaluation of eight microsatellite loci polymorphism in four Japanese quail (Coturnix japonica) strain in Iran. Pak. J. Biol. Sci. 10:1195-1199.
  5. Babar, M. E., A. Nadeem, T. Hussain, A. Wajid, S. A. Shah, A. Iqbal, Z. Sarfraz, and M. Akram. 2012. Microsatellite marker based genetic diversity among four varieties of Pakistan Aseel chicken. Pak. Vet. J. 32:237-241.
  6. Bai, Y. J., Y. Z. Pang, S. J. Wu, M. Q. Yu, X. H. Zhang, S. J. Zhao, and H. W. Xu. 2013. Polymorphism Analysis of Chinese yellow quail using microsatellite markers. J. Anim. Plant Sci. 23:1072-1076.
  7. Botstein, D., R. L. White, M. Skolnik, and R. W. Davis. 1980. Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am. J. Hum. Genet. 32:314-331.
  8. Chang, G. B., H. Chang, X. P. Liu, W. M. Zhao, D. J. Ji, Y. J. Mao, G. H. Song, and X. K. Shi. 2007. Genetic diversity of wild quail in China ascertained with microsatellite DNA markers. Asian Australas. J. Anim. Sci. 20:1783-1790.
  9. Charati, H., A. E. Koshkoiyeh, R. J. Ori, H. Moradian, and A. A. Menrgardi. 2014. Detection of quantitative trait loci affecting carcass traits and internal organs on chromosome 3 in an F2 intercross of Japanese quail. Anim. Sci. Pap. Rep. 32:369-383.
  10. Chen, G. H., X. S. Wu, D. Q. Wang, J. Qin, S. L. Wu, Q. L. Zhou, F. Xie, R. Cheng, Q. Xu, B. Liu, X. Y. Zhang, and O. Olowofeso. 2004. Cluster analysis of 12 Chinese native chicken populations using microsatellite markers. Asian Australas. J. Anim. Sci. 17:1047-1052.
  11. Davila, S. G., M. G. Gil, P. Resino-Talavan, and J. L. Campo. 2009. Evaluation of diversity between different Spanish chicken breeds, a tester line and a White Leghorn population based on microsatellite markers. Poult. Sci. 88:2518-2525.
  12. Earl, D. A. and B. M. vonHoldt. 2012. STRUCTURE HARVESTER: A website and program for visualizing STRUCTURE output and implementing the Evanno method. Conserv. Genet. Resour. 4:359-361.
  13. Evanno, G., S. Regnaut, and J. Goudet. 2005. Detecting the number of cluster of individuals using the software STRUCTURE: a simulation study. Mol. Ecol. 14:2611-2620.
  14. Farrag, S. A., A. B. Tanatarov, M. E. Soltan, M. Ismail, and O. M. Zayed. 2011. Microsatellite analysis of genetic diversity in three populations of Japanese quail (Coturnix coturnix japonica) from Kazakhstan. J. Anim. Vet. Adv. 10:2376-2383.
  15. Gomes, M. L., T. Haranaka, W. N. deCampos, and A. P. Wasko. 2013. Assessing paternity in Japanese quails (Coturnix Japonica) using microsatellite markers - inferences for its mating system and reproductive success. Rev. Bras. Cienc. Avic. 15:329-338.
  16. Gruszczynska, J. and E. Michalska. 2013. Application of chicken microsatellite markers to molecular monitoring of the experimental population of Japanese quail (Coturnix japonica). Anim. Sci. Pap. Rep. 31:73-84.
  17. Hartl, D. L. and A. G. Clark. 1997. Principles of Population Genetics. 3rd edn. Sinauer Associates, Inc. Publishers, Sunderland, MA, USA.
  18. Kalinowski, S. T., M. L. Taper, and T. C. Marshall. 2007. Revising how to computer program CERVUS accommodates genotyping error increases success in paternity assignment. Mol. Ecol. 16:1099-1106.
  19. Kayang, B. B., M. Inoue-Murayama. T. Hoshi, K. Matsuo, H. Takahashi, M. Minezawa, M. Mizutani, and S. Ito. 2002. Microsatellite loci in Japanese quail and cross-species amplification in chicken and guinea fowl. Genet. Sel. Evol. 34:233-253.
  20. Kim, S. H., K. M. T. Cheng, C. Ritland, K. Ritland, and F. G. Silversides. 2007. Inbreeding in Japanese quail estimated by pedigree and microsatellite analyses. J. Hered. 98:378-381.
  21. Nei, M. 1987. Molecular Evolutionary Genetics. Columbia University Press, NY, USA.
  22. Pritchard, J. K., M. Stephens, and P. Donnelly. 2000. Inference of population structure using multilocus genotype data. Genetics 155:945-959.
  23. Rosenberg, N. A. 2004. Distruct: A program for the graphical display of population structure. Mol. Ecol. Notes 4:137-138.
  24. Tadano, R., M. Nunome, M. Mizutani, R. Kawahara-Miki, A. Fujiwara, S. Takahashi, T. Kawashima, K. Nirasawa, T. Ono, T. Y. Kono, and Y. Matsuda. 2014. Cost-effective development of highly polymorphic microsatellite in Japanese quail facilitated by next-generation sequencing. Anim. Genet. 45:881-884.