Skip to main content
SpringerLink
Log in

Mining and Polymorphic Analysis of Di-Nucleotide Microsatellites from Yak Genome

  • ANIMAL GENETICS
  • Published:
Russian Journal of Genetics Aims and scope Submit manuscript

Abstract

Bos grunniens (Yak) are the most important domesticated species, which adapt to the alpine climates on the Qinghai–Tibetan Plateau for thousands of years, and the researches on their genetic resources has been greatly restricted due to lack of identification and mining DNA markers from yak genome, especially effective and reliable microsatellite markers (MS). Thirty polymorphic microsatellite loci, each with di-nucleotide repeat motifs, were identified and used to analyze polymorphisms of sampled Maiwa yak population. These microsatellites comprised of 18 perfect repeats (60%), 10 imperfect repeats (33.33%) and 2 compound repeats (6.67%). All the loci exhibited different level of polymorphisms in a sampled breeding population of Maiwa yak. The Ho (observed heterozygosity) for different locus varied from 0.0000 to 0.9333 and the PIC (polymorphic information content) arranged from 0.1971 to 0.8611. The genotyping of all yak individuals and population structure analysis revealed the monomorphic genetic structure for the sampled yak population. The newly characterized microsatellites from yak genome will display potential values in molecular breeding and developing of genetic resources of yak population in the future.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1.
Fig. 2.

Similar content being viewed by others

REFERENCES

  1. Cai, X., Mipam, T., Zhang, H., and Yue, B., Abundant variations of MC4R gene revealed by phylogenies of yak (Bos grunniens) and other mammals, Mol. Biol. Rep., 2011, vol. 38, no. 4, pp. 2733—2738.

    Article  CAS  PubMed  Google Scholar 

  2. Behl, R., Behl, J., Gupta, N., and Gupta, S.C., Genetic relationships of five Indian horse breeds using microsatellite markers, Animal, 2007, vol. 1, no. 4, pp. 483—488.

    Article  CAS  PubMed  Google Scholar 

  3. Boitard, S., Chevalet, C., Mercat, M.J., et al., Genetic variability, structure and assignment of Spanish and French pig populations based on a large sampling, Anim. Genet., 2010, vol. 41, no. 8, pp. 608—618.

    Article  CAS  PubMed  Google Scholar 

  4. Ren, D.R., Yang, Q.Y., Ye, J.H., et al., Strong heterozygote deficit in Tibetan Mastiff of China based on microsatellite loci, Animal, 2009, vol. 3, no. 9, pp. 1213—1215.

    Article  CAS  PubMed  Google Scholar 

  5. Gómez, Y.M., Fernandez, M., Rivera, D., et al., Genetic characterization of Colombian Bahman cattle using microsatellites markers, Genetika, 2013, vol. 49, no. 7, pp. 846—855.

    PubMed  Google Scholar 

  6. Suh, S., Kim, Y.S., Cho, C.Y., et al., Assessment of genetic diversity, relationships and structure among Korean native cattle breeds using microsatellite markers, Asian-Australas. J. Anim. Sci., 2014, vol. 27, no. 11, pp. 1548—1553.

    Article  PubMed  PubMed Central  Google Scholar 

  7. Nguyen, T.T., Genini, S., Ménétrey, F., et al., Application of bovine microsatellite markers for genetic diversity analysis of Swiss yak (Poephagus grunniens), Anim. Genet., 2005, vol. 36, no. 6, pp. 484—489.

    Article  CAS  PubMed  Google Scholar 

  8. Tu, P.A., Lin, D.Y., Li, G.F., et al., Characterization of the genetic diversity and population structure for the yellow cattle in Taiwan based on microsatellite markers, Anim. Biotechnol., 2014, vol. 25, no. 4, pp. 234—249.

    Article  PubMed  Google Scholar 

  9. Cai, X., Mipam, T., Zhao, F.F., and Sun, L., Isolation and characterization of polymorphic microsatellites in the genome of yak (Bos grunniens), Mol. Biol. Rep., 2014, vol. 41, no. 6, pp. 3829—3837.

    Article  CAS  PubMed  Google Scholar 

  10. Müllenbach, R., Lagoda, P.J., and Welter, C., An efficient salt chloroform extraction of DNA from blood and tissues, Trends Genet., 1989, vol. 5, no. 12, p. 391.

    PubMed  Google Scholar 

  11. Li, Q. and Wan, J.M., SSRHunter: development of a local searching software for SSR sites. Yi Chuan, 2005, vol. 27, no. 5, pp. 808—810.

    PubMed  Google Scholar 

  12. Rozen, S. and Skaletsky, H.J., PRIMER 3 on the WWW for general users and for biologist programmers, Methods Mol. Biol., 2000, vol. 132, pp. 365—386.

    CAS  PubMed  Google Scholar 

  13. Kalinowski, S.T., Taper, M.L., and Marshall, T.C., Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment, Mol. Ecol., 2007, vol. 16, no. 5, pp. 1099—1106.

    Article  PubMed  Google Scholar 

  14. Pritchard, J.K., Stephens, M., and Donnelly, P., Inference of population structure using multilocus genotype data, Genetics, 2000, vol. 155, no. 2, pp. 945—959.

    CAS  PubMed  PubMed Central  Google Scholar 

  15. Evanno, G., Regnaut, S., and Goudet, J., Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study, Mol. Ecol., 2005, vol. 14, no. 8, pp. 2611—2620.

    Article  CAS  PubMed  Google Scholar 

  16. Leeflang, E.P., Zhang, L., Tavaré, S., et al., Single sperm analysis of the trinucleotide repeats in the Huntington’s disease gene: quantification of the mutation frequency spectrum, Hum. Mol. Genet., 1995, vol. 4, no. 9, pp. 1519—1526.

    Article  CAS  PubMed  Google Scholar 

  17. Maurer, D.J., O’Callaghan, B.L., and Livingston, D.M., Orientation dependence of trinucleotide CAG repeat instability in yeast, Mol. Cell Biol., 1996, vol. 16, no. 12, pp. 6617—6622.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Trans, H.T., Keen, J.D., Kricker, M., et al., Hypermutability of homonucleotide runs in mismatch repair and DNA polymerase proofreading yeast mutants, Mol. Cell Biol., 1997, vol. 17, no. 5, pp. 2859—2865.

    Article  Google Scholar 

  19. Wierdle, M., Dominska, M., and Petes, T.D., Microsatellite instability in yeast: dependence on the length of the microsatellite, Genetics, 1997, vol. 146, no. 3, pp. 769—779.

    Google Scholar 

  20. Lovett, S.T., Drapkin, P.T., Sutera, V.A., Jr., and Gluckman-Peskind, T.J., A sister-stand exchange mechanism for recA-independent deletion of repeated DNA sequences in Escherchia coli, Genetics, 1993, vol. 135, no. 3, pp. 631—642.

    CAS  PubMed  PubMed Central  Google Scholar 

  21. D’Alencon, E., Petranovic, M., Michel, B., et al., Copy-choice illegitimate DNA recombination revisited, EMBO J., 1994, vol. 13, no. 11, pp. 2725—2734.

    Article  PubMed  PubMed Central  Google Scholar 

  22. Bierne, H., Vilette, D., Ehrlich, S.D., and Michel, B., Isolation of a dnaE mutation which enhances RecA-independent homologous recombination in the Escherichia coli chromosome, Mol. Mocrobiol., 1997, vol. 24, no. 6, pp. 1225—1234.

    Article  CAS  Google Scholar 

  23. Shinde, D., Lai, Y., and Sun, F., Taq DNA polymerase slippage mutation rates measured by PCR and quasi-likelihood analysis: (CA/GT)n and (A/T)n microsatellites, Nucleic Acids Res., 2003, vol. 31, no. 3, pp. 974—980.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Funding

This work was supported by the grants from China Postdoctoral Science Foundation funded project (no. 20090461336) and China Postdoctoral Special Science Foundation funded project (no. 201003703).

Author information

Authors and Affiliations

  1. School of Life Science and Engineering, Southwest University of Science and Technology, 621010, Mianyang, Sichuan, China

    B. Asma, F. Zhao, X. Cai & X. Luo

Authors
  1. B. Asma
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. F. Zhao
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. X. Cai
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. X. Luo
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to X. Cai or X. Luo.

Ethics declarations

Conflict of interests. The authors declare that they have no conflict of interest.

Statement on the welfare of animals. All applicable international, national, and/or institutional guidelines for the care and use of animals were followed.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Asma, B., Zhao, F., Cai, X. et al. Mining and Polymorphic Analysis of Di-Nucleotide Microsatellites from Yak Genome. Russ J Genet 55, 891–898 (2019). https://doi.org/10.1134/S1022795419070044

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1134/S1022795419070044

Keywords:

Search

Navigation