Individual identification and population assignment with microsatellite markers in three Indian donkey populations


Abstract views: 106 / PDF downloads: 52

Authors

  • RAHUL BEHL ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana 132 001 India
  • S K NIRANJAN ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana 132 001 India
  • JYOTSNA BEHL ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana 132 001 India
  • R K VIJH ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana 132 001 India

https://doi.org/10.56093/ijans.v90i4.104204

Keywords:

Breed-assignment, Indian-donkeys, Individual identification

Abstract

Ability of the microsatellite markers for individual identification and their potential for breed assignment of individuals was evaluated in three Indian donkey populations. The probability of identity of two random individuals within a population (G1), taking into consideration all eleven loci was 5.91×10–13, 1.06×10–12 and 3.67×10–14 in Ladakhi, Spiti and Andhra-brown donkeys, respectively. Similarly, the probability of identity of two random individuals from two different populations (G2) between Spiti and Ladakhi donkeys, the two most closely related populations, was only 8.05×10–21 . However, the population assignment precision using this set of 11 loci, the correct assignments ranged between 73.08 (Andhra-brown) to 96% (Ladakhi) with frequency method and between 88.46 (Andhra-brown) to 100% (Ladakhi) with Baysian approach. These results suggest that this set of markers can be a promising tool for identification of individuals and their products. Although G2 values were higher than the G1 values but when this set was specifically evaluated for breed allocation purposes, our results indicated that it may require further substantiation before this set can be safely employed for breed/population allocation of individuals in Indian donkey populations.

Downloads

Download data is not yet available.

References

Aranguren-Mendez J, Jordana J and Gomez M. 2001. Genetic diversity in Spanish donkey breeds using microsatellite DNA markers. Genetics Selection Evolution 33: 433–42. DOI: https://doi.org/10.1186/1297-9686-33-4-433

Banks M A and Eichert W. 2000. Whichrun–a computer program for population assignment of individuals based on multilocus genotype data. Journal of Heredity 91: 87–89. DOI: https://doi.org/10.1093/jhered/91.1.87

Behl R, Behl J, Gupta N and Gupta S C. 2008. Evaluation of microsatellite genotyping based individual assignment in five Indian horse breeds. Indian Journal of Animal Sciences 78: 384–87.

Behl R, Niranjan S K, Behl J, Sharma H, Tantia M S, Arora R, Ranjan P, Bharati V K, Iqbal M, Vijh R K and Sharma A. 2019. Genetic characterization of Ladakhi donkeys using microsatellite markers. Indian Journal of Animal Sciences 89: 157–60.

Behl R, Niranjan S K, Behl J, Tantia M S, Arora R, Dharma-Rao M V, Reddy P P, Vijh R K and Sharma A. 2017a. Genetic characterization of Brown type donkeys of Andhra Pradesh. Indian Journal of Animal Sciences 87: 1102–05.

Behl R, Sadana D K, Behl J, Banerjee P, Joshi J, Vijh R K, Attri P N, Nadda S and Joshi B K. 2017b. Characterization and microsatellite analysis for genetic diversity and bottlenecks of Spiti donkeys. Indian Journal of Animal Sciences 87: 1221– 25.

Bjornstad G and Roed K H. 2001. Breed demarcation and potential for breed allocation of horses assessed by microsatellite markers. Animal Genetics 32: 59–65. DOI: https://doi.org/10.1046/j.1365-2052.2001.00705.x

Bjornstad G and Roed K H. 2002. Evaluation of factors affecting individual assignment precision using microsatellite data from horse breeds and simulated breed crosses. Animal Genetics 33: 264–70. DOI: https://doi.org/10.1046/j.1365-2052.2002.00868.x

Colli P G, Negrini R, Bomba L, Bigi D, Zambonelli P, Verini S A, Liotta L and Ajmore-Marron P. 2013. Detecting population structure and recent demographic history in endangered livestock breeds: the case of the Italian autochthonous donkeys. Animal Genetics 44: 69–78. DOI: https://doi.org/10.1111/j.1365-2052.2012.02356.x

Canon J, Checa M L, Carleos C, Vega-Pla J L, Vallejo M and Dunner S. 2000. The genetic structure of Spanish Celtic horse breeds inferred from microsatellite data. Animal Genetics 31: 39–48. DOI: https://doi.org/10.1046/j.1365-2052.2000.00591.x

Cornuet J M, Piry S, Luikart G, Estoup A and Solignac M. 1999. New methods employing multilocus genotypes to select or exclude populations as origins of individuals. Genetics 153: 1989–2009. DOI: https://doi.org/10.1093/genetics/153.4.1989

FAO. 2011. ISAG-FAO recommended microsatellite markers – Donkey (Appendix 7). FAO animal production and health guidelines (No 9)—Molecular genetic characterization of animal genetic resources, FAO Publications, Rome. pp. 78– 79.

Ivankovic A, Kavar T, Caput P, Mioc B, Pavic V and Dovc P. 2002. Genetic diversity of three donkey populations in the Croatian coastal region. Animal Genetics 33: 169–77. DOI: https://doi.org/10.1046/j.1365-2052.2002.00879.x

Jordana J, Folch P and Aranguren J A. 2001. Microsatellite analysis of genetic diversity in Catalonian donkey breeds. Journal of Animal Breeding and Genetics 118: 57–63. DOI: https://doi.org/10.1046/j.1439-0388.2001.00266.x

Krüger K, Gaillard C, Stranzinger G and Rieder S. 2005. Phylogenetic analysis and species allocation of individual equids using microsatellite data. Journal of Animal Breeding and Genetics 122(Suppl 1): 78–86. DOI: https://doi.org/10.1111/j.1439-0388.2005.00505.x

Nei M, Tajima F and Tateno Y. 1983. Accuracy of estimated phylogenetic trees from molecular data. Journal of Molecular Evolution 19: 153–70. DOI: https://doi.org/10.1007/BF02300753

Paetkau D, Calvert W, Stirling I and Strobeck C. 1995. Microsatellite analysis of population structure in Canadian polar bears. Molecular Ecology 4: 347–54. DOI: https://doi.org/10.1111/j.1365-294X.1995.tb00227.x

Piry S and Cornuet J M. 1998. GENECLASS, A program for assignation and exclusion using molecular markers, available at http: //www.ensam.inra.fr/CBGP. Campus International de Baillarguet, Cedex, France.

Rannala B and Mountain J L. 1997. Detecting immigration by using multilocus genotypes. Proceedings of National Academy of Sciences USA 94: 9197–221. DOI: https://doi.org/10.1073/pnas.94.17.9197

Tozaki T, Takezaki N, Hasegawa T, Ishida N, Kurusawa M, Saitou N and Mukoyama H. 2003. Microsatellite variation in Japanese and Asian horses and their phylogenetic relationship using a European horse outgroup. Journal of Heredity 94: 374–80. DOI: https://doi.org/10.1093/jhered/esg079

Van-Zeveran A, Peelman L, Van de Weghe A and Bouquet Y. 1995. A genetic study on four Belgian pig populations by means of seven microsatellite loci. Journal of Animal Breeding and Genetics 112: 191–204. DOI: https://doi.org/10.1111/j.1439-0388.1995.tb00558.x

Yeh F C, Boyle T, Rongcal Y, Ye Z and Xian J M. 1999. Popgene, version 3.31, a Microsoft Windows based freeware for population genetic analysis (https://sites.ualberta.ca/~fyeh/ popgene.html).

Zhang R F, Xie W M, Zhang T and Lei C Z. 2016. High polymorphism at microsatellite loci in the Chinese donkey. Genetics and Molecular Research 15: gmr15028291. DOI: https://doi.org/10.4238/gmr.15028291

Downloads

Submitted

2020-09-01

Published

2020-09-01

Issue

Section

Articles

How to Cite

BEHL, R., NIRANJAN, S. K., BEHL, J., & VIJH, R. K. (2020). Individual identification and population assignment with microsatellite markers in three Indian donkey populations. The Indian Journal of Animal Sciences, 90(4), 584-587. https://doi.org/10.56093/ijans.v90i4.104204
Citation