Genetic characterization of Ladakhi donkeys using microsatellite markers
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Keywords:
Diversity, Donkey, Ladakh, MicrosatellitesAbstract
The donkeys of Ladakh region of Jammu and Kashmir, are well adapted to the cold, arid and hypoxic conditions of this region. The genomic DNA, isolated from 25 blood samples collected from these donkeys, were amplified by PCR using FAM and HEX labeled primers and resolved for alleles on automatic DNA sequencer. Total 20 loci of the horse origin were tested and only 13 loci gave scorable results. Rest of the loci either did not amplify well (HMS3, HMS7, ASB17 and COR22) or showed less than four alleles (HMS5, HMS6, HTG4), in the studied population. At the 13 loci included in the final analysis, the PCR product size ranged from 79–85 bp at locus HTG6 to 257–275 bp at locus COR18. The observed number of alleles varied from 4 (HTG15, HTG6, HTG10 and VHL20) to 9 (HTG7 and COR71) with a mean of 5.92±1.80. The observed heterozygosity ranged from 0.44 (VHL209) to 0.90 (AHT5) with a mean of 0.76±0.13. The mean genetic diversity estimate (FIS) was –0.076. The cumulative exclusion probability (PE) of these loci was 0.999838 indicating their suitability for parentage testing in these donkeys. The sign test, standardized differences test, the Wilcoxon test using the allelic frequency data under two phased mutation model and sequential mutation model at the studied loci as well as normal ‘L’ shaped distribution of the allelic frequency indicated the absence of any recent genetic bottleneck in donkeys of Ladakh region. When these donkeys were compared to Spiti donkeys of Himachal Pradesh and Brown type donkeys of Andhra Pradesh on the basis of allelic frequency data at these loci, they showed Nei’s minimum genetic distances of 0.115 and 0.165, respectively, from these population.Downloads
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
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.
Botstein D, White R L, Skolnick M and Davies R W. 1980. Construction of a genetic linkage map in man using restriction length polymorphism. American Journal of Human Genetics 32: 314–31.
Colli, Perrotta 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
Cornuet J M and Luikart G. 1996. Description and power analysis of two tests for detecting recent population bottlenecks from allelic frequency data. Genetics 144: 2001–14. DOI: https://doi.org/10.1093/genetics/144.4.2001
Goldstein D B and Schlotterer C. 1999. Microsatelltes: evolution and applications. Oxford University Press, Oxford.
Goudet J. 2001. Fstat, version 2.9.3. A program to estimate and test gene diversities and fixation indices (http://www.unil.ch/ popgen/softwares/fstat.html). Lausanne University, Lausanne, Switzerland.
ICAR-NBAGR Newsletter. 2017. Characterization of Ladakhi donkeys. ICAR-NBAGR Newsletter 14(1): 2.
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
Jamieson A and Taylor C S. 1997. Comparison of three probability formulae for parentage exclusion. Animal Genetics 28: 397– 400. DOI: https://doi.org/10.1111/j.1365-2052.1997.00186.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
Langella O. 2002. POPULATIONS, version 1.2.31. Available from http://www.pge.cnrs-gif.fr/bioinformatics/populations/ Livestock Census. 2012. 19th Livestock Census. Department of Animal Husbandry, Dairying and Fisheries, Ministry of Agriculture, Government of India.
Luikart G, Allendorf F W, Cornuet J M and Sherwin W B. 1998.Distortion of allele frequency distribution provides a test for recent population bottlenecks. Journal of Heredity 89: 238– 47. DOI: https://doi.org/10.1093/jhered/89.3.238
Nei M. 1973. The theory and estimation of genetic distance. Genetic Structure of Populations. (Ed.) Morton N E. University Press of Hawaii, Honululu. Pp 45–54.
Piry S, Luikart G and Cornuet J M. 1999. Bottleneck: a computer program for detecting recent reductions in effective population size using allele frequency data (http://www1.montpellier. inra.fr/CBGP/softwares/Bottleneck). Journal of Heredity 90: 502–03. DOI: https://doi.org/10.1093/jhered/90.4.502
Raymond M and Rousset F. 1995. Genepop, version 3.4. Population genetic software for exact tests and ecumenicism (http://biomed.curtin.edu.au/genepop). Journal of Heredity 86: 248–49. DOI: https://doi.org/10.1093/oxfordjournals.jhered.a111573
Reynolds J, Weir B S and Cockerham C C. 1983. Estimation of the coancestry coefficients: basis for a short term genetic distance. Genetics 105: 769–79. DOI: https://doi.org/10.1093/genetics/105.3.767
Rosenbam S, Costa V, Al-Araimi N, Kefena E, Abdel-Moniem A S, Abdalla M A, Bakhiet A and Pereira-Beja A. 2015. Genetic diversity of donkey populations from putative centers of domestication. Animal Genetics 46: 30–36. DOI: https://doi.org/10.1111/age.12256
Rousset F. 2008. Genepop, 007: a complete reimplementation of the Genepop software for Windows and Linux (http://genepop.curtin.edu.au). Molecular Ecology Resources 8: 103–06. DOI: https://doi.org/10.1111/j.1471-8286.2007.01931.x
Takezaki N and Nei M. 1996. Genetic distances and reconstruction of phylogenetic trees from microsatellite DNA. Genetics 144: 389–99. DOI: https://doi.org/10.1093/genetics/144.1.389
Weir B S and Cockerham C C. 1984. Estimating F statistics for analysis of population structure. Evolution 38: 1358–70. DOI: https://doi.org/10.1111/j.1558-5646.1984.tb05657.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).
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