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Moradi, M., Farahani, A., Nejati-Javaremi, A. (2017). Genome-wide evaluation of effective population size in some Iranian sheep breeds using linkage disequilibrium information. , 48(1), 39-49. doi: 10.22059/ijas.2017.213736.653464
Mohammad Hossein Moradi; Amir Hossein Farahani; Ardeshir Nejati-Javaremi. "Genome-wide evaluation of effective population size in some Iranian sheep breeds using linkage disequilibrium information". , 48, 1, 2017, 39-49. doi: 10.22059/ijas.2017.213736.653464
Moradi, M., Farahani, A., Nejati-Javaremi, A. (2017). 'Genome-wide evaluation of effective population size in some Iranian sheep breeds using linkage disequilibrium information', , 48(1), pp. 39-49. doi: 10.22059/ijas.2017.213736.653464
Moradi, M., Farahani, A., Nejati-Javaremi, A. Genome-wide evaluation of effective population size in some Iranian sheep breeds using linkage disequilibrium information. , 2017; 48(1): 39-49. doi: 10.22059/ijas.2017.213736.653464

Genome-wide evaluation of effective population size in some Iranian sheep breeds using linkage disequilibrium information

علوم دامی ایران
Article 5, Volume 48, Issue 1, June 2017, Pages 39-49    PDF (628.27 K)
Document Type: Research Paper
DOI: 10.22059/ijas.2017.213736.653464
Authors
Mohammad Hossein Moradi* 1; Amir Hossein Farahani1; Ardeshir Nejati-Javaremi2
1Assistant Professor, Department of Animal Science, Faculty of Agriculture and Natural Resources, Arak University, Arak 38156-8-8349, Iran
2Associate Professor, Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Iran
Abstract
The aim of the present study was to estimate the effective population size (Ne) in some Iranian sheep breeds using genome wide SNP data. A total of 217 animal samples consisting of 45, 37, 34, 35, 45 and 11 samples from Zel, Afshari, Moghani, Qezel, Lori-Bakhtiari and a wild-type of Iranian sheep breeds, genotyped by Illumina OvineSNP50K Beadchip assay were used in this study respectively. This study has been performed in collaboration with the Ovine HapMap project. The Ne was estimated using linkage disequilibrium across 4 up to 3500 generations ago. The result of principal component analysis (PCA) indicated that all breeds will be separated from each other in the first two principal components. Average expected and observed heterozygosity for different breeds ranged 0.36-0.37 and 0.37-0.43 respectively. The Ne results showed a decreasing trend over the last 3500 generations for all breeds, with an increasingly slope since about last 550 generations. The Ne in Iranian sheep breeds for 4 generations ago were ranged from 9 up to 89. The highest historically effective population size was found for Zel breed (89 heads) and the lowest for Afshari (44 heads) and wild_type (9 heads) sheep breeds. Generally, the results indicated that although a considerable genetic variation exists in these populations, however Ne has been decreased strongly in Iranian sheep breeds especially in Afshari and wild-type sheep breeds during recent years and designing of appropriate programs is necessary to conserve remaining purebred animals of these indigenous sheep breeds. 
Keywords
effective population size; genetic conservation; genome wide evaluation; Iranian sheep breeds
References
  1. Al-Mamun, H. A., Clark, S. A., Kwan, P. & Gondro, C. (2015). Genome-wide linkage disequilibrium and genetic diversity in five populations of Australian domestic sheep. Genetic Selection and Evolution, 47, 90.
  2. Barbato, M., Wengel, P. O., Tapio, M. & Bruford, M. W. (2015). SNeP: a tool to estimate trends in recent effective population size trajectories using genome-wide SNP data. Frontier in Genetics, 6, 109.
  3. Browning, B. L. & Browning, S. R. (2009). A unified approach to genotype imputation and haplotype-phase inference for large data sets of trios and unrelated individuals. American Journal of Human Genetics, 84, 210-223.
  4. Burren, A., Signer-Hasler, H., Neuditschko, M., Tetens, J., Kijas, J. W., Drögemüller, C. & et al. (2014). Fine-scale population structure analysis of seven local Swiss sheep breeds using genome-wide SNP data. Animal Genetic Resources, 55, 67-76.
  5. Corbin, L. J., Liu, A. Y. H., Bishop, S. C. & Woolliams, J. A. (2012). Estimation of historical effective population size using linkage disequilibria with marker data. Journal of Animal Breeding Genetics, 129, 257-270.
  6. Danchin-Burge, C., Palhière, I., François, D., Bibé, B., Leroy, G. & Verrier, E. (2010). Pedigree analysis of seven small French sheep populations and implications for the management of rare breeds. Journal of Animal Science, 88, 505-516.
  7. Esmaeilkhanian, E. & Banabazi, M. H. (2006). Genetic variation within and between five Iranian sheep populations using microsatellite markers. Pakistan Journal of Biological Science, 9(3), 2488-2492.
  8. Flury, C., Tapio, M., Sonstegard, T., Drögemüller, C., Leeb, T., Simianer, H. & et al., (2010). Effective population size of an indigenous Swiss cattle breed estimated from linkage disequilibrium. Journal of Animal Breeding Genetics, 127, 339-347.
  9. Frankham, R. (2005). Genetics and extinction. Biological Conservation, 126, 131-140.
  10. Frankham, R., Bradshaw, C. J. A.  & Brook, B. W. (2014). Genetics in conservation and management: Revised recommendations for the 50/500 rules, Red List criteria and population viability analyses. Biological Conservation, 170, 56-63.
  11. Ghafouri-Kesbi, F. (2012). Using pedigree information to study genetic diversity and reevaluating a selection program in an experimental flock of Afshari sheep. Archiv fur Tierzucht, 55: 375-384.
  12. Hayes, B. J., Visscher, P. M., McPartlan, H. C. & Goddard, M. E. (2003). Novel multilocus measure of linkage disequilibrium to estimate past effective population size. Genome Research, 13, 635–643.
  13. Helms, C. (1990). Salting out Procedure for Human DNA extraction. In: The Donis-Keller Lab - Lab Manual Homepage. From http://humgen.wustl.edu/hdk_lab_manual/dna/dna2.html.
  14. Hill, W. G. & Robertson, A. (1968). Linkage Disequilibrium in Finite Populations. Theoretical Applied Genetics, 38, 226-231.
  15. Hill, W. G. (1981). Estimation of effective population size from data on linkage disequilibrium. Genetic Resources, 38, 209-216.
  16. Karimi, K., Esmaeelizadeh, A. K. & Asadi Fozi, M. (2015). Estimation of effective population size in Sarabi cattle based on single nucleotide polymorphism markers. Iranian Journal of Animal Science, 46(3), 335-343. (in Farsi)
  17. Kijas, J. W., Lenstra, J. A., Hayes, B. J., Boitard, S., Porto Neto, L. R., San Cristobal, M. & et al. (2012). Genome-wide analysis of the world’s sheep breeds reveals high levels of historic mixture and strong recent selection. PLoS Bio, 10, e1001258.
  18. Kijas, J. W., Townley, D., Dalrymple, B. P., Heaton, M. P., Maddox, J. F. & et al. (2009). A genome wide survey of SNP variation reveals the genetic structure of sheep breeds. PLoS ONE, 4, e4668.
  19.  Lachance, J. & Tishkoff, S. A. (2013). SNP ascertainment bias in population genetic analyses: Why it is important, and how to correct it. Bioessays, 35 (9), 780-786.
  20. Lee, S. H., Cho, Y. M., Lim, D., Kim, H. C., Choi, B. H. & et al. (2011). Linkage disequilibrium and effective population size in Hanwoo Korean cattle. Asian Australas Journal of Animal Science, 24, 1660-1665.
  21. Leroy, G., Mary-Huard, T., Verrier, E., Danvy, S., Charvolin, E. & Danchin-Burge, C. (2013). Methods to estimate effective population size using pedigree data: examples in dog, sheep, cattle and horse. Genetic Selection and Evolution, 45, 1-10.
  22. Marquez, G. C., Speidel, S. E., Enns, R. M. & Garrick, D. J. (2010). Genetic diversity and population structure of American Red Angus cattle. Journal of Animal Science, 88, 59-68.
  23. Mohammadi, A. R., Abbasi, M. A., Moghaddam, A. A. & Zare Shahneh A. (2009). Estimation of growth traits in Iranian Afshari sheep breed under rural production system. Journal of Animal and Veterinary advances, 8(7), 1449-54.
  24. Mokhtari, M. S., Miraei-Ashtiani, S. R., Jafaroghli, M. & Gutiérrez, J. P. (2015). Studying genetic diversity in Moghani sheep using pedigree analysis. Journal of Agricultural Science and Technology, 17, 1151-1160.
  25. Moradi, M. H., Nejati-Javaremi, A., Moradi-Shahrbabak, M., Dodds K. G. & McEwan. J. C. (2012). Genomic scan of selective sweeps in thin and fat tail sheep breeds for identifying of candidate regions associated with fat deposition. BMC Genetics, 13, 10.
  26. Moradi, M. H., Rostamzadeh, J., Rashidi, A., Vahabi, K. & Farahmand, H. (2013). Analysis of genetic diversity in Iranian Mohair goat and its color types using Inter Simple Sequence Repeat (ISSR) markers. Journal of Agricultural Communications, 1, 2.
  27. Nei, M. (1978). Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics, 89, 583-590.
  28. Ohta, T. & Kimura, M. (1971). Linkage disequilibrium between two segregating nucleotide sites under the steady flux of mutations in a finite population. Genetics, 68, 571-580.
  29. Pons, A. L., Landi, V., Martinez, A. & Delgado, J. V. (2015). The biodiversity and genetic structure of Balearic sheep breeds. Journal of Animal Breeding Genetics, 132(3), 268-76.
  30. Purcell, S., Neale, B., Todd-Brown, K., Thomas, L., Ferreira, M. A. R., Bender, D. & et al. (2007). PLINK: a tool set for whole-genome association and population-based linkage analyses. American Journal of Human Genetics, 81, 559-575.
  31. Qanbari, S.,  Pimentel, E. C., Tetens, J., Thaller, G., Lichtner, P., Sharifi, A. R. & Simianer, H. (2010). The pattern of linkage disequilibrium in German Holstein cattle. Animal Genetics, 41, 346-356.
  32. Saatchi, M., McClure, M. C., McKay, S. D., Rolf, M. M., Kim, J. & et al. (2011). Accuracies of genomic breeding values in American Angus beef cattle using K-means clustering for cross-validation. Genetic Selection and Evolution, 43, 40.
  33. Sved, J. A. (1971). Linkage disequilibrium and homozygosity of chromo-some segments in finite populations. Theoretical Population Biology, 141, 125-141.
  34. Tahmoorespur, M. & Sheikhloo, M. (2011). Pedigree analysis of the closed nucleus of Iranian Baluchi sheep. Small Ruminant Research, 99, 1-6.
  35. Tenesa, A., Navarro, P.,  Hayes, B. J.,  Duffy, D. L., Clarke, G. M., Goddard, M. E. &  Visscher P. M. (2007). Recent human effective population size estimated from linkage disequilibrium. Genome Research, 17, 520-526.
  36. Teo, Y. Y., Fry, A. E., Clark, T. G., Tai, E. S. & Seielstad, M. (2007). On the usage of HWE for identifying genotyping errors. Annals of Human Genetics, 71, 701-703.
  37. Uimari, P. & Tapio, M. (2011). Extent of linkage disequilibrium and effective population size in Finnish Landrace and Finnish Yorkshire pig breeds. Journal of Animal Science, 89, 609-614.
  38. Villa-Angulo, R., Matukumalli, L. M., Gill, C. A., Choi, G., Van Tassle, C. P. & Grefenstette, J. J. (2009). High-resolution haplotype block structure in the cattle genome. BMC Genetics, 10, 19.
  39. Weir, B. S. & Hill, W. G. (1980). Effect of mating structure on variation in linkage disequilibrium. Genetics, 95, 477-488.
  40. Zeder, M. A. (1999). Animal domestication in the Zagros: a review of past and current research. Pale´orient, 25, 11-26.
  41. Zhao, F., Wang, G., Zeng, T., Wei, C., Zhang, L.&et al. (2014). Estimations of genomic linkage disequilibrium and effective population sizes in three sheep populations. Livestock Science, 170, 22-2.
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