The pattern of linkage disequilibrium in three native Iranian sheep breeds

Document Type : Research Paper

Authors

1 M. Sc. Student, Professor, Department of Animal Science, University College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran

2 Professor, Department of Animal Science, University College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran

3 Associate Professor, Department of Animal Science, University College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran

4 Assistant Professor, Department of Animal Science, University of Arak, Iran

5 Assistant Professor, Department of Animal Science, University of Sari, Iran

6 Assistant Professor, Department of Animal Science, University College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran

Abstract

Understanding the pattern of linkage disequilibrium (LD) in different populations provides useful information for genomic selection (GS), genome wide association studies (GWAS) and identification of genetic architecture of traits by estimating the persistence of LD phase between markers and quantitative trait loci (QTL). The aim of this research was to estimate of the extent of LD in three Iranian native sheep breeds. Therefore, 186 blood samples were taken from three sheep breeds (96 Baluchi, 45 lori-Bakhtiari and 45 Zel) and genotyped by Illumina ovine 50K SNPChip, then linkage disequilibrium in any breed were measured using r2. The results showed that the highest average values of r2 at inter marker distance of less than 10Kb were 0.392± 0.323, 0.360±0.308 and 0.340±0.306 in Baluchi, Lori-Bakhtiari and Zel, respectively. The highest average values of r2 in autosome chromosomes of each breed were obtained for chromosome 24 and 25 in Baluchi, 9 and 21 in Lori-Bakhtiari and 23 and 24 in Zel. The amount of LD reduced with increasing the distance between markers, the extent of LD was less than 0.1 at inter marker distances greater than 100Kb. The comparison of correlation coefficients LD between different breeds showed a strong persistence of LD phase between Zel and Lori-Bakhtiari breeds which is probably due to recent common ancestors between these two breeds.  Generally, with increase amount of LD means that lower marker density in association studies will be required. The results of this study showed to achieve genomic prediction accuracy of 85%  (assuming there is no other accuracy limiting factor) and robust GWAS results, the density of markers must be higher than 50K SNPChip.

Keywords

References

  1. Alhaddad, H., Khan, R., Grahn, R. A., Gandolfi, B., Mullikin, J. C., Cole, S. A., ... & Lyons, L. A. (2013). Extent of linkage disequilibrium in the domestic cat, Felis silvestris catus, and its breeds. PLoS One, 8(1), e53537
  2. Al-Mamun, H. A., Clark, S., Kwan, P. & Gondro, C. (2015). Genome-wide linkage disequilibrium and genetic diversity in five populations of Australian domestic sheep. Genetics Selection Evolution, 47(1), 1.
  3. Ardlie, K. G., Kruglyak, L. & Seielstad, M. (2002). Patterns of linkage disequilibrium in the human genome. Nature Reviews Genetics, 3(4), 299-309.
  4. Badke, Y. M., Bates, R. O., Ernst, C. W., Schwab, C. & Steibel, J. P. (2012). Estimation of linkage disequilibrium in four US pig breeds. BMC genomics, 13(1), 1.
  5. Barrett, J. C., Fry, B., Maller, J. D. M. J. & Daly, M. J. (2005). Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics, 21(2), 263-265.
  6. BEAGLE 3.3.2 (2011). Department of Medicine Division of Medical Genetics University of Washington. Browning, B. L.
  7. Biegelmeyer, P., Gulias-Gomes, C. C., Caetano, A. R., Steibel, J. P. & Cardoso, F. F. (2016). Linkage disequilibrium, persistence of phase and effective population size estimates in Hereford and Braford cattle. BMC genetics, 17(1), 1.
  8. Bohmanova, J., Sargolzaei, M. & Schenkel, F. S. (2010). Characteristics of linkage disequilibrium in North American Holsteins. BMC genomics, 11(1), 1.
  9. Brito, L. F., Jafarikia, M., Grossi, D. A., Kijas, J. W., Porto-Neto, L. R., Ventura, R. V., ... & Schenkel, F. S. (2015). Characterization of linkage disequilibrium, consistency of gametic phase and admixture in Australian and Canadian goats. BMC genetics, 16(1), 1.
  10. Corbin, L. J., Blott, S. C., Swinburne, J. E., Vaudin, M., Bishop, S. C. & Woolliams, J. A. (2010). Linkage disequilibrium and historical effective population size in the Thoroughbred horse. Animal Genetics, 41(s2), 8-15.
  11. Fu, W., Dekkers, J. C., Lee, W. R. & Abasht, B. (2015). Linkage disequilibrium in crossbred and pure line chickens. Genetics Selection Evolution, 47(1), 1.
  12. Gabriel, S. B., Schaffner, S. F., Nguyen, H., Moore, J. M., Roy, J., Blumenstiel, B., ... & Liu-Cordero, S. N. (2002). The structure of haplotype blocks in the human genome. Science, 296(5576), 2225-2229.
  13. Gholizadeh, M., Rahimi-Mianji, G., Nejati-Javaremi, A., de Koning, D. J. & Jonas, E. (2014). Genome-wide association study to detect QTL for twinning rate in Baluchi sheep. Journal of genetics, 93(2), 489.
  14. Gouveia, J. J. D. S., Silva, M. V. G. B. D., Paiva, S. R. & Oliveira, S. M. P. D. (2014). Identification of selection signatures in livestock species. Genetics and molecular biology, 37(2), 330-342.
  15. Hayes, B. J. & Goddard, M. E. (2001). Prediction of total genetic value using genome-wide dense marker maps. Genetics, 157(4), 1819-1829.
  16. Jasielczuk, I., Gurgul, A., Szmatoła, T., Ząbek, T., Pawlina, K., Semik, E. & Bugno-Poniewierska, M. (2016). Linkage disequilibrium and haplotype block structure in Limousin, Simmental and native Polish Red cattle. Livestock Science, 191, 57-63.
  17. Karimi, K., Koshkoiyeh, A. E. & Gondro, C. (2015). Comparison of linkage disequilibrium levels in Iranian indigenous cattle using whole genome SNPs data. Journal of Animal Science and Technology, 57(1), 1.
  18. Khatkar, M. S., Nicholas, F. W., Collins, A. R., Zenger, K. R., Cavanagh, J. A., Barris, W., ... & Raadsma, H. W. (2008). Extent of genome-wide linkage disequilibrium in Australian Holstein-Friesian cattle based on a high-density SNP panel. BMC genomics, 9(1), 1.
  19. Lewontin, R. C. (1964). The interaction of selection and linkage. I. General considerations; heterotic models. Genetics, 49(1), 49-67.
  20. Mokry, F. B., Buzanskas, M. E., de Alvarenga Mudadu, M., do Amaral Grossi, D., Higa, R. H., Ventura, R. V., ... & da Silva, M. V. G. B. (2014). Linkage disequilibrium and haplotype block structure in a composite beef cattle breed. BMC genomics, 15(7), 1.
  21. 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(1), 1.
  22. Nilsen, H., Hayes, B., Berg, P. R., Roseth, A., Sundsaasen, K. K., Nilsen, K. & Lien, S. (2008). Construction of a dense SNP map for bovine chromosome 6 to assist the assembly of the bovine genome sequence. Animal genetics, 39(2), 97-104.
  23. Niu, H., Zhu, B., Guo, P., Zhang, W., Xue, J., Chen, Y., ... & Li, J. (2016). Estimation of linkage disequilibrium levels and haplotype block structure in Chinese Simmental and Wagyu beef cattle using high-density genotypes. Livestock Science, 190, 1-9.
  24. Pfahler, S. & Distl, O. (2015). Effective Population Size, Extended Linkage Disequilibrium and Signatures of Selection in the Rare Dog Breed Lundehund. PloS one, 10(4), e0122680.
  25. Purcell, S., Neale, B., Todd-Brown, K., Thomas, L., Ferreira, M. A., Bender, D., ... & Sham, P. C. (2007). PLINK: a tool set for whole-genome association and population-based linkage analyses. The American Journal of Human Genetics, 81(3), 559-575.
  26. Qanbari, S., Hansen, M., Weigend, S., Preisinger, R. & Simianer, H. (2010). Linkage disequilibrium reveals different demographic history in egg laying chickens. BMC Genetics, 11(1), 1.
  27. Qanbari, S., Pimentel, E. C. G., Tetens, J., Thaller, G., Lichtner, P., Sharifi, A. R. & Simianer, H. (2010). The pattern of linkage disequilibrium in German Holstein cattle. Animal genetics, 41(4), 346-356.
  28. Shrestha, J. N. B. & Fahmy, M. H. (2005). Breeding goats for meat production: a review: 1. Genetic resources, management and breed evaluation. Small Ruminant Research, 58(2), 93-106.
  29. Skipper, L., Wilkes, K., Toft, M., Baker, M., Lincoln, S., Hulihan, M., ... & Farrer, M. (2004). Linkage disequilibrium and association of MAPT H1 in Parkinson disease. The American Journal of Human Genetics, 75(4), 669-677.
  30. Wang, L., Sørensen, P., Janss, L., Ostersen, T. & Edwards, D. (2013). Genome-wide and local pattern of linkage disequilibrium and persistence of phase for 3 Danish pig breeds. BMC Genetics, 14(1), 115.
  31. Zygoyiannis, D. (2006). Sheep production in the world and in Greece. Small Ruminant Research, 62(1), 143-147.

Files

History

  • Receive Date: 04 December 2016
  • Revise Date: 20 January 2017
  • Accept Date: 22 January 2017

Share

How to cite

Statistics