Invistigation of effictive populatioin, linkage disequilibrium and haplotype block structure in Azarbaijani breed buffalo using high density SNP markers

Document Type : Research Paper

Authors

1 M. Sc. Student, College of Agriculture & Natural Resources, University of Tehran, Karaj, Iran

2 Assistant Professor, College of Agriculture & Natural Resources, University of Tehran, Karaj, Iran

3 Professor, College of Agriculture & Natural Resources, University of Tehran, Karaj, Iran

4 Assistant Professor, Department of Animal Science, College of Agriculture Abureyhan, University of Tehran, Iran

Abstract

The aim of this study was to determine genomewide linkage disequilibrium (LD), Haplotype block and effective population size using the information obtained from 243 Azarbaijani breed buffalo using a high density SNP panel (Axiom® Buffalo Genotyping 90K). After quality control of SNP markers data, 62,141 SNP markers remained for identification of linkage disequiliberum, haplotype blocks and effective population size. LD was measured by the square of the correlation coefficient (r2) between alleles. The maximum LD measured by r2 varied from 0.25 to 0.29 at a distance of < 2.5 kb, and the minimum average values of r2 varied from 0.012 to 0.014 at distances ranging from 900 to 1000 kb, clearly showing that the average r2 reduced with the increase in SNP pair distances. Overall,  1693 blocks were observed through the genome. Eleven percent of all SNPs were clustered into haplotype blocks, covering 202 ±3.4 Mb of the total autosomal genome size. Effective population size (Ne) was estimated based on expected linkage disequilibrium. Ne was estimated to be 422 in our population.        

Keywords

References

  1. Alberts, C., Ribeiro-Paes, J., Aranda-Selverio, G., Cursino-Santos, J., Moreno-Cotulio, V., Oliveira, A., Porchia, B., Santos, W. & Souza, EBd. (2010). DNA extraction from hair shafts of wild Brazilian felids and canids. Genetics and Molecular Research, 9(4), 2429-2435.
  2. Amaral, A. J., Megens, H. J., Crooijmans, R. A., Heuven, H. M. & Groenen, M. M. (2008). Linkage     disequilibrium decay and haplotype block structure in the pig. Genetics, 179(1), 569-579.
  3. Ardlie, K. G., Kruglyak, L. & Seielstad, M. (2002). Patterns of linkage disequilibrium in the human genome. Nature Reviews Genetics, 3, 299-309.
  4. Barrett, J. C., Fry, B., Maller, J. & Daly, M. J. (2005). Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics, 21(2), 263-265.
  5. Browning, S. R. & Browning, B. L. (2007). Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering. The American Journal of Human Genetics, 81, 1084-1097.
  6. 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, 8-15.
  7. De La Vega, F. M., Dailey, D., Ziegle, J., Williams, J., Madden, D. & Gilbert, D. A. (2002). New generation pharmacogenomic tools: a SNP linkage disequilibrium Map, validated SNP assay resource, and high-throughput instrumentation system for large-scale genetic studies. Biotechniques, 48(50), 52-54.
  8. Espigolan, R., Baldi, F., Boligon, A. A., Souza, F. R., Gordo, D. G., Tonussi, R. L., Cardoso, D. F., Oliveira, H. N., Tonhati, H., Sargolzaei, M., Schenkel, F. S., Carvalheiro, R., Ferro, J. A. & Albuquerque, LG. (2013). Study of whole genome linkage disequilibrium in Nellore cattle. BMC Genomics, 14, 305-313.
  9. Farnir, F., Coppieters, W., Arranz, J., Berzi, P., Cambisano, N., Grisart, B., Karim, L., Marcq, F., Moreau, L., Mni, M., Nezer, C., Simon, P., Vanmanshoven, P., Wagenaar, D. & Georges, M. (2000). Extensive Genome-wide Linkage Disequilibrium in Cattle. Genome Research, 10, 220-227.
  10. Furrer, R., Nychka, D. & Sain, S. (2009). Fields: Tools for spatial data. R package version, 6(11).
  11. Gabriel, S. B., Schaffner, S. F., Nguyen, H., Moore, J. M., Roy, J. & Blumenstiel, B. (2002). The structure of haplotype blocks in the human genome. Science, 296(5576), 2225-2229.
  12. Hedrick, P. W. (2005). Genetics Of Populations. Jones and Bartlett Publishers. Biological Science (Jones and Bartlett) Series.
  13. Khatkar, M. S., Collins, A. & Cavanagh, J. A. L. (2006). A first generation metric linkage disequilibriu­m map of bovine chromosome 6. Genetics, 174, 79-85.
  14. Khatkar, M. S., Zenger, K. R. & Hobbs, M. (2007). A primary assembly of a bovine haplotype block map based on a 15,036 single nucleotide polymorphism panel genotyped in Holstein Friesian cattle. Genetics, 176, 763-772.
  15. Kim, E. S. & Kirkpatrick, B. W. (2009). Linkage disequilibrium in the North American Holstein population. Animal Genetics, 40, 279-88.
  16. Lu, D., Sargolzaei, M., Kelly, M., Li, C., Vander Voort, G., Wang, Z., Plastow, G., Moore, S. & Miller, S. P. (2012). Linkage disequilibrium in Angus, Charolais, and Crossbred beef cattle. Frontiers in Genetics, 3(152), 3389-3399.
  17. Mahon, G. A. T. & Cunningham, E. P. (1982). Inbreeding and the inheritance of fertility in the thoroughbred mare. Livestock Production Science, 9, 743-54.
  18. Marques, E., Schnabel, R. & Stothard, P. (2008). High density linkage disequilibrium maps of chromosome 14 in Holstein and Angus cattle. BMC Genetics, 9, 45-57.
  19. Mokhber, M. (2015). Genome-wide survey of signature of positive selection in Khuzestani and Mazandrani buffalo breeds. Ph.D. thesis. Faculty of Agriculture Tehran University, Iran. (In Farsi).
  20. Moradi, M. H., Nejati-Javaremi, A., Moradi-Shahrbabak, M., Dodds, K. G. & McEwan, J. (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), 1186-1201.
  21. Mokry, F. B., Buzanskas, M., de-Alvarenga, M. & Sargolzaei, M.  (2014). Linkage disequilibrium and haplotype block structure in a composite beef cattle breed. BMC Genomics, 10, 1186-1197.
  22. Patil, N., Berno, A. J., Hinds, D. A., Barrett, W. A., Doshi, J. M., Hacker, C. R., Kautzer, C. R., Lee, D. H., Thomas, D. J., Trulson, M. O., Vyas, K. R., Frazer, K. A., Fodor, S. P. & Cox, D. R. (2001). Blocks of limited haplotype diversity revealed by high-resolution scanning of human chromosome 21. Science, 294(5547), 1719-1723.
  23. 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, 346-356.
  24. Rahmaninia, J. (2015). Population structure analysis within Iranian Buffalo breeds Using dense SNP markers. Ph.D. thesis. Faculty of Agriculture Tehran University, Iran. (in Farsi)
  25. Villa-Angulo, R., Matukumalli, L. K., Gill, C. A., Choi, J., Van Tassell, C. P. & Grefenstette, J. J. (2009). High-resolution haplotype block structure in the cattle genome. BMC Genetic, 10(19), 1471-2156.
Iranian Journal of animal Science
Volume 49, Issue 2 - Serial Number 2
September 2018
Pages 247-255

Files

History

  • Receive Date: 20 August 2016
  • Revise Date: 04 November 2017
  • Accept Date: 04 November 2017

Share

How to cite

Statistics