Genes & Genomics

, Volume 37, Issue 9, pp 759–765 | Cite as

Genome-wide linkage disequilibrium analysis of indigenous cattle breeds of Ethiopia and Korea using different SNP genotyping BeadChips

  • Zewdu Edea
  • Hailu Dadi
  • Tadelle Dessie
  • Seung-Hwan Lee
  • Kwan-Suk Kim
Research Article

Abstract

Knowledge of the extent of linkage disequilibrium (LD) between markers is crucial for determining the number of markers required for quantitative trait loci mapping, genome-wide association studies, and application of marker-assisted selection. In this study, we surveyed genome-wide LD using three genotyping BeadChips (9, 50, and 80 K) in 11 indigenous Ethiopian cattle populations and the Korean (Hanwoo) cattle breed. The overall mean r2 values were 0.05 ± 0.12, 0.12 ± 0.20, and 0.20 ± 0.24 in the Ethiopian cattle populations for the 9, 50, and 80 K genotyping BeadChips, respectively. In Hanwoo cattle, these values were respectively 0.06 ± 0.13, 0.15 ± 0.23, and 0.15 ± 0.26. The level of LD was significantly affected by breed, genotyping BeadChip, and chromosome (P < 0.0001). For Ethiopian cattle populations, a moderate level of LD (r2 = 0.22) extended at marker distances of 20–40 kb for the indicine-derived 80 K BeadChip, whereas it was only 0.14 for the 50 K BeadChip. As a consequence of the moderate r2, genome-wide association studies in Ethiopian cattle populations require 75,000–150,000 indicine-derived SNPs (with a MAF ≥ 0.05). We suggest that indicine-derived SNPs maybe more suitable for genome-wide association studies and genomic selection in indigenous Ethiopian (or African) cattle populations.

Keywords

Ethiopian cattle Hanwoo Linkage disequilibrium Single-nucleotide polymorphism 

Supplementary material

13258_2015_304_MOESM1_ESM.doc (87 kb)
Supplementary material 1 (DOC 87 kb)

References

  1. Arias JA, Keehan M, Fisher P, Coppieters W, Spelman R (2009) A high density linkage map of the bovine genome. BMC Genet 10:18PubMedCentralCrossRefPubMedGoogle Scholar
  2. Boichard D, Chung H, Dassonneville R, David X, Eggen A, Fritz S, Gietzen KJ, Lawley CT, Sonstegard TS, Van Tassell CP et al (2012) Design of a bovine low-density SNP array optimized for imputation. PLoS One 7:e34130PubMedCentralCrossRefPubMedGoogle Scholar
  3. Dadi H, Lee SH, Lee SS, Park C, Kim KS (2014) Inter- and Intra- population genetic divergence of East Asian cattle populations: focusing on Korean cattle. Genes Genom 36:261–265CrossRefGoogle Scholar
  4. Edea Z, Dadi H, Kim SW, Dessie T, Lee T, Kim H, Kim JJ, Kim KS (2013) Genetic diversity, population structure and relationships in indigenous cattle populations of Ethiopia and Korean Hanwoo breeds using SNP markers. Front Genet 4:35PubMedCentralCrossRefPubMedGoogle Scholar
  5. Edea Z, Dadi H, Kim SW, Park JH, Shin GH, Dessie T, Kim KS (2014) Linkage disequilibrium and genomic scan to detect selective loci in cattle populations adapted to different ecological conditions in Ethiopia. J Anim Breed Genet 131:358–366CrossRefPubMedGoogle Scholar
  6. Edea Z, Bhuiyan MAS, Dessie T, Rothschild MF, Dadi H, Kim KS (2015) Genome-wide genetic diversity, population structure and admixture analysis in African and Asian cattle breeds. Animal 9:218–226CrossRefPubMedGoogle Scholar
  7. Espigolan R, Baldi F, Boligon AA, Souza RP, Gordo GM, Tonussi RL, Cardoso DF, Oliveira HN, Tonhati H, Sargolzaei M et al (2013) Study of whole genome linkage disequilibrium in Nellore cattle. BMC Genomics 14:305PubMedCentralCrossRefPubMedGoogle Scholar
  8. Farnir F, Coppieters W, Arranz JJ (2000) Extensive genome-wide linkage disequilibrium in cattle. Genome Res 10:220–227CrossRefPubMedGoogle Scholar
  9. García-Gámez E, Sahana G, Gutiérrez-Gil B, Arranz JJ (2012) Linkage disequilibrium and inbreeding estimation in Spanish Churra sheep. BMC Genet 13:43PubMedCentralCrossRefPubMedGoogle Scholar
  10. Goddard ME, Hayes BJ (2012) Genome-wide association studies and linkage disequilibrium in cattle. In: Womack JE (ed) Bovine genomics. Wiley-Blackwell, Oxford. doi:10.1002/9781118301739.ch13 Google Scholar
  11. Hayes BJ, Chamberlain AJ, Maceachern S, Savin K, McPartlan H, MacLeod I, Sethuraman L, Goddard ME (2009) A genome map of divergent artificial selection between Bos taurus dairy cattle and Bos Taurus beef cattle. Anim Genet 40:176–184CrossRefPubMedGoogle Scholar
  12. Hill WG, Robertson A (1986) Linkage disequilibrium in finite populations. Theor Appl Genet 38:226–231CrossRefGoogle Scholar
  13. Khatkar MS, Nicholas FW, Collins AR, Zenger KR, Cavanagh JA, Barris W, Schnabel RD, Taylor JF, Raadsma HW (2008) Extent of genome-wide linkage disequilibrium in Australian Holstein-Friesian cattle based on a high-density SNP panel. BMC Genomics 9:187PubMedCentralCrossRefPubMedGoogle Scholar
  14. Kim ES, Berger PJ, Kirkpatrick BW (2009) Genome-wide scan for bovine twinning rate QTL using linkage disequilibrium. Anim Genet 40:300–307CrossRefPubMedGoogle Scholar
  15. Lee SH, Cho YM, Lim D, Kim HC, Choi BH, Park HS, Kim OH, Kim S, Kim TH, Yoon D et al (2011) Linkage disequilibrium and effective population size in Hanwoo Korean cattle. Asian-Aust J Anim Sci 24:1660–1665CrossRefGoogle Scholar
  16. Lee SH, Park BH, Sharma A, Dang CG, Lee SS, Choi TJ, Choy YH, Kim HC, Jeon KJ, Kim SD et al (2014) Hanwoo cattle: origin, domestication, breeding strategies and genomic selection. J Anim Sci Technol 56:2PubMedCentralCrossRefPubMedGoogle Scholar
  17. Lu D, Sargolzaei M, Kelly M, Li C, Voort GV, Wang Z, Plastow G, Moore S, Miller SP (2012) Linkage disequilibrium in Angus, Charolais, and Crossbred beef cattle. Front Genet 3:152PubMedCentralCrossRefPubMedGoogle Scholar
  18. Meuwissen TH, Hayes BJ, Goddard ME (2001) Prediction of total genetic value using genome-wide dense marker maps. Genetics 157:1819–1829PubMedCentralPubMedGoogle Scholar
  19. Porto-Neto LR, Kijas JW, Reverter A (2014) The extent of linkage disequilibrium in beef cattle breeds using high-density SNP genotypes. Genet Sel Evol 46:22PubMedCentralCrossRefPubMedGoogle Scholar
  20. Prasad A, Schnabel RD, McKay SD, Murdoch B, Stothard P, Kolbehdari D, Wang Z, Taylor JF, Moore SS (2008) Linkage disequilibrium and signatures of selection on chromosomes 19 and 29 in beef and dairy cattle. Anim Genet 39:597–605PubMedCentralCrossRefPubMedGoogle Scholar
  21. Qanbari S, Pimentel EC, Tetens J, Thaller G, Lichtner P, Sharifi AR, Simianer H (2010) The pattern of linkage disequilibrium in German Holstein cattle. Anim Genet 41:346–356PubMedGoogle Scholar
  22. Tenesa A, Knott SA, Ward D, Smith D, Williams JL, Visscher PM (2003) Estimation of linkage disequilibrium in a sample of the United Kingdom dairy cattle population using unphased genotypes. J Anim Sci 81:617–623PubMedGoogle Scholar
  23. The Bovine HapMap Consortium (2009) Genome-wide survey of SNP variation uncovers the genetic structure of cattle breeds. Science 324:528–532PubMedCentralCrossRefGoogle Scholar
  24. Wiggans GR, Cooper TA, Vanraden PM, Olson KM, Tooker ME (2012) Use of the Illumina Bovine 3 K BeadChip in dairy genomic evaluation. J Dairy Sci 95:1552–1558CrossRefPubMedGoogle Scholar
  25. Zavattari P, Deidda E, Whalen M, Lampis R, Mulargia A, Loddo M, Eaves I, Mastio G, Todd JA, Cucca F (2000) Major factors influencing linkage disequilibrium by analysis of different chromosome regions in distinct populations: demography, chromosome recombination frequency and selection. Hum Mol Genet 9:2947–2957CrossRefPubMedGoogle Scholar
  26. Zhu M, Zhu B, Wang YH, Wu Y, Xu L, Guo LP, Yuan ZR, Zhang LP, Cao X, Gao HJ et al (2013) Linkage disequilibrium estimation of Chinese beef Simmental cattle using high-density SNP panels. Asian-Aust J Anim Sci 26:772–779CrossRefGoogle Scholar

Copyright information

© The Genetics Society of Korea and Springer-Science and Media 2015

Authors and Affiliations

  • Zewdu Edea
    • 1
    • 2
  • Hailu Dadi
    • 3
  • Tadelle Dessie
    • 2
  • Seung-Hwan Lee
    • 4
  • Kwan-Suk Kim
    • 1
  1. 1.Department of Animal ScienceChungbuk National UniversityCheongjuKorea
  2. 2.International Livestock Research Institute (ILRI)Addis AbabaEthiopia
  3. 3.Department of BiotechnologyAddis Ababa Science and Technology UniversityAddis AbabaEthiopia
  4. 4.Animal Science & BiotechnologyChungnam National UniverstiyDaejeonKorea

Personalised recommendations