Effective population size of an indigenous Swiss cattle breed estimated from linkage disequilibrium

Journal of Animal Breeding and Genetics

Volumn 127, Issue 5, 2010, Pages 339-347

  Flury, C ^a   Tapio, M ^b   Sonstegard, T ^c   Drogemuller C ^d   Leeb, T ^d   Simianer, H ^e   Hanotte, O ^b,f   Rieder, S ^a  

^a Swiss College of Agriculture   (Switzerland)

^b International Livestock Research Institute (ILRI)   (United States)

^c AGRICULTURAL RESEARCH SERVICE   (United States)

^d UNIVERSITY OF BERN   (Switzerland)

^e UNIVERSITY OF GÖTTINGEN   (Germany)

^f UNIVERSITY OF NOTTINGHAM   (United Kingdom)

Author keywords

Effective population size; Linkage disequilibrium; Local breed; SNP

Indexed keywords

ANIMAL; ARTICLE; BREEDING; CATTLE; FEMALE; GENE LINKAGE DISEQUILIBRIUM; GENETIC RECOMBINATION; GENETICS; GENOTYPE; MALE; POPULATION DENSITY; SINGLE NUCLEOTIDE POLYMORPHISM;

ANIMALS; BREEDING; CATTLE; FEMALE; GENOTYPE; LINKAGE DISEQUILIBRIUM; MALE; POLYMORPHISM, SINGLE NUCLEOTIDE; POPULATION DENSITY; RECOMBINATION, GENETIC;

BOS;

EID: 77956497351     PISSN: 09312668     EISSN: 14390388     Source Type: Journal    
DOI: 10.1111/j.1439-0388.2010.00862.x     Document Type: Article

References (28)

1. Barrett JC, Fry B, Maller J, Daly MJ. Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics 2005, 21:263-265.
2. Crawford DC, Bhangale T, Li N, Hellenthal G, Rieder MJ, Nickerson DA, Stephens M. Evidence for substantial fine-scale variation in recombination rates across the human genome. Nat. Genet. 2004, 36:700-706.
3. Farnir F, Coppiettiers W, Arranz JJ, Berzi P, Cambisano N, Grisart B, Karim L, Marcq F, Moreau L, Mni M, Nezer C, Simon P, Vannanshoven P, Wagenaar D, Georges M. Extensive genome-wide linkage disequilibrium in cattle. Genome Res. 2000, 10:220-227.
4. Felius M. Cattle Breeds: An Encyclopedia 1995, Misset, Doetinchem
5. Farm animal genetic resources in Switzerland. Booklet in the order of the Federal Office of Agriculture for the First Technical Conference on Animal Genetic Resources, Interlaken, 2007. 2007, http://www.blw.admin.ch/themen/00013/00082/00087/index.html?lang=en, (available at: ; last accessed 12 February 2010)
6. Förderung der Tierzucht durch den Bund und die Kantone im Jahre 2007. Federal Office of Agriculture FOAG. 2008, http://www.blw.admin.ch/themen/00013/00082/00087/index.html?lang=de, (available at: ; last accessed 12 February 2010)
7. Gautier M, Faraut T, Moazami-Goudarzi K, Navratil V, Foglio M, Grohs C, Boland A, Garnier JG, Boichard D, Lathrop GM, Gut IG, Eggen A. Genetic and haplotypic structure in 14 European and African cattle breeds. Genetics 2007, 177:1059-1070.
8. Gutiérrez JP, Goyache F. A note on ENDOG: a computer program for analysing pedigree information. J. Anim. Breed. Genet. 2005, 122:172-176.
9. Hagger C. Estimates of genetic diversity in the brown cattle population of Switzerland obtained from pedigree information. J. Anim. Breed. Genet. 2005, 122:405-413.
10. Hayes BJ, Visscher PM, McPartlan HC, Goddard ME. Novel multilocus measure of linkage disequilibrium to estimate past effective population size. Genome Res. 2003, 13:635-643.
11. Hayes BJ, Bowman PJ, Chamberlain AJ, Goddard ME. Genomic selection in dairy cattle: progress and challenges. J. Dairy Sci. 2009, 92:433-443.
12. Hill WG. Estimation of effective population size from data on linkage disequilibrium. Genet. Res. 1981, 38:209-216.
13. Khatkar MS, Nicholas FW, Collins AR, Zenger KR, Cavanagh JA, Barris W, Schnabel R, Taylor JF, Raadsma HW. Extent of genome-wide linkage disequilibrium in Australian Holstein-Friesian cattle based on a high-density SNP-panel. BMC Genomics 2008, 9:187.
14. König S, Simianer H. Approaches to the management of inbreeding and relationship in the German Holstein dairy cattle population. Lives. Sci. 2006, 103:40-53.
15. Li N, Stephens M. Modelling linkage disequilibrium, and identifying recombination hotspots using SNP data. Genetics 2003, 165:2213-2233.
16. Matukumalli LK, Lawley CT, Schnabel RD, Taylor JF, Allan MF, Heaton MP, O'Connell J, Moore SS, Smith TPL, Sonstegard TS, Van Tassell CP. Development and characterization of a high density SNP genotyping assay for cattle. PLoS ONE 2009, 4:e5350.
17. Nomura T, Honda T, Mukai F. Inbreeding and effective population size of Japanese Black cattle. J. Anim. Sci. 2001, 79:366-370.
18. Pérez-Enciso M. Use of the uncertain relationship matrix to compute effective population size. J. Anim. Breed. Genet. 1995, 112:327-332.
19. Sargolzaei M, Schenkel FS, Jansen GB, Schaeffer LR. Extent of linkage disequilibrium in Holstein cattle in North America. J. Dairy Sci. 2008, 91:2106-2117.
20. Simianer H, Szyda J, Ramon G, Lien S. Evidence for individual and between family variability of the recombination rate. Mamm. Genome 1997, 8:830-835.
21. Sved JA. Linkage disequilibrium and homozygosity of chromosome segments in finite populations. Theor. Popul. Biol. 1971, 2:125-141.
22. Tenesa A, Knott SA, Ward D, Smith D, Williams JL, Visscher PM. Estimation of linkage disequilibrium in a sample of the United Kingdom dairy cattle population using unphased genotypes. J. Anim. Sci. 2003, 81:617-623.
23. Genome-wide survey of SNP variation uncovers the genetic structure of cattle breeds. Science 2009, 324:528-532.
24. Thévenon S, Dayo GK, Sylla S, Sidibe I, Berthier D, Legros H, Boichard D, Eggen A, Gautier M. The extent of linkage disequilibrium in a large cattle population of western Africa and its consequences for association studies. Anim. Genet. 2007, 38:277-286.
25. Visscher PM. Principles of QTL-Mapping, Manual QTL-course held in Salzburg 2003 2003, University of Edinburgh, Edinburgh
26. Wang J. Estimation of effective ppulation sizes from data on genetic markers. Philos. Trans. R. Soc. Lond. B Biol. Sci. 2005, 360:1395-1409.
27. Weir BS, Hill WG. Effect of mating structure on variation in linkage disequilibrium. Genetics 1980, 95:477-488.
28. Zenger KR, Khatkar MS, Cavanagh JA, Hawken RJ, Raadsma HW. Genome-wide genetic diversity of Holstein Friesian cattle reveals new insights into Australian and global population variability, including impact of selection. Anim. Genet. 2007, 38:7-14.