A comparison of approaches to estimate the inbreeding coefficient and pairwise relatedness using genomic and pedigree data in a sheep population

PLoS ONE

Volumn 6, Issue 11, 2011, Pages

  Li, Meng Hua ^a,b   Strandén, Ismo ^a   Tiirikka, Timo ^a   Sevón Aimonen, Marja Liisa ^a   Kantanen, Juha ^a  

^a FINNISH FOREST RESEARCH INSTITUTE   (Finland)

^b INSTITUTE OF ZOOLOGY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CONTROLLED STUDY; FINLAND; GENEALOGY; GENETIC ANALYSIS; GENETIC ASSOCIATION; GENOTYPE; INBREEDING; INTERMETHOD COMPARISON; NONHUMAN; PEDIGREE ANALYSIS; SAMPLE SIZE; SHEEP; SINGLE NUCLEOTIDE POLYMORPHISM; SKIN COLOR; ANIMAL; BIOLOGY; COMPARATIVE STUDY; GENETICS; GENOMICS; HAIR COLOR; PEDIGREE;

ANIMALIA; OVIS; OVIS ARIES;

ANIMALS; COMPUTATIONAL BIOLOGY; GENOMICS; HAIR COLOR; INBREEDING; PEDIGREE; POLYMORPHISM, SINGLE NUCLEOTIDE; SHEEP;

EID: 80655128543     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0026256     Document Type: Article

References (27)

1. Hindorff LA, Sethupathy P, Junkins HA, Ramos EM, Mehta JP, et al. (2009) Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc Natl Acad Sci USA 106: 9362-9367.
2. Ku CS, Loy EY, Pawitan Y, Chia KS, (2010) The pursuit of genome-wide association studies: where are we now? J Hum Genet 55: 195-206.
3. Manichaikul A, Mychaleckyj JC, Rich SS, Daly K, Sale M, et al. (2010) Robust relationship inference in genome-wide association studies. Bioinformatics 26: 2867-2873.
4. Leutenegger AL, Prum B, Génin E, Verny C, Lemainque A, et al. (2003) Estimation of the inbreeding coefficient through use of genomic data. Am J Hum Genet 73: 516-523.
5. Maijala K, Osterberg S, (1977) Productivity of pure Finnsheep in Finland and abroad. Livest Prod Sci 4: 355-377.
6. Maijala K, (1984) Review of experience about the use of Finnsheep in improving fertility. In: Hofmeys JH, Meyer EHH, editors. Proc. 2nd World Congr. Sheep, Beef, Cattle Breed South African Stud Book Livest. Improve. Assoc., Pretoria, South Africa pp. 519-531.
7. Maijala K, (1988) History, recent development and uses of Finnsheep. J Agric Sci in Finland 60: 449-454.
8. Maijala K, (1997) Genetic aspects of domestication, common breeds and their origin. In: Piper L, Ruvinsky A, editors. The Genetics of Sheep CAB Int., Wallingford, UK pp. 13-49.
9. Tapio M, Miceikiené I, Vilkki J, Kantanen J, (2003) Comparison of microsatellite and blood protein diversity in sheep: inconsistencies in fragmented breeds. Mol Ecol 12: 2045-2056.
10. Tapio M, Tapio I, Grislis Z, Holm LE, Jeppsson S, et al. (2005) Native breeds demonstrate high contributions to the molecular variation in northern European sheep. Mol Ecol 14: 3951-3963.
11. Tapio M, Marzanov N, Ozerov M, Cinkulov M, Gonzarenko G, et al. (2006) Sheep mitochondrial DNA variation in European, Caucasian, and Central Asian areas. Mol Biol Evol 23: 1776-1783.
12. Li MH, Strandén I, Kantanen J, (2009) Genetic diversity and pedigree analysis of the Finnsheep breed. J Anim Sci 87: 1598-1605.
13. Muir WM, Wong GK, Zhang Y, Wang J, Groenen MA, et al. (2008) Genome-wide assessment of worldwide chicken SNP genetic diversity indicates significant absence of rare alleles in commercial breeds. Proc Natl Acad Sci USA 105: 17312-17317.
14. McPeek MS, Sun L, (2000) Statistical tests for detection of misspecified relationships by use of genome-screen data. Am J Hum Genet 66: 1076-1094.
15. Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, et al. (2007) PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 81: 559-575.
16. Adalsteinsson S, (1970) Colour inheritance in Icelandic sheep. J Agric Res Icel 2: 1-135.
17. Kijas JW, Townley D, Dalrymple BP, Heaton MP, Maddox JF, et al. (2009) A genome wide survey of SNP variation reveals the genetic structure of sheep breeds. PLoS One 4: e4668.
18. Diez-Tascón C, Littlejohn RP, Almeida PA, Crawford AM, (2000) Genetic variation within the Merino sheep breed: analysis of closely related populations using microsatellites. Anim Genet 31: 243-251.
19. Norberg E, Sorensen AC, (2007) Inbreeding trend and inbreeding depression in the Danish populations of Texel, Shropshire, and Oxford Down. J Anim Sci 85: 299-304.
20. Polasek O, Hayward C, Bellenguez C, Vitart V, Kolcić I, et al. (2010) Comparative assessment of methods for estimating individual genome-wide homozygosity-by-descent from human genomic data. BMC Genomics 11: 139.
21. Crawford AM, Cuthbertson RP, (1996) Mutations in sheep microsatellites. Genome Res 1996 6: 876-879.
22. Stranden I, Vuori K, (2006) RelaX2: Pedigree analysis program. Proc. 8th World Congr. Genet. Appl. Livest. Prod., Belo Horizonte, Brazil, Abstract and CD-ROM.
23. MacCluer JW, Boyce AJ, Dyke B, Weitkamp LR, Pfennig DW, et al. (1983) Inbreeding and pedigree structure in Standardbred horses. J Hered 74: 394-399.
24. Pritchard JK, Stephens M, Donnelly P, (2000) Inference of population structure using multilocus genotype data. Genetics 155: 945-959.
25. Evanno G, Regnaut S, Goudet J, (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14: 2611-2620.
26. Li MH, Kantanen J, (2010) Genetic structure of Eurasian cattle (Bos taurus) based on microsatellites: clarification for their breed classification. Anim Genet 41: 150-158.
27. Excoffier L, Lischer HL, (2010) Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Mol Ecol Resour 10: 564-567.