A genome-wide association study reveals loci influencing height and other conformation traits in horses

PLoS ONE

Volumn 7, Issue 5, 2012, Pages

  Signer Hasler, Heidi ^a   Flury, Christine ^a   Haase, Bianca ^b,c   Burger, Dominik ^d   Simianer, Henner ^e   Leeb, Tosso ^b   Rieder, Stefan ^d  

^a BERN UNIVERSITY OF APPLIED SCIENCES   (Switzerland)

^b UNIVERSITY OF BERN   (Switzerland)

^c UNIVERSITY OF SYDNEY   (Australia)

^d Swiss National Stud Farm SNSTF   (Switzerland)

^e UNIVERSITY OF GÖTTINGEN   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

GENOMIC DNA;

ARTICLE; BACK; BODY HEIGHT; CHROMOSOME 3; CHROMOSOME 9; DOMESTIC ANIMAL; ECA 3 GENE; ECA 6 GENE; ECA 9 GENE; GAIT; GENE; GENETIC ANALYSIS; GENETIC ASSOCIATION; GENETIC HETEROGENEITY; HEAD; HORSE; LCORL GENE; LEG; MANDIBLE; MORPHOLOGICAL TRAIT; NCAPG GENE; NONHUMAN; QUANTITATIVE TRAIT LOCUS; SINGLE NUCLEOTIDE POLYMORPHISM; ZFAT GENE; ANIMAL; FEMALE; GENETICS; HISTOLOGY; MALE; PHENOTYPE;

ANIMALIA; EQUIDAE;

ANIMALS; FEMALE; GENOME-WIDE ASSOCIATION STUDY; HORSES; MALE; PHENOTYPE; QUANTITATIVE TRAIT LOCI;

EID: 84861215022     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0037282     Document Type: Article

References (37)

1. Chowdhary BP, Raudsepp T, (2008) The Horse Genome Derby: racing from map to whole genome sequence. Chromosome Res 16: 109-127.
2. Wade CM, Giulotto E, Sigurdsson S, Zoli M, Gnerre S, et al. (2009) Genome Sequence, Comparative Analysis, and Population Genetics of the Domestic Horse. Science 326: 865-867.
3. Binns MM, Boehler DA, Lambert DH, (2010) Identification of the myostatin locus (MSTN) as having a major effect on optimum racing distance in the Thoroughbred horse in the USA. Anim Genet 41 (Suppl 2): 154-158.
4. Hill EW, McGivney BA, Gu J, Whiston R, MacHugh DE, (2010) A genome-wide SNP-association study confirms a sequence variant (g.66493737C&T) in the equine myostatin (MSTN) gene as the most powerful predictor of optimum racing distance for Thoroughbred racehorses. BMC Genomics 11: 552.
5. Tozaki T, Hill EW, Hirota K, Kakoi H, Gawahara H, et al. (2012) A cohort study of racing performance in Japanese Thoroughbred racehorses using genome information on ECA18. Anim Genet 43: 42-52.
6. Rieder S, (2009) Molecular tests for coat colours in horses. J Anim Breed Genet 126: 415-424.
7. Bellone RR, (2010) Pleiotropic effects of pigmentation genes in horses. Anim Genet 41 (Suppl 2): 100-110.
8. Brosnahan MM, Brooks SA, Antczak DF, (2010) Equine clinical genomics: A clinician's primer. Equine Vet J 42: 658-670.
9. Saastamoinen MT, Barrey E, (2000) Genetics of Conformation, Locomotion and Physiological Traits. In: Bowling AT, Ruvinsky A, editors. The Genetics of the Horse pp. 439-472 CABI, Wallingford, UK.
10. Koenen EPC, van Veldhuizen AE, Brascamp EW, (1995) Genetic parameters of linear scored conformation traits and their relation with dressage and show-jumping in the Dutch Warmblood riding horse population. Livest Prod Sci 43: 85-94.
11. Visscher PM, McEvoy B, Yang J, (2010) From Galton to GWAS: quantitative genetics of human height. Genet Res (Camb) 92: 371-379.
12. Lango Allen H, Estrada K, Lettre G, Berndt SI, Weedon MN, et al. (2010) Hundreds of variants clustered in genomic loci and biological pathways affect human height. Nature 467: 832-838.
13. Manolio TA, Collins FS, Cox NJ, Goldstein DB, Hindorff LA, et al. (2009) Finding the missing heritability of complex diseases. Nature 461: 747-753.
14. Kutalik Z, Whittaker J, Waterworth D, Beckmann JS, et al. GIANT consortium (2011) Novel method to estimate the phenotypic variation explained by genome-wide association studies reveals large fraction of the missing heritability. Genet Epidemiol 35: 341-349.
15. Yang J, Benyamin B, McEvoy BP, Gordon S, Henders AK, et al. (2010) Common SNPs explain a large proportion of the heritability for human height. Nat Genet 42: 565-569.
16. Pausch H, Flisikowski K, Jung S, Emmerling R, Edel C, et al. (2011) Genome-wide association study identifies two major loci affecting calving ease and growth-related traits in cattle. Genetics 187: 289-297.
17. Pryce JE, Hayes BJ, Bolormaa S, Goddard ME, (2011) Polymorphic regions affecting human height also control stature in cattle. Genetics 187: 981-984.
18. Karim L, Takeda H, Lin L, Druet T, Arias JAC, et al. (2011) Variants modulating the expression of a chromosome domain encompassing PLAG1 influence bovine stature. Nat Genet 43: 405-413.
19. Visscher PM, Goddard ME, (2011) Cattle gain stature. Nat Genet 43: 397-398.
20. Habier D, (2010) More than a third of the WCGALP presentations on genomic selection. J Anim Breed Genet 127: 336-337.
21. Heffner EL, Lorenz AI, Jannink J-L, Sorrells ME, (2010) Plant breeding with genomic selction: potential gain per unit time and cost. Crop Sci 50: 1681-1690.
22. Hayes BJ, Bowman PJ, Charmberlain AJ, Goddard ME, (2009) Genomic selection in dairy cattle: Progress and challenges. J Dairy Sci 92: 433-443.
23. Habier D, Tetens J, Seefried F-R, Lichtner P, Thaller G, (2010) The impact of genetic relationship information on genomic breeding values in German Holstein cattle. Genet Sel Evol 42: 5.
24. Meuwissen THE, Hayes BJ, Goddard ME, (2001) Prediction of total genetic value using genome-wide dense marker maps. Genetics 157: 1819-1829.
25. VanRaden PM, (2008) Efficient Methods to Compute Genomic Predictions. J Dariy Sci 91: 4414-4423.
26. Hayes BJ, Pryce J, Chamberlain AJ, Bowman PJ, Goddard ME, (2010) Genetic architecture of complex traits and accuracy of genomic prediction: coat colour, milk-fat percentage, and type in Holstein cattle as contrasting model traits. PLoS Genet 6: e1001139.
27. Hasler H, Flury C, Menet S, Haase B, Leeb T, et al. (2011) Genetic diversity in an indigenous horse breed -implications for mating strategies and the control of future inbreeding. J Anim Breed Genet 128: 394-406.
28. Hayes B, Goddard ME, (2001) The distribution of the effects of genes affecting quantitative traits in livestock. Genet Sel Evol 33: 209-229.
29. Setoguchi K, Furuta M, Hirano T, Nagao T, Watanabe T, et al. (2009) Cross-breed comparisons identified a critical 591-kb region for bovine carcass weight QTL (CW-2) on chromosome 6 and the Ile-442-Met substitution in NCAPG as a positional candidate. BMC Genet 10: 43.
30. Libioulle C, Louis E, Hansoul S, Sandor C, Farnir F, et al. (2007) Novel Crohn disease locus identified by genome-wide association maps to a gene desert on 5p13.1 and modulates expression of PTGER4. PLoS Genet 3: e58.
31. Henderson CR, (1975) Best linear unbiased prediction under a selection model. Biometrics 31: 423-447.
32. Poncet PA, Pfister W, Muntwyler J, Glowatzki-Mullis ML, Gaillard C, (2006) Analysis of pedigree and conformation data to explain genetic variability of the horse breed Franches-Montagnes. J Anim Breed Genet 123: 114-121.
33. Garrick DJ, Taylor JF, Fernando RL, (2009) Deregressing estimated breeding values and weighting information for genomic regression analyses. Genet Sel Evol 41: 55.
34. Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, et al. (2007) PLINK: a toolset for whole-genome association and population-based linkage analysis. Am J Hum Genet 81: 559-575.
35. Sargolzaei M, Iwaisaki H, Colleau JJ, (2006) CFC: a tool for monitoring genetic diversity. Proc. 8th World Congr. Genet. Appl. Livest. Prod., CD-ROM Communication no 27-28. Belo Horizonte, Brazil, Aug. 13-18, 2006.
36. Aulchenko YS, Ripke S, Isaacs A, van Duijn CM, (2007) GenABEL: An R library for genome-wide association analysis. Bioinformatics 23: 1294-1296.
37. Yang J, Manolio TA, Pasquale LR, Boerwinkle E, Caporaso N, et al. (2011) Genome partitioning of genetic variation for complex traits using common SNPs. Nat Genet 43: 519-525.