Multivariate analysis of a genome-wide association study in dairy cattle

Journal of Dairy Science

Volumn 93, Issue 8, 2010, Pages 3818-3833

  Bolormaa, S ^a   Pryce, J E ^a   Hayes, B J ^a   Goddard, M E ^a,b  

^a DEPARTMENT OF PRIMARY INDUSTRIES   (Australia)

^b UNIVERSITY OF MELBOURNE   (Australia)

Author keywords

Multivariate genome wide association study; Pleiotropy; Principal component

Indexed keywords

ANIMAL; ANIMAL DISEASE; ARTICLE; AUSTRALIA; CATTLE; COMPARATIVE STUDY; FEMALE; GENETIC ASSOCIATION; GENETIC MARKER; GENETICS; MALE; METHODOLOGY; MULTIVARIATE ANALYSIS; POPULATION GENETICS; QUANTITATIVE TRAIT LOCUS; SINGLE NUCLEOTIDE POLYMORPHISM; BOVINAE; PROCEDURES; VETERINARY;

ANIMALS; AUSTRALIA; CATTLE; FEMALE; GENETIC MARKERS; GENETICS, POPULATION; GENOME-WIDE ASSOCIATION STUDY; MALE; MULTIVARIATE ANALYSIS; POLYMORPHISM, SINGLE NUCLEOTIDE; QUANTITATIVE TRAIT LOCI;

BOS;

GENETIC MARKER;

EID: 77955047597     PISSN: 00220302     EISSN: 15253198     Source Type: Journal    
DOI: 10.3168/jds.2009-2980     Document Type: Article

References (29)

1. ADHIS. 2010. Australian Dairy Herd Improvement Scheme. Accessed Nov. 1, 2009. http://www.adhis.org.au/.
2. Benjamini Y., Hochberg Y. Controlling the false discovery rate: A practical and powerful approach to multiple testing. J. R. Stat. Soc., B 1995, 57:289-300.
3. Chagas L.M., Lucy M.C., Back P.J., Blache D., Lee J.M., Gore P.J., Sheahan A.J., Roche J.R. Insulin resistance in divergent strains of Holstein-Friesian dairy cows offered fresh pasture and increasing amounts of concentrate in early lactation. J. Dairy Sci. 2009, 92:216-222.
4. Chamberlain A.J., Meuwissen T.H.E., Goddard M.E. Estimation of the distribution of QTL effects. Proc. Assoc. Advmt. Anim. Breed. Genet. 2005, 16:103-106.
5. Chase K., Carrier D.R., Adler F.R., Jarvik T., Ostrander E.A., Lorentzen T.D. Genetic basis for systems of skeletal quantitative traits: Principal component analysis of the canid skeleton. Proc. Natl. Acad. Sci. USA 2002, 99:9930-9935.
6. Cole J.B., VanRaden P.M., O'Connell J.R., Van Tassell C.P., Sonstegard T.S., Schnabel R.D., Taylor J.F., Wiggans G.R. Distribution and location of genetic effects for dairy traits. J. Dairy Sci. 2009, 92:2931-2946.
7. de Roos A.P., Hayes B., Spelman R., Goddard M. Linkage disequilibrium and persistence of phase in Holstein-Friesian, Jersey and Angus cattle. Genetics 2008, 179:1503-1512.
8. Gilmour A.R., Gogel B.J., Gullis B.R., Welham S.J., Thompson R. ASReml User Guide. Release 1.0. 2002, VSN International Ltd., Hemel Hempstead, UK.
9. Grisart B., Coppitiers W., Farnir F., Karim L., Ford C., Berzi P., Cambisano N., Mni M., Reid S., Simon P., Spelman R., Georges M., Snell R. Positional candidate cloning of a QTL in dairy cattle: Identification of a missense mutation in the bovine DGAT1 gene with major effect on milk yield and composition. Genome Res. 2002, 12:222-231.
10. Hayes B., Bowman P., Chamberlain A., Goddard M. A validated genome-wide association study to breed cattle adapted to an environment altered by climate change. PLoS One 2009, 4:e6676.
11. Karlsson E.K., Baranowska I., Wade C.M., Hillbertz N.H.C.S., Zody M.C., Anderson N., Biagi T.M., Patterson N., Pielberg G.R., Kulbokas E.J., Comstock K.E., Keller E.T., Mesirov J.P., von Euler H., Kaumlmpe O., Hedhammar A., Lander E.S., Andersson G., Andersson L., Lindblad-Toh K. Efficient mapping of mendelian traits in dogs through genome-wide association. Nat. Genet. 2007, 39:1321-1328.
12. Knott S.A., Haley C.S. Multitrait least squares for quantitative trait loci detection. Genetics 2000, 156:899-911.
13. Korol A.B., Ronin Y.I., Itskovich A.M., Peng J., Nevo E. Enhanced efficiency of quantitative trait loci mapping analysis based on multivariate complexes of quantitative traits. Genetics 2001, 157:1789-1803.
14. Lettre G., Jackson A., Gieger C., Schumacher F., Berndt S., Sanna S., Eyheramendy S., Voight B., Butler J., Guiducci C., Illig T., Hackett R., Heid I., Jacobs K., Lyssenko V., Uda M. Identification of ten loci associated with height highlights new biological pathways in human growth. Nat. Genet. 2008, 40:584-591.
15. Lillehammer M., Goddard M., Nilsen H., Sehested E., Olsen G., Lien S., Meuwissen T. QTL by environment interaction for milk yield traits on Bos Taurus Autosome 6. Genetics 2008, 0.1534/genetics.1107.084483.
16. MacLeod I.M., Hayes B.J., Savin K.W., Chamberlain A.J., McPartlan H.C., Goddard M.E. Power of a genome scan to detect and locate quantitative trait loci in cattle using dense single nucleotide polymorphisms. J. Anim. Breed. Genet. 2009, 127:133-142.
17. Matukumalli L.K., Lawley C., Schnabel R., Taylor J., Allan M., Heaton M., O'Connell J., Moore S., Smith T., Sonstegard T., Van Tassell C. Development and characterization of a high density SNP genotyping assay for cattle. PLoS ONE 2009, 4:e5350.
18. Musani S.K., Zhang H., Hsu H., Yi N., Gorman B.S., Allison D.B., Mountz J.D. Principal component analysis of quantitative trait loci for immune response to adenovirus in mice. Hereditas 2006, 143:189-197.
19. Osborne, J. 2006. Estimating the false discovery rate using SAS. 190-30 in SAS Conference Proceedings: SAS Users Group International 31. Accessed Aug. 10, 2009. http://www2.sas.com/proceedings/sugi31/190-31.pdf.
20. Payne R.W., Murray D.A., Harding S.A., Baird D.B., Soutar D.M. GenStat for Windows 2007, VSN International, Hemel Hempstead, UK. 10th ed.
21. Pryce J., Haile-Mariam M., Verbyla K., Bowman P., Goddard M., Hayes B. Genetic markers for lactation persistency in primiparous Australian dairy cows. J. Dairy Sci. 2010, 93:2202-2214.
22. Pryce J.E., Bolormaa S., Chamberlain A., Bowman P., Savin K., Goddard M., Hayes B. A validated genome-wide association study in two dairy cattle breeds for milk production and fertility traits using variable length haplotypes. J. Dairy Sci. 2010, 93:3331-3345.
23. Scheet P., Stephens M. A fast and flexible statistical model for large-scale population genotype data: Applications to inferring missing genotypes and haplotypic phase. Am. J. Hum. Genet. 2006, 78:629-644.
24. Spelman R.J., Ford C., McElhinney P., Gregory G., Snell R. Characterization of the DGAT1 gene in the New Zealand dairy population. J. Dairy Sci. 2002, 85:3514-3517.
25. Stearns T.M., Beever J.E., Southey B.R., Ellis M., McKeith F.K., Rodriguaz-Zas S.L. Evaluation of approaches to detect quantitative traits loci for growth, carcass, and meat quality on swine chromosome 2, 6, 13 and 18. II. Multivariate and principal component analyses. J. Anim. Sci. 2005, 83:2471-2481.
26. Storey J.D. A direct approach to false discovery rates. J. R. Stat. Soc. B 2002, 64:479-498.
27. Genome-wide survey of SNP variation uncovers the genetic structure of cattle breeds. Science 2009, 324:528-532. The Bovine HapMap Consortium.
28. Visscher P.M., Thompson R., Haley C.S. Confidence interval in QTL mapping by bootstrapping. Genetics 1996, 143:1013-1020.
29. Weedon M.N., Lango H., Lindgren C., Wallace C., Evans D., Mangino M., Freathy R., Perry J., Stevens S., Hall A., Samani N., Shields B., Prokopenko I., Farrall M., Dominiczak A. Genome-wide association analysis identifies 20 loci that influence adult height. Nat. Genet. 2008, 40:575-583.