How old are quantitative trait loci and how widely do they segregate?

Journal of Animal Breeding and Genetics

Volumn 132, Issue 2, 2015, Pages 121-134

  Kemper, K E ^a   Hayes, B J ^b,c,d   Daetwyler, H D ^b,c   Goddard, M E ^a,b  

^a UNIVERSITY OF MELBOURNE   (Australia)

^b LA TROBE UNIVERSITY   (Australia)

^c LA TROBE UNIVERSITY   (Australia)

^d Department of Civil and Environmental Engineering   (Australia)

Author keywords

Dairy cattle; Genetic architecture; Genomic prediction; Genomic sequence variants; QTL mapping

Indexed keywords

BOS;

ANIMAL; BOVINE; FEMALE; GENETIC ASSOCIATION; GENETICS; MALE; METABOLISM; MILK; PHYSIOLOGY; QUANTITATIVE TRAIT LOCUS; SINGLE NUCLEOTIDE POLYMORPHISM;

ANIMALS; CATTLE; FEMALE; GENOME-WIDE ASSOCIATION STUDY; MALE; MILK; POLYMORPHISM, SINGLE NUCLEOTIDE; QUANTITATIVE TRAIT LOCI;

EID: 84925968000     PISSN: 09312668     EISSN: 14390388     Source Type: Journal    
DOI: 10.1111/jbg.12152     Document Type: Article

References (32)

1. Blott S., Kim J.J., Moisio S., Schmidt-Kuntzel A., Cornet A., Berzi P., Cambisano N., Ford C., Grisart B., Johnson D., Karim L., Simon P., Snell R., Spelman R., Wong J., Vilkki J., Georges M., Farnir F., Coppieters W. (2003) Molecular dissection of a quantitative trait locus: a phenylalanine-to-tyrosine substitution in the transmembrane domain of the bovine growth hormone receptor is associated with a major effect on milk yield and composition. Genetics, 163, 253-266.
2. Bolormaa S., Pryce J., Kemper K., Hayes B., Zhang Y., Tier B., Barendse W., Reverter A., Goddard M. (2013a) Detection of quantitative trait loci in Bos indicus and Bos taurus cattle using genome-wide association studies. Genet. Sel. Evol., 45, 43.
3. Bolormaa S., Pryce J.E., Kemper K.E., Savin K., Hayes B.J., Barendse W., Zhang Y., Reich C.M., Mason B.A., Bunch R.J., Harrison B.E., Reverter A., Herd R.M., Tier B., Graser H.U., Goddard M.E. (2013b) Accuracy of prediction of genomic breeding values for residual feed intake, carcass and meat quality traits in Bos taurus, Bos indicus and composite beef cattle. J. Anim. Sci., 91, 3088-3104.
4. Bolormaa S., Pryce J.E., Reverter A., Zhang Y., Barendse W., Kemper K., Tier B., Savin K., Hayes B.J., Goddard M.E. (2014) Multi-trait, meta-analysis for GWAS reveals four broad classes of pleiotropic effects for SNP associated with stature, fatness and reproductive traits in beef cattle. PLoS Genet., 10, e1004198.
5. Bradley D.G., MacHugh D.E., Cunningham P., Loftus R.T. (1996) Mitochondrial diversity and the origins of African and European cattle. Proc. Natl Acad. Sci. USA, 93, 5131-5135.
6. Browning S.R., Browning B.L. (2007) Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering. Am. J. Hum. Genet., 81, 1084-1097.
7. Daetwyler H.D., Capitan A., Pausch H., Stothard P., van Binsbergen R., Brondum R.F., Liao X., Djari A., Rodriguez S.C., Grohs C., Esquerre D., Bouchez O., Rossignol M.-N., Klopp C., Rocha D., Fritz S., Eggen A., Bowman P.J., Coote D., Chamberlain A.J., Anderson C., VanTassell C.P., Hulsegge I., Goddard M.E., Guldbrandtsen B., Lund M.S., Veerkamp R.F., Boichard D.A., Fries R., Hayes B.J. (2014) Whole-genome sequencing of 234 bulls facilitates mapping of monogenic and complex traits in cattle. Nat. Genet., 46, 858-865.
8. Druet T., Ahariz N., Cambisano N., Tamma N., Michaux C., Coppieters W., Charlier C., Georges M. (2014) Selection in action: dissecting the molecular underpinnings of the increasing muscle mass of Belgian Blue Cattle. BMC Genom., 15, 796.
9. Fuchsberger C., Abecasis G.R., Hinds D.A. (2015) minimac2: faster genotype imputation. Bioinformatics, 31, 782-784.
10. Gautier M., Vitalis R. (2012) rehh: an R package to detect footprints of selection in genome-wide SNP data from haplotype structure. Bioinformatics, 28, 1176-1177.
11. Grisart B., Coppieters W., Farnir F., Karim L., Ford C., Berzi P., Cambisano N., Mni M., Reid S., Simon P., Spelman R., Georges M., Snell R. (2002) 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., 12, 222-231.
12. Haile-Mariam M., Nieuwhof G.J., Beard K.T., Konstatinov K.V., Hayes B.J. (2013) Comparison of heritabilities of dairy traits in Australian Holstein-Friesian cattle from genomic and pedigree data and implications for genomic evaluations. J. Anim. Breed. Genet., 130, 20-31.
13. Hayes B.J., Visscher P.M., McPartlan H.C., Goddard M.E. (2003) Novel multilocus measure of linkage disequilibrium to estimate past effective population size. Genome Res., 13, 635-643.
14. Kang H.M., Sul J.H., Service S.K., Zaitlen N.A., Kong S.-Y., Freimer N.B., Sabatti C., Eskin E. (2010) Variance component model to account for sample structure in genome-wide association studies. Nat. Genet., 42, 348-354.
15. Kaupe B., Winter A., Fries R., Erhardt G. (2004) DGAT1 polymorphism in Bos indicus and Bos taurus cattle breeds. J. Dairy Res., 71, 182-187.
16. Kemper K.E., Saxton S.J., Bolormaa S., Hayes B.J., Goddard M.E. (2014) Selection for complex traits leaves little or no classic signatures of selection. BMC Genom., 15, 246.
17. Kemper K.E., Reich C.M., Bowman P.J., Vander Jagt C.J., Chamberlain A.C., Mason B.A., Hayes B.J., Goddard M.E. (in press) Improved precision of QTL mapping using a nonlinear Bayesian method in a multi-breed population leads to greater accuracy for across-breed genomic predictions. Genet. Sel. Evol.
18. Khansefid M., Pryce J.E., Bolormaa S., Miller S.P., Wang Z., Li C., Goddard M.E. (2014) Estimation of genomic breeding values for residual feed intake in a multibreed cattle population. J. Anim. Sci., 92, 3270-3283.
19. Kimura M., Ohta T. (1973) The age of a neutral mutation persisting in a finite population. Genetics, 75, 199-212.
20. Littlejohn M.D., Tiplady K., Lopdell T., Law T.A., Scott A., Harland C., Sherlock R., Henty K., Obolonkin V., Lehnert K., MacGibbon A., Spelman R.J., Davis S.R., Snell R.G. (2014) Expression variants of the lipogenic AGPAT6 gene affect diverse milk composition phenotypes in Bos taurus. PLoS One, 9, e85757.
21. McLaren W., Pritchard B., Rios D., Chen Y., Flicek P., Cunningham F. (2010) Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor. Bioinformatics, 26, 2069-2070.
22. O'Rourke B.A., Greenwood P.L., Arthur P.F., Goddard M.E. (2012) Inferring the recent ancestry of myostatin alleles affecting muscle mass in cattle. Anim. Genet., 44, 86-90.
23. Pritchard J.K. (2001) Are rare variants responsible for susceptibility to complex diseases? Am. J. Hum. Genet., 69, 124-137.
24. R Core Team. (2012). R Foundation for Statistical Computing, R Core Team, Vienna, Austria.
25. Raven L.-A., Cocks B.G., Hayes B.J. (2014) Multibreed genome wide association can improve precision of mapping causative variants underlying milk production in dairy cattle. BMC Genom., 15, 62.
26. Rocha D., Billerey C., Samson F., Boichard D., Boussaha M. (2014) Identification of the putative ancestral allele of bovine single-nucleotide polymorphisms. J. Anim. Breed. Genet., 131, 483-486.
27. de Roos A.P.W., Hayes B.J., Spelman R.J., Goddard M.E. (2008) Linkage disequilibrium and persistence of phase in Holstein-Friesian, Jersey and Angus cattle. Genetics, 179, 1503-1512.
28. Saatchi M., Schnabel R., Taylor J., Garrick D. (2014) Large-effect pleiotropic or closely linked QTL segregate within and across ten US cattle breeds. BMC Genom., 15, 442.
29. Sabeti P.C., Reich D.E., Higgins J.M., Levine H.Z., Richter D.J., Schaffner S.F., Gabriel S.B., Platko J.V., Patterson N.J., McDonald G.J., Ackermann H.C., Campbell S.J., Altshuler D., Cooper R., Kwiatkowski D., Ward R., Lander E.S. (2002) Detecting recent positive selection in the human genome from haplotype structure. Nature, 419, 832-837.
30. The Bovine HapMap Consortium (2009) Genome-wide survey of SNP variation uncovers the genetic structure of cattle breeds. Science, 324, 528-532.
31. Voight B.F., Kudaravalli S., Wen X., Pritchard J.K. (2006) A map of recent positive selection in the human genome. PLoS Biol., 4, e72.
32. Wang X., Wurmser C., Pausch H., Jung S., Reinhardt F., Tetens J., Thaller G., Fries R. (2012) Identification and dissection of four major QTL affecting milk fat content in the German Holstein-Friesian population. PLoS One, 7, e40711.