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Volumn 96, Issue 10, 2013, Pages 6703-6715

Combining cow and bull reference populations to increase accuracy of genomic prediction and genome-wide association studies

Author keywords

Genome wide association study; Genomic selection; Multitrait; Reference population

Indexed keywords

ANIMALIA;

EID: 84884357067     PISSN: 00220302     EISSN: 15253198     Source Type: Journal    
DOI: 10.3168/jds.2012-6013     Document Type: Article
Times cited : (36)

References (50)
  • 2
    • 84861884687 scopus 로고    scopus 로고
    • Merging and characterising phenotypic data on conventional and rare traits from dairy cattle experimental resources in three countries
    • Banos G., Coffey M.P., Veerkamp R.F., Berry D.P., Wall E. Merging and characterising phenotypic data on conventional and rare traits from dairy cattle experimental resources in three countries. Animal 2012, 6:1040-1048.
    • (2012) Animal , vol.6 , pp. 1040-1048
    • Banos, G.1    Coffey, M.P.2    Veerkamp, R.F.3    Berry, D.P.4    Wall, E.5
  • 3
    • 84863448955 scopus 로고    scopus 로고
    • Genome-wide associations for fertility traits in Holstein-Friesian dairy cows using data from experimental research herds in four European countries
    • Berry D.P., Bastiaansen J.W.M., Veerkamp R.F., Wijga S., Wall E., Berglund B., Calus M.P.L. Genome-wide associations for fertility traits in Holstein-Friesian dairy cows using data from experimental research herds in four European countries. Animal 2012, 6:1206-1215.
    • (2012) Animal , vol.6 , pp. 1206-1215
    • Berry, D.P.1    Bastiaansen, J.W.M.2    Veerkamp, R.F.3    Wijga, S.4    Wall, E.5    Berglund, B.6    Calus, M.P.L.7
  • 5
    • 35348817330 scopus 로고    scopus 로고
    • Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering
    • Browning S.R., Browning B.L. Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering. Am. J. Hum. Genet 2007, 81:1084-1097.
    • (2007) Am. J. Hum. Genet , vol.81 , pp. 1084-1097
    • Browning, S.R.1    Browning, B.L.2
  • 6
    • 84858076112 scopus 로고    scopus 로고
    • Genomic selection strategies in dairy cattle: Strong positive interaction between use of genotypic information and intensive use of young bulls on genetic gain
    • Buch L.H., Sørensen M.K., Berg P., Pedersen L.D., Sørensen A.C. Genomic selection strategies in dairy cattle: Strong positive interaction between use of genotypic information and intensive use of young bulls on genetic gain. J. Anim. Breed. Genet 2012, 129:138-151.
    • (2012) J. Anim. Breed. Genet , vol.129 , pp. 138-151
    • Buch, L.H.1    Sørensen, M.K.2    Berg, P.3    Pedersen, L.D.4    Sørensen, A.C.5
  • 7
    • 76849094999 scopus 로고    scopus 로고
    • Genomic breeding value prediction: Methods and procedures
    • Calus M.P.L. Genomic breeding value prediction: Methods and procedures. Animal 2010, 4:157-164.
    • (2010) Animal , vol.4 , pp. 157-164
    • Calus, M.P.L.1
  • 8
    • 84872077949 scopus 로고    scopus 로고
    • Predicted accuracy of and response to genomic selection for new traits in dairy cattle
    • Calus M.P.L., de Haas Y., Pszczola M., Veerkamp R.F. Predicted accuracy of and response to genomic selection for new traits in dairy cattle. Animal 2013, 7:183-191.
    • (2013) Animal , vol.7 , pp. 183-191
    • Calus, M.P.L.1    de Haas, Y.2    Pszczola, M.3    Veerkamp, R.F.4
  • 9
    • 84856008520 scopus 로고    scopus 로고
    • Identification of Mendelian inconsistencies between SNP and pedigree information of sibs
    • Calus M.P.L., Mulder H.A., Bastiaansen J.W.M. Identification of Mendelian inconsistencies between SNP and pedigree information of sibs. Genet. Sel. Evol 2011, 43:34.
    • (2011) Genet. Sel. Evol , vol.43 , pp. 34
    • Calus, M.P.L.1    Mulder, H.A.2    Bastiaansen, J.W.M.3
  • 10
    • 80455127261 scopus 로고    scopus 로고
    • Accuracy of multi-trait genomic selection using different methods
    • Calus M.P.L., Veerkamp R.F. Accuracy of multi-trait genomic selection using different methods. Genet. Sel. Evol 2011, 43:26.
    • (2011) Genet. Sel. Evol , vol.43 , pp. 26
    • Calus, M.P.L.1    Veerkamp, R.F.2
  • 12
    • 80054724376 scopus 로고    scopus 로고
    • Genome-wide evaluation of populations
    • Wageningen University, Wageningen, the Netherlands
    • Daetwyler H.D. Genome-wide evaluation of populations. PhD Thesis 2009, Wageningen University, Wageningen, the Netherlands.
    • (2009) PhD Thesis
    • Daetwyler, H.D.1
  • 13
    • 54449097329 scopus 로고    scopus 로고
    • Accuracy of predicting the genetic risk of disease using a genome-wide approach
    • Daetwyler H.D., Villanueva B., Woolliams J.A. Accuracy of predicting the genetic risk of disease using a genome-wide approach. PLoS ONE 2008, 3:e3395.
    • (2008) PLoS ONE , vol.3
    • Daetwyler, H.D.1    Villanueva, B.2    Woolliams, J.A.3
  • 14
    • 84867101935 scopus 로고    scopus 로고
    • Improved accuracy of genomic prediction for dry matter intake of dairy cattle from combined European and Australian data sets
    • de Haas Y., Calus M.P.L., Veerkamp R.F., Wall E., Coffey M.P., Daetwyler H.D., Hayes B.J., Pryce J.E. Improved accuracy of genomic prediction for dry matter intake of dairy cattle from combined European and Australian data sets. J. Dairy Sci 2012, 95:6103-6112.
    • (2012) J. Dairy Sci , vol.95 , pp. 6103-6112
    • de Haas, Y.1    Calus, M.P.L.2    Veerkamp, R.F.3    Wall, E.4    Coffey, M.P.5    Daetwyler, H.D.6    Hayes, B.J.7    Pryce, J.E.8
  • 15
    • 84876390765 scopus 로고    scopus 로고
    • Whole-genome regression and prediction methods applied to plant and animal breeding
    • de los Campos G., Hickey J.M., Pong-Wong R., Daetwyler H.D., Calus M.P.L. Whole-genome regression and prediction methods applied to plant and animal breeding. Genetics 2013, 193:327-345.
    • (2013) Genetics , vol.193 , pp. 327-345
    • de los Campos, G.1    Hickey, J.M.2    Pong-Wong, R.3    Daetwyler, H.D.4    Calus, M.P.L.5
  • 16
    • 84884350830 scopus 로고    scopus 로고
    • Genomic selection in dairy cattle
    • Wageningen University, Wageningen, the Netherlands
    • de Roos A.P.W. Genomic selection in dairy cattle. PhD Thesis 2011, Wageningen University, Wageningen, the Netherlands.
    • (2011) PhD Thesis
    • de Roos, A.P.W.1
  • 17
    • 21144478473 scopus 로고
    • Solution of multiple trait animal models with missing data on some traits
    • Ducrocq V., Besbes B. Solution of multiple trait animal models with missing data on some traits. J. Anim. Breed. Genet 1993, 110:81-92.
    • (1993) J. Anim. Breed. Genet , vol.110 , pp. 81-92
    • Ducrocq, V.1    Besbes, B.2
  • 18
    • 0035403306 scopus 로고    scopus 로고
    • Weighting factors of sire daughter information in international genetic evaluations
    • Fikse W.F., Banos G. Weighting factors of sire daughter information in international genetic evaluations. J. Dairy Sci 2001, 84:1759-1767.
    • (2001) J. Dairy Sci , vol.84 , pp. 1759-1767
    • Fikse, W.F.1    Banos, G.2
  • 19
    • 77949854404 scopus 로고    scopus 로고
    • Deregressing estimated breeding values and weighting information for genomic regression analyses
    • Garrick D.J., Taylor J.F., Fernando R.L. Deregressing estimated breeding values and weighting information for genomic regression analyses. Genet. Sel. Evol 2009, 41:55.
    • (2009) Genet. Sel. Evol , vol.41 , pp. 55
    • Garrick, D.J.1    Taylor, J.F.2    Fernando, R.L.3
  • 20
    • 67349287476 scopus 로고    scopus 로고
    • Genomic selection: Prediction of accuracy and maximisation of long term response
    • Goddard M. Genomic selection: Prediction of accuracy and maximisation of long term response. Genetica 2009, 136:245-257.
    • (2009) Genetica , vol.136 , pp. 245-257
    • Goddard, M.1
  • 22
    • 59349098163 scopus 로고    scopus 로고
    • Invited review: Genomic selection in dairy cattle: Progress and challenges
    • Hayes B.J., Bowman P.J., Chamberlain A.J., Goddard M.E. Invited review: Genomic selection in dairy cattle: Progress and challenges. J. Dairy Sci 2009, 92:433-443.
    • (2009) J. Dairy Sci , vol.92 , pp. 433-443
    • Hayes, B.J.1    Bowman, P.J.2    Chamberlain, A.J.3    Goddard, M.E.4
  • 24
    • 84863423405 scopus 로고    scopus 로고
    • Genotyping strategies for genomic selection in dairy cattle
    • Jiménez-Montero J.A., Gonzalez-Recio O., Alenda R. Genotyping strategies for genomic selection in dairy cattle. Animal 2012, 6:1216-1224.
    • (2012) Animal , vol.6 , pp. 1216-1224
    • Jiménez-Montero, J.A.1    Gonzalez-Recio, O.2    Alenda, R.3
  • 25
    • 79952597275 scopus 로고    scopus 로고
    • Whole-genome association analysis of susceptibility to paratuberculosis in Holstein cattle
    • Kirkpatrick B.W., Shi X., Shook G.E., Collins M.T. Whole-genome association analysis of susceptibility to paratuberculosis in Holstein cattle. Anim. Genet 2011, 42:149-160.
    • (2011) Anim. Genet , vol.42 , pp. 149-160
    • Kirkpatrick, B.W.1    Shi, X.2    Shook, G.E.3    Collins, M.T.4
  • 26
    • 0040028143 scopus 로고    scopus 로고
    • Genetic covariance functions for live weight, condition score, and dry-matter intake measured at different lactation stages of Holstein Friesian heifers
    • Koenen E.P.C., Veerkamp R.F. Genetic covariance functions for live weight, condition score, and dry-matter intake measured at different lactation stages of Holstein Friesian heifers. Livest. Prod. Sci 1998, 57:67-77.
    • (1998) Livest. Prod. Sci , vol.57 , pp. 67-77
    • Koenen, E.P.C.1    Veerkamp, R.F.2
  • 27
    • 70349925402 scopus 로고    scopus 로고
    • Application of selection index calculations to determine selection strategies in genomic breeding programs
    • König S., Swalve H.H. Application of selection index calculations to determine selection strategies in genomic breeding programs. J. Dairy Sci 2009, 92:5292-5303.
    • (2009) J. Dairy Sci , vol.92 , pp. 5292-5303
    • König, S.1    Swalve, H.H.2
  • 28
    • 38949168198 scopus 로고    scopus 로고
    • Computing strategies in genome-wide selection
    • Legarra A., Misztal I. Computing strategies in genome-wide selection. J. Dairy Sci 2008, 91:360-366.
    • (2008) J. Dairy Sci , vol.91 , pp. 360-366
    • Legarra, A.1    Misztal, I.2
  • 30
    • 27544441647 scopus 로고    scopus 로고
    • Short communication: Difficulties in estimating across-country genetic correlations for weakly linked bull populations
    • Mark T., Madsen P., Jensen J., Fikse W.F. Short communication: Difficulties in estimating across-country genetic correlations for weakly linked bull populations. J. Dairy Sci 2005, 88:3303-3305.
    • (2005) J. Dairy Sci , vol.88 , pp. 3303-3305
    • Mark, T.1    Madsen, P.2    Jensen, J.3    Fikse, W.F.4
  • 31
    • 2442597278 scopus 로고    scopus 로고
    • Mapping multiple QTL using linkage disequilibrium and linkage analysis information and multitrait data
    • Meuwissen T.H.E., Goddard M.E. Mapping multiple QTL using linkage disequilibrium and linkage analysis information and multitrait data. Genet. Sel. Evol 2004, 36:261-279.
    • (2004) Genet. Sel. Evol , vol.36 , pp. 261-279
    • Meuwissen, T.H.E.1    Goddard, M.E.2
  • 32
    • 0035045051 scopus 로고    scopus 로고
    • Prediction of total genetic value using genome-wide dense marker maps
    • Meuwissen T.H.E., Hayes B.J., Goddard M.E. Prediction of total genetic value using genome-wide dense marker maps. Genetics 2001, 157:1819-1829.
    • (2001) Genetics , vol.157 , pp. 1819-1829
    • Meuwissen, T.H.E.1    Hayes, B.J.2    Goddard, M.E.3
  • 33
    • 70449382559 scopus 로고    scopus 로고
    • Database of cattle candidate genes and genetic markers for milk production and mastitis
    • Ogorevc J., Kunej T., Razpet A., Dovc P. Database of cattle candidate genes and genetic markers for milk production and mastitis. Anim. Genet 2009, 40:832-851.
    • (2009) Anim. Genet , vol.40 , pp. 832-851
    • Ogorevc, J.1    Kunej, T.2    Razpet, A.3    Dovc, P.4
  • 34
    • 82155163139 scopus 로고    scopus 로고
    • Reliability of direct genomic values for animals with different relationships within and to the reference population
    • a
    • Pszczola M., Strabel T., Mulder H.A., Calus M.P.L. Reliability of direct genomic values for animals with different relationships within and to the reference population. J. Dairy Sci 2012, 95:389-400. a.
    • (2012) J. Dairy Sci , vol.95 , pp. 389-400
    • Pszczola, M.1    Strabel, T.2    Mulder, H.A.3    Calus, M.P.L.4
  • 35
    • 84865320793 scopus 로고    scopus 로고
    • The impact of genotyping different groups of animals on accuracy when moving from traditional to genomic selection
    • b
    • Pszczola M., Strabel T., van Arendonk J.A.M., Calus M.P.L. The impact of genotyping different groups of animals on accuracy when moving from traditional to genomic selection. J. Dairy Sci 2012, 95:5412-5421. b.
    • (2012) J. Dairy Sci , vol.95 , pp. 5412-5421
    • Pszczola, M.1    Strabel, T.2    van Arendonk, J.A.M.3    Calus, M.P.L.4
  • 36
    • 84884353443 scopus 로고    scopus 로고
    • Best use of conventional EBV of bull dams and combination with direct genomic values
    • Pages 123-126 in Interbull Bulletin no. 40. Proc. of the Interbull International Workshop-Genomic Information in Genetic Evaluations, Barcelona, Spain. Interbull, Uppsala, Sweden
    • Rensing, S., E. Pasman, and F. Reinhardt. 2009. Best use of conventional EBV of bull dams and combination with direct genomic values. Pages 123-126 in Interbull Bulletin no. 40. Proc. of the Interbull International Workshop-Genomic Information in Genetic Evaluations, Barcelona, Spain. Interbull, Uppsala, Sweden.
    • (2009)
    • Rensing, S.1    Pasman, E.2    Reinhardt, F.3
  • 37
    • 0036835912 scopus 로고    scopus 로고
    • Interval and composite interval mapping of somatic cell score, yield, and components of milk in dairy cattle
    • Rodriguez-Zas S.L., Southey B.R., Heyen D.W., Lewin H.A. Interval and composite interval mapping of somatic cell score, yield, and components of milk in dairy cattle. J. Dairy Sci 2002, 85:3081-3091.
    • (2002) J. Dairy Sci , vol.85 , pp. 3081-3091
    • Rodriguez-Zas, S.L.1    Southey, B.R.2    Heyen, D.W.3    Lewin, H.A.4
  • 38
    • 0034760719 scopus 로고    scopus 로고
    • Multiple quantitative trait locus analysis of bovine chromosome 6 in the Israeli Holstein population by a daughter design
    • Ron M., Kliger D., Feldmesser E., Seroussi E., Ezra E., Weller J.I. Multiple quantitative trait locus analysis of bovine chromosome 6 in the Israeli Holstein population by a daughter design. Genetics 2001, 159:727-735.
    • (2001) Genetics , vol.159 , pp. 727-735
    • Ron, M.1    Kliger, D.2    Feldmesser, E.3    Seroussi, E.4    Ezra, E.5    Weller, J.I.6
  • 39
    • 0018154846 scopus 로고
    • Simultaneous estimation of variance and covariance components from multitrait mixed model equations
    • Schaeffer L.R., Wilton J.W., Thompson R. Simultaneous estimation of variance and covariance components from multitrait mixed model equations. Biometrics 1978, 34:199-208.
    • (1978) Biometrics , vol.34 , pp. 199-208
    • Schaeffer, L.R.1    Wilton, J.W.2    Thompson, R.3
  • 41
    • 79960637076 scopus 로고    scopus 로고
    • Multiple-trait genomic evaluation of linear type traits using genomic and phenotypic data in US Holsteins
    • Tsuruta S., Misztal I., Aguilar I., Lawlor T.J. Multiple-trait genomic evaluation of linear type traits using genomic and phenotypic data in US Holsteins. J. Dairy Sci 2011, 94:4198-4204.
    • (2011) J. Dairy Sci , vol.94 , pp. 4198-4204
    • Tsuruta, S.1    Misztal, I.2    Aguilar, I.3    Lawlor, T.J.4
  • 42
    • 84858984749 scopus 로고    scopus 로고
    • Makeup of the genetic correlation between milk production traits using genome-wide single nucleotide polymorphism information
    • van Binsbergen R., Veerkamp R.F., Calus M.P.L. Makeup of the genetic correlation between milk production traits using genome-wide single nucleotide polymorphism information. J. Dairy Sci 2012, 95:2132-2143.
    • (2012) J. Dairy Sci , vol.95 , pp. 2132-2143
    • van Binsbergen, R.1    Veerkamp, R.F.2    Calus, M.P.L.3
  • 43
    • 77952760672 scopus 로고    scopus 로고
    • International genomic evaluation methods for dairy cattle
    • VanRaden P.M., Sullivan P.G. International genomic evaluation methods for dairy cattle. Genet. Sel. Evol 2010, 42:7.
    • (2010) Genet. Sel. Evol , vol.42 , pp. 7
    • VanRaden, P.M.1    Sullivan, P.G.2
  • 44
    • 55849133422 scopus 로고    scopus 로고
    • Efficient methods to compute genomic predictions
    • VanRaden P.M. Efficient methods to compute genomic predictions. J. Dairy Sci 2008, 91:4414-4423.
    • (2008) J. Dairy Sci , vol.91 , pp. 4414-4423
    • VanRaden, P.M.1
  • 45
    • 84867045246 scopus 로고    scopus 로고
    • Genome-wide associations for feed utilisation complex in primiparous Holstein-Friesian dairy cows from experimental research herds in four European countries
    • Veerkamp R.F., Coffey M.P., Berry D.P., de Haas Y., Strandberg E., Bovenhuis H., Calus M.P.L., Wall E. Genome-wide associations for feed utilisation complex in primiparous Holstein-Friesian dairy cows from experimental research herds in four European countries. Animal 2012, 6:1738-1749.
    • (2012) Animal , vol.6 , pp. 1738-1749
    • Veerkamp, R.F.1    Coffey, M.P.2    Berry, D.P.3    de Haas, Y.4    Strandberg, E.5    Bovenhuis, H.6    Calus, M.P.L.7    Wall, E.8
  • 46
    • 77952974808 scopus 로고    scopus 로고
    • Predicting energy balance for dairy cows using high-density single nucleotide polymorphism information
    • Verbyla K.L., Calus M.P.L., Mulder H.A., de Haas Y., Veerkamp R.F. Predicting energy balance for dairy cows using high-density single nucleotide polymorphism information. J. Dairy Sci 2010, 93:2757-2764.
    • (2010) J. Dairy Sci , vol.93 , pp. 2757-2764
    • Verbyla, K.L.1    Calus, M.P.L.2    Mulder, H.A.3    de Haas, Y.4    Veerkamp, R.F.5
  • 47
    • 75649126894 scopus 로고    scopus 로고
    • Accuracy of genomic selection using stochastic search variable selection in Australian Holstein Friesian dairy cattle
    • Verbyla K.L., Hayes B.J., Bowman P.J., Goddard M.E. Accuracy of genomic selection using stochastic search variable selection in Australian Holstein Friesian dairy cattle. Genet. Res. (Camb.) 2009, 91:307-311.
    • (2009) Genet. Res. (Camb.) , vol.91 , pp. 307-311
    • Verbyla, K.L.1    Hayes, B.J.2    Bowman, P.J.3    Goddard, M.E.4
  • 48
    • 0034487852 scopus 로고    scopus 로고
    • Testing for the presence of previously identified QTL for milk production traits in new populations
    • Wiener P., Maclean I., Williams J., Woolliams J. Testing for the presence of previously identified QTL for milk production traits in new populations. Anim. Genet 2000, 31:385-395.
    • (2000) Anim. Genet , vol.31 , pp. 385-395
    • Wiener, P.1    Maclean, I.2    Williams, J.3    Woolliams, J.4


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