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Volumn 47, Issue 1, 2015, Pages

Sequence- vs. chip-assisted genomic selection: Accurate biological information is advised

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY ASSESSMENT; ANIMAL; CHROMOSOME; GENETIC ANALYSIS; GENOMICS; PLANT;

EID: 84928969287     PISSN: 0999193X     EISSN: 12979686     Source Type: Journal    
DOI: 10.1186/s12711-015-0117-5     Document Type: Article
Times cited : (131)

References (40)
  • 1
    • 59349098163 scopus 로고    scopus 로고
    • Invited review: Genomic selection in dairy cattle: Progress and challenges
    • 1:CAS:528:DC%2BD1MXit1Kju7s%3D 19164653
    • Hayes BJ, Bowman PJ, Chamberlain AJ, Goddard ME. Invited review: Genomic selection in dairy cattle: progress and challenges. J Dairy Sci. 2009;92:433-43.
    • (2009) J Dairy Sci , vol.92 , pp. 433-43
    • Hayes, B.J.1    Bowman, P.J.2    Chamberlain, A.J.3    Goddard, M.E.4
  • 2
    • 84899113044 scopus 로고    scopus 로고
    • Short communication: Use of young bulls in the United States
    • 1:CAS:528:DC%2BC2cXjslOmtLk%3D 24612804
    • Hutchison JL, Cole JB, Bickhart DM. Short communication: Use of young bulls in the United States. J Dairy Sci. 2014;97:3213-20.
    • (2014) J Dairy Sci , vol.97 , pp. 3213-20
    • Hutchison, J.L.1    Cole, J.B.2    Bickhart, D.M.3
  • 3
    • 77955482663 scopus 로고    scopus 로고
    • Accurate prediction of genetic values for complex traits by whole-genome resequencing
    • 2881142 1:CAS:528:DC%2BC3cXhsFOnu73M 20308278
    • Meuwissen T, Goddard M. Accurate prediction of genetic values for complex traits by whole-genome resequencing. Genetics. 2010;185:623-31.
    • (2010) Genetics , vol.185 , pp. 623-31
    • Meuwissen, T.1    Goddard, M.2
  • 4
    • 84905483050 scopus 로고    scopus 로고
    • Whole-genome sequencing of 234 bulls facilitates mapping of monogenic and complex traits in cattle
    • 1:CAS:528:DC%2BC2cXhtFGqsbjI 25017103
    • Daetwyler HD, Capitan A, Pausch H, Stothard P, van Binsbergen R, Brøndum RF, et al. Whole-genome sequencing of 234 bulls facilitates mapping of monogenic and complex traits in cattle. Nat Genet. 2014;46:858-65.
    • (2014) Nat Genet , vol.46 , pp. 858-65
    • Daetwyler, H.D.1    Capitan, A.2    Pausch, H.3    Stothard, P.4    Van Binsbergen, R.5    Brøndum, R.F.6
  • 5
    • 84890312913 scopus 로고    scopus 로고
    • Toward genomic prediction from whole-genome sequence data: Impact of sequencing design on genotype imputation and accuracy of predictions
    • 1:CAS:528:DC%2BC3sXhvFCqsr7N
    • Druet T, Macleod IM, Hayes BJ. Toward genomic prediction from whole-genome sequence data: impact of sequencing design on genotype imputation and accuracy of predictions. Heredity (Edinb). 2014;112:39-47.
    • (2014) Heredity (Edinb) , vol.112 , pp. 39-47
    • Druet, T.1    Macleod, I.M.2    Hayes, B.J.3
  • 8
    • 65449132092 scopus 로고    scopus 로고
    • Genome-wide survey of SNP variation uncovers the genetic structure of cattle breeds
    • 1:CAS:528:DC%2BD1MXkvVGmtLY%3D 19390050
    • Gibbs RA, Taylor JF, Van Tassell CP, Barendse W, Eversole KA, Gill CA, et al. Genome-wide survey of SNP variation uncovers the genetic structure of cattle breeds. Science. 2009;324:528-32.
    • (2009) Science , vol.324 , pp. 528-32
    • Gibbs, R.A.1    Taylor, J.F.2    Van Tassell, C.P.3    Barendse, W.4    Eversole, K.A.5    Gill, C.A.6
  • 9
    • 0036245438 scopus 로고    scopus 로고
    • Genealogical trees, coalescent theory and the analysis of genetic polymorphisms
    • 1:CAS:528:DC%2BD38Xjs1yhtLY%3D 11988763
    • Rosenberg NA, Nordborg M. Genealogical trees, coalescent theory and the analysis of genetic polymorphisms. Nat Rev Genet. 2002;3:380-90.
    • (2002) Nat Rev Genet , vol.3 , pp. 380-90
    • Rosenberg, N.A.1    Nordborg, M.2
  • 10
    • 61449135985 scopus 로고    scopus 로고
    • Fast and flexible simulation of DNA sequence data
    • 2612967 1:CAS:528:DC%2BD1MXptFWisQ%3D%3D 19029539
    • Chen GGK, Marjoram P, Wall JDJ. Fast and flexible simulation of DNA sequence data. Genome Res. 2009;19:136-42.
    • (2009) Genome Res , vol.19 , pp. 136-42
    • Chen, G.G.K.1    Marjoram, P.2    Wall, J.D.J.3
  • 11
    • 84897606419 scopus 로고    scopus 로고
    • Genomic relationships computed from either next-generation sequence or array SNP data
    • 24397314
    • Pérez-Enciso M. Genomic relationships computed from either next-generation sequence or array SNP data. J Anim Breed Genet. 2014;131:85-96.
    • (2014) J Anim Breed Genet , vol.131 , pp. 85-96
    • Pérez-Enciso, M.1
  • 12
    • 34447546660 scopus 로고    scopus 로고
    • The distribution of fitness effects of new mutations
    • 1:CAS:528:DC%2BD2sXnvVekt7s%3D 17637733
    • Eyre-Walker A, Keightley PD. The distribution of fitness effects of new mutations. Nat Rev Genet. 2007;8:610-8.
    • (2007) Nat Rev Genet , vol.8 , pp. 610-8
    • Eyre-Walker, A.1    Keightley, P.D.2
  • 13
    • 84859611693 scopus 로고    scopus 로고
    • Understanding and predicting the fitness decline of shrunk populations: Inbreeding, purging, mutation, and standard selection
    • 3316656 22298709
    • García-Dorado A. Understanding and predicting the fitness decline of shrunk populations: inbreeding, purging, mutation, and standard selection. Genetics. 2012;190:1461-76.
    • (2012) Genetics , vol.190 , pp. 1461-76
    • García-Dorado, A.1
  • 14
    • 0034957069 scopus 로고    scopus 로고
    • The distribution of the effects of genes affecting quantitative traits in livestock
    • 2705405 1:CAS:528:DC%2BD3MXltFWksL4%3D 11403745
    • Hayes B, Goddard ME. The distribution of the effects of genes affecting quantitative traits in livestock. Genet Sel Evol. 2001;33:209-29.
    • (2001) Genet Sel Evol , vol.33 , pp. 209-29
    • Hayes, B.1    Goddard, M.E.2
  • 16
    • 55849133422 scopus 로고    scopus 로고
    • Efficient methods to compute genomic predictions
    • 1:CAS:528:DC%2BD1cXhtlajtLzO 18946147
    • VanRaden PM. Efficient methods to compute genomic predictions. J Dairy Sci. 2008;91:4414-23.
    • (2008) J Dairy Sci , vol.91 , pp. 4414-23
    • Vanraden, P.M.1
  • 17
    • 0035045051 scopus 로고    scopus 로고
    • Prediction of total genetic value using genome-wide dense marker maps
    • 1:CAS:528:DC%2BD3MXjsFemtbY%3D 11290733
    • Meuwissen TH, Hayes BJ, Goddard ME. Prediction of total genetic value using genome-wide dense marker maps. Genetics. 2001;157:1819-29.
    • (2001) Genetics , vol.157 , pp. 1819-1829
    • Meuwissen, T.H.1    Hayes, B.J.2    Goddard, M.E.3
  • 18
    • 38949168198 scopus 로고    scopus 로고
    • Technical note: Computing strategies in genome-wide selection
    • 1:CAS:528:DC%2BD1cXhsVGitA%3D%3D 18096959
    • Legarra A, Misztal I. Technical note: Computing strategies in genome-wide selection. J Dairy Sci. 2008;91:360-6.
    • (2008) J Dairy Sci , vol.91 , pp. 360-6
    • Legarra, A.1    Misztal, I.2
  • 19
    • 84879743015 scopus 로고    scopus 로고
    • Priors in whole-genome regression: The bayesian alphabet returns
    • 3697965 1:CAS:528:DC%2BC3sXht1ChsrnN 23636739
    • Gianola D. Priors in whole-genome regression: the bayesian alphabet returns. Genetics. 2013;194:573-96.
    • (2013) Genetics , vol.194 , pp. 573-596
    • Gianola, D.1
  • 20
    • 84897110582 scopus 로고    scopus 로고
    • Re-sequencing studies of non-model organisms using closely-related reference genomes: Optimal experimental designs and bioinformatics approaches for population genomics
    • 1:STN:280:DC%2BC2cnpslWmsg%3D%3D 24795998
    • Nevado B, Ramos-Onsins S, Perez-Enciso M. Re-sequencing studies of non-model organisms using closely-related reference genomes: optimal experimental designs and bioinformatics approaches for population genomics. Mol Ecol. 2014;23:1764-79.
    • (2014) Mol Ecol , vol.23 , pp. 1764-79
    • Nevado, B.1    Ramos-Onsins, S.2    Perez-Enciso, M.3
  • 22
    • 77956295988 scopus 로고    scopus 로고
    • The genome analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
    • 2928508 1:CAS:528:DC%2BC3cXhtFeru7jM 20644199
    • McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, et al. The genome analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010;20:1297-303.
    • (2010) Genome Res , vol.20 , pp. 1297-303
    • McKenna, A.1    Hanna, M.2    Banks, E.3    Sivachenko, A.4    Cibulskis, K.5    Kernytsky, A.6
  • 23
    • 84923070606 scopus 로고    scopus 로고
    • Pipeliner: Software to evaluate the performance of bioinformatics pipelines for next-generation resequencing
    • 1:STN:280:DC%2BC2cjosVGrtw%3D%3D 24890372
    • Nevado B, Perez-Enciso M. Pipeliner: Software to evaluate the performance of bioinformatics pipelines for next-generation resequencing. Mol Ecol Resour. 2015;15:99-106.
    • (2015) Mol Ecol Resour , vol.15 , pp. 99-106
    • Nevado, B.1    Perez-Enciso, M.2
  • 24
    • 0036275126 scopus 로고    scopus 로고
    • BeadArray technology: Enabling an accurate, cost-effective approach to high-throughput genotyping
    • Oliphant A, Barker DL, Stuelpnagel JR, Chee MS. BeadArray technology: Enabling an accurate, cost-effective approach to high-throughput genotyping. Biotechniques. 2002;Suppl 56:60-61.
    • (2002) Biotechniques , vol.56 , pp. 60-61
    • Oliphant, A.1    Barker, D.L.2    Stuelpnagel, J.R.3    Chee, M.S.4
  • 25
    • 67650108558 scopus 로고    scopus 로고
    • Comparison of identical single nucleotide polymorphisms genotyped by the GeneChip Targeted Genotyping 25K, Affymetrix 500K and Illumina 550K platforms
    • 1:CAS:528:DC%2BD1MXotlOlt7k%3D 19394417
    • Kim KK, Won HH, Cho SS, Park JH, Kim MJ, Kim S, et al. Comparison of identical single nucleotide polymorphisms genotyped by the GeneChip Targeted Genotyping 25K, Affymetrix 500K and Illumina 550K platforms. Genomics. 2009;94:89-93.
    • (2009) Genomics , vol.94 , pp. 89-93
    • Kim, K.K.1    Won, H.H.2    Cho, S.S.3    Park, J.H.4    Kim, M.J.5    Kim, S.6
  • 26
    • 84865285342 scopus 로고    scopus 로고
    • Rates of assay success and genotyping error when single nucleotide polymorphism genotyping in non-model organisms: A case study in the Antarctic fur seal
    • 1:STN:280:DC%2BC38jkt1yhtA%3D%3D 22727236
    • Hoffman JI, Tucker R, Bridgett SJ, Clark MS, Forcada J, Slate J. Rates of assay success and genotyping error when single nucleotide polymorphism genotyping in non-model organisms: a case study in the Antarctic fur seal. Mol Ecol Resour. 2012;12:861-72.
    • (2012) Mol Ecol Resour , vol.12 , pp. 861-72
    • Hoffman, J.I.1    Tucker, R.2    Bridgett, S.J.3    Clark, M.S.4    Forcada, J.5    Slate, J.6
  • 28
    • 42649123990 scopus 로고    scopus 로고
    • Sizing up human height variation
    • 1:CAS:528:DC%2BD1cXltFyksrY%3D 18443579
    • Visscher PM. Sizing up human height variation. Nat Genet. 2008;40:489-90.
    • (2008) Nat Genet , vol.40 , pp. 489-90
    • Visscher, P.M.1
  • 30
    • 84915821124 scopus 로고    scopus 로고
    • The effects of demography and long-term selection on the accuracy of genomic prediction with sequence data
    • 25233989
    • MacLeod IM, Hayes BJ, Goddard ME. The effects of demography and long-term selection on the accuracy of genomic prediction with sequence data. Genetics. 2014;198:1671-84.
    • (2014) Genetics , vol.198 , pp. 1671-84
    • Macleod, I.M.1    Hayes, B.J.2    Goddard, M.E.3
  • 32
    • 84863652334 scopus 로고    scopus 로고
    • Using whole-genome sequence data to predict quantitative trait phenotypes in Drosophila melanogaster
    • 3342952 1:CAS:528:DC%2BC38Xnt1Oiu7w%3D 22570636
    • Ober U, Ayroles JF, Stone EA, Richards S, Zhu D, Gibbs RA, et al. Using whole-genome sequence data to predict quantitative trait phenotypes in Drosophila melanogaster. PLoS Genet. 2012;8:e1002685.
    • (2012) PLoS Genet , vol.8 , pp. 1002685
    • Ober, U.1    Ayroles, J.F.2    Stone, E.A.3    Richards, S.4    Zhu, D.5    Gibbs, R.A.6
  • 34
    • 79955783956 scopus 로고    scopus 로고
    • A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species
    • 3087801 1:CAS:528:DC%2BC3MXmtVKru7Y%3D 21573248
    • Elshire RJ, Glaubitz JC, Sun Q, Poland JA, Kawamoto K, Buckler ES, et al. A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS One. 2011;6:e19379.
    • (2011) PLoS One , vol.6 , pp. 19379
    • Elshire, R.J.1    Glaubitz, J.C.2    Sun, Q.3    Poland, J.A.4    Kawamoto, K.5    Buckler, E.S.6
  • 35
    • 55749084543 scopus 로고    scopus 로고
    • Tilting at quixotic trait loci (QTL): An evolutionary perspective on genetic causation
    • 2516055 18711218
    • Weiss KM. Tilting at quixotic trait loci (QTL): An evolutionary perspective on genetic causation. Genetics. 2008;179:1741-56.
    • (2008) Genetics , vol.179 , pp. 1741-56
    • Weiss, K.M.1
  • 37
    • 84897377942 scopus 로고    scopus 로고
    • Selection for complex traits leaves little or no classic signatures of selection
    • 3986643 24678841
    • Kemper KE, Saxton SJ, Bolormaa S, Hayes BJ, Goddard ME. Selection for complex traits leaves little or no classic signatures of selection. BMC Genomics. 2014;15:246.
    • (2014) BMC Genomics , vol.15 , pp. 246
    • Kemper, K.E.1    Saxton, S.J.2    Bolormaa, S.3    Hayes, B.J.4    Goddard, M.E.5
  • 38
    • 84881616630 scopus 로고    scopus 로고
    • SNP ascertainment bias in population genetic analyses: Why it is important, and how to correct it
    • 1:CAS:528:DC%2BC3sXht12gsb3O 23836388
    • Lachance J, Tishkoff S. SNP ascertainment bias in population genetic analyses: why it is important, and how to correct it. Bioessays. 2013;35:780-6.
    • (2013) Bioessays , vol.35 , pp. 780-6
    • Lachance, J.1    Tishkoff, S.2
  • 39
    • 84906497659 scopus 로고    scopus 로고
    • The distribution of deleterious genetic variation in human populations
    • Lohmueller KE. The distribution of deleterious genetic variation in human populations. bioRxiv. 2014;29:139-46.
    • (2014) BioRxiv , vol.29 , pp. 139-146
    • Lohmueller, K.E.1
  • 40
    • 40149087235 scopus 로고    scopus 로고
    • Data and theory point to mainly additive genetic variance for complex traits
    • 2265475 18454194
    • Hill WG, Goddard ME, Visscher PM. Data and theory point to mainly additive genetic variance for complex traits. PLoS Genet. 2008;4:e1000008.
    • (2008) PLoS Genet , vol.4 , pp. 1000008
    • Hill, W.G.1    Goddard, M.E.2    Visscher, P.M.3


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