메뉴 건너뛰기




Volumn 45, Issue 1, 2013, Pages

Use of partial least squares regression to impute SNP genotypes in Italian Cattle breeds

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY ASSESSMENT; CATTLE; DATA SET; GENOMICS; GENOTYPE; POPULATION GENETICS; POPULATION STRUCTURE; REPRODUCTIVE BEHAVIOR; SOFTWARE;

EID: 84878455126     PISSN: 0999193X     EISSN: 12979686     Source Type: Journal    
DOI: 10.1186/1297-9686-45-15     Document Type: Article
Times cited : (8)

References (34)
  • 1
    • 59349098163 scopus 로고    scopus 로고
    • Genomic selection in dairy cattle: Progress and challenges
    • 10.3168/jds.2008-1646 19164653
    • Genomic selection in dairy cattle: progress and challenges. Hayes BJ, Bowman PJ, Chamberlain AJ, Goddard ME, J Dairy Sci 2009 92 433 443 10.3168/jds.2008-1646 19164653
    • (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
  • 2
    • 79956268263 scopus 로고    scopus 로고
    • Whole-genome association study for milk protein composition in dairy cattle
    • 10.3168/jds.2010-4030 21605784
    • Whole-genome association study for milk protein composition in dairy cattle. Schopen GCB, Visker MHPW, Koks PD, Mullaart E, van Aredonk JAM, Bovenhuis H, J Dairy Sci 2011 94 3148 3158 10.3168/jds.2010-4030 21605784
    • (2011) J Dairy Sci , vol.94 , pp. 3148-3158
    • Schopen, G.C.B.1    Visker, M.2    Koks, P.D.3    Mullaart, E.4    Van Aredonk, J.A.M.5    Bovenhuis, H.6
  • 5
    • 78649372542 scopus 로고    scopus 로고
    • Imputation of genotypes from different single nucleotide polymorphism panels in dairy cattle
    • 10.3168/jds.2010-3255 20965360
    • Imputation of genotypes from different single nucleotide polymorphism panels in dairy cattle. Druet T, Schrooten C, de Roos APW, J Dairy Sci 2010 93 5443 5454 10.3168/jds.2010-3255 20965360
    • (2010) J Dairy Sci , vol.93 , pp. 5443-5454
    • Druet, T.1    Schrooten, C.2    De Roos, A.P.W.3
  • 6
    • 80052679688 scopus 로고    scopus 로고
    • Imputation of missing genotypes from sparse to high density using long-range phasing
    • 10.1534/genetics.111.128082 21705746
    • Imputation of missing genotypes from sparse to high density using long-range phasing. Daetwyler HD, Wiggans GR, Hayes BJ, Woolliams JA, Goddard ME, Genetics 2011 189 317 327 10.1534/genetics.111.128082 21705746
    • (2011) Genetics , vol.189 , pp. 317-327
    • Daetwyler, H.D.1    Wiggans, G.R.2    Hayes, B.J.3    Woolliams, J.A.4    Goddard, M.E.5
  • 7
    • 79960051527 scopus 로고    scopus 로고
    • A combined long-range phasing and long haplotype imputation method to impute phase for SNP genotypes
    • 10.1186/1297-9686-43-12 21388557
    • A combined long-range phasing and long haplotype imputation method to impute phase for SNP genotypes. Hickey JM, Kinghorn BP, Tier B, Wilson JF, Dunstan N, van der Werf JHJ, Genet Sel Evol 2011 43 12 10.1186/1297-9686-43-12 21388557
    • (2011) Genet Sel Evol , vol.43 , pp. 12
    • Hickey, J.M.1    Kinghorn, B.P.2    Tier, B.3    Wilson, J.F.4    Dunstan, N.5    Van Der Werf, J.H.J.6
  • 8
    • 33644974019 scopus 로고    scopus 로고
    • A fast and flexible statistical model for large-scale population genotype data: Applications to inferring missing genotypes and haplotypic phase
    • 10.1086/502802 16532393
    • A fast and flexible statistical model for large-scale population genotype data: applications to inferring missing genotypes and haplotypic phase. Scheet P, Stephens M, Am J Hum Genet 2006 78 629 644 10.1086/502802 16532393
    • (2006) Am J Hum Genet , vol.78 , pp. 629-644
    • Scheet, P.1    Stephens, M.2
  • 9
    • 62649155943 scopus 로고    scopus 로고
    • A unified approach to genotype imputation and haplotype-phase inference for large data sets of trios and unrelated individuals
    • 10.1016/j.ajhg.2009.01.005 19200528
    • A unified approach to genotype imputation and haplotype-phase inference for large data sets of trios and unrelated individuals. Browning BL, Browning SR, Am J Hum Genet 2009 84 210 223 10.1016/j.ajhg.2009.01.005 19200528
    • (2009) Am J Hum Genet , vol.84 , pp. 210-223
    • Browning, B.L.1    Browning, S.R.2
  • 10
    • 77950613737 scopus 로고    scopus 로고
    • A hidden Markov model combining linkage and linkage disequilibrium information for haplotype reconstruction and quantitative trait locus fine mapping
    • 10.1534/genetics.109.108431 20008575
    • A hidden Markov model combining linkage and linkage disequilibrium information for haplotype reconstruction and quantitative trait locus fine mapping. Druet T, Georges M, Genetics 2010 184 789 798 10.1534/genetics.109. 108431 20008575
    • (2010) Genetics , vol.184 , pp. 789-798
    • Druet, T.1    Georges, M.2
  • 11
  • 12
    • 77952054021 scopus 로고    scopus 로고
    • Prediction of unobserved single nucleotide polymorphism genotypes of Jersey cattle using reference panels and population-based imputation algorithms
    • 10.3168/jds.2009-2849 20412938
    • Prediction of unobserved single nucleotide polymorphism genotypes of Jersey cattle using reference panels and population-based imputation algorithms. Weigel KA, Van Tassell CP, O'Connell JR, VanRaden PM, Wiggans GR, J Dairy Sci 2010 93 2229 2238 10.3168/jds.2009-2849 20412938
    • (2010) J Dairy Sci , vol.93 , pp. 2229-2238
    • Weigel, K.A.1    Van Tassell, C.P.2    O'Connell, J.R.3    Vanraden, P.M.4    Wiggans, G.R.5
  • 13
    • 78649235216 scopus 로고    scopus 로고
    • Accuracy of direct genomic values derived from imputed single nucleotide polymorphism genotypes in Jersey cattle
    • 10.3168/jds.2010-3149 20965358
    • Accuracy of direct genomic values derived from imputed single nucleotide polymorphism genotypes in Jersey cattle. Weigel KA, De los Campos G, Vazquez AI, Rosa GJM, Gianola D, Van Tassell CP, J Dairy Sci 2010 93 5423 5435 10.3168/jds.2010-3149 20965358
    • (2010) J Dairy Sci , vol.93 , pp. 5423-5435
    • Weigel, K.A.1    De Los Campos, G.2    Vazquez, A.I.3    Rosa, G.J.M.4    Gianola, D.5    Van Tassell, C.P.6
  • 14
    • 78649359717 scopus 로고    scopus 로고
    • Marker imputation with low-density marker panels in Dutch Holstein cattle
    • 10.3168/jds.2010-3501 20965364
    • Marker imputation with low-density marker panels in Dutch Holstein cattle. Zhang Z, Druet T, J Dairy Sci 2010 93 5487 5494 10.3168/jds.2010-3501 20965364
    • (2010) J Dairy Sci , vol.93 , pp. 5487-5494
    • Zhang, Z.1    Druet, T.2
  • 15
    • 84865330571 scopus 로고    scopus 로고
    • Reliability of genomic prediction using imputed genotypes for German Holsteins: Illumina 3K to 54K bovine chip
    • Reliability of genomic prediction using imputed genotypes for German Holsteins: Illumina 3K to 54K bovine chip. Chen J, Liu Z, Reinhardt F, Reents R, Interbull Bull 2011 44 http://www-interbull.slu.se/ojs/index.php/ib/article/ view/1191
    • (2011) Interbull Bull , pp. 44
    • Chen, J.1    Liu, Z.2    Reinhardt, F.3    Reents, R.4
  • 16
    • 84865322262 scopus 로고    scopus 로고
    • Reliability of genomic prediction for German Holsteins using imputed genotypes from low-density chips
    • 10.3168/jds.2012-5466 22916947
    • Reliability of genomic prediction for German Holsteins using imputed genotypes from low-density chips. Segelke D, Chen J, Liu Z, Reinhadt F, Thaller G, Reents R, J Dairy Sci 2012 95 5403 5411 10.3168/jds.2012-5466 22916947
    • (2012) J Dairy Sci , vol.95 , pp. 5403-5411
    • Segelke, D.1    Chen, J.2    Liu, Z.3    Reinhadt, F.4    Thaller, G.5    Reents, R.6
  • 17
    • 79953822348 scopus 로고    scopus 로고
    • Accuracy of direct genomic values in Holstein bulls and cows using subsets of SNP markers
    • 10.1186/1297-9686-42-37 20950478
    • Accuracy of direct genomic values in Holstein bulls and cows using subsets of SNP markers. Moser G, Khatkar MS, Hayes BJ, Raadsma HW, Genet Sel Evol 2010 42 37 10.1186/1297-9686-42-37 20950478
    • (2010) Genet Sel Evol , vol.42 , pp. 37
    • Moser, G.1    Khatkar, M.S.2    Hayes, B.J.3    Raadsma, H.W.4
  • 18
    • 79958788991 scopus 로고    scopus 로고
    • Use of partial least squares regression to predict single nucleotide polymorphism marker genotypes when some animals are genotyped with a low-density panel
    • 10.1017/S1751731110002600 22440021
    • Use of partial least squares regression to predict single nucleotide polymorphism marker genotypes when some animals are genotyped with a low-density panel. Dimauro C, Steri R, Pintus MA, Gaspa G, Macciotta NPP, Animal 2011 5 833 837 10.1017/S1751731110002600 22440021
    • (2011) Animal , vol.5 , pp. 833-837
    • Dimauro, C.1    Steri, R.2    Pintus, M.A.3    Gaspa, G.4    Macciotta, N.P.P.5
  • 19
    • 6344222582 scopus 로고    scopus 로고
    • Partial least square (PLS) regression
    • Thousand Oaks: Sage Lewis-Beck M, Bryman A, Futing T
    • Partial least square (PLS) regression. Abdi H, Encyclopedia for Research Methods for the Social Sciences Thousand Oaks: Sage, Lewis-Beck M, Bryman A, Futing T, 2003 792 795
    • (2003) Encyclopedia for Research Methods for the Social Sciences , pp. 792-795
    • Abdi, H.1
  • 20
    • 79959332314 scopus 로고    scopus 로고
    • Effect of imputing markers from a low-density chip on the reliability of genomic breeding values in Holsteins populations
    • 10.3168/jds.2011-4299 21700057
    • Effect of imputing markers from a low-density chip on the reliability of genomic breeding values in Holsteins populations. Dassonneville R, Brøndum RF, Druet T, Fritz S, Guillaume F, Guldbrandtsen B, Lund MS, Ducrocq V, Su G, J Dairy Sci 2011 94 3679 3686 10.3168/jds.2011-4299 21700057
    • (2011) J Dairy Sci , vol.94 , pp. 3679-3686
    • Dassonneville, R.1    Brøndum, R.F.2    Druet, T.3    Fritz, S.4    Guillaume, F.5    Guldbrandtsen, B.6    Lund, M.S.7    Ducrocq, V.8    Su, G.9
  • 21
    • 75949112012 scopus 로고    scopus 로고
    • Genomic prediction of simulated multibreed and purebred performance using observed fifty thousand single nucleotide polymorphism genotypes
    • 10.2527/jas.2009-2064 19820059
    • Genomic prediction of simulated multibreed and purebred performance using observed fifty thousand single nucleotide polymorphism genotypes. Kizilkaya K, Fernando RL, Garrick DJ, J Anim Sci 2010 88 544 551 10.2527/jas.2009-2064 19820059
    • (2010) J Anim Sci , vol.88 , pp. 544-551
    • Kizilkaya, K.1    Fernando, R.L.2    Garrick, D.J.3
  • 24
    • 0035045051 scopus 로고    scopus 로고
    • Prediction of total genetic value using genome-wide dense marker maps
    • Prediction of total genetic value using genome-wide dense marker maps. Meuwissen TH, Hayes BJ, Goddard ME, Genetics 2001 157 1819 1829 11290733 (Pubitemid 32298846)
    • (2001) Genetics , vol.157 , Issue.4 , pp. 1819-1829
    • Meuwissen, T.H.E.1    Hayes, B.J.2    Goddard, M.E.3
  • 25
    • 67650518081 scopus 로고    scopus 로고
    • Total PLS based contribution plots for fault diagnosis
    • 10.3724/SP.J.1004.2009.00759
    • Total PLS based contribution plots for fault diagnosis. Li G, Qin SZ, Ji YD, Zhou DH, Acta Automat Sinica 2009 35 759 765 10.3724/SP.J.1004.2009.00759
    • (2009) Acta Automat Sinica , vol.35 , pp. 759-765
    • Li, G.1    Qin, S.Z.2    Ji, Y.D.3    Zhou, D.H.4
  • 26
    • 84856199438 scopus 로고    scopus 로고
    • Imputation of genotypes with low-density chips and its effect on reliability of direct genomic values in Dutch Holstein cattle
    • 10.3168/jds.2011-4490 22281352
    • Imputation of genotypes with low-density chips and its effect on reliability of direct genomic values in Dutch Holstein cattle. Mulder HA, Calus MPL, Druet T, Schrooten C, J Dairy Sci 2012 95 876 889 10.3168/jds.2011-4490 22281352
    • (2012) J Dairy Sci , vol.95 , pp. 876-889
    • Mulder, H.A.1    Calus, M.P.L.2    Druet, T.3    Schrooten, C.4
  • 27
    • 84859051417 scopus 로고    scopus 로고
    • Imputation performances of 3 low-density marker panels in beef and dairy cattle
    • 10.3168/jds.2011-5133 22720970
    • Imputation performances of 3 low-density marker panels in beef and dairy cattle. Dassonneville R, Fritz S, Ducroq V, Boichard D, J Dairy Sci 2012 95 4136 4140 10.3168/jds.2011-5133 22720970
    • (2012) J Dairy Sci , vol.95 , pp. 4136-4140
    • Dassonneville, R.1    Fritz, S.2    Ducroq, V.3    Boichard, D.4
  • 29
    • 68349139652 scopus 로고    scopus 로고
    • Genetic diversity of European cattle breeds highlights the conservation value of traditional unselected breeds with high effective population size
    • 10.1111/j.1365-294X.2009.04286.x 19659482
    • Genetic diversity of European cattle breeds highlights the conservation value of traditional unselected breeds with high effective population size. Medugorac I, Medugorac A, Russ I, Veit-Kensch CE, Taberlet P, Luntz B, Mix HM, Förster M, Mol Ecol 2009 18 3394 3410 10.1111/j.1365-294X.2009.04286.x 19659482
    • (2009) Mol Ecol , vol.18 , pp. 3394-3410
    • Medugorac, I.1    Medugorac, A.2    Russ, I.3    Veit-Kensch, C.E.4    Taberlet, P.5    Luntz, B.6    Mix, H.M.7    Förster, M.8
  • 30
    • 28144452828 scopus 로고    scopus 로고
    • Estimates of genetic diversity in the brown cattle population of Switzerland obtained from pedigree information
    • DOI 10.1111/j.1439-0388.2005.00552.x
    • Estimates of genetic diversity in the brown cattle population of Switzerland obtained from pedigree information. Hagger C, J Anim Breed Genet 2005 122 405 413 10.1111/j.1439-0388.2005.00552.x 16274425 (Pubitemid 41695732)
    • (2005) Journal of Animal Breeding and Genetics , vol.122 , Issue.6 , pp. 405-413
    • Hagger, C.1
  • 31
    • 52049096371 scopus 로고    scopus 로고
    • Linkage disequilibrium and persistence of phase in Holstein-Friesian, Jersey and Angus cattle
    • 10.1534/genetics.107.084301 18622038
    • Linkage disequilibrium and persistence of phase in Holstein-Friesian, Jersey and Angus cattle. de Roos APW, Hayes BJ, Spelman RJ, Goddard ME, Genetics 2008 179 1503 1512 10.1534/genetics.107.084301 18622038
    • (2008) Genetics , vol.179 , pp. 1503-1512
    • De Roos, A.P.W.1    Hayes, B.J.2    Spelman, R.J.3    Goddard, M.E.4
  • 33
    • 77949782994 scopus 로고    scopus 로고
    • Accuracy of genomic breeding values in multi-breed dairy cattle populations
    • 10.1186/1297-9686-41-51 19930712
    • Accuracy of genomic breeding values in multi-breed dairy cattle populations. Hayes BJ, Bowman PJ, Chamberlain AJ, Verbyla K, Goddard ME, Genet Sel Evol 2009 41 51 10.1186/1297-9686-41-51 19930712
    • (2009) Genet Sel Evol , vol.41 , pp. 51
    • Hayes, B.J.1    Bowman, P.J.2    Chamberlain, A.J.3    Verbyla, K.4    Goddard, M.E.5
  • 34
    • 79960147440 scopus 로고    scopus 로고
    • Imputation of genotypes from low- to high-density genotyping platforms and implications for genomic selection
    • 10.1017/S1751731111000309 22440168
    • Imputation of genotypes from low- to high-density genotyping platforms and implications for genomic selection. Berry DP, Kearney JF, Animal 2011 5 1162 1169 10.1017/S1751731111000309 22440168
    • (2011) Animal , vol.5 , pp. 1162-1169
    • Berry, D.P.1    Kearney, J.F.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.