Genomic Selection Accuracy using Multifamily Prediction Models in a Wheat Breeding Program

Plant Genome

Volumn 4, Issue 1, 2011, Pages

  Heffner, Elliot L ^a   Jannink, Jean Luc ^a   Sorrells, Mark E ^a  

^a Department of Molecular Biology and Genetics   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 85167520539     PISSN: None     EISSN: 19403372     Source Type: Journal    
DOI: 10.3835/plantgenome2010.12.0029     Document Type: Article

References (76)

1. Anderson, J.A., Sorrells, M.E., and Tanksley, S.D. 1993. RFLP analysis of genomic regions associated with resistance to preharvest sprouting in wheat. Crop Sci. 33:453–459.10.2135/cropsci1993.0011183X003300030008x. http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=agrocropsoil&KeyUT=A1993LM11100008&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=523bbf5d2a868de7bbaeea0bc70ec0e4
2. Beavis, W.D. 1998. QTL analyses: Power, precision, and accuracy. p. 145–162. In Paterson, A.H. (ed.) Molecular Dissection of Complex Traits. CRC Press, Boca Raton, FL.
3. Bernardo, R. 2008. Molecular markers and selection for complex traits in plants: Learning from the last 20 years. Crop Sci. 48:1649.10.2135/cropsci2008.03.0131. http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=agrocropsoil&KeyUT=000259792100001&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=523bbf5d2a868de7bbaeea0bc70ec0e4
4. Bernardo, R., and Yu, J. 2007. Prospects for genomewide selection for quantitative traits in maize. Crop Sci. 47:1082.10.2135/cropsci2006.11.0690. http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=agrocropsoil&KeyUT=000247424200020&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=523bbf5d2a868de7bbaeea0bc70ec0e4
5. Breseghello, F., and Sorrells, M.E. 2006. Association analysis as a strategy for improvement of quantitative traits in plants. Crop Sci. 46:1323–1330.10.2135/cropsci2005.09-0305. http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=agrocropsoil&KeyUT=000237375900040&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=523bbf5d2a868de7bbaeea0bc70ec0e4
6. Brim, C., Johnson, H.W., and Cockerham, C.C. 1959. Multiple selection criteria in soybeans. Agron. J. 51:42.10.2134/agronj1959.00021962005100010015x
7. Calus, M. 2010. Genomic breeding value prediction: Methods and procedures. Animal4:157–164.10.1017/S1751731109991352. http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=agrocropsoil&KeyUT=000274461500001&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=523bbf5d2a868de7bbaeea0bc70ec0e4
8. Crossa, J., de los Campos, G., Pérez, P., Gianola, D., Atlin, G., Burgueño, J., Araus, J.L., Makumbi, D., Singh, R., Dreisigacker, S., Yan, J., Arief, V., Banziger, M., and Braun, H.J. 2010. Prediction of genetic values of quantitative traits in plant breeding using pedigree and molecular markers. Genetics doi:10.1534/genetics.110.118521
9. Daetwyler, H.D., Pong-Wong, R., Villanueva, B., and Woolliams, J.A. 2010. The impact of genetic architecture on genome-wide evaluation methods. Genetics185:1021–1031.10.1534/genetics.110.116855. http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=agrocropsoil&KeyUT=000281906800025&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=523bbf5d2a868de7bbaeea0bc70ec0e4
10. Dekkers, J.C.M. 2007. Prediction of response to marker-assisted and genomic selection using selection index theory. J. Anim. Breed. Genet. 124:331–341.10.1111/j.1439-0388.2007.00701.x. http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=agrocropsoil&KeyUT=000251432800003&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=523bbf5d2a868de7bbaeea0bc70ec0e4
11. Dekkers, J.C.M., Garrick, D.J., and Fernando, R.L. 2009. Use of high-density SNP genotyping for genetic improvement of livestock. A short course organized by the Animal Breeding & Genetics Department of Animal Science Iowa State University June 1–10. http://taurus.ansci.iastate.edu/groups/genomicselectioninlivestock/wiki/129ad/Course_Information.html (verified 21 Feb. 2011). Iowa State Univ., Ames, IA.
12. Eathington, S.R., Crosbie, T.M., Edwards, M.D., Reiter, R.S., and Bull, J.K. 2007. Molecular markers in a commercial breeding program. Crop Sci. 47:S154–S163.http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=agrocropsoil&KeyUT=000253124800013&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=523bbf5d2a868de7bbaeea0bc70ec0e4
13. Federer, W.T. 1956. Augmented (or hoonuiaku) designs. Hawaiian Planter 's Records 55:191–208.
14. Fraley, C., and Raferty, A.E. 2002. Model-based clustering, discriminant analysis, and density estimation. J. Am. Stat. Assoc. 97:611–631.10.1198/016214502760047131. http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=agrocropsoil&KeyUT=000176078300027&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=523bbf5d2a868de7bbaeea0bc70ec0e4
15. Fraley, C., and Raferty, A.E. 2006. MCLUST version 3 for R: Normal mixture modeling and model-based clustering. Technical Report No. 504, Department of Statistics, University of Washington. http://www.stat.washington.edu/research/reports/2006/tr504.pdf. (verified 21 Feb. 2011). Univ. of Washington, Seattle, WA.
16. Gianola, D., de los Campos, G., Hill, W.G., Manfredi, E., and Fernando, R. 2009. Additive genetic variability and the Bayesian alphabet. Genetics183:347.10.1534/genetics.109.103952. http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=agrocropsoil&KeyUT=000272067000031&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=523bbf5d2a868de7bbaeea0bc70ec0e4
17. Gilmour, A.R., Gogel, B.J., Cullis, B.R., and Thompson, R. 2009. ASReml user guide release 3.0 VSN Intl. Ltd., Hemel Hempstead, UK.
18. Goddard, M. 2009. Genomic selection: Prediction of accuracy and maximisation of long term response. Genetica (The Hague) 136:245–257.
19. Gudbjartsson, D.F., Walters, G.B., Thorleifsson, G., Stefansson, H., and Halldorsson, B.V. et al 2008. Many sequence variants affecting diversity of adult human height. Nat. Genet. 40:609–615.10.1038/ng.122
20. Guttieri, M.J., Souza, E.J., and Sneller, C. 2008. Nonstarch polysaccharides in wheat flour wire-cut cookie making. J. Agric. Food Chem. 56:10927–10932.10.1021/jf801677a. http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=agrocropsoil&KeyUT=000261056700073&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=523bbf5d2a868de7bbaeea0bc70ec0e4
21. Habier, D., Fernando, R., and Dekkers, J. 2007. The impact of genetic relationship information on genome-assisted breeding values. Genetics 177:2389.http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=agrocropsoil&KeyUT=000251949800035&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=523bbf5d2a868de7bbaeea0bc70ec0e4
22. Harris, D.L. 1964. Expected and predicted progress from index selection involving estimates of population parameters. Biometrics 20:46–72.10.2307/2527617. http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=agrocropsoil&KeyUT=A19647269A00019&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=523bbf5d2a868de7bbaeea0bc70ec0e4
23. Hartigan, J., and Wong, M. 1978. Algorithm AS: A K-mean clustering algorithm. Appl. Stat 28:100–108.
24. Hayes, B.J., Bowman, P.J., Chamberlain, A.J., and Goddard, M.E. 2009a. Invited review: Genomic selection in dairy cattle: Progress and challenges. J. Dairy Sci. 92:433–443.
25. Hayes, B.J., Bowman, P.J., Chamberlain, A.J., Verbyla, K., and Goddard, M.E. 2009b. Accuracy of genomic breeding values in multi-breed dairy cattle populations. Genet. Sel. Evol. 41:51–60.
26. Hayes, B.J., Visscher, P.M., and Goddard, M.E. 2009c. Increased accuracy of artificial selection by using the realized relationship matrix. Genet. Res. 91:47–60.http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=agrocropsoil&KeyUT=000264226300006&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=523bbf5d2a868de7bbaeea0bc70ec0e4
27. Hazel, L. 1943. The genetic basis for constructing selection indexes. Genetics 28:476.
28. Heffner, E.L., Lorenz, A.J., Jannink, J.L., and Sorrells, M.E. 2010. Plant breeding with genomic selection: Gain per unit time and cost. Crop Sci. 50:1681–1690.10.2135/cropsci2009.11.0662. http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=agrocropsoil&KeyUT=000281060300010&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=523bbf5d2a868de7bbaeea0bc70ec0e4
29. Heffner, E.L., Sorrells, M.E., and Jannink, J.L. 2009. Genomic selection for crop improvement. Crop Sci. 49:1–12.10.2135/cropsci2008.08.0512. http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=agrocropsoil&KeyUT=000263344300001&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=523bbf5d2a868de7bbaeea0bc70ec0e4
30. Henderson, C. 1984. Application of linear models in animal breeding. University of Guelph, Guelph, ON, Canada.
31. Holland, J.B. 2004. Implementation of molecular markers for quantitative traits in breeding programs—Challenges and opportunities. In New directions for a diverse planet. Proc. Intl. Crop Sci. Congress, 4th, Brisbane, Australia. 26 Sept. – 1 Oct. 2004. The Regional Institute Ltd, Gosford, NSW, Australia.
32. Hospital, F., Moreau, L., Lacoudre, F., Charcosset, A., and Gallais, A. 1997. More on the efficiency of marker-assisted selection. Theor. Appl. Genet. 95:1181–1189.10.1007/s001220050679. http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=agrocropsoil&KeyUT=000071281000001&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=523bbf5d2a868de7bbaeea0bc70ec0e4
33. Jannink, J.L. 2010. Dynamics of long-term genomic selection. Genet. Sel. Evol. 42:35.10.1186/1297-9686-42-35
34. Jannink, J.L., Bink, M.C., and Jansen, R.C. 2001. Using complex plant pedigrees to map valuable genes. Trends Plant Sci. 6:337.10.1016/S1360-1385(01)02017-9. http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=agrocropsoil&KeyUT=000170479900003&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=523bbf5d2a868de7bbaeea0bc70ec0e4
35. Jannink, J.L., Lorenz, A.J., and Iwata, H. 2010. Genomic selection in plant breeding: From theory to practice. Brief. Funct. Genomics 9:166.
36. Kang, H.M., Zaitlen, N.A., Wade, C.M., Kirby, A., Heckerman, D., Daly, M.J., and Eskin, E. 2008. Efficient control of population structure in model organism association mapping. Genetics 178:1709.10.1534/genetics.107.080101. http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=agrocropsoil&KeyUT=000254921600050&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=523bbf5d2a868de7bbaeea0bc70ec0e4
37. Knapp, S., and Bridges, W. 1990. Using molecular markers to estimate quantitative trait locus parameters: Power and genetic variances for unreplicated and replicated progeny. Genetics 126:769–777.http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=agrocropsoil&KeyUT=A1990EF29100026&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=523bbf5d2a868de7bbaeea0bc70ec0e4
38. Lande, R., and Thompson, R. 1990. Efficiency of marker-assisted selection in the improvement of quantitative traits. Genetics 124:743–756.http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=agrocropsoil&KeyUT=A1990CQ97500027&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=523bbf5d2a868de7bbaeea0bc70ec0e4
39. Lettre, G., Jackson, A.U., Gieger, C., Schumacher, F.R., and Berndt, S.I. et al 2008. Identification of ten loci associated with height highlights new biological pathways in human growth. Nat. Genet. 40:584–591.10.1038/ng.125
40. Lin, C.Y. 1978. Index selection for genetic improvement of quantitative characters. Theor. Appl. Genet. 73:556–562.
41. Lorenz, A.J., Chao, S., Asoro, F.G., Heffner, E.L., Hayashi, T., Iwata, H., Smith, K.P., Sorrells, M.E., and Jannink, J.L. 2011. Genomic selection in plant breeding: Knowledge and prospects. Adv. Agron 110:77–123.10.1016/B978-0-12-385531-2.00002-5
42. Lorenzana, R.E., and Bernardo, R. 2009. Accuracy of genotypic value predictions for marker-based selection in biparental plant populations. Theor. Appl. Genet. 120:151–161.10.1007/s00122-009-1166-3. http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=agrocropsoil&KeyUT=000271939900013&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=523bbf5d2a868de7bbaeea0bc70ec0e4
43. Luan, T., Woolliams, J.A., Lien, S., Kent, M., Svendsen, M., and Meuwissen, T.H.E. 2009. The accuracy of genomic selection in Norwegian red cattle assessed by cross-validation. Genetics 183:1119.10.1534/genetics.109.107391. http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=agrocropsoil&KeyUT=000272295800029&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=523bbf5d2a868de7bbaeea0bc70ec0e4
44. Lynch, M., and Walsh, B. 2008. Theory of selection index. Evolution and selection of quantitative traits: II. Advanced topics in breeding and evolution. Available at http://nitro.biosci.arizona.edu/zbook/NewVolume_2/newvol2.html (verified 7 Feb. 2011). Bruce Walsh, Seattle, WA.
45. Meuwissen, T.H.E. 2009. Accuracy of breeding values of ‘unrelated’ individuals predicted by dense SNP genotyping. Genet. Sel. Evol. 41:35.10.1186/1297-9686-41-35
46. Meuwissen, T.H.E., Hayes, B., and Goddard, M. 2001. Prediction of total genetic value using genome-wide dense marker maps. Genetics 157:1819.http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=agrocropsoil&KeyUT=000168223400036&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=523bbf5d2a868de7bbaeea0bc70ec0e4
47. Mohring, J., and Piepho, H.P. 2009. Comparison of weighting in two-stage analysis of plant breeding trials. Crop Sci. 49:1977–1988.10.2135/cropsci2009.02.0083. http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=agrocropsoil&KeyUT=000271607300004&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=523bbf5d2a868de7bbaeea0bc70ec0e4
48. Moreau, L., Charcosset, A., Hospital, F., and Gallais, A. 1998. Marker-assisted selection efficiency in populations of finite size. Genetics 148:1353–1365.http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=agrocropsoil&KeyUT=000072638000036&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=523bbf5d2a868de7bbaeea0bc70ec0e4
49. Moser, G., Tier, B., Crump, R.E., Khatkar, M.S., and Raadsma, H.W. 2009. A comparison of five methods to predict genomic breeding values of dairy bulls from genome-wide SNP markers. Genet. Sel. Evol. 41:56.10.1186/1297-9686-41-56
50. Muir, W.M. 2007. Comparison of genomic and traditional BLUP-estimated breeding value accuracy and selection response under alternative trait and genomic parameters. J. Anim. Breed. Genet. 124:342–355.10.1111/j.1439-0388.2007.00700.x. http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=agrocropsoil&KeyUT=000251432800004&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=523bbf5d2a868de7bbaeea0bc70ec0e4
51. Munkvold, J.D., Tanaka, J., Benscher, D., and Sorrells, M.E. 2009. Mapping quantitative trait loci for preharvest sprouting resistance in white wheat. Theor. Appl. Genet. 119:1223–1235.10.1007/s00122-009-1123-1. http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=agrocropsoil&KeyUT=000271029300007&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=523bbf5d2a868de7bbaeea0bc70ec0e4
52. Panse, V. 1946. An application of the discriminant function for selection in poultry. J. Genet. 47:242–248.10.1007/BF02986249. http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=agrocropsoil&KeyUT=A1946XX16600002&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=523bbf5d2a868de7bbaeea0bc70ec0e4
53. Piepho, H. 2009. Ridge regression and extensions for genomewide selection in maize. Crop Sci. 49:1165.10.2135/cropsci2008.10.0595. http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=agrocropsoil&KeyUT=000268109800003&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=523bbf5d2a868de7bbaeea0bc70ec0e4
54. Podlich, D.W., Winkler, C.R., and Cooper, M. 2004. Mapping as you go: An effective approach for marker-assisted selection of complex traits. Crop Sci. 44:1560.10.2135/cropsci2004.1560. http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=agrocropsoil&KeyUT=000223586200008&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=523bbf5d2a868de7bbaeea0bc70ec0e4
55. R Development Core Team. 2009. R: A language and environment for statistical computingR Foundation for Statistical Computing, Vienna, Austria.
56. Rafalski, A. 2009. Applications of single nucleotide polymorphisms in crop genetics. Curr. Opin. Plant Biol. 5:94.
57. Schaeffer, L.R. 2006. Strategy for applying genome-wide selection in dairy cattle. J. Anim. Breed. Genet. 123:218–223.10.1111/j.1439-0388.2006.00595.x. http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=agrocropsoil&KeyUT=000239006300002&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=523bbf5d2a868de7bbaeea0bc70ec0e4
58. Schön, C., Utz, S., Groh, B., Truberg, S., Openshaw, S., and Melchinger, A. 2004. QTL mapping based on resampling in a vast maize testcross experiment confirms the infinitesimal model of quantitative genetics for complex traits. Genetics 167:485–498.10.1534/genetics.167.1.485. http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=agrocropsoil&KeyUT=000221851100040&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=523bbf5d2a868de7bbaeea0bc70ec0e4
59. Sebastian, S., Streit, L., Stephens, P., Thompson, J., Hedges, B., Fabrizius, M., Soper, J., Schmidt, D., Kallem, R., and Hinds, M. 2010. Context-specific marker-assisted selection for improved grain yield in elite soybean populations. Crop Sci. 50:1196.10.2135/cropsci2009.02.0078. http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=agrocropsoil&KeyUT=000279138200010&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=523bbf5d2a868de7bbaeea0bc70ec0e4
60. Smith, H.F. 1936. A discriminant function for plant selection. Ann. Eugen 7:0–250.
61. Su, G., Guldbrandtsen, B., Gregersen, V., and Lund, M. Preliminary investigation on reliability of genomic estimated breeding values in the Danish Holstein population. J. Dairy Sci 93:1175–1183.
62. Sved, J.A. 1971–2010. Linkage disequilibrium and homozygosity of chromosome segments in finite populations. Theor. Popul. Biol. 2:125–141.10.1016/0040-5809(71)90011-6
63. van Eeuwijk, F.A., Boer, M., Totir, L.R., Bink, M., Wright, D., Winkler, C.R., Podlich, D., Boldman, K., Baumgarten, A., Smalley, M., Arbelbide, M. 2010. C.J.F. ter Braak, and M. Cooper Mixed model approaches for the identification of QTLs within a maize hybrid breeding program. Theor. Appl. Genet. 120:429–440.10.1007/s00122-009-1205-0
64. vanRaden, P. 2004. Invited review: Selection on net merit to improve lifetime profit. J. Dairy Sci. 87:3125–3131.10.3168/jds.S0022-0302(04)73447-5. http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=agrocropsoil&KeyUT=000224011800002&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=523bbf5d2a868de7bbaeea0bc70ec0e4
65. vanRaden, P., van Tassell, C., Wiggans, G., Sonstegard, T., Schnabel, R., Taylor, J., and Schenkel, F. 2009. Invited review: Reliability of genomic predictions for North American Holstein bulls. J. Dairy Sci. 92:16.10.3168/jds.2008-1514
66. Verbyla, K.L., Bowman, P.J., Hayes, B.J., and Goddard, M.E. Sensitivity of genomic selection to using different prior distributions. BMC Proc 4(Suppl 1) S5.
67. Visscher, P.M. 2007-2008. Sizing up human height variation. Nat. Genet. 40:489–490.10.1038/ng0508-489
68. Weedon, M.N., Lango, H., Lindgren, C.M., Wallace, C., Evans, D.M., Mangino, M., Freathy, R.M., Perry, J.R.B., Stevens, S., and Hall, A.S. 2008. Genome-wide association analysis identifies 20 loci that influence adult height. Nat. Genet. 40:575–583.10.1038/ng.121
69. Whittaker, J.C., Thompson, R., and Denham, M.C. 2000. Marker-assisted selection using ridge regression. Genet. Res. 75:249–252.10.1017/S0016672399004462
70. Williams, J. 1962. The evaluation of a selection index. Biometrics 18:375–393.10.2307/2527479. http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=agrocropsoil&KeyUT=A19627263A00031&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=523bbf5d2a868de7bbaeea0bc70ec0e4
71. Wong, C.K., and Bernardo, R. 2008. Genomewide selection in oil palm: Increasing selection gain per unit time and cost with small populations. Theor. Appl. Genet. 116:815–824.10.1007/s00122-008-0715-5. http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=agrocropsoil&KeyUT=000254262600008&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=523bbf5d2a868de7bbaeea0bc70ec0e4
72. Xu, S. 2003. Theoretical basis of the Beavis effect. Genetics 165:2259.http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=agrocropsoil&KeyUT=000187805300048&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=523bbf5d2a868de7bbaeea0bc70ec0e4
73. Xu, Y., and Crouch, J.H. 2008. Marker-assisted selection in plant breeding: From publications to practice. Crop Sci. 48:391.10.2135/cropsci2007.04.0191. http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=agrocropsoil&KeyUT=000254855500001&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=523bbf5d2a868de7bbaeea0bc70ec0e4
74. Yang, J., Benyamin, B., McEvoy, B.P., Gordon, S., Henders, A.K., Nyholt, D.R., Madden, P.A., Heath, A.C., Martin, N.G., and Montgomery, G.W. 2010. Common SNPs explain a large proportion of the heritability for human height. Nat. Genet. 42:565–569.10.1038/ng.608
75. Zhao, K., Aranzana, M.J., Kim, S., Lister, C., Shindo, C., Tang, C., Toomajian, C., Zheng, H., Dean, C., and Marjoram, P. An Arabidopsis example of association mapping in structured samples. PLoS Genet. 3:e4
76. Zhong, S., Dekkers, J., Fernando, R.L., and Jannink, J.L. 2009. Factors affecting accuracy from genomic selection in populations derived from multiple inbred lines: A barley case study. Genetics 182:355.10.1534/genetics.108.098277. http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=agrocropsoil&KeyUT=000270213800030&DestLinkType=FullRecord&DestApp=WOS_CPL&UsrCustomerID=523bbf5d2a868de7bbaeea0bc70ec0e4