Optimal design of preliminary yield trials with genome-wide markers

Crop Science

Volumn 54, Issue 1, 2014, Pages 48-59

  Endelman, J B ^a   Atlin, G N ^c   Beyene, Y ^d   Semagn, K ^d   Zhang, X ^e   Sorrells, M E ^b   Jannink, J L ^f  

^a UNIVERSITY OF WISCONSIN MADISON   (United States)

^b Department of Obstetrics Gynecology   (United States)

^c BILL AND MELINDA GATES FOUNDATION   (United States)

^d INTERNATIONAL MAIZE AND WHEAT IMPROVEMENT CENTER CIMMYT   (Kenya)

^e INTERNATIONAL MAIZE AND WHEAT IMPROVEMENT CENTER CIMMYT   (Mexico)

^f ROBERT W HOLLEY CENTER FOR AGRICULTURE AND HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84887611798     PISSN: 0011183X     EISSN: 14350653     Source Type: Journal    
DOI: 10.2135/cropsci2013.03.0154     Document Type: Article

References (31)

1. Bernardo, R., and J. Yu. 2007. Prospects for genomewide selection for quantitative traits in maize. Crop Sci. 47:1082-1090. doi:10.2135/cropsci2006.11.0690
2. Bos, I. 1983. The optimum number of replications when testing lines or families on a fixed number of plots. Euphytica 32:311-318. doi:10.1007/BF00021439
3. Bulmer, M.G. 1980. The mathematical theory of quantitative genetics. Clarendon Press, Oxford.
4. Clark, S.A., J.M. Hickey, H.D. Daetwyler, and J.H.J. van der Werf. 2012. The importance of information on relatives for the prediction of genomic breeding values and the implications for the makeup of reference data sets in livestock breeding schemes. Genet., Sel., Evol. 44:4. doi:10.1186/1297-9686-44-4
5. Daetwyler, H.D., R. Pong-Wong, B. Villanueva, and J.A. Woolliams. 2010. The impact of genetic architecture on genomewide evaluation methods. Genetics 185:1021-1031. doi:10.1534/ genetics.110.116855
6. Dekkers, J.C.M. 2007. Prediction of response to markerassisted and genomic prediction using selection index theory. J. Anim. Breed. Genet. 124:331-341. doi:10.1111/j.1439-0388.2007.00701.x
7. Endelman, J.B. 2011. Ridge regression and other kernels for genomic selection with R package rrBLUP. Plant Gen. 4:250-255. doi:10.3835/plantgenome2011.08.0024
8. Endelman, J.B., and J.-L. Jannink. 2012. Shrinkage estimation of the realized relationship matrix. G3: Genes, Genomes, Genet. 2:1405-1413. doi:10.1534/g3.112.04269
9. Gauch, H.G., Jr., and R.W. Zobel. 1996. Optimal replication in selection experiments. Crop Sci. 36:838-843. doi:10.2135/crop sci1996.0011183X003600040002x
10. Gordillo, G.A., and H.H. Geiger. 2008. MBP (Version 1.0): A software package to optimize maize breeding procedures based on doubled haploid lines. J. Hered. 99:227-231. doi:10.1093/ jhered/esm103
11. Habier, D., R.L. Fernando, and J.C.M. Dekkers. 2007. The impact of genetic relationship information on genome-assisted breeding values. Genetics 177:2389-2397.
12. Jannink, J.-L., A.J. Lorenz, and H. Iwata. 2010. Genomic selection in plant breeding: From theory to practice. Brief. Funct. Genomics 9:166-177. doi:10.1093/bfgp/elq001
13. 2 lines from a maize population. Maydica 34:5-14.
14. Knapp, S.J. 1998. Marker-assisted selection as a strategy for increasing the probability of selecting superior genotypes. Crop Sci. 38:1164-1174. doi:10.2135/cropsci1998.0011183X003800050009x
15. Lande, R., and R. Thompson. 1990. Efficiency of marker-assisted selection in the improvement of quantitative traits. Genetics 124:743-756.
16. Longin, C.F.H., H.F. Utz, J.C. Reif, W. Schipprack, and A.E. Melchinger. 2006. Hybrid maize breeding with doubled haploids: I. One-stage versus two-stage selection for testcross performance. Theor. Appl. Genet. 112:903-912. doi:10.1007/ s00122-005-0192-z
17. Lorenz, A.J., S. Chao, F.G. Asoro, E.L. Heffner, T. Hayashi, H. Iwata, et al. 2011. Genomic selection in plant breeding: Knowledge and prospects. Adv. Agron. 110:77-123. doi:10.1016/ B978-0-12-385531-2.00002-5
18. Lorenzana, R.E., and R. Bernardo. 2009. Accuracy of genotypic value predictions for marker-based selection in biparental plant populations. Theor. Appl. Genet. 120:151-161. doi:10.1007/ s00122-009-1166-3
19. Massman, J.M., A. Gordillo, R.E. Lorenzana, and R. Bernardo. 2013. Genomewide predictions from maize single-cross data. Theor. Appl. Genet. 126:13-22. doi:10.1007/s00122-012-1955-y
20. Moreau, L., S. Lemarié, A. Charcosset, and A. Gallais. 2000. Economic efficiency of one cycle of marker-assisted selection. Crop Sci. 40:329-337. doi:10.2135/cropsci2000.402329x
21. Nagaraja, H.N., and H.A. David. 1994. Distribution of the maximum of concomitants of selected order statistics. Ann. Stat. 22:478-494. doi:10.1214/aos/1176325380
22. R Development Core Team. 2012. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna.
23. Rice, J.A. 2007. Mathematical statistics and data analysis. 3rd ed. Duxbury, Belmont, CA.
24. Riedelsheimer, C., J.B. Endelman, M. Stange, M.E. Sorrells, J.-L. Jannink, and A.E. Melchinger. 2013. Genomic predictability of interconnected bi-parental maize populations. Genetics 194:493-503. doi:10.1534/genetics.113.150227
25. Robson, D.S., L. Powers, and N.S. Urquhart. 1967. The proportion of genetic deviates in the tails of a normal population. Theor. Appl. Genet. 37:205-216. doi:10.1007/BF00329530
26. Searle, S.R., G. Casella, and C.E. McCulloch. 1992. Variance components. John Wiley & Sons, Hoboken, NJ.
27. Tinker, N.A., D.E. Mather, B.G. Rossnagel, K.J. Kasha, A. Kleinhofs, P.M. Hayes, et al. 1996. Regions of the genome that affect agronomic performance in two-row barley. Crop Sci. 36:1053-1062. doi:10.2135/cropsci1996.0011183X003600040040x
28. VanRaden, P.M. 2008. Efficient methods to compute genomic predictions. J. Dairy Sci. 91:4414-4423. doi:10.3168/jds.2007-0980
29. VSN International. 2009. ASReml 3. VSN Intl., Hemel Hempstead, UK.
30. Xie, C., and S. Xu. 1998. Efficiency of multistage marker-assisted selection in the improvement of multiple quantitative traits. Heredity 80:489-498. doi:10.1046/j.1365-2540.1998.00308.x
31. Zhao, Y., M. Gowda, W. Liu, T. Würschum, H.P. Maurer, F.H. Longin, et al. 2013. Choice of shrinkage parameter and prediction of genomic breeding values in elite maize breeding populations. Plant Breed. 132:99-106. doi:10.1111/pbr.12008