Abstract
Genomic selection (GS) is a method to predict the genetic value of selection candidates based on the genomic estimated breeding value (GEBV) predicted from high-density markers positioned throughout the genome. Unlike marker-assisted selection, the GEBV is based on all markers including both minor and major marker effects. Thus, the GEBV may capture more of the genetic variation for the particular trait under selection.
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Meuwissen THE, Hayes BJ, Goddard ME (2001) Prediction of total genetic value using genome-wide dense marker maps. Genetics 157:1819–1829
VanRaden PM, Van Tassell CP, Wiggans GR, Sonstegard TS, Schnabel RD, Taylor JF, Schenkel FS (2009) Invited review: reliability of genomic predictions for North American Holstein bulls. J Dairy Sci 92:16–24
Lorenzana RE, Bernardo R (2009) Accuracy of genotypic value predictions for marker-based selection in biparental plant populations. Theor Appl Genet 120:151–161
de los Campos G, Naya G, Gianola D, Crossa J, Legarra A, Manfredi E, Weigel K, Cotes JM (2009) Predicting quantitative traits with regression models for dense molecular markers and pedigrees. Genetics 182:375–385
Asoro FG, Newell MA, Beavis WD, Scott MP, Jannink J-L (2011) Accuracy and training population design for genomic selection on quantitative traits in elite North American oats. Plant Genome 4:132–144
Lorenz AJ, Smith KP, Jannink J-L (2012) Potential and optimization of genomic selection for Fusarium Head Blight resistance in six-row barley. Crop Sci 52:1609–1621
Hayes BJ, Bowman PJ, Chamberlain AC, Goddard ME (2009) Invited review: genomic selection in dairy cattle: progress and challenges. J Dairy Sci 92:433–443
Daetwyler HD, Pong-Wong R, Villanueva B, Woolliams JA (2010) The impact of genetic architecture on genome-wide evaluation methods. Genetics 185:1021–1031
Habier D, Fernando R, Dekkers J (2007) The impact of genetic relationship information on genome-assisted breeding values. Genetics 177:2389–2397
Habier D, Tetens J, Seefried FR, Lichtner P, Thaller G (2010) The impact of genetic relationship information on genomic breeding values in German Holstein cattle. Genet Sel Evol 42:5
Clark SA, Hickey JM, Daetwyler HD, van der Werf JHJ (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
de Roos APW, Hayes BJ, Goddard ME (2009) Reliability of genomic breeding values across multiple populations. Genetics 183:1545–1553
Hayes BJ, Bowman PJ, Chamberlain AC, Verbyla K, Goddard ME (2009) Accuracy of genomic breeding values in multi-breed dairy cattle populations. Genet Sel Evol 41:51
Yu J, Pressoir G, Briggs WH, Bi IV, Yamasaki M, Doebley JF, McMullen MD, Gaut BS, Nielsen DM, Holland JB, Kresovich S, Buckler ES (2006) A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nat Genet 38:203–208
Jannink J-L (2010) Dynamics of long-term genomic selection. Genet Sel Evol 42:35
Bijma P (2012) Accuracies of estimated breeding values from ordinary genetic evaluations do not reflect the correlation between true and estimated breeding values in selected populations. J Anim Breed Genet 129:345–358
Sonesson AK, Woolliams JA, Meuwissen THE (2012) Genomic selection requires genomic control of inbreeding. Genet Sel Evol 44:27
Heffner EL, Lorenz AJ, Jannink J-L, Sorrells ME (2010) Plant breeding with genomic selection: gain per unit time and cost. Crop Sci 50:1681–1690
Endelman J (2011) Ridge regression and other kernels for genomic selection with R package rrBLUP. Plant Genome 4:250–255
Wickham H (2009) ggplot2: elegant graphics for data analysis. Springer, New York
Lorenz A, Chao S, Asoro F, Heffner E, Hayashi T, Iwata H, Smith K, Sorrells M, Jannink J-L (2011) Genomic selection in plant breeding: knowledge and prospects. In: Sparks DL (ed) Advances in agronomy. Academic, San Diego, CA, pp 77–123
Acknowledgments
Funding for the data used in this chapter came from a US Department of Agriculture, National Institute of Food and Agriculture agreement, No. 2006-55606-16722 “Barley Coordinated Agricultural Project: Leveraging Genomics, Genetics, and Breeding for Gene Discovery and Barley Improvement.” Mark Newell’s contributed work was funded by “The Samuel Roberts Noble Foundation.”
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Newell, M.A., Jannink, JL. (2014). Genomic Selection in Plant Breeding. In: Fleury, D., Whitford, R. (eds) Crop Breeding. Methods in Molecular Biology, vol 1145. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-0446-4_10
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DOI: https://doi.org/10.1007/978-1-4939-0446-4_10
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