Abstract
Estimating marker effects based on routinely generated phenotypic data of breeding programs is a cost-effective strategy to implement genomic selection. Truncation selection in breeding populations, however, could have a strong impact on the accuracy to predict genomic breeding values. The main objective of our study was to investigate the influence of phenotypic selection on the accuracy and bias of genomic selection. We used experimental data of 788 testcross progenies from an elite maize breeding program. The testcross progenies were evaluated in unreplicated field trials in ten environments and fingerprinted with 857 SNP markers. Random regression best linear unbiased prediction method was used in combination with fivefold cross-validation based on genotypic sampling. We observed a substantial loss in the accuracy to predict genomic breeding values in unidirectional selected populations. In contrast, estimating marker effects based on bidirectional selected populations led to only a marginal decrease in the prediction accuracy of genomic breeding values. We concluded that bidirectional selection is a valuable approach to efficiently implement genomic selection in applied plant breeding programs.
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References
Albrecht T, Wimmer V, Auinger H-J, Erbe M, Knaak C, Ouzunova M, Simianer H, Schön CC (2011) Genome-based prediction of testcross values in maize. Theor Appl Genet 123:339–350
Crossa J, Campos G, Pérez P, Gianola D, Burgueño J, Araus JL, Makumbi D, Singh RP, Dreisigacker S, Yan J, Arief V, Banziger M, Braun H-J (2010) Prediction of genetic values of quantitative traits in plant breeding using pedigree and molecular markers. Genetics 186:713–724
Crossa J, Pérez P, Campos G, Mahuku G, Dreisigacker S, Magorokosho C (2011) Genomic selection and prediction in plant breeding. J Crop Improv 25:239–261
Dekkers JCM (2007) Prediction of response to marker-assisted and genomic selection using selection index theory. J Animal Breed Genet 124:331–341
Hayes BJ, Bowman PJ, Chamberlain AJ, Goddard ME (2009) Invited review: genomic selection in dairy cattle: progress and challenges. J Dairy Sci 92:433–443
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
Henderson CR (1984) Application of linear models in animal breeding. University of Guelph, Guelph
Jannink JL, Lorenz AJ, Iwata H (2010) Genomic selection in plant breeding: from theory to practice. Brief Funct Genomics 9:166–177
Lander ES, Botstein D (1989) Mapping Mendelian factors underlying quantitative traits using RFLP linkage maps. Genetics 121:185–199
Lebowitz RL, Soller M, Beckmann JS (1987) Trait-based analysis for the detection of linkage between marker loci and quantitative trait loci in cross between inbred lines. Theor Appl Genet 73:556–562
Longin CFH, Utz HF, Reif JC, Schipprack W, Melchinger AE (2006) Hybrid maize breeding with doubled haploids: I. One-stage versus two-stage selection for testcross performance. Theor Appl Genet 112:903–912
Longin CFH, Utz HF, Reif JC, Wegenast T, Schipprack W, Melchinger AE (2007) Hybrid maize breeding with doubled haploids: III. Efficiency of early testing prior to doubled haploid production in two-stage selection for testcross performance. Theor Appl Genet 115:519–527
Lorenzana R, Bernardo R (2009) Accuracy of genotypic value predictions for marker-based selection in biparental plant populations. Theor Appl Genet 120:151–161
Luan T, Wooliams JA, Lien S, Kent M, Svendsen M, Meuwissen THE (2009) The accuracy of genomic selection in Norwegian red cattle assessed by cross validation. Genetics 183:1119–1126
Melchinger AE, Gumber RK, Leipert RB, Vuylsteke M, Kuiper M (1998) Prediction of test cross means and variances among F3 progenies of F1 crosses from test cross means and genetic distances of their parents in maize. Theor Appl Genet 96:503–512
Melchinger AE, Orsini E, Schön CC (2012) QTL mapping under truncation selection in homozygous lines derived from biparental crosses. Theor Appl Genet 124:543–553
Meuwissen THE, Hayes BJ, Goddard ME (2001) Prediction of total genetic value using genome-wide dense marker maps. Genetics 157:1819–1829
Miedaner T, Schneider B, Oettler G (2006) Means and variances for Fusarium head blight resistance of F2-derived bulks from winter triticale and winter wheat crosses. Euphytica 152:405–411
Mihaljevic R, Schön CC, Utz HF, Melchinger AE (2005) Correlations and QTL correspondence between line per se and testcross performance for agronomic traits in four populations of European maize. Crop Sci 45:114–122
Navabi A, Mather DE, Bernier J, Spaner DM, Atlin AN (2009) QTL detection with bidirectional and unidirectional selective genotyping: marker-based and trait-based analyses. Theor Appl Genet 118:347–358
Sillanpää MJ, Hoti F (2007) Mapping quantitative trait loci from a single-tail sample of the phenotype distribution including survival data. Genetics 177:2361–2377
Steinhoff J, Liu W, Maurer HP, Würschum T, Longin CFH, Reif JC (2011) Multiple-line cross QTL-mapping in European elite maize. Crop Sci 51:2505–2516
Sun Y, Wang J, Crouch JH, Xu Y (2010) Efficiency of selective genotyping for genetic analysis of complex traits and potential applications in crop improvement. Mol Breed 26:451–493
Utz HF, Bohn M, Melchinger AE (2001) Predicting progeny means and variances of winter wheat crosses from phenotypic values of their parents. Crop Sci 41:1470–1478
Zhao Y, Gowda M, Liu W, Würschum T, Maurer HP, Longin CFH, Ranc N, Reif JC (2012a) Accuracy of genomic selection in European maize elite breeding populations. Theor Appl Genet 124:769–776
Zhao Y, Gowda M, Liu W, Würschum T, Maurer HP, Longin CFH, Ranc N, Reif JC (2012b) Choice of shrinkage parameter and prediction of genomic breeding values in maize elite breeding populations. Theor Appl Genet (in review)
Acknowledgments
This research was conducted within the Biometric and Bioinformatic Tools for Genomics based Plant Breeding project supported by the German Federal Ministry of Education and Research (BMBF) within the framework of GABI–FUTURE initiative. Y. Zhao and M. Gowda were supported by BMBF within the HYWHEAT project (Grant ID: FKZ0315945D).
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Communicated by J. Wang.
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Zhao, Y., Gowda, M., Longin, F.H. et al. Impact of selective genotyping in the training population on accuracy and bias of genomic selection. Theor Appl Genet 125, 707–713 (2012). https://doi.org/10.1007/s00122-012-1862-2
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DOI: https://doi.org/10.1007/s00122-012-1862-2