Evaluation of genomic selection training population designs and genotyping strategies in plant breeding programs using simulation

AbstrAct Genomic selection offers great potential for increasing the rate of genetic improvement in plant breeding programs. This research used simulation to evaluate the effectiveness of dif-ferent strategies for genotyping and phenotyp-ing to enable genomic selection in early genera -tion individuals (e.g., F 2 ) in breeding programs involving biparental or similar (e.g., backcross or top cross) populations. By using phenotypes that were previously collected in other bipa-rental populations, selection decisions could be made without waiting for phenotypes that pertain directly to the selection candidate to be collected, a process that would take at least three growing seasons. If these phenotypes were collected in biparental populations that were closely related to the selection candidates, only a small number of markers (e.g., 200–500) and a small number of phenotypes (e.g., 1000) were needed to achieve effective accuracy of estimated breeding values. If these phenotypes were collected in biparental populations that were not closely related to the selection can-didates, as many as 10,000 markers and 5000 to 20,000 phenotypes were needed. Increasing marker density beyond 10,000 markers did not show benefit and in some scenarios reduced the accuracy of prediction. This study provides a guide, enabling resource allocation to be opti -mized between genotyping and phenotyping investment dependent on the population under development.J.M. Hickey, The Roslin Institute and Royal (Dick) School of Vet-erinary Studies, Univ. of Edinburgh, Easter Bush Research Center, Midlothian EH25 9RG, UK; S. Dreisigacker, Global Wheat Program, International Maize and Wheat Improvement Center (CIMMYT), Apdo. 06600 Mexico D.F., Mexico; J. Crossa and K. Mathews, Biomet -rics and Statistics Unit, International Maize and Wheat Improvement Center (CIMMYT), Apdo. 06600 Mexico D.F., Mexico; S. Hearne, Genetic Resources Program, International Maize and Wheat Improve -ment Center (CIMMYT), Apdo. 06600 Mexico D.F., Mexico; R. Babu and B.M. Prasanna, Global Maize Program, International Maize and Wheat Improvement Center (CIMMYT), Apdo. 06600 Mexico D.F., Mexico; M. Grondona and A. Zambelli, Center for Biotechnol-ogy Research, Advanta Semillas, Ruta 226 Km 60.5, (7620) Balcarce, Argentina; V.S. Windhausen, Saaten Union Recherche, 160 Avenue de Flandre, 60190 Estrees Saint Denis, France; Gregor Gorjanc, Biotech-nical Faculty, University of Ljubljana, Domzale, Slovenia. Received 22 Mar. 2013. *Corresponding author (john.hickey@roslin.ed.ac.uk).