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. 2015 Feb 17;11(2):e1004982. doi: 10.1371/journal.pgen.1004982

Fig 2. Example of irrigated rice breeding pipeline that incorporates genomic selection.

Fig 2

Parents are selected and crossed to create an F1 population. ∼20,000 F1 lines are fixed over 7–8 generations with selection of families for heritable traits with ∼25% of the pedigree lines eventually selected for entry into the observational yield trial (OYT). GEBVs can be used at two or more generations during fixation as resources permit to perform selection. Here we propose using GEBVs at the F3 and F6 generations. GEBVs are also used to select the fixed lines from the F8 to advance to the OYT. The top lines advanced to the OYT based on GEBV are cycled back into the crossing block in order to continue to improve the population. From the OYT, the best performing lines based on phenotype are advanced to the replicated yield trials (RYT), and the best performing lines from the RYT are advanced to the multi-environment trials (MET). Lines from the MET are then selected based on GEBV as parents for the next generation of recurrent selection. Models are built at each stage in which GEBVs are used for selection based on a subset of the lines in the population (∼300 individuals representing different families) that are both genotyped and phenotyped to form the training set. The rest of the individuals in the population are genotyped only in order to calculate GEBVs.