Illustrative scheme of three strategies used in calibration sets of genomic selection training analyses.

Letters F2, A, S and BC represent the base population of allogamous, self-pollinated and backcrossing species. The index from 1 to 4 represents breeding cycles. In the right square, strategy 2 is the training set composed of species that used the contemporary or outdated genotypic and phenotypic values from the population itself (Si, Ai and Bci; i = 1,2,3,4), and validation was performed in the same population (Sn, An and Bcn) and in each advanced population (Sn+1, An+1 and Bcn+1). The last strategy used three different kinds of calibration data sets (D1t, D2t, D3t), which considered multigenerational sets for prediction. In the first training data set (D1t), the total of 1000 individuals, 500 from the first generation of allogamous or autogamous species and 500 individuals from the F2 population (D1t = A1/S1+ F2) were used to estimate the marker effect. Validation was performed on 500 individuals (D1v) from each outdated population (D1v = A1/S1, A2/S2, A3/S3 and A4/S4). In the second and third kinds of calibration data sets (D2t and D3t), data sets were added using generations two (D2t = A1/S1+ A2/S2 + F2) and three (D3t = A1/S1+ A2/S2 + A3/S3 + F2).