Simulation-based establishment of base pools for a hybrid breeding program in winter rapeseed

Abstract

Simulation planned pre-breeding can increase the efficiency of starting a hybrid breeding program. Starting a hybrid breeding program commonly comprises a grouping of the initial germplasm in two pools and subsequent selection on general combining ability. Investigations on pre-breeding steps before starting the selection on general combining ability are not available. Our goals were (1) to use computer simulations on the basis of DNA markers and testcross data to plan crosses that separate genetically two initial germplasm pools of rapeseed, (2) to carry out the planned crosses, and (3) to verify experimentally the pool separation as well as the increase in testcross performance. We designed a crossing program consisting of four cycles of recombination. In each cycle, the experimentally generated material was used to plan the subsequent crossing cycle with computer simulations. After finishing the crossing program, the initially overlapping pools were clearly separated in principal coordinate plots. Doubled haploid lines derived from the material of crossing cycles 1 and 2 showed an increase in relative testcross performance for yield of about 5% per cycle. We conclude that simulation-designed pre-breeding crossing schemes, that were carried out before the general combining ability-based selection of a newly started hybrid breeding program, can save time and resources, and in addition conserve more of the initial genetic variation than a direct start of a hybrid breeding program with general combining ability-based selection.

Fig. 1

Crossing scheme for material development in one pool. Each parental line was used in two crosses, and 50 F1 genotypes were generated (recombination R1). From the F1 genotypes, 50 cycle 1 (C1) families of size 10 were generated (recombination R2). Two genotypes of each family were selected and crossed with selected genotypes from other families (recombination R3). The procedure was repeated (recombination R4) resulting in 50 C3 families of size 10

Fig. 2

Heatmaps of the MRD (red: $\text{MRD}=0$ and white: $\text{MRD}=1$) between the parental lines ordered by hierarchical clustering. The crosses in recombination step R1 identified as favorable by the target functions $T^{\prime }$ (top) and T (bottom) in pool 1 (left) and pool 2 (right) are marked by black dots in the heatmaps

Fig. 3

Principal coordinate plots of the two pools during the material development. In the first row, the parental lines and the F1 are shown. The latter three rows show cycles C1–C3. In the left column simulation, results were presented and, in the right column, the corresponding experimental data. Red symbols in generations P and F1, and yellow/red/brown coloring in generation C1–C3 were used for pool 1. Green symbols in generations P and F1, and green/blue coloring were used for pool 2. In generations C1–C3, different geometric shapes were used for genotypes that belong to different families

Fig. 4

Relative testcross performance for yield for the parental lines and doubled haploid lines derived from cycles C1 and C2 (C1-DH and C2-DH). 100% is the mean performance of the three standards Ludger, DK Excited, and LG Aviron

Fig. 5

Illustration of the target functions $T^{\prime }$ and T for selecting crosses in recombination R1. The lines of pool 1 are green, and the lines of pool 2 are red. P1_i-1 and P2_i-1 (light blue) are the parental lines of the $i-1$th cross. P1_i and P2_i (blue) are the parental lines of the ith cross, with ${\text{P2}}_{i-1}\equiv {\text{P1}}_i$. This illustration is a simplification in two respects: (1) It is using a two-dimensional space with an euclidean distance, whereas for the actual calculations, the MRD in a multi-dimensional space was used. (2) The opposite pool is represented by its centroid, whereas for the actual calculations, the average distance of a line to all lines of the opposite pool was used

Fig. 6

Crosses of the F1 genotypes. The black lines (top) connect F1 genotypes that were selected as crossing partners of crosses of type I (“best x best”). The gray lines (bottom) connect genotypes selected as parents of crosses of type II (“improve the worst”)