Genome properties and prospects of genomic prediction of hybrid performance in a breeding program of maize

Abstract

Maize (Zea mays L.) serves as model plant for heterosis research and is the crop where hybrid breeding was pioneered. We analyzed genomic and phenotypic data of 1254 hybrids of a typical maize hybrid breeding program based on the important Dent × Flint heterotic pattern. Our main objectives were to investigate genome properties of the parental lines (e.g., allele frequencies, linkage disequilibrium, and phases) and examine the prospects of genomic prediction of hybrid performance. We found high consistency of linkage phases and large differences in allele frequencies between the Dent and Flint heterotic groups in pericentromeric regions. These results can be explained by the Hill-Robertson effect and support the hypothesis of differential fixation of alleles due to pseudo-overdominance in these regions. In pericentromeric regions we also found indications for consistent marker-QTL linkage between heterotic groups. With prediction methods GBLUP and BayesB, the cross-validation prediction accuracy ranged from 0.75 to 0.92 for grain yield and from 0.59 to 0.95 for grain moisture. The prediction accuracy of untested hybrids was highest, if both parents were parents of other hybrids in the training set, and lowest, if none of them were involved in any training set hybrid. Optimizing the composition of the training set in terms of number of lines and hybrids per line could further increase prediction accuracy. We conclude that genomic prediction facilitates a paradigm shift in hybrid breeding by focusing on the performance of experimental hybrids rather than the performance of parental lines in test crosses.

Keywords: GenPred, shared data resources; genomic prediction; heterotic groups; hybrid breeding; linkage phases; training set design.

Figure 1

Schematic visualization of the strategy for distinguishing the tested hybrids in the training set and T2, T1, and T0 hybrids in the validation set.

Figure 2

(A and B) Average minor allele frequency (MAF) of SNP within consecutive bins of 5-Mb width along the chromosomes, for Dent lines (A) and Flint lines (B). (C) Average absolute difference of reference allele frequency between Dent and Flint lines in the same 5-Mb bins. The different colors of the points and the heat map in the bottom of each subplot indicate the marker density within the bin (Mb⁻¹). The green, dashed vertical bars indicate the physical positions of the centromeres, and the solid, black bars separate the chromosomes.

Figure 3

(A and B) Boxplots of pairwise LD, measured as r², between markers on the same chromosomes, with distances in megabases (Mb), for the set of Dent (A) and Flint (B) lines. Marker pairs were binned according to physical distance, each bin corresponding to an interval of 0.125 Mb.

Figure 4

(A and B) Average pairwise LD (measured as r²) within consecutive bins of 5-Mb width along the chromosomes, for Dent lines (A) and Flint lines (B). (C) Proportion of marker pairs with equal linkage phase (equal sign of r statistic) between Dent and Flint lines in the same 5-Mb bins. The different colors of the points and the heat map in the bottom of each subplot indicate the marker density within the bin (Mb⁻¹). The green, dashed vertical bars indicate the physical positions of the centromeres, and the solid, black bars separate the chromosomes. The horizontal line in C indicates the value of 0.50.

Figure 5

Scatterplot of posterior means of additive effects of markers located within 12.5 Mb of the centromeres in the Dent and Flint lines, estimated simultaneously with BayesB, using a subset of 1617 markers in total and all 1254 hybrids. Marker effects shown are for grain yield (A) and grain moisture content (B).