Genomewide marker estimates of the level of dominance in maize heterosis

Heterosis is the superiority of an F₁ hybrid over its parents, and overdominance and dominance are the two main hypotheses for the genetic basis of heterosis. Our objectives were to determine if genomewide marker effects accurately reflect the level of dominance at quantitative trait loci (QTL) and assess the distribution of per-marker estimates of the level of dominance in maize (Zea mays L.). We simulated different levels of dominance at QTL that were in coupling, repulsion, and random linkage phases. Genomewide marker effects from ridge regression-best linear unbiased prediction led to accurate estimates of the level of dominance when all linkages were in coupling phase, but repulsion and random linkage phases led to an upward bias. We then estimated levels of dominance from genomewide marker effects in a reciprocal testcross experiment with 1642 hybrids genotyped with 4805 single nucleotide polymorphism markers, and in a legacy Design III experiment with 351 backcross progenies (subjected to three generations of random mating to dissipate linkages) genotyped with 160 simple sequence repeats. In both experiments, the level of dominance was higher for yield than for moisture. For each trait, some loci showed little or no dominance, others showed partial to complete dominance, and others showed overdominance. A high level of dominance was typically due to a small difference between homozygote values. Overall, the results were consistent with previous QTL mapping results indicating that heterosis in maize is due to varying levels of dominance rather than a prevalent level of dominance.