Revisiting hybrid breeding designs using genomic predictions: simulations highlight the superiority of incomplete factorials between segregating families over topcross designs

Theor Appl Genet. 2020 Jun;133(6):1995-2010. doi: 10.1007/s00122-020-03573-5. Epub 2020 Mar 17.


Simulations showed that hybrid performances issued from an incomplete factorial between segregating families of two heterotic groups enable to calibrate genomic predictions of hybrid value more efficiently than tester-based designs. Genomic selection offers new opportunities to revisit hybrid breeding by replacing extensive phenotyping of hybrid combinations by genomic predictions. A key question remains to identify the best design to calibrate genomic prediction models. We proposed to use single-cross hybrids issued from an incomplete factorial design between segregating populations and compared this strategy with a conventional approach based on topcross evaluation. Two multiparental segregating populations of lines, each specific of one heterotic group, were simulated. Hybrids considered as training sets were generated using either (1) a parental line from the opposite group as tester or (2) following an incomplete factorial design. Different specific combining ability (SCA) proportions were simulated by considering different levels of group divergence and dominance effects for the simulated QTL. For the incomplete factorial design, for a same number of hybrids, we considered different numbers of parental lines and different contributions of lines (one to four) to calibration hybrids. We evaluated for different training set sizes prediction accuracies of new hybrids and genetic gains along three generations. At a given training set size, factorial design was as efficient (considering accuracy) as tester design in additive scenarios, but significantly outperformed tester design when SCA was present. The contribution number of each parental line to the incomplete factorial design had a small impact on accuracies. Our simulations confirmed experimental results and showed that calibrating models on hybrids between two multiparental populations is a cost-efficient way to perform genomic predictions in both groups, opening prospects for revisiting reciprocal recurrent selection schemes.

MeSH terms

  • Algorithms
  • Alleles
  • Computer Simulation
  • Crosses, Genetic
  • Genome, Plant
  • Genomics / methods*
  • Genotype
  • Hybrid Vigor
  • Hybridization, Genetic*
  • Models, Genetic
  • Phenotype
  • Plant Breeding
  • Polymorphism, Single Nucleotide
  • Quantitative Trait Loci*
  • Zea mays / genetics*