Identification of heterotic group-specific haplotypes and impact of residual inbreeding on grain yield of maize elite hybrids
Modern hybrid maize (Zea mays L.) breeding programs are based on the management of distinct complementary heterotic groups to maximize heterosis in high-performing hybrids. This practice lowers shared genetic segments and increases divergence between groups to limit inbreeding in hybrids. However, most breeding programs have not always enforced strict separation between heterotic groups in the past. Competitor commercial hybrids were notably a common elite germplasm source for inbred development, which would diminish divergence between groups. This study proposes a new haplotype-based approach to assess hybrids residual inbreeding based on parental similarity. The new haplotype method has a stronger significant negative effect on hybrids grain yield than raw SNP data. Evaluation of modern experimental hybrids uncovered related inbreds contributing to superior rates of residual inbreeding. Analysis of these inbreds revealed haplotype transfers between heterotic groups, originating notably from the use of a Stiff Stalk-Iodent commercial hybrid as breeding starts material in both Stiff Stalk and Non-Stiff Stalk breeding populations. The introduction of this intergroup parent generated heterotic-group-specific haplotype migration between crossing pools. These fragments caused significant genome-wide residual inbreeding in experimental hybrids across selection cycles. This study highlights the necessity for accurate evaluation of external sources of diversity to minimize haplotype transfers and admixture between crossing pools. We demonstrate the consequences of using commercial hybrids in inbred development, particularly regarding residual inbreeding, and their effects on hybrid performance. Insights from these results can assist breeders in optimizing the choice of parents for introducing genetic diversity in a reciprocal recurrent selection scheme. KEY MESSAGEHaplotype-based hybrids parental similarity better predicts grain yield than marker-based identity-by-state. Utilization of commercial hybrids as breeding start material resulted in higher hybrid residual inbreeding even after several selection cycles