CUBIC: an atlas of genetic architecture promises directed maize improvement

<jats:title>Abstract</jats:title><jats:sec> <jats:title>Background</jats:title> <jats:p>Identifying genotype-phenotype links and causative genes from quantitative trait loci (QTL) is challenging for complex agronomically important traits. To accelerate maize gene discovery and breeding, we present the Complete-diallel design plus Unbalanced Breeding-like Inter-Cross (CUBIC) population, consisting of 1404 individuals created by extensively inter-crossing 24 widely used Chinese maize founders.</jats:p> </jats:sec><jats:sec> <jats:title>Results</jats:title> <jats:p>Hundreds of QTL for 23 agronomic traits are uncovered with 14 million high-quality SNPs and a high-resolution identity-by-descent map, which account for an average of 75% of the heritability for each trait. We find epistasis contributes to phenotypic variance widely. Integrative cross-population analysis and cross-omics mapping allow effective and rapid discovery of underlying genes, validated here with a case study on leaf width.</jats:p> </jats:sec><jats:sec> <jats:title>Conclusions</jats:title> <jats:p>Through the integration of experimental genetics and genomics, our study provides useful resources and gene mining strategies to explore complex quantitative traits.</jats:p> </jats:sec>