Abstract：

Hybrid maize displays superior heterosis and contributes over 30% oftotal worldwide cereal production. However, the molecular mechanismsof heterosis remain obscure. Here we show that structural variants (SVs)between the parental lines have a predominant role underpinning maizeheterosis. De novo assembly and analyses of 12 maize founder inbred lines(FILs) reveal abundant genetic variations among these FILs and, throughexpression quantitative trait loci and association analyses, we identifyseveral SVs contributing to genomic and phenotypic differentiationsof various heterotic groups. Using a set of 91 diallel-cross F1 hybrids, wefound strong positive correlations between better-parent heterosis of theF1 hybrids and the numbers of SVs between the parental lines, providing concrete genomic support for a prevalent role of geneticcomplementation underlying heterosis. Further, we document evidence that SVs in both ZAR1 and ZmACO2 contribute to yield heterosis in an overdominance fashion. Our results should promote genomics-based breeding of hybrid maize.