Single-cross maize hybrids display superior heterosis and are produced from crossing two parental inbred lines belonging to genetically different heterotic groups. Here we assembled 1,604 historically utilized maize inbred lines belonging to various female heterotic groups (FHGs) and male heterotic groups (MHGs), and conducted phenotyping and genomic sequencing analyses. We found that the FHGs and MHGs have undergone both convergent and divergent changes for different sets of agronomic traits. Using genome-wide selection scans and association analyses, we identified a large number of candidate genes that contributed to the improvement of agronomic traits of the FHGs and MHGs. Moreover, we observed increased genetic differentiation between the FHGs and MHGs across the breeding eras, and we found a positive correlation between increasing heterozygosity levels in the differentiated genes and heterosis in hybrids. Furthermore, we validated the function of two selected genes and a differentiated gene. This study provides insights into the genomic basis of modern hybrid maize breeding.

单交玉米杂交种显示出优越的杂种优势，是通过杂交属于遗传上不同杂种优势群的两个亲本近交系而产生的。在这里，我们组装了属于各种雌性杂种优势群 (FHG) 和雄性杂种优势群 (MHG) 的 1,604 个历史上使用的玉米自交系，并进行了表型分析和基因组测序分析。我们发现 FHGs 和 MHGs 对于不同的农艺性状集发生了趋同和发散的变化。使用全基因组选择扫描和关联分析，我们确定了大量有助于改善 FHG 和 MHG 农艺性状的候选基因。此外，我们观察到整个育种时期 FHG 和 MHG 之间的遗传分化增加，并且我们发现分化基因中增加的杂合度水平与杂种中的杂种优势之间呈正相关。此外，我们验证了两个选定基因和一个分化基因的功能。本研究为现代杂交玉米育种的基因组基础提供了见解。