Breeding ideotype maize with enhanced yield through genomics-guided pyramiding of favorable alleles

Breeding ideotype maize for high-density planting is crucial for increasing yield but is hindered by a limited understanding of plant architecture regulation. Here we uncover a prominent role for the accumulation of homozygous favorable alleles in genes regulating four principal shoot traits constituting a maize ideotype, and we identify and functionally validate eight architecture-regulating genes. Guided by genomics, we selected the elite hybrid Yufeng303 as a chassis to develop five improved parental lines by pyramiding favorable alleles of these eight genes together with genome-wide loci associated with these traits. These improved parental lines led to the creation of four new hybrids better suited for high-density planting, achieving 4.1-9.2% higher plot yields than Yufeng303 across eight environments. This study exemplifies the power of genomics-guided breeding of ideotype maize for high densities and serves as a template for informed hybrid improvement of other appropriate crops.