Zea mays subsp. mays Genome sequencing

To explore the genomic basis underlying the dramatic yield increase in maize, we conducted a comprehensiven analysis of the genomic and phenotypic changes associated with modern maize breeding through across a chronological sampling of 350 elite inbred lines representing multiple eras of both Chinese and U.S. germplasm. We document a number of convergent phenotypic changes in both countries. Using genome-wide association and selection scan methods, we identify 160 loci underlying adaptive agronomic phenotypes and more than 1,800 genomic regions representing the targets of selection during modern breeding. This work We functionally validate two candidate genes underpinning variation in ear height and tassel branch number using CRISPR knockout mutants. In sum, this work demonstrates the utility of breeding-era approach for identifying breeding signatures and lays the foundation for future genomics-enabled maize breeding.