Genome-wide selection and genetic improvement during modern maize breeding

Nat Genet. 2020 Jun;52(6):565-571. doi: 10.1038/s41588-020-0616-3. Epub 2020 Apr 27.


Since the development of single-hybrid maize breeding programs in the first half of the twentieth century1, maize yields have increased over sevenfold, and much of that increase can be attributed to tolerance of increased planting density2-4. To explore the genomic basis underlying the dramatic yield increase in maize, we conducted a comprehensive analysis of the genomic and phenotypic changes associated with modern maize breeding through chronological sampling of 350 elite inbred lines representing multiple eras of germplasm from both China and the United States. We document several 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 demonstrates the use of the breeding-era approach for identifying breeding signatures and lays the foundation for future genomics-enabled maize breeding.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • CRISPR-Cas Systems
  • China
  • Genome, Plant
  • Genome-Wide Association Study*
  • Linkage Disequilibrium
  • Phenotype
  • Plant Breeding / methods*
  • Plant Proteins / genetics
  • Plants, Genetically Modified
  • Polymorphism, Single Nucleotide
  • Quantitative Trait, Heritable
  • Reproducibility of Results
  • United States
  • Zea mays / genetics*
  • Zea mays / physiology


  • Plant Proteins