Contributions of Zea mays subspecies mexicana haplotypes to modern maize

Maize was domesticated from lowland teosinte ( Zea mays ssp. parviglumis ), but the contribution of highland teosinte ( Zea mays ssp. mexicana , hereafter mexicana ) to modern maize is not clear. Here, two genomes for Mo17 (a modern maize inbred) and mexicana are assembled using a meta-assembly strategy after sequencing of 10 lines derived from a maize-teosinte cross. Comparative analyses reveal a high level of diversity between Mo17, B73, and mexicana , including three Mb-size structural rearrangements. The maize spontaneous mutation rate is estimated to be 2.17 × 10 −8 ~3.87 × 10 −8 per site per generation with a nonrandom distribution across the genome. A higher deleterious mutation rate is observed in the pericentromeric regions, and might be caused by differences in recombination frequency. Over 10% of the maize genome shows evidence of introgression from the mexicana genome, suggesting that mexicana contributed to maize adaptation and improvement. Our data offer a rich resource for constructing the pan-genome of Zea mays and genetic improvement of modern maize varieties.