Neocentromere Formation and Rapid Turnover of Centromere Repeats are Linked to Maize Domestication

Using anti-cenH3 ChIP-seq to map the functional centromeres in domesticated maize inbreds we demonstrate frequent neocentromere formation that is linked to tandem repeat loss at the ancestral centromere locations. Neocentromeres are dominated by centromere-specific retrotransposons that insert following neocentromere formation. The presence of only one or two pre-domestication haplotypes at seven of the ten centromeres in domesticated maize suggests that strong selection for centromere-linked genes drives this process.