Zea mays subsp. mays Genome sequencing

The success of modern maize breeding has been well demonstrated by a remarkable increase of productivity over the last four decades. Yet the underlying genetic changes correlated with the genetic gain throughout the breeding process remain largely unknown at the genome-wide level. We report here the sequencing of 278 temperate maize inbred lines from different stages of breeding history, including deep resequencing of four lines with known pedigree information. Our results show that modern breeding has introduced highly dynamic genetic changes into the maize genome. Artificial selection has affected thousands of targets including genes and non-genic regions, leading to apparent reduction of nucleotide diversity and increase in the proportion of rare alleles. Genetic changes during breeding happen rapidly, with extensive variation (SNPs, Indels and CNVs) even within the identity-by-descent regions.