The Maize Genome: New Complexities and Opportunities.

A project to generate a near-complete sequence of the maize inbred B73 utilized a minimal tiling path of approximately 16,000 mapped BAC clones. The project focused on producing high-quality sequence coverage of the genic regions, which were ordered, oriented and anchored to physical and genetic maps. Project methodologies and outputs will be briefly reviewed before addressing a genome-enabled investigation of genome structure. Following its domestication ~10,000 years ago, breeders have exploited the extensive genetic diversity of maize. The roles of structural variation, including insertions, deletions and copy number variation on the phenotypic diversity and plasticity of this important crop have not been elucidated. Whole-genome array-based comparative genomic hybridizations (aCGH) have revealed that structural variation between the B73 and Mo17 inbreds is not evenly distributed across the genome. Analysis of altered segments of DNA identified hundreds of sequences that exhibit copy number variation among the two genotypes, as well as thousands of sequences that are present in B73 but not Mo17 (presence/absence variation). Sequences present in the B73 genome, but absent from the Mo17 genome, include single-copy, full-length genes. Implications for plant breeding will be discussed.