Maize Inbreds Exhibit High Levels of Copy Number Variation (CNV) and Presence/Absence Variation (PAV) in Genome Content

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Abstract
Following the domestication of maize over the past ∼10,000 years, breeders have exploited the extensive genetic diversity of this species to mold its phenotype to meet human needs. The extent of structural variation, including copy number variation (CNV) and presence/absence variation (PAV), which are thought to contribute to the extraordinary phenotypic diversity and plasticity of this important crop, have not been elucidated. Whole-genome, array-based, comparative genomic hybridization (CGH) revealed a level of structural diversity between the inbred lines B73 and Mo17 that is unprecedented among higher eukaryotes. A detailed analysis of altered segments of DNA conservatively estimates that there are several hundred CNV sequences among the two genotypes, as well as several thousand PAV sequences that are present in B73 but not Mo17. Haplotype-specific PAVs contain hundreds of single-copy, expressed genes that may contribute to heterosis and to the extraordinary phenotypic diversity of this important crop. There is a growing appreciation for the role of genome structural variation in creating phenotypic variation within a species. Comparative genomic hybridization was used to compare the genome structures of two maize inbred lines, B73 and Mo17. The data reinforce the view that maize is a highly polymorphic species, but also show that there are often large genomic regions that have little or no variation. We identify several hundred sequences that, while present in both B73 and Mo17, have copy number differences in the two genomes. In addition, there are several thousand sequences, including at least 180 sequences annotated as single-copy genes, that are present in one genome but entirely missing in the other genome. This genome content variation leads to differences in transcript content between inbred lines and likely contributes to phenotypic diversity and heterosis in maize.