Discovery and Mapping of Presence-Absence Variants (PAV) in the Founders of the Maize NAM Population

Genomic structural variation is increasingly being recognized as a major contributor to phenotypic variation across species. In plants structural variants contribute to traits including soybean resistance to soybean cyst nematode, barley boron tolerance and flowering time, wheat dwarfism and flowering time, and maize aluminum tolerance. Presence-absence variants (PAV), a form of structural variation where a DNA sequence is present in one genome but entirely missing from another, has been found to contribute to a number of genetic diseases in humans However, the association between PAV and phenotype is still being explored in plants with very few documented examples, including flavor quality in strawberries and submergence tolerance in rice. We enabled global explorations of the association between PAVs and phenotypic variation by conducting RNA-sequencing on the 27 inbred founders of the maize Nested Association Mapping (NAM) population.  This exploration identified thousands of putative expressed PAVs that are absent from B73, the maize reference. In collaboration with Roche-Nimblegen these putative PAVs were used to design a Zeanome sequence capture array. Using this array, sequence capture of the NAM founders identified ~12,000 genomic PAVs that are absent from B73. Characterization of these PAVs shows that many have similarities to characterized proteins. Using the Fluidigm BioMark Dynamic Array, we have genotyped presence-absence variation for a subset of PAVs and genetically mapped them in the NAM RILs. This resource will allow us to test for associations between PAVs and with phenotypic variation in yield-related traits.