The Maize W22 Genome: A Foundation for Gene Discovery and Functional Genomics

Co-authors: The Maize W22 Sequencing Consortium

The maize W22 inbred has served as a platform for maize genetics since the mid twentieth century, initially as a model to understand factors contributing to epigenetic inheritance and currently as a platform for transposon-mediated forward and reverse genetics.  To maximize the utility of W22 in gene discovery, we have sequenced and de novo assembled a color-converted W22 reference genome using small read sequencing technologies.  We show that significant structural heterogeneity exists in comparisons to the B73 reference genome at multiple scales, from transposon composition and copy number variation to single nucleotide polymorphisms.  The generation of this high quality reference genome has enabled the accurate placement of several thousand Mutator and Dissociation transposable elements from transposon mutagenesis projects that enable the use of both engineered and endogenous elements for reverse and forward genetics in maize.  Annotation of the genome has been informed by RNAseq analysis, differential nuclease sensitivity profiling, and bisulfite sequencing to fine map open reading frames, open chromatin sites, and DNA methylation profiles, respectively.  Several independent assessments of the quality of the genome assembly including comparisons to high resolution genetic maps, Sanger-sequenced regions of high complexity and transposon site insertion mapping coupled with the integration of global epigenetic and gene expression annotation reveal that the W22 genome now represents the highest quality maize reference genome in the public domain.