The maize W22 genome provides a foundation for functional genomics and transposon biology

Abstract

The maize W22 inbred has served as a platform for maize genetics since the mid twentieth century. To streamline maize genome analyses, we have sequenced and de novo assembled a W22 reference genome using short-read sequencing technologies. We show that significant structural heterogeneity exists in comparison to the B73 reference genome at multiple scales, from transposon composition and copy number variation to single-nucleotide polymorphisms. The generation of this reference genome enables accurate placement of thousands of Mutator (Mu) and Dissociation (Ds) transposable element insertions for reverse and forward genetics studies. Annotation of the genome has been achieved using RNA-seq analysis, differential nuclease sensitivity profiling and bisulfite sequencing to map open reading frames, open chromatin sites and DNA methylation profiles, respectively. Collectively, the resources developed here integrate W22 as a community reference genome for functional genomics and provide a foundation for the maize pan-genome.

Classifying cold‐stress responses of inbred maize seedlings using RGB imaging

“…Within our selected genotypes, there were representatives from multiple heterotic groups and genotypes that resulted from breeding programs at very distinct latitudes that likely faced variable levels of early season cold stress (Figure 4a; Supporting Information Table S1). The genotypes used in this study included 20 of the 25 nested association mapping population parent lines (McMullen et al, 2009), and lines with sequenced genomes such as B73 (Jiao et al, 2017;Schnable et al, 2009), PH207 (Hirsch et al, 2016), W22 (Springer et al, 2018), F7 (Unterseer et al, 2017), and Mo17 (Sun et al, 2018). All plants were grown in conditions described in the methods with a 2-day cold stress as the treatment group.…”

European maize genomes unveil pan-genomic dynamics of repeats and genes

“…Hence, the B73 reference sequence captures only a portion of the maize pan-genome. To overcome these limitations, a draft genome of the Iodent line PH207 [15], and -more recently-reference sequences of Mo17 and W22, two additional US dent lines, have been released [16,17]. Genomewide comparisons confirmed the high dynamics of the maize genome emphasizing the need for several high-quality genome sequences to characterize and exploit the pan-genomic variability in maize.…”

An updated gene atlas for maize reveals organ‐specific and stress‐induced genes

“…Within the MGR, a sequence retrieval tool for the AGPv4 genome, gene models, and surrounding gene model regions are provided. A BLAST server is also available to allow users to search Z. mays B73, including older versions, PH207 (Hirsch et al ., ), Mo17 (Sun et al ., ), W22 (Springer et al ., ), and other assemblies and annotation. All data sets are also available for download including the WGCNA and DE gene lists.…”