Population Level Variation of Transposable Elements in a Maize Diversity Panel

Intact transposable elements (TEs) account for 65% of the maize genome and can impact gene function and regulation. Although TEs comprise the majority of the maize genome and affect important phenotypes, genome wide patterns of TE polymorphisms in maize have only been studied in a handful of maize genotypes, due in part to the challenging nature of assessing highly repetitive sequences. We implemented a method to use short read sequencing data from 509 diverse inbred lines to classify the presence/absence of 494,564 non-redundant TEs that were previously annotated in four genome assemblies including B73, Mo17, PH207, and W22. Different orders of TEs (i.e. LTRs, Helitrons, TIRs) had different frequency distributions within the population. Across the different orders, TE family size was negatively correlated with average population frequency of TEs in the family and nested TEs are at lower frequency than non-nested TEs. Age of LTR elements was positively correlated with population frequency. Comparison with SNP data revealed that while a majority of TEs are tagged by nearby SNPs (r2 > 0.9) there are also many TEs in low to moderate linkage disequilibrium with nearby SNPs. This study provides a population scale genome-wide assessment of TE variation in maize, and provides valuable insight on variation in TEs in maize and factors that contribute to this variation.