Genome-wide characterization of non-reference transposable element insertion polymorphisms reveals genetic diversity in tropical and temperate maize

BACKGROUND: Maize was originally domesticated in a tropical environment but is now widely cultivated at temperate latitudes. Temperate and tropical maize populations have diverged both genotypically and phenotypically. Tropical maize lines grown in temperate environments usually exhibit delayed flowering, pollination, and seed set, which reduces their grain yield relative to temperate adapted maize lines. One potential mechanism by which temperate maize may have adapted to a new environment is novel transposable element insertions, which can influence gene regulation. Recent advances in sequencing technology have made it possible to study variation in transposon content and insertion location in large sets of maize lines. RESULTS: In total, 274,408 non-redundant TEs (NRTEs) were identified using resequencing data generated from 83 maize inbred lines. The locations of DNA TEs and copia-superfamily retrotransposons showed significant positive correlations with gene density and genetic recombination rates, whereas gypsy-superfamily retrotransposons showed a negative correlation with these two parameters. Compared to tropical maize, temperate maize had fewer unique NRTEs but higher insertion frequency, lower background recombination rates, and higher linkage disequilibrium, with more NRTEs close to flowering and stress-related genes in the genome. Association mapping demonstrated that the presence/absence of 48 NRTEs was associated with flowering time and that expression of neighboring genes differed between haplotypes where a NRTE was present or absent. CONCLUSIONS: This study suggests that NRTEs may have played an important role in creating the variation in gene regulation that enabled the rapid adaptation of maize to diverse environments. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12864-017-4103-x) contains supplementary material, which is available to authorized users.