Evolutionary dynamics and genetic diversity of transposable elements revealed by resequencing data in maize population

Zea mays (maize) is a globally significant crop with a complex genome enriched with transposable elements (TEs), which are crucial drivers of genomic diversity and plant evolution. In this study, we identified the TE insertion loci (TILs) from resequencing data of 103 maize accessions with the developed pipeline, and 64 293 non-redundant unique TILs were obtained in 82 maize accessions after filtering; approximately 80% (51 361) of loci showed insertion polymorphisms within the population. All TE superfamilies have low frequency in the maize population except for short interspersed nuclear elements, while some TE families have high fixed TE insertions, revealing distinct evolutionary dynamics among TE superfamilies and families. Genetic analysis using the transposon insertion polymorphism information from the maize population showed that the TE polymorphism loci can reflect their geographical origin and evolutionary relationships. Furthermore, TE insertions could also significantly impact gene expression, implying functional consequences for maize phenotypes and adaptation. These findings provide valuable insights into the evolutionary dynamics and genetic diversity of maize genomes, offering a valuable resource for molecular markers and association studies.