Artificial Seed Drying Conditions and Maize Seed Viability and Vigor after Storage

Abstract

Transposable elements (TEs) are DNA sequences that can change positions within the genome and may induce mutations. In Maize and Arabidopsis genomes, environmental stressors may cause an increase in transposition events. We used X-ray radiation on maize (W22) and arabidopsis (TAIR10) and then assembled a bioinformatic pipeline to test for an increase in TEs. Arabidopsis was exposed to 80 Gy of radiation and Maize was exposed to 10 Gy. Each plant was grown and self-crossed for three generations before sample collection was performed to ensure the fixation of activated TEs. Oxford Nanopore long-read sequencing was performed, and reads were aligned to their respective reference genome using minimap2. SVIM, a bioinformatics tool for detecting structural variants, was used to find instances of novel insertions (NI) in the genomes. The NI were then compared to the reference genome using the BLAST software, and the BLAST hits showed where the NI aligned with the reference genome. The BLAST hits were then compared to the annotated transposons via bedtools intersect and R code. Instances where the start and endpoints of the BLAST hits are close to the start and endpoints of the annotated transposons will be identified in order to locate active transposons.