Maize Genomics and Genetics 2024, Vol.15, No.3, 123-135 http://cropscipublisher.com/index.php/mgg 127 Figure 3 Relationship between TE frequency and relative position to the nearest gene (Adopted from Qiu et al., 2021) Image caption: Helitrons (A), TIRs (B), and LTRs (C) were categorized using the following hierarchy: gene completely within the TE, TE completely within the 5’ UTR, completely within the 3’ UTR, completely within an exon, completely within an intron, completely encompassed by a gene, 0–1 kb upstream of a gene, 1–5 kb upstream of a gene, 5–10 kb upstream of a gene, 0–1 kb downstream of a gene, 1–5 kb downstream of a gene, 5–10 kb downstream of a gene, intergenic (not shown in figure). Full colored bars (left bars) contain frequencies for TEs in each genomic region and transparent bars (right bars) contain frequencies for genome-wide background rates based on 100 bootstrap iterations. (D) Proportion of LTRs with low LTR similarity (LTR similarity <95%), moderate LTR similarity (LTR similarity between 95 and 99%), and high LTR similarity (LTR similarity >99%) in each gene proximity category (Adopted from Qiu et al., 2021) TEs can influence the epigenetic landscape of the genome. For example, the insertion of a TE can attract epigenetic modifications such as DNA methylation, which can spread to nearby genes and alter their expression. This epigenetic influence can be heritable, adding another layer of complexity to the genetic variation generated by TEs (Su et al., 2019). 4.2 Examples of phenotypic changes in maize due to TE activity The activity of TEs in maize has been linked to several notable phenotypic changes, illustrating their role in driving genetic diversity and evolution. One classic example is the role of TEs in the pigmentation of maize kernels. The insertion of a TE in the regulatory region of the C1 gene, which controls anthocyanin biosynthesis, can lead to variegated kernel coloration. When the TE excises, it can restore the gene's function, resulting in patches of pigmented tissue (Schrader and Schmitz, 2018).
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