Maize Genomics and Genetics 2024, Vol.15, No.3, 123-135 http://cropscipublisher.com/index.php/mgg 124 study aims to highlight the dual nature of TEs as both genomic parasites and beneficial elements, and to elucidate their contributions to the genetic and phenotypic diversity of maize. Through this study hope to advance the understanding of TEs in maize and their broader implications for plant genomics and evolution. 2 Types of Transposable Elements inZea 2.1 DNA transposons DNA transposons, also known as Class II transposable elements, move within the genome through a "cut-and-paste" mechanism. This process involves the excision of the transposon from one location and its reinsertion at another site within the genome. DNA transposons are characterized by terminal inverted repeats (TIRs) and the presence of a transposase enzyme that facilitates their movement. In maize, DNA transposons have been shown to play significant roles in genome evolution by inducing structural variations and generating allelic diversity. For instance, the Activator (Ac) and Dissociation (Ds) elements are well-studied DNA transposons in maize that can cause complex chromosomal rearrangements, leading to variations in gene expression and phenotypic diversity (Fedoroff, 2012; Su et al., 2019; Sharma and Peterson, 2022) 2.2 Retrotransposons Retrotransposons, or Class I transposable elements, move within the genome via an RNA intermediate. This "copy-and-paste" mechanism involves the transcription of the retrotransposon into RNA, which is then reverse-transcribed into DNA and inserted at a new location. Retrotransposons are further classified into long terminal repeat (LTR) and non-LTR retrotransposons. In maize, retrotransposons constitute a significant portion of the genome, contributing to its large size and complexity. They are often associated with regulatory elements that can influence gene expression. For example, studies have shown that retrotransposon-derived sequences can act as cis-regulatory elements, affecting the transcriptional regulation of nearby genes (Zhao et al., 2018; Stitzer et al., 2019; Noshay et al., 2020). 2.3 Specific TEs identified in maize (e.g., Ac/Ds, Spm/En) In maize, several specific transposable elements have been identified and extensively studied for their roles in genetic diversity and evolution. The Ac/Ds system is one of the most well-known DNA transposon systems in maize. The Ac element encodes a transposase that can mobilize both Ac and Ds elements. The movement of these elements can cause mutations, gene disruptions, and chromosomal rearrangements, contributing to genetic diversity (Fedoroff, 2012; Wang et al., 2020; Sharma and Peterson, 2022). Another significant DNA transposon system in maize is the Suppressor-mutator (Spm) or Enhancer (En) system. Similar to Ac/Ds, the Spm/En elements can induce mutations and alter gene expression, further adding to the genetic variability within maize populations (Fedoroff, 2012; Sharma and Peterson, 2022). Retrotransposons also play a crucial role in maize genome dynamics. For instance, the long terminal repeat (LTR) retrotransposons are abundant in the maize genome and have been implicated in the regulation of gene expression. These elements can insert near genes and provide regulatory sequences that enhance or repress gene activity. The presence of retrotransposon-derived cis-regulatory elements has been shown to significantly impact the transcriptional landscape of maize, highlighting their importance in genome evolution (Zhao et al., 2018; Stitzer et al., 2019; Noshay et al., 2020). The diverse array of transposable elements in maize, including both DNA transposons and retrotransposons, underscores their critical role in shaping the genetic architecture and evolutionary trajectory of this species. By generating genetic diversity and influencing gene expression, transposable elements contribute to the adaptability and phenotypic plasticity of maize, making them a key focus of genomic and evolutionary studies (Fedoroff, 2012; Zhao et al., 2018; Stitzer et al., 2019; Wang et al., 2020; Noshay et al., 2020; Sharma and Peterson, 2022). 3 Mechanisms of Transposition 3.1 How TEs move within the genome Transposable elements (TEs) are dynamic components of the genome that can move from one location to another, a process known as transposition. This movement can occur through two primary mechanisms: "cut-and-paste"
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