Triticeae Genomics and Genetics, 2025, Vol.16, No.6, 237-244 http://cropscipublisher.com/index.php/tgg 247 Even without sequence control, it can still force both ends together, but problems such as messy insertion points and base loss are hard to avoid. In addition, copy-related mechanisms such as FoSTeS or MMBIR often get involved. When the copy fork stalls or templates switch, inversions or complex concatenation follow (Burssed et al., 2022). There are many types of rearrangements, and to a large extent, it depends on which repair mechanism takes the lead. 3.3 Transposons and repetitive sequences driving genome structural dynamics Sometimes, chromosomal rearrangement is not even caused by "correction errors", but rather that certain sequences themselves are "too noisy". Transposons and repetitive DNA fragments are like this. They not only keep jumping in the genome but also tend to cluster together. This kind of accumulation often provides ready-made "anchor points" for rearrangement. Especially for repetitive units like LINE and satellite sequences, if non-allelic recombination (NAHR) occurs, large fragment structural changes are almost inevitable (Luo, 2025). For instance, retrotransposons particularly tend to aggregate around centromeres. This behavior intensifies regional duplication and instability, providing a "testing ground" for the structural evolution of the genome (Gozashti et al., 2025). In other words, they not only participate in structural changes but may also profoundly influence gene functions and even species adaptation. 4 Roles of Chromosome Rearrangements in Hexaploid Wheat Evolution 4.1 Genome conflicts and structural stabilization after polyploidization The step of doubling did not immediately stabilize the hexaploid wheat. At the very beginning, there were many contradictions among the genomes and their structures were also very unstable. Especially among the three subgenomes A, B and D, integration is not an easy task. Chromosomal translocations such as 4A, 5A, and 7B, as well as the rearrangement of centromeric positions, are actually gradually explored during the process of genomic "self-repair" (Zhao et al., 2023; Liu et al., 2025). And the accumulation of those specific centromere repeat sequences is not a useless decoration. It plays a significant role in cell division, especially in the later stage of hybridization. With them present, chromosomes are more likely to separate correctly and the genome is more complete. 4.2 Effects of chromosome rearrangements on gene expression and trait variation Sometimes, gene expression can be "dragged down" by structures. Once chromosomal rearrangement alters the position of regulatory elements or the openness of chromatin, the expression of genes also fluctuates accordingly. Especially for those genes involved in translocation, they evolve at a faster rate and the recombination frequency may also change, making it easy for new phenotypes to "emerge". However, it doesn't always bring good things. In some cases, structural changes may instead disrupt the original balance. However, in breeding, this kind of interference sometimes becomes a means instead. For example, by using the infiltration of rye chromosome fragments, disease resistance was successfully introduced (Figure 1) (Wang et al., 2023). In addition, the activity of transposers and fragment duplication are often involved, which alter the regulatory logic of the genome and make wheat more flexible at the expression level. 4.3 Contributions of rearrangements to adaptive evolution and environmental stress responses Not every adaptation to the environment relies on sudden changes. In fact, changes in the structure of chromosomes themselves can also help species adapt. For hexaploid wheat, chromosomal rearrangement is like a "quick adjustment" tool. When the external environment undergoes drastic changes or the pressure of breeding selection increases, it can rapidly bring about genetic variations. For instance, genetic segments from wild species, combined with some complex rearrangements, not only enhance disease resistance but also affect yield and quality. These seemingly chaotic changes actually have certain directionality behind them (Zhao et al., 2023; Liu et al., 2025). Moreover, the transposon in the wheat genome is also very active. Coupled with the fact that the centromeric region itself is prone to "movement", the flexibility of the overall structure is also enhanced accordingly. It can be said that throughout the evolution of wheat, these "constantly adjusting" mechanisms have never ceased.
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