Triticeae Genomics and Genetics, 2025, Vol.16, No.6, 237-244 http://cropscipublisher.com/index.php/tgg 246 2 Structural Characteristics of the Hexaploid Wheat Genome 2.1 Composition and functional divergence of the A, B, and D genomes The three subgenomes - A, B, and D - each undertake different "tasks" in hexaploid wheat. They come from different ancestors, and this background itself determines that they will not be exactly the same. Not all gene families can find "common points" with each other in wheat germplasm. In fact, the truly universally shared part accounts for only about 23% (Cheng et al., 2025). The D genome is particularly special. It shows more genetic variations during the formation of hexaploids, which is quite crucial in breeding. Furthermore, the distribution of transposition elements and the phenomenon of gene duplication were not evenly distributed among the three subgenomes A, B, and D. These differences ultimately contributed to the functional complexity and plasticity of the wheat genome (Liu et al., 2025). 2.2 Relationships and regulatory mechanisms of homologous chromosomes and genes In hexaploid wheat, homologous chromosomes from different subgenomes do not live independently of each other. There are indeed interactions among them, but the ways are rather complex. The interactions between these chromosomes largely depend on sequence similarity and some transposable elements specific to subgenomes. In other words, although homologous genes may seem similar, their expression level is often limited by the chromatin environment of the subgenome where they are located (Wang et al., 2025). For instance, if the genes are from wild relatives, the situation is even more different: the introduced genes may have reduced expression due to regulatory disorders, and the original homologous copies may not be able to "fill in" (Coombes et al., 2021; Jia et al., 2021). In addition, three-dimensional structures like topological associative domains (Tads) also play a regulatory and stabilizing role behind the scenes. 2.3 Features of large-scale genome duplication, deletion, and expansion The hexaploid wheat genome itself is not "calm". It has experienced many fluctuations after multiplexing, including large-scale repetition, fragment deletion and amplification. This state of "constant change" has actually shaped its complexity today. The insertion of transposition elements and the repetition of fragments not only bring about new genes but also rewrite functions. Structural variations such as presence/absence variations and copy number variations have now been found in the wheat genome with more than 1.9 million non-redundant events, especially concentrated around the centromere (De Oliveira et al., 2020; Cheng et al., 2025). Sometimes, large fragment deletions may also be the result of human manipulation, such as gamma-ray induction or gene infiltration breeding. Such variations sometimes directly affect agronomic traits (Komura et al., 2022). So, to some extent, the "turmoil" of structure is also one of the sources of the diversity and adaptability of wheat. 3 Major Types and Mechanisms of Chromosome Rearrangements 3.1 Structural variations such as inversions, translocations, duplications, and deletions It is actually not a rare thing for the structure of chromosomes to change. Once a double-strand break occurs in DNA, if the subsequent repair is not handled properly, problems are very likely to arise. Either an extra section was inserted or the position was connected wrongly. Thus, the common types of rearrangement such as inversion, transposition, repetition and absence were thus formed. At certain times, rearrangement occurs very intensely, such as large-scale chromosome breakage and recombination. Within just one cell cycle, the structural appearance may change significantly (Pellestor, 2019; Pellestor et al., 2021; Krupina et al., 2023). Inversion duplication is sometimes not complicated. It is that the DNA at the breakpoint turns back and "self-initiates" synthesis, resulting in a wrong connection again. This pattern is also common (al-Zain et al., 2023). To figure out where these rearrangements come from, high-resolution breakpoint analysis is needed; otherwise, the ins and outs won't be clear. 3.2 Roles of homologous and non-homologous recombination in chromosomal rearrangements When it comes to the "behind-the-scenes drivers" of rearrangement, homologous recombination (HR) and non-homologous end join (NHEJ) are basically the "main forces". HR is supposed to be a fine-tuning tool that precisely repairs by similar sequences. However, unfortunately, it sometimes "makes mistakes", and multiple intrusions may cause structural troubles such as translocation (Kot et al., 2021). NHEJ is more straightforward.
RkJQdWJsaXNoZXIy MjQ4ODYzNA==