Triticeae Genomics and Genetics, 2025, Vol.16, No.6, 237-244 http://cropscipublisher.com/index.php/tgg 249 5.3 SV, CNV, and translocation identification based on reference genome analysis pipelines The rearrangement recognition processes that rely on algorithms are also indispensable to the reference genome. High-throughput sequencing data, such as double-end sequencing or long-read assembly, can quickly identify large fragment variations, but only if there is a control reference to facilitate the comparison of which variations are specific and which may be common but harmless (Mitsuhashi et al., 2020; Jilani and Haspel, 2021; Eisfeldt et al., 2024). These processes can not only locate the breakpoints but also restore the direction and connection sequence of the variant fragments, which is particularly important when it is necessary to distinguish between pathogenicity and natural diversity. Of course, it is difficult to cover all aspects by relying solely on such processes. Only by integrating them with optical, Hi-C, FISH and other data can the accuracy of detection and the analytical ability for complex rearrangements be improved, especially in genomes with intense structural dynamics like those of hexaploid wheat. 6 Case Studies: Chromosome Rearrangements in Wheat Origin and Breeding 6.1 Evidence of chromosomal rearrangements during A, B, and D genome fusion inTriticum aestivumorigin The evolutionary process of wheat is not as simple as just putting together three sets of genes. Before the fusion of the A, B and D genomes, each had distinct chromosomal structures. However, after the fusion, these differences triggered a series of rearrangements. Translocation and inversion among 4A, 5A, and 7B are not isolated phenomena but structural features that are widely present in hexaploid wheat and its wild relatives (Shi et al., 2022). Evidence from techniques such as FISH and chromosome staining also indicates that these rearrangements do not only occur in modern wheat; they began as early as the stage when subgenomic D was introduced (Figure 2). These changes not only helped stabilize the newly formed wheat genome but also accelerated the integration among the three subgenomes. Figure 2 Characterization of chromosomal translocations 4AS∙4AL-1DS and 1DL∙1DS-4AL derived from wheat cultivar Bima 4 (Adopted from Shi et al., 2022) 6.2 Application of wheat–rye translocations in disease resistance breeding Not all chromosomal rearrangements occur naturally; they can also be "artificially" created in breeding work. For instance, chromosomal translocations like 1BL/1RS in rye and wheat have long been widely used for disease resistance improvement. This translocation brought the resistance gene from rye into wheat and incidentally improved some yield-related traits (Jiao et al., 2024). What's more interesting is that the repetitive sequence of chromosome 1RS is particularly active, with many deletions and variations, indicating that it is not a static structure but is constantly evolving. However, these changes did not affect its status as a "darling" in breeding; instead, due to its significant effects, it was retained for a long time. 6.3 Structural variations associated with yield and stress tolerance in modern cultivated wheat Structural variations are almost everywhere in the wheat varieties grown today. Not only the inversions or translocations that are very "conspicuous" at first glance, but even the increase or decrease in copy number is often found to be linked to yield and stress resistance. Through pan-genome comparison, many variations have
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