Triticeae Genomics and Genetics, 2025, Vol.16, No.6, 237-244 http://cropscipublisher.com/index.php/tgg 248 Figure 1 Plants (a), spikes (b), and seeds (c) images of Yukuri, MY11and six wheat-rye addition lines (Adopted from Wang et al., 2023) 5 Detection Technologies and Analytical Methods for Chromosome Rearrangements 5.1 Application of optical mapping, Hi-C, and long-read sequencing in structural variation detection How to detect structural variations has always been an unavoidable problem in the study of genomic rearrangement. Especially for crops like wheat, which have a large and complex genome, relying solely on a single technology often leads to neglecting one aspect for another. For instance, optical spectra can reveal which regions are broken, how they are rearranged, and also indicate the direction, distinguishing between equilibrium and non-equilibrium rearrangements. However, this needs to be combined with other methods, and there are blind spots when used alone (Qu et al., 2023). Hic is not only capable of creating three-dimensional structure diagrams. It can also identify rearrangement types such as translocation and inversion, even see the breakpoints, and extract copy number information from the same dataset (Burden et al., 2025; Galbraith et al., 2025). Long-read sequencing, such as PacBio and Oxford Nanopore, has more advantages when dealing with repetitive and disordered fragments. It can accurately locate breakpoints and has become a standard feature in many high-standard national-level testing processes. 5.2 Visualization value of cytogenetic techniques such as FISH and GISH When it comes to which method is the most intuitive, the visualization technology at the cellular level is still irreplaceable. Methods like FISH and GISH, although "old-fashioned", can really directly identify where the problem lies on the chromosome. The resolution of FISH can reach the level of thousands of bases, and it is effortless to locate structural problems such as translocation and inversion (Qu et al., 2023; Xia, 2025). GISH is particularly useful for polyploid species. In a subgenomic mixed crop like wheat, the components of each genome can be clearly distinguished, and even which fragments are introduced from exogenous sources, such as wild species transplanting fragments (Hu et al., 2020). Although they are not as information-rich as high-throughput technologies, they have irreplaceable intuitive value in the judgment of spatial position and chromosomal background.
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