Triticeae Genomics and Genetics, 2025, Vol.16, No.2, 54-62 http://cropscipublisher.com/index.php/tgg 56 portion. On average, each variety contains around 128 656 genes (Montenegro et al., 2017). While this may sound like a large number of genes, what's even more interesting is that these "nonessential" genes are actually a treasure trove of genes associated with traits. Abilities such as drought resistance, disease resistance, and adaptability to diverse environments are often found in these genes with greater variability. Figure 1 Wheat Panache screenshot showing an Aegilops ventricosa introgression at the beginning of chromosome 2 in cultivars Stanley, Jagger, Mace, and SY Mattis. Black boxes were added to show the region missing in cultivars where the introgression replaced parts of chromosome 2A. The graph assembly started with the IWGSC v1 assembly leading to linearized regions following the same naming scheme as the IWGSC v1.0 assembly (chr1A_part1, chr1A_part2, chr2A_part1, …). CS, ‘Chinese Spring’. Shown here is the beginning of the first part of chr2A. Black blocks are gene models. White regions correspond to regions that are present in the graph but contain no genes (Adopted from Bayer et al., 2022) 3.2 Structural variants (SVs) and their distribution The differences between genomes are sometimes not minor repairs but radical alterations. Pan-genome research shows that the number of structural variations among wheat varieties is astonishing. Chromosomal rearrangement is one type, and the other type is the mixture of genetic fragments from wild relatives (Przewieslik-Allen et al., 2021). In other words, some varieties may carry a portion of "wild" genes. The relationship between these structural variations and phenotypes is not loose. Traits such as stress resistance and yield can often find clues in SV. However, their distribution in the genome is not uniform. In some areas, there is almost no movement, while in others, the frequency of variation is so high that it seems like a "hotspot". Often, these highly variable regions are precisely linked to the adaptability and breeding history of wheat (Zanini et al., 2021). This makes one can't help but suspect that our previous research might have missed quite a few important positions. 3.3 Gene presence-absence variation (PAV) and copy number variation (CNV) Not every wheat variety has the same genes. Some genes are completely absent in certain varieties but actively present in others. This is known as PAV (Bayer et al., 2022). This difference is one of the important sources of genetic diversity in wheat. Especially among the genes related to disease resistance and environmental stress response, the proportion of PAV is even higher. In other words, it is precisely these differences that enable wheat to display its unique abilities in various environments. As for CNV-the variation in gene copy number-although it seems like a technical detail, its impact is not small at all. The same gene may have only one copy in one variety, but several copies may be replicated in another. This "more" or "less" will change the intensity of gene expression and thereby affect the manifestation of traits. Of course, these differences only count if they can be seen.
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