Triticeae Genomics and Genetics, 2025, Vol.16, No.2, 54-62 http://cropscipublisher.com/index.php/tgg 58 5.2 Population structure and geographic differentiation The differences in the appearance and performance of wheat in different places are not only caused by the environment, but also the involvement of genes is obvious. The pan-genome can help us track these differences and see if certain genes are only present in varieties of specific regions and cannot be found anywhere else (Schreiber et al., 2024). PAV and SNP data record this "presence" and "absence", "similarity" and "difference". When put together, they can depict the relationships among wheat populations and how they gradually adapt to local conditions. However, this is not a simple issue of geographical grouping. Core genes and helper genes each have their own roles in regional adaptability. The absence of either type would be incomplete. More importantly, the pan-genome not only helps us review history, but also monitors the present, enabling us to identify in advance those variations that may be particularly crucial for future breeding. 5.3 Gene family expansion and functional innovation If genetic diversity is regarded as a warehouse, then the expansion of gene families is like adding new goods to the warehouse. Pan-genome research has found that many gene families in wheat have become more "fancy" in function, especially those related to stress coping. The changes are not only reflected in quantity but also in the situation of "changing jobs". Some genes that originally operated in organelles have entered the cell nucleus through polyploidy or gene transfer (Chen et al., 2023). These members, known as nuclear organelle genes (NOGs), have taken on new tasks, giving wheat more leeway in performing under adverse conditions. These changes may not seem obvious on the surface, but for breeding, they mean more functional reserves that can be utilized. The environment changes and genes adjust accordingly. The pan-genome can precisely bring out such details, making improvement more operational. 6 Case Study 6.1 Significance of the project for pangenome construction Everyone knew from the beginning that wheat was too complex and that a single reference genome was definitely not enough. But to really break through this limitation, it still had to be driven by specific projects. The "Ten+ Wheat Genome Project" was launched in this context. It tested more than ten varieties, both common and highly representative. To be honest, previous data were often "out of focus", especially when faced with global wheat variations. This project, through sequencing and assembly, has revealed the true appearance of each variety, from structural rearrangements to differences in the number of genes. It involves everything. It cannot be said that all problems have been solved, but at least the foundation of the pan-genome has been laid more firmly, allowing researchers to understand the overall genetic structure of wheat more systematically. 6.2 Key discoveries and interpretations As soon as the data came out, several details quickly caught the attention of the research team. For instance, some structural variations are not merely conventional genetic alterations. Some are chromosomal rearrangements, and others directly result from gene infiltration of wild relatives (Figure 2) (Walkowiak et al., 2020). This makes people realize that the evolutionary path of wheat is far more tortuous and complex than imagined. There were also some discoveries that, at first hearing, were quite unexpected. The reference genome of spring wheat in China is actually lacking quite a few genes. However, in some varieties, completely "exclusive" genes can still be found (White et al., 2024). These results not only helped clarify the boundary between core genes and variable genes, but also filled the gap in the previous map. The team also specifically analyzed genes related to disease and pest resistance. Genes like Sm1 have been detailedly characterized, and the results proved that its existence does indeed bring about real functional differences. As for the expression level, the activity levels of different subgenomes are not consistent, and the expression patterns among different tissues and varieties also vary significantly. The results of the transcriptome almost remind us that wheat is a naturally "restless" crop. 6.3 Broader implications for research and breeding These achievements are not simply a few more records in the database. They have left more room for maneuver in the search for trait markers, the development of new markers, and the exploration of superior alleles. Breeders can select the appropriate ones from a wider range of options and also improve varieties in a more targeted manner,
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