Triticeae Genomics and Genetics, 2025, Vol.16, No.2, 54-62 http://cropscipublisher.com/index.php/tgg 57 Pan-genome databases like Wheat Panache can now visually display and compare PAV with CNV. Researchers and breeders can directly query and quickly compare, which makes the study of genetic diversity and the targeted breeding of new varieties more confident (Bayer and Edwards, 2023). 4 Implications for Wheat Breeding and Crop Improvement 4.1 Enhanced trait association and marker development Some traits, such as drought resistance, salt tolerance, or the taste of the grains, are visible and tangible to everyone, but they are often the result of complex genes at work. The traditional reference genome is not omnipotent-some key variations cannot be found at all because they only occur in a few species (Tiwari et al., 2024). This is precisely where the pan-genome comes into play. It can make up for the missing part in the past, such as the presence of a deletion variation (PAV) or a newly emerged allele. Many new genetic markers have been unearthed from these differences. Tools like genome-wide association analysis (GWAS), with these markers, make it as easy to locate traits as "matching them" (Montenegro et al., 2017). The current k-mer analysis method can even directly identify the key genes that affect the protein content of grains. With these targets in place, quality improvement is no longer just a matter of luck but has a clear direction. 4.2 Improving genomic selection and prediction accuracy If one could know the destination of breeding earlier, a lot of time and resources could be saved. The introduction of the pan-genome is actually helping us look at the map in advance. The common genomic selection model has a drawback-it cannot cover all genes, especially those "non-mainstream" genes that are absent from the reference genome. The pan-genome can precisely fill this gap and make the prediction results closer to reality (Zhang et al., 2024). Machine learning is not omnipotent, but when combined with the pan-genome, it does have more advantages in dealing with complex traits (Bayer et al., 2021). This combination can help us avoid detours and screen out potential materials in advance. The breeding cycle has been shortened and the accuracy of seed selection has also improved. More importantly, these more abundant genetic information enable us to select materials that are both disease-resistant and of high quality with decent yields, no longer relying solely on experience for judgment, but rather backed by data. 4.3 Facilitating adaptation to climate change and emerging threats The climate is becoming increasingly unpredictable, and the changes in pests and diseases are also rapid. New problems in agriculture are increasing year by year. Wheat, as the staple food, is naturally the first to face the challenge. The pan-genome enables us to extract valuable genetic information from modern cultivated varieties and wild relatives. Many genes that are drought-tolerant, disease-resistant and adaptable to extreme climates have actually been hidden in those unnoticed varieties long ago (Mangal et al., 2024). In the past, it might have taken several years to find these genes. Now, with the "accelerator" of the pan-genome, the speed is much faster and the application is more precise. In the context of unstable climate and increasing threats, this ability is almost a necessity (Fernandez et al., 2021). Only by identifying and making good use of these "hidden" useful alleles can we possibly ensure the stability of future wheat yields and quality. 5 Evolutionary and Ecological Insights from the Wheat Pangenome 5.1 Understanding domestication and divergence The more refined the breeding, the more simple the inheritance-this is a common saying in the industry. The data from the pan-genome basically also confirm this statement. Those superior varieties that have undergone long-term domestication and strict screening have indeed "tightened" their genetic diversity significantly (Montenegro et al., 2017). However, this is not the whole truth. There are still many variations in the so-called "non-essential" gene regions. Although not every breed has these genes, they are often closely related to adaptability or specific traits. If we only look at modern varieties, this story actually cannot be told completely. If we compare wild relatives and local species together, we can see more details: some genes have been retained all the way, while others have quietly disappeared during the process of evolution. Behind every retention or loss, the shadow of human breeding selection can almost always be found.
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