Triticeae Genomics and Genetics, 2025, Vol.16, No.3, 101-109 http://cropscipublisher.com/index.php/tgg 105 5 Application of PAV Knowledge in Barley Breeding 5.1 Use of PAV markers in marker-assisted and genomic selection Often, traditional SNP markers are sufficient, but the genetic basis of some important traits cannot be fully explained by SNPS. At this point, the PAV marking becomes particularly crucial. Especially for expressive PAV, its linkage relationship with peripheral sequences is not strong; instead, it can independently reflect certain unique genetic differences. Some studies have attempted to combine PAV data with SNPS and gene expression levels, and the results show that the prediction effect for some key agronomic traits has become more accurate and stable. For breeding materials, low-coverage mRNA sequencing methods can quickly and cost-effectively extract these PAV information. In some scenarios, it may even replace SNP as the main characterization method. For instance, the genes Ryd2 and Ryd3 of barley that resist yellow dwarf virus were screened out by this PAV-based labeling method (Scheurer et al., 2001). 5.2 Incorporating PAVs into pangenome-informed breeding strategies The traditional reference genome cannot encompass all variations of genes. It was only by constructing the pan-genome of barley that researchers identified millions of PAV tags, which gradually revealed the true genetic diversity. Sometimes, mining these rare PAVs from wild and local varieties is more direct and effective than looking for variations from modern varieties. Machine learning has also played a driving role in this-it enables us to screen out useful PAVs more quickly and use them for trait localization. Once PAV is anchored to a certain phenotype, it can be used for subsequent selection breeding, such as controlling traits like flowering time, plant height or grain size. This approach is also gradually changing the "blind selection" model of breeders in the past, making the improvement of target traits more controllable and efficient. 5.3 Examples of trait improvement through PAV-based introgression Disease-resistant breeding is one of the typical application scenarios of PAV. For instance, barley varieties carrying Ryd2 and Ryd3 showed almost no significant decline in yield when infected by BYDV-PAV virus, while susceptible varieties often suffered a severe reduction in yield. The infiltration process of these genes is an example of combining traditional methods with genomic approaches (Wei, 2024). More notably, even in some "superior varieties" that were originally considered to have a very similar genetic background, the use of PAV markers can also uncover potential resistance differences (Ghanem et al., 2018; Alquicer et al., 2023). In addition, PAVs related to agronomic traits such as heading time and plant height have also begun to play a role in precise selection, enhancing the efficiency and pertinence of the entire breeding process. 6 Case Study 6.1 Identification of heat-responsive genes absent in susceptible genotypes The hot weather has arrived. Some barley can withstand it, while others wilt quickly. This difference is often related to whether a group of key "heat response" genes are present, such as heat shock proteins, antioxidant enzymes, and those factors that maintain cell membrane stability and regulate hormone signals (Figure 2). These genes are common in heat-resistant varieties, but may not exist at all in some susceptible varieties. This is very likely the fault of PAV. In fact, similar situations have also been seen in other crops. In pearl millet, pan-genomic studies have identified some structural variations and PAVs, involving genes related to endoplasmic reticulum function, RWP-RK-type transcription factors, etc., which are either absent or underexpressed in heat-resistant materials (Yan et al., 2023). These findings suggest that barley may also have such a situation where "one or two key genes are missing". If the same PAV screening approach is applied, it might be possible to identify the core genes that determine its thermal adaptability. 6.2 Field validation of heat tolerance in pav-harboring lines under stress Of course, merely looking at genes is not enough. What really works still needs to be tested in the fields. Especially when it comes to the property of heat resistance-its performance may vary in different years and on different plots. In some breeding projects, researchers plant materials carrying specific PAVs under high-temperature stress conditions to observe indicators such as grain filling speed, canopy temperature and yield stability (Driedonks et al., 2016). Although there are not many cases of barley in this regard, in other crops, it is
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