Triticeae Genomics and Genetics, 2025, Vol.16, No.3, 101-109 http://cropscipublisher.com/index.php/tgg 102 So, the purpose of in-depth research on PAV is actually quite straightforward-to find new clues that are useful for breeding. Combining PAV information with transcriptome and other genomic data is expected to make the prediction of complex traits more accurate and open up new paths for genomic selection and marker-assisted breeding. The ultimate goal is also very realistic, which is to screen out barley varieties that are more productive, more resilient and more nutritious. This is not only for the income of farmers, but also for food security and the sustainable development of future agriculture. Characterizing and utilizing PAV can accelerate the development of barley varieties with excellent agronomic performance and adaptability, supporting food security and sustainable agriculture. 2 Molecular Basis and Detection of Presence/Absence Variations in Barley 2.1 Definition and genomic mechanisms leading to PAVs Not all genotypes contain exactly the same gene fragments. In barley, some DNA regions, such as an entire gene segment, may be "standard configuration" in one type of material but not present at all in another. This is known as PAV (Presence/Absence Variation). This kind of variation is not uncommon, and the mechanisms involved behind it are rather complex: factors such as transpostion activity, fragment repetition or loss, and even some "accidental operations" during the DNA repair process may all create these differences. The factor of seat rotation is particularly worth mentioning. It can not only change the position of DNA, but sometimes it is also directly related to the increase or decrease of genes. Those genes that are not "essential", such as certain transcription factors, are prone to "get on board" when transposons are inserted. In addition, mechanisms such as single-chain annealing and template sliding are also involved (Munoz-Amatriain et al., 2013; Tong et al., 2024). In other words, the generation of PAV does not rely on a single method but is the result of the combined effect of multiple processes. 2.2 Technological advances enabling PAV discovery Finding these PAVs is not something that can be achieved simply by flipping through a genomic manual. Only when we have high-quality genetic assemblies of multiple barley varieties, wild types, and local strains can these hidden variations come to light (Figure 1). The establishment of the pan-genome is precisely based on the integration of this diversity, which helps us systematically classify PAVs across the entire species range. Of course, sequencing technology is also constantly advancing. High-throughput methods such as whole-genome resequencing and mRNA sequencing not only help us improve resolution but also enable us to identify genotypic and non-genotypic PAVs more quickly and accurately. Most importantly, they can also reveal whether these variations are related to traits such as disease resistance, plant height or flowering period (Jayakodi et al., 2020; Zhang et al., 2022). 2.3 Bioinformatics tools and pipelines for accurate identification and validation of PAVs Experimental methods alone are not enough. To a large extent, the identification of PAVs also depends on data processing. Some commonly used tools and methods nowadays, such as comparative genomic hybridization, k-mer whole-genome scanning, and even some new technologies that do not rely on reference genomes (like AgRenSeq), can already achieve highly accurate detection. Assembling multiple genomes for comparison not only enables the "targeted" positioning of PAV but also allows for the rapid comparison of differences among various haplotypes. If one wants to save costs and improve efficiency, the method based on mRNA sequencing is a good choice-it can not only capture structural variations but also directly obtain expression information, which is particularly suitable for large-scale screening in breeding materials (Weisweiler et al., 2019). 3 Distribution and Evolutionary Significance of PAVs in Barley 3.1 Variation of PAVs across landraces, cultivars, and wild relatives Not all genes are present in every type of barley. In fact, whether it is local varieties, modern cultivated varieties or wild relatives, there are considerable differences in the number of genes among them. Researchers analyzed multiple inbred lines of spring barley using mRNA sequencing. The results showed that more than half of the genes had PAV phenomena-some genes only appeared in specific varieties, while others were not present at all. Strangely, these PAVs have little to do with the surrounding sequence variations, indicating that such variations
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