Triticeae Genomics and Genetics, 2025, Vol.16, No.3, 101-109 http://cropscipublisher.com/index.php/tgg 101 Research Insight Open Access Exploring Presence/Absence Variations in Barley for Agronomic Trait Improvement Wenyu Yang, Chunxiang Ma Modern Agricultural Research Center, Cuixi Academy of Biotechnology, Zhuji, 311800, Zhejiang, China Corresponding email: chunxiang.ma@cuixi.org Triticeae Genomics and Genetics, 2025, Vol.16, No.3 doi: 10.5376/tgg.2025.16.0011 Received: 09 Mar., 2025 Accepted: 21 Apr., 2025 Published: 06 May, 2025 Copyright © 2025 Yang and Ma, This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Preferred citation for this article: Yang W.Y., and Ma C.X., 2025, Exploring presence/absence variations in barley for agronomic trait improvement, Triticeae Genomics and Genetics, 16(3): 101-109 (doi: 10.5376/tgg.2025.16.0011) Abstract Presence/absence variations (PAVs), a form of structural genomic variation, play a critical role in shaping phenotypic diversity in plants, including crop species like barley (Hordeum vulgare), which serves both as a globally important cereal crop and a model organism for genomic studies. In this review, we examined the molecular mechanisms underlying PAV formation, such as transposable element activity and large-scale deletions, and highlighted recent advances in technologies-including pangenome assemblies and high-throughput sequencing-that have enabled the comprehensive detection of PAVs. We further discussed the distribution patterns of PAVs among landraces, cultivars, and wild relatives of barley, emphasizing their evolutionary significance in domestication and adaptation. Functionally, PAVs were found to influence key agronomic traits such as disease resistance, abiotic stress tolerance, and yield-related characteristics. The integration of PAV knowledge into modern breeding programs was explored, with a focus on marker-assisted selection and pangenome-based strategies, including a case study on improving heat tolerance through PAV-informed breeding. Lastly, we considered the potential of combining PAV analysis with multi-omics data and phenotyping platforms, and the role of machine learning in modeling genotype-phenotype relationships. This study underscores the value of PAVs as a genomic resource for precision breeding and highlights future directions in expanding pangenomic datasets and developing breeder-friendly tools to facilitate their practical application. Keywords Presence/absence variation (PAV); Barley (Hordeum vulgare); Structural genomic variation; Agronomic trait improvement; Pangenome-based breeding 1 Introduction Sometimes, some important genetic information is not reflected in the familiar single nucleotide polymorphisms (SNPS). For instance, certain fragments in the genome appear in some barley individuals but cannot be found at all in others-this is what is called presence/absence variation (PAV). Although this variation sounds simple, it may directly affect a plant's stress resistance, yield, and even determine whether it can grow well under certain climatic conditions (Cai, 2024). Research also found that the number of PAVs in barley is not small. These variations not only change the number of genes but also affect the expression mode of genes (Jayakodi et al., 2020). In fact, the significance of these structural variations is far more than just scientific exploration. Barley (Hordeum vulgare), as the fourth largest grain in the world, has a strong environmental adaptability by itself. This diversity of genetic background is precisely a resource that breeding research highly values (Desta et al., 2024). Especially in some regions with less favorable climatic conditions, barley can still be stably produced as feed, malt and human food. Behind this "tenacity" lies a genetic code at various structural levels. PAV happens to be one of the keys to unlocking these "codes". Of course, SNPS remain important, but an increasing number of studies have shown that if PAV is ignored, recessive variations associated with important agronomic traits may be missed (Weisweiler et al., 2019). The emergence of the pan-genome has enabled us to no longer be confined to the "reference genome" version alone and has also made the mining of PAVs more feasible. This difference may be reflected in core indicators such as when the ears start to spike, how tall they grow, and whether they are resistant to diseases.
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