Triticeae Genomics and Genetics, 2025, Vol.16, No.2, 54-62 http://cropscipublisher.com/index.php/tgg 54 Research Insight Open Access Pangenome Construction of Triticum aestivum and Its Implications for Genetic Diversity 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.2 doi: 10.5376/tgg.2025.16.0006 Received: 08 Jan., 2025 Accepted: 20 Feb., 2025 Published: 05 Mar., 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, Pangenome construction of Triticum aestivum and its implications for genetic diversity, Triticeae Genomics and Genetics, 16(2): 54-62 (doi: 10.5376/tgg.2025.16.0006) Abstract Common wheat (Triticum aestivum) is a globally important staple food crop. However, the use of a single reference genome limits our understanding of its extensive genomic diversity. This study explores the construction of a wheat pan-genome, utilizing advanced sequencing technology, map-based genomic characterization, and integrated bioinformatics processes to capture core genes and non-essential gene content. We analyzed structural variations, gene presence and deletion variations (PAV), and copy number variations (CNV), revealing significant genetic diversity in common wheat (T. aestivum). These findings have profound significance for wheat breeding, enhancing trait association research, genomic selection, and adaptability to climate change. We further discussed the evolutionary insights gained from pan-genome data, including domestication events, population structure and gene family expansion, and highlighted the key contributions of the "10+ Wheat Genome Project". A comprehensive understanding of the wheat genome highlights the necessity of continuously developing inclusive and scalable pan-genomes, integrating multi-omics data, and conducting international cooperation, ultimately aiming to support sustainable agriculture and crop improvement. Keywords Triticum aestivum; Pangenome; Genetic diversity; Wheat breeding; Structural variation 1 Introduction The name "wheat" (Triticum aestivum) might sound somewhat academic, but it is actually the bread wheat that people eat in their daily lives. Its status needs no exaggeration. A large part of the daily calories and proteins of billions of people are supplied by it (Cavalet-Giorsa et al., 2023). For many places, the stability of wheat production determines the stability of food security. The problem is that the population is still growing and the climate is becoming increasingly difficult to predict. The requirements for wheat have naturally increased-not only high yield, but also disease resistance, drought resistance, and preferably better nutrition (Bayer et al., 2022). These demands may sound self-evident, but the scientific research foundation behind them was actually not as solid as imagined before (Huang et al., 2024). Over the past few decades, most research on wheat genomes has revolved around a reference genome. In other words, we use a "standard sample" to represent all wheat (Zanini et al., 2021). It sounds convenient, but the problem is obvious-there are significant genetic differences among different varieties, and even among some of its wild relatives. Using one sample to infer the situation of an entire species is like using one person's height to represent the height distribution of all mankind. This approach misses a lot of things, such as whether certain genes exist or not, changes in gene structure, or new genes closely related to agronomic traits (Przewieslik-Allen et al., 2021). In this case, the idea of "pan-genome" was proposed. It does not focus on a single genome but rather assembles multiple gene groups from different sources to view the complete genetic picture within a species. Genes that are present in all varieties are core genes, while those that are only found in some varieties are auxiliary genes. Regulatory elements and structural variations can also be captured in the pan-genome. Nowadays, the pan-genome data and map databases of wheat can be presented in a visual way. Researchers can use them to compare the genetic differences of different varieties, and breeders can also select more suitable materials based on this (Barabaschi et al., 2025).
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