Triticeae Genomics and Genetics, 2025, Vol.16, No.2, 54-62 http://cropscipublisher.com/index.php/tgg 55 The starting point of this study is very straightforward-by constructing the wheat pan-genome, to clarify which gene differences are related to important traits. Not only modern wheat, but also ancient subspecies are included. After comparison, some new gene loci and structural variations that were not noticed in the past can be found, and useful alleles can also be unearthed, enriching the genetic chassis of wheat. Nowadays, sequencing and analysis technologies are much more mature than before, and the assembly of the pan-genome will become increasingly precise, which is precisely an important step in promoting sustainable wheat production. 2 Advances in Pangenome Construction Technologies 2.1 Sequencing platforms and assembly methods If it were ten years ago, to say that all the genetic diversity of wheat should be fully understood, more people would have thought it was a fairy tale. The genome of wheat is large and complex, with triploids and hexaploids mixed together. However, in recent years, the situation has changed. Sequencing technology has been updated rapidly and the cost is not as terrifying as before. The conditions for conducting such research have become much more lenient. The three commonly used assembly methods did not exist from the very beginning but gradually evolved through research and practice. For instance, de novo assembly-completely independent of existing reference genomes, directly piecing together a version that belongs to a certain variety itself; Reference-based iterative assembly-first use the existing version as the foundation, and then add new segments of other varieties. There is also the increasingly popular atlas pan-genome in recent years, which can directly "draw" the differences among different varieties (Hu et al., 2024). But don't think that having a method will solve the problem once and for all. The genome of wheat is full of repetitive sequences, interspersed with deletions and diversity changes, and it is particularly difficult to assemble these things. Often, it is still necessary to rely on high-throughput and high-precision platforms to support the entire process. 2.2 Data integration and graph-based pangenomes To assemble the genes of multiple varieties into a large map sounds like building with blocks, but in fact, it is not at all easy. However, the amount of information brought by this method is indeed astonishing, especially in terms of gene deletions (PAVs) and structural variations, where the differences can be seen at a glance (Zanini et al., 2021). Nowadays, some platforms have turned this idea into tools, such as Wheat Panache, and many researchers are already using it. Its advantage is that the operation is intuitive-it can directly compare the genetic regions of different varieties, and even complex variations can be detected (Figure 1) (Bayer et al., 2022). Moreover, this kind of map is not just for "watching the spectacle". It can mark which regions are encoded and which are regulated, and can also integrate transcriptome and epigenome data together. To put it bluntly, this is no longer a simple jigsaw puzzle; it's more like opening a door for in-depth research. 2.3 Challenges in constructing a wheat pangenome The problem, of course, has always existed. The genome of wheat is inherently large, and with its high repetition rate and polyploid structure, the difficulty of analysis can be imagined. Some people might say, "Isn't technology getting more and more advanced?" Yes, but the volume of data is also expanding at a rapid pace. Just for storage and management, very strong computing resources are required. The real challenge lies in how to precisely identify variations from piles of sequences, complete integration, and then produce clear and usable visual results. Moreover, not every researcher is proficient in operating those complex data tools, which leads to a lot of data being "useful but not applicable". It is precisely for this reason that many teams nowadays emphasize the need to build "user-friendly" analysis platforms. Only when more people can make it accessible and smooth for them to use can pan-genome research be truly implemented. 3 Genetic Diversity Uncovered by the Wheat Pangenome 3.1 Core and dispensable gene content Wheat's genes are more than just present or absent. Pan-genome studies reveal that they actually consist of two components: core genes common to all wheat varieties, and a subset of genes found only in certain varieties, often referred to as nonessential genes or, more bluntly, "variable genes." To give specific numbers, the pan-genome of hexaploid bread wheat contains approximately 140 500 genes, of which approximately 81 070 are in the core
RkJQdWJsaXNoZXIy MjQ4ODYzNA==