Rice Genomics and Genetics 2025, Vol.16, No.3, 159-179 http://cropscipublisher.com/index.php/rgg 161 To build a pan-genome, scientists’ sequence multiple individuals and bring all their genetic data together. This helps uncover genes that aren’t in the usual reference genome-genes that might otherwise go unnoticed. Studies in rice and other crops have shown that using only one reference leaves out important parts of the genetic puzzle. By adding those missing pieces, the pan-genome gives a clearer picture of a species’ full genetic makeup. What stands out is that many of these variable genes are linked to how plants handle stress from their surroundings. They may not be essential all the time, but they give plants the flexibility to adapt. That’s what makes the pan-genome such a powerful tool for exploring biodiversity. 2.2 Core genome vs. dispensable genome In plant genomes, including rice, the core genome comprises the genes that are consistently present in every accession examined. These genes typically encode fundamental cellular and developmental functions. The dispensable genome (also called the accessory genome) contains genes that are missing in one or more accessions. Dispensable genes often relate to environmental interactions, such as disease resistance, stress tolerance, or secondary metabolism, which may not be needed under all conditions. The balance between core and dispensable content can be quantified as more genomes are sequenced. Early pan-genome research on Asian rice showed that the shared set of genes-the so-called core genome-makes up just over half of all genes found across different varieties. For instance, a study of 453 rice genomes identified about 12 770 gene families (roughly 53.5%) that were common to all samples. The rest varied from one variety to another. Similarly, the 3 000 Rice Genomes Project found more than 19 000 genes that weren’t in the reference genome but were present in at least one of the varieties studied (Wang et al., 2023). This shows that rice genomes can differ a lot depending on the variety. Many of these variable genes appear in only certain groups and often reflect the plant’s evolutionary history or responses to environmental pressures. These genes aren’t just extras-they can be key to specific traits like disease resistance that help a plant thrive in particular conditions. Understanding which genes are common to all rice types and which are more specialized is crucial. It helps researchers see both the essentials for rice survival and the sources of diversity that allow different varieties to adapt. 2.3 Development and application of pan-genomes in major crops Pan-genomic approaches have been successfully applied to many major crop species, leading to key biological and practical insights (Shi et al., 2022). In tomato (Solanum lycopersicum), a pan-genome analysis of 725 accessions uncovered dozens of novel genes, including a rare allele for fruit flavor that had been lost during domestication. In maize (Zeamays), initial pan-genome studies revealed that a significant fraction of genes is not shared among all lines, explaining heterosis and trait variation in hybrids. For soybean (Glycine max), pan-genomics helped identify structural variations and presence/absence variants linked to seed composition and stress responses. In wheat (Triticum aestivum)– a complex hexaploid crop-assembly of multiple genomes provided a wheat pan-genome that captures global variation from modern breeding; this work identified genomic regions and genes affected by selection in different breeding programs. Similarly, a pan-genome of barley (Hordeum vulgare) revealed “hidden” structural variants accumulated through decades of mutation breeding, some of which underlie agronomic traits. Pan-genomes aren’t just theoretical-they’re useful tools for crop improvement. In rapeseed, comparing different ecotypes revealed genetic differences between spring and winter varieties, especially in traits like flowering time and glucosinolate levels. These insights help breeders target beneficial genes. Pan-genome data also support better genotyping tools, including presence/absence markers, which boost the accuracy of GWAS and genomic predictions in crops like rice and maize. Building crop pan-genomes has opened the door to understanding more of the genetic variation that exists-and has given breeders stronger resources to work with across many species. 2.4 Advances in computational methods and sequencing technologies In recent years, plant pan-genomics has made great progress, largely thanks to advances in DNA sequencing and data analysis. Early studies depended on short-read methods like Illumina, which were precise but often missed big structural changes or repetitive regions in the genome. That changed with the arrival of long-read technologies
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