Rice Genomics and Genetics 2025, Vol.16, No.3, 159-179 http://cropscipublisher.com/index.php/rgg 169 and panicle architecture. In conclusion, structural variations often act as large-effect cis-regulatory mutations: by changing gene copy number, disrupting chromosomal context, or introducing new regulatory DNA, SVs rewire gene expression networks in ways that can produce significant phenotypic outcomes. 6 Comparative Pan-genome Analysis Across Rice Subspecies 6.1 Core and variable genome components across subspecies Comparative pan-genome analysis allows us to quantify how much of the rice genome is shared between subspecies (core) and how much is unique to each lineage (variable). When examining indica and japonica rice, researchers find a substantial core genome common to both, alongside significant subspecies-specific content. For example, a recent pan-genome reference constructed from both Asian and African rice reported about 28 900 core genes that were found in all accessions examined (Guo et al., 2025). Beyond this core, thousands of genes were restricted to particular groups-around 10 101 genes were specific to Asian rice (indica/japonica) and not present in African rice, and conversely about 1 259 genes appeared unique to African rice. Focusing within O. sativa, indica andjaponica share the majority of their genes, but each has lost or gained some genes relative to the other. The 3K pan-genome analysis, for instance, showed that japonica varieties lack some genes that are present in indica (and vice versa), which correlates with their independent domestication bottlenecks and breeding histories. The aus subpopulation (considered an early-diverging group of indica) and aromatic group (Basmati-type) also contribute unique genes to the pan-genome. Aus rice was found to carry novel alleles and even novel genes not observed in mainstreamindica, reflecting its separate evolutionary trajectory. Meanwhile, aromatic rices, which include the basmati and sadri types, have some genomic segments more similar to japonica (due to historical introgression) but also unique content. Wild relatives dramatically expand the variable genome: incorporating O. rufipogon adds many wild-specific genes (e.g., ~13k genes unique to wild in one study), most of which are absent from all cultivated lines. These wild-specific genes include those related to stress tolerances or life history traits (like seed shattering or perennial growth) that were not retained during domestication. In summary, the core genome forms the backbone of rice’s biological functions, while the variable genome–differing across subspecies and populations–provides the genomic basis for the diverse phenotypes and local adaptations observed in rice. 6.2 SV enrichment in lineage-specific regions When comparing genomes of different rice subspecies, certain genomic regions emerge as enriched for structural variation unique to one lineage. These often correspond to regions that experienced differential selection or drift after the indica–japonica split. For example, genomic regions around known reproductive isolation genes show lineage-specific SVs. The S5 locus on chromosome 6, implicated in hybrid sterility between indica and japonica, contains an inversion and a small deletion in indica relative to japonica that cause meiotic failure in hybrids. Such structural differences act as barriers maintaining lineage separation. More broadly, a pan-genome inversion analysis identified nearly 1 769 inversions across Asian rice, some of which are fixed in one subpopulation but absent in others. These inversions are essentially lineage-specific markers; they can suppress recombination locally, contributing to subpopulation structure. Researchers have also observed that some chromosomes harbor clusters of subspecies-specific SVs. A striking example is on chromosome 11 and 12 where indica carries private large deletions affecting seed dormancy and shattering genes, whereas japonica carries ancestral versions of those loci. In the rice super-pan-genome, an analysis of SV hotspot distribution found that certain deletions or copy-number changes were exclusively present in the indica subgroup (denoted O. sativa indica, Osi) but completely absent in the japonica subgroup (Osj), and vice versa. For instance, Shang et al. (2022) noted a large deletion in the flowering gene DTH8 only in indica accessions, and a copy-number expansion of the grain length gene GL7 only in japonica accessions. These lineage-specific SVs often align with QTLs that differ between subspecies–e.g., DTH8 deletion contributes to early flowering in some indica, GL7 duplication contributes to longer grains in japonica. Hence, structural variation is not evenly spread: it tends to cluster in genomic neighborhoods that have undergone separate evolutionary paths in indica versus japonica (or other subgroups), representing the genetic signatures of lineage divergence.
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