Rice Genomics and Genetics 2025, Vol.16, No.3, 159-179 http://cropscipublisher.com/index.php/rgg 170 6.3 Evolutionary forces shaping the rice pan-genome Several evolutionary forces have shaped the composition and variation of the rice pan-genome. Natural selection during domestication and diversification has had a profound impact. Domestication imposed bottlenecks and strong selection for certain traits, which in turn fixed some structural variants and eliminated others. For instance, as rice was domesticated from O. rufipogon, alleles conferring non-shattering, reduced dormancy, and erect growth were favored-many of these traits, as discussed, involved structural changes such as insertions or deletions at key loci. This directional selection reduced diversity around those loci in cultivated rice relative to wild rice, effectively making wild-specific haplotypes (and their SVs) disappear from the cultivated gene pool. The relatively larger bottleneck in japonica (a narrower genetic base) compared to indica means japonica lost more genomic variation (including SVs) during domestication (Guo et al., 2025). This is reflected in the pan-genome by fewer private alleles and SVs in japonica and a smaller effective pan-gene set for japonica alone, as opposed to indica which retained or acquired more variation via introgression. Speaking of introgression, gene flow between different rice populations has also shaped the pan-genome. Indica rice is thought to have picked up domestication alleles through hybridization with japonica (for example, the sd1 dwarf allele was originally japonica and transferred to indica breeding lines). Such introgressions are structural events at the population level-large chromosomal segments (containing multiple genes and variants) moved between gene pools. Introgression with wild relatives (either deliberate in breeding or natural in sympatric growth) has introduced new structural variants into cultivated rice, such as the aforementioned Sub1A locus for flood tolerance from wild O. rufipogon. Another force is transposable element activity and genome turnover. Rice genomes have high transposon content, and bursts of transposition can generate new insertions that differentiate lineages. Over evolutionary time, active transposons in one subpopulation but not another will lead to accumulation of private insertions, expanding the pan-genome. Similarly, gene duplication and divergence (a form of mutation and selection combined) contribute to the pan-genome as new gene copies arise (e.g., disease resistance gene duplications in response to pathogen pressure). If those duplicates confer advantage, they may be retained in some populations (under positive selection) but could be lost in others (neutral loss or lack of selection). Genetic drift, especially in small farmer-maintained landrace populations, can also result in random loss of genes or fixation of structural peculiarities in certain lineages without adaptive reason. 6.4 Insights into indica–japonica divergence and hybridization Through comparing pan-genomes, we can better understand how indica and japonica rice diverged and how hybridization played a role in shaping their genomes. Genomic studies show that both types of rice-indica and japonica-likely came from the same original domestication event of Oryza rufipogon. Indica seems to have formed later, by mixing with domesticated japonica. The pan-genome supports this single-origin idea by showing that key domestication genes-like those affecting seed shattering, pericarp color, and plant structure-are mostly the same in both types (Lu et al., 2022). This suggests that japonica passed these useful traits to early indica through hybridization. For instance, both types carry the non-shattering sh4 allele and the white-pericarp Rc mutation, which are nearly fixed. These shared traits point to a common history, rather than separate domestication paths. So, rather than being independently domesticated, indica likely inherited key domestication traits fromjaponica or a related early domesticate. However, after their split, indica and japonica pursued largely separate evolutionary paths, accumulating distinct sets of structural variants. Indica–japonica comparative analyses show about 13 853 presence/absence variants differentiating the two groups, many of which can be traced back to divergence between their wild progenitor populations or post-domestication selection (Kou et al., 2025). These include differences such as the aforementioned DTH8 deletion (indica-specific) and GL7 duplication (japonica-specific), as well as numerous small indels in regulatory regions. Hybrid sterility loci like S5 on chromosome 6 illustrate how certain SVs reinforce divergence: S5 involves a gene complex where indica and japonica have incompatible alleles (including
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