Rice Genomics and Genetics 2025, Vol.16, No.3, 159-179 http://cropscipublisher.com/index.php/rgg 168 revealed different structural variants upstream of SHAT1 were selected in each domestication event. Asian cultivated rice (both indica and japonica) carries a specific ~126 bp insertion about 4.5 kb upstream of SHAT1, while African cultivated rice evolved a different ~70 bp insertion ~3.5 kb upstream of the orthologous gene (Shang et al., 2022). These insertions, which likely alter regulatory elements, contributed to the loss of shattering in domesticated rice-a prime example of parallel domestication using distinct SVs. Another case involves adaptation to flooding. Deepwater rice varieties, which grow in flood-prone areas, evolved the ability to elongate when submerged. The discovery of the SNORKEL1/2 genes (absent in standard cultivars) in certain traditional rice indicated that introgression of these genes (a structural gain) gave plants a novel adaptation-a dramatic elongation response to rising water. This structural gain from wild rice was likely selected by farmers in regions with deep floods. Domestication also often entailed selective sweeps around beneficial structural variants. For instance, a well-known quantitative trait locus for rice plant architecture, PROG1, underwent a causative 2-bp deletion in coding sequence (not a large SV, but a mutational variant) that changed plant growth from prostrate (in wild rice) to erect (in domesticated rice). While that example is a small indel, structural changes such as copy-number variation at the Fragrance gene (badh2) locus or deletion of dormancy genes have been identified as contributors to domestication syndrome traits (loss of seed dormancy, white pericarp, etc.). Looking at rice evolution, researchers have found that certain structural changes in the genome-like insertions, deletions, or duplications-are closely tied to domestication. These changes often show up repeatedly in breeding programs, suggesting they’ve been under strong selection pressure. For example, removing part of a gene that controls starch breakdown helps rice sprout better in flooded fields, which is great for direct seeding. Whether adapting rice for upland or lowland fields, or tropical versus temperate regions, structural variations-like SNPs-have clearly played a major role in shaping the crop we rely on today. 5.4 Regulatory roles of SVs in gene expression networks Structural variants can influence gene expression in myriad ways, acting as a form of structural regulation. Inversions, for example, can disrupt the local synteny and place genes in new regulatory contexts or prevent their recombination with certain regulatory alleles. If a transcription factor gene is caught in an inversion, its expression might change due to altered chromatin environment or the breaking of linkage with distant enhancers. In rice, large inversions identified in the pan-genome have been correlated with expression differences for genes inside the inverted regions. This suggests some inversions may underlie eQTL (expression quantitative trait loci) by modifying how genes contact enhancers or insulators in the 3D genome architecture. Copy number variations (duplications) can directly alter gene expression levels by gene dosage. A rice variety carrying a duplication of a transcription factor gene will often express that factor at higher levels, potentially amplifying its downstream effects (Qin et al., 2021). A case in point is the green revolution semi-dwarf gene Sd1 (though the classic semi-dwarf allele is a loss-of-function SNP, one can imagine a duplication of a growth repressor gene leading to a similar dwarf phenotype via increased dosage). CNVs can also foster neofunctionalization: duplicated gene copies may diverge-one maintaining the original function, another taking on a new expression pattern-thereby rewiring networks. Another regulatory impact of SVs comes from transposable element (TE) insertions in regulatory regions. Rice genomes contain many TEs, and new TE insertions can bring regulatory motifs that either enhance or repress nearby gene expression. For example, if a TE carrying a strong promoter inserts 5′ of a gene, it can cause overexpression of that gene. In maize, the famous tb1 gene controlling apical dominance was upregulated by an adjacent transposon insertion; analogous phenomena are likely present in rice as well (such as hopping of MITEs near stress-responsive genes contributing stress inducibility). In pan-genome data, many structural insertions are in non-coding regions and may represent novel regulatory sequences. A recent study demonstrated that presence/absence of a ~366 bp promoter insertion in foxtail millet (SiGW3 gene) led to expression variation and differences in grain weight-a concept transferable to rice, where promoter indels can modulate traits like grain size
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