Rice Genomics and Genetics 2025, Vol.16, No.3, 159-179 http://cropscipublisher.com/index.php/rgg 167 enhancer regions can modulate trait expression. For instance, the rice pan-genome analysis by Gao et al. (2025) identified structural variants associated with grain weight differences: one variety group had an ~126 bp insertion upstream of the gene SHAT1, altering its expression and contributing to different grain shattering tendencies (Shang et al., 2022). Independent selection of such upstream insertions in Asian vs. African rice suggests their role in domestication of seed non-shattering. Structural variants can also be linked to flowering time. A notable deletion in the flowering repressor gene DTH8 (also known as Ghd8) is present in some indica cultivars but not in japonica, leading to earlier flowering under long-day conditions; breeders have utilized this deletion allele for adapting rice to temperate climates. Furthermore, presence/absence of entire gene clusters, such as photoperiod-sensitivity genes or hormone regulators, can create qualitative trait differences. A striking example outside of cultivated rice is the SNORKEL1 and SNORKEL2 genes from deepwater wild rice: these genes (encoding ethylene response factors) are absent in most cultivars, but when present as an introgression, they allow rice plants to rapidly elongate internodes under flooding. This trait is vital for survival in deepwater environments. Overall, structural variation provides a rich source of phenotypic variation in rice-by changing gene dosage, creating novel chimeric genes, or modifying gene regulation, SVs underlie many quantitative trait loci (QTLs) that breeders have historically selected for improved yield, plant architecture, or stress responses. 5.2 SVs affecting gene presence/absence and gene family evolution One of the most significant consequences of structural variation in a pan-genomic context is gene presence/absence variation (PAV). Because of large insertions and deletions, some genes are completely missing in certain rice genomes while present in others. This leads to differences in gene content that can influence phenotypes and adaptation. Many of these PAVs involve genes in multigene families that are known to evolve rapidly. For example, plant disease resistance genes (notably the NBS-LRR class) often occur in clusters that are subject to duplication and deletion. As a result, any given rice variety typically has a unique repertoire of NBS-LRR genes-some genes in these families are present in one cultivar but absent in another (Shang et al., 2022). A species-wide study in the model plant Arabidopsis thaliana found dozens of immune receptor genes present only in certain accessions, revealing extreme cases of presence/absence variation in a plant’s immune gene repertoire. Similarly in rice, pan-genome analysis has identified entire clusters of defense-related genes that are part of the dispensable genome. These PAVs drive gene family evolution: through duplication (a type of CNV), new gene copies can arise and diverge in function; conversely, through deletion, some lineages lose certain gene family members. An illustrative case is the LRR-RLK gene family (Leucine-Rich Repeat Receptor-Like Kinases) involved in pathogen recognition-different rice subpopulations have gained or lost specific members of this family via structural variations over time, reflecting local adaptation to pathogen pressure (Zhao et al., 2018). Presence/absence polymorphisms also extend to genes controlling metabolic profiles, such as fragrance: the well-known fragrance allele in aromatic rice is caused by an 8 bp deletion in the BADH2 gene (technically a small indel), which in homozygous form leads to fragrance. While a small mutation, it underscores how loss-of-function via deletion can disseminate as a favorable trait. On a larger scale, the rice pan-genome has revealed that each new genome added contributes on average several hundred “novel” genes that were absent from prior references (Gao et al., 2025). Many of these novel genes belong to expanded gene families or are duplicated copies that acquired new functions. Thus, structural variation and PAV are intimately linked with gene family evolution, constantly shaping and reshaping the gene content of rice populations. 5.3 Case studies of SVs linked to domestication and adaptation Structural variants have played conspicuous roles in rice domestication-the process by which wild rice was transformed into cultivated rice-and in subsequent adaptation to diverse agricultural environments. One hallmark of domestication in cereals is loss of seed shattering (to facilitate harvesting). In rice, a key domestication gene is SHATTERING 1 (SHAT1), a regulator of seed detachment. A comparative analysis between Asian and African rice
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