Background: The genomic region spanning 1.1-1.3 Mb on chromosome 6 in rice is a known structural variation (SV) hotspot associated with resistance to Rice Black-Streaked Dwarf Virus (RBSDV). However, the precise molecular mechanisms underlying this resistance have remained elusive, largely due to the limitations of the japonica-based reference genome, which lacks the critical causative variants. Methods: Utilizing a neuro-symbolic-driven analysis of T2T pangenome datasets and the LGEMP engine, we performed a high-resolution comparative genomic study between indica (9311) and japonica (Nipponbare) across this high-diversity locus. Results: We identified a 3.3 kb large-scale insertion uniquely present in the 9311 genome at the 1.21 Mb locus. This SV, likely mediated by transposable elements, exhibits extreme sequence divergence (24% identity) compared to the Nipponbare reference. Importantly, this insertion event facilitated a dramatic functional shift: while the japonica allele encodes a basic DUF590 transporter, the indica allele has evolved into a complete CC-NBS-LRR (NLR) immune receptor. Transcriptomic analysis confirmed the generation of six novel isoforms (T01-T06) derived from the SV sequence. Validation across 16 representative T2T reference genomes demonstrated that this 3.3kb SV is an indica-specific evolutionary "patch," explaining the significant resistance gap between rice subpopulations. Conclusion: Our findings uncover a novel mechanism of gene birth through structural re-organization at genomic hotspots. This study not only fills a critical gap in rice immunity databases but also provides a high-value molecular marker for the molecular breeding of virus-resistant rice varieties.