Chromosome-Level Genome Assembly Identifies RIRE2 and CACTA Transposable Elements at the Sub1 Locus in Submergence-Tolerant Rice Varieties.

Rice (Oryza sativa), despite being adapted to waterlogged conditions, is vulnerable to complete submergence, which represents one of the greatest threats to crop yield under climate change after drought. The Sub1A-1 allele within the Sub1 QTL on chromosome 9 confers submergence tolerance and has been successfully introduced into many elite varieties; however, a complete reference sequence of the Sub1 locus including its flanking regulatory regions has not been reported. Here we show that the Sub1 locus contains two previously uncharacterized transposable elements, an LTR-retrotransposon (RIRE2 family) and CACTA element, that are conserved across submergence-tolerant indica varieties and harbor candidate regulatory sequences that could modulate Sub1A activity. Using chromosome-level assemblies of IR64-Sub1 (98.6% completeness) and its background genotype IR64sj (98.3% completeness), we identified a RIRE2 positioned ~ 500 bp downstream of Sub1A in opposite orientation, which was inserted into the indica genome approximately 179,000 years ago, and a ~ 12 kb CACTA element containing two genes that exhibit expression patterns similar to Sub1A-1 under submergence. Motif analysis further revealed a strong enrichment of ERF-family binding motifs within the CACTA sequence, with most CACTA-associated ERF motifs concentrated in the ~ 2 kb promoter regions of the two embedded genes, whereas EIL-binding motifs were rare. Together, these findings provide the first complete reference sequence of the Sub1 QTL and nominate the TE-associated regulatory sequences as plausible contributors to submergence-responsive transcription, establishing a genomic foundation for the development of flood-resilient rice varieties.