Population-level analysis of rice transposon polymorphisms reveals an LTR-retrotransposon insertion linked to grain length

Transposable elements (TEs) constitute a major source of genetic variability in plants by generating insertion polymorphisms that contribute to genome evolution. LTR-retrotransposons are the most abundant plant TEs, but their association with traits has not been comprehensively studied. In this study, we take advantage of the large available genomic resources of rice to characterize LTR-retrotransposon polymorphisms in indica subspecies and uncover their relationship with trait variability. Using genome-wide association studies based on TE-polymorphisms (TIP-GWAS), we identified a non-reference LTR-retrotransposon insertion strongly associated with grain length in a region without previously known QTLs. The insertion is present in the upstream region of the IQD19 gene, which belongs to the calmodulin-binding domain family proteins. The insertion reduces IQD19 gene expression through a DNA-methylation-independent mechanism, likely by interfering with transcription factor regulation. In this study, we identify a potential novel grain length regulator in a region that can be targeted to design genetic markers for rice breeding. We also provide high-quality genome assemblies for two indica related accessions for which the TE is polymorphic. Finally, our results underscore the importance of incorporating TE polymorphisms to the pool of genetic variants used for rice association mapping.