A Domestication-Selected Retrotransposon for Quenching Genomic Immunity in Rice [MeDIP-seq]

Transposable elements (TEs) are genomic parasites that constitute the most abundant portions of higher plant genomes. However, whether TE selection occurred during crop domestication remains unknown. HUO is active under normal growth conditions, present at low copy numbers, inserts preferentially into regions capable of transcription, but absent in almost all modern varieties, indicating its removal during rice domestication and modern rice breeding. HUO triggers genomic immunity and dramatically alters genome-wide methylation levels and small RNA biogenesis, as well as global gene expression. Its presence specifically affects agronomic traits by decreasing yield performance and disease resistance but enhancing salt tolerance, which mechanistically explains its domestication removal. Thus, our study reveals a unique retrotransposon as a negative target for maintaining genetic and epigenetic stability during crop domestication and selection. Overall design: Whole genome methylation maps of WT line 308D and the 3 copies of HUO retrotransposon insertion lines 307T3 were generated using methylcytosine immunoprecipetation combined with Illumina sequencing (MeDIP-seq)