Transposable element polymorphisms underlie epigenetic variation and phenotypic diversification during foxtail millet domestication [miRNA-Seq]

Here we show that TE-associated genetic variants drive heritable epigenetic changes underlying key domestication traits in foxtail millet (Setaria italica), a cereal domesticated from green millet within the past ~11,000 years. By analyzing DNA methylation, transcriptome, small RNA, and structural variation data across 60 wild and domesticated accessions of foxtail millet, we identify 76,815 differentially methylated regions (DMRs), which associated with extensive polymorphic TE insertions.

The epigenomic variation enable the discovery of a polymorphic TE inventory linked to key domestication traits, including seed shattering, branching, and growth habit. Functional analyses reveal two DNA/PIF-Harbinger elements insertions in the 5’ UTR regions of pleiotropic gene SiGW3 modulate its expression and regulate the plant architecture, panicle morphology, and grain size. Our findings highlight that naturally occurring TE polymorphisms can generate epigenetic variations and contributing to phenotypic evolution during crop domestication, offering insights for crop improvement and adaptive breeding.