A Natural LTR Retrotransposon Insertion in the Promoter of GhNAC140-Dt Boosts Cotton Lint Yield

Transposable elements (TEs) are fundamental drivers of crop evolution and domestication. Whereas the underlying mechanisms of TE-mediated gene activation remain poorly understood. Lint percentage is an important yield component in cotton. Here, we report a retrotransposon insertion in the promoter of GhNAC140-Dt, a secondary wall NAC encoding gene, to promote the lint production by elevating its expression. We confirm that a 60 bp core cis-regulatory module within the TE's LTR (long terminal repeat) specifically recruits the transcription factor GhMYB46 and increases downstream genes' expression. GhNAC140-Dt overexpression activates the expressions of secondary cell wall development related genes, including GhCESA4-Dt, GhCESA4-At, and GhCOBL9-At, promotes cellulose deposition, and enhances lint percentage. This retrotransposon insertion massively emerges on the domestication transition from Gossypium hirsutum races to cultivated cotton accessions, with > 80% fixation in modern cultivars. This work deepens our understanding of TE-mediated gene activation; it also provides direct molecular evidence for "transposon-driven yield evolution" in crop domestication.