Tandem duplication and increased expression of Shattering2 led to evolution of high seed shattering in a U.S. weedy rice group

Weedy rice ( Oryza spp.), a weedy relative of cultivated rice, exhibits strong competitiveness while invading rice fields, driven in part by its high seed shattering abilities. Despite its impact, the locus responsible for the evolution of this shattering trait has remained elusive. We focused on a large-effect QTL (Quantitative Trait Locus) identified in a cross between shattering SH weedy rice, a prominent weedy rice group in the U.S., and non-shattering indica cultivated rice – the known ancestors of SH weeds. We identified a tandem duplication, whose presence/absence is strongly associated with variation in seed shattering. A transcription factor, Shattering2 , located within the duplication, can impact the formation of the abscission zone, a crucial structure where falling organs detach from plants. Increased expression of Shattering2 resulting from its duplication leads to longer abscission zones in weedy compared cultivated rice. Detection of the tandem duplication in multiple SH individuals suggests its potential role in the evolution of high seed shattering in the group. The newly identified shattering gene and its associated genetic variation reveal the genetic mechanisms by which a complex trait like seed shattering can be easily modified.