Genomic divergence during feralization reveals both conserved and distinct mechanisms of parallel weediness evolution

Agricultural weeds are the most important biotic constraints to global crop production, and chief among these is weedy rice. Despite increasing yield losses from weedy rice in recent years worldwide, the genetic basis of weediness evolution remains unclear. Using whole-genome sequence analyses, we examined the origins and adaptation of Japanese weedy rice. We find evidence for a weed origin from tropical japonica crop ancestry, which has not previously been documented in surveys of weedy rice worldwide. We further show that adaptation occurs largely through different genetic mechanisms between independently-evolved temperate japonica- and tropical japonica-derived strains; most genomic signatures of positive selection are unique within weed types. In addition, some weedy rice strains have evolved through hybridization between weedy and cultivated rice with adaptive introgression from the crop. Surprisingly, introgression from cultivated rice confers not only crop-like adaptive traits (such as shorter plant height, facilitating crop mimicry) but also weedy-like traits (such as seed dormancy). These findings reveal how hybridization with cultivated rice can promote persistence and proliferation of weedy rice. Imaizumi et al. examine the origin and evolution of Japanese weedy rice and document the role of hybridization in weedy rice origins. Their results show that there is parallel evolution in rice feralization, and document the temperate and tropical japonica origins of weedy rice in Japan.

Automated summary

The study explores the origin and adaptation mechanism of Japanese weedy rice through whole-genome sequence analysis, revealing different genetic mechanisms between weed types and the importance of hybridization between weedy and cultivated rice in weedy rice evolution. Hybridization with cultivated rice not only confers crop-like adaptive traits but also weedy-like traits to weedy rice, promoting its persistence and proliferation.