Genomic revolution of US weedy rice in response to 21st century agricultural technologies

Weedy rice, a close relative of cultivated rice, significantly impacts rice productivity globally. In the southern US, two strains (strawhull and blackhull-awned) were historically dominant. However, the introduction of hybrid rice and herbicide-resistant (HR) rice technologies in the 21st century has drastically altered the selective landscape. This study uses whole-genome sequences of 48 contemporary weedy rice accessions to investigate genomic consequences of crop-weed hybridization and selection for herbicide resistance. The findings reveal a shift in population dynamics, with most contemporary weeds being crop-weed hybrid derivatives whose genomes have evolved to resemble their weedy ancestors. Extensive adaptive introgression of cultivated alleles at the resistance gene ALS is observed, alongside evidence of convergent molecular evolution in accessions without hybrid origin. This research suggests a new era of weedy rice evolution in the US.

Marshall J. Wedger, Nilda Roma-Burgos, Kenneth M. Olsen