Population Genomics of Weedy Crop Relatives: Insights from Weedy Rice

Weedy crop relatives can evolve as a byproduct of the domestication process, and most modern crop species have conspecific or congeneric weedy relatives. These weedy relatives invade crop fields and aggressively outcompete desirable cultivars through a suite of weediness traits. Weedy rice (Oryza sativa f. spontanea) is a highly morphologically diverse group of undesirable rice strains that infest rice production areas and causes heavy yield loss worldwide. In this chapter, we focus on recent phenotypic and genomic characterizations of weedy rice, with special emphasis on its evolutionary origins and adaptive mechanisms. While weedy rice strains can be broadly divided into “crop mimic” and “wild-like” forms, genetic surveys around the world have revealed that most strains have evolved through de-domestication from cultivated rice and that this process has occurred multiple times from different genetically distinct rice varieties. Weedy strains have further evolved and adapted with varying degrees of input from domesticated and wild Oryza populations. The weediness traits can evolve independently in weedy rice through a combination of de novo mutation, standing genetic variation, and adaptive introgression. Recent advances in high-throughput sequencing platforms have made it possible to perform genome-enabled QTL mapping and comparative population genomics approaches to identify weediness-related genes in independently evolved weedy strains. We hope that perspectives raised in this review can provide a point of comparison for future studies of other weedy species.