Weedy rice, a damaging conspecific weed of cultivated rice, has arisen multiple times independently around the world. Understanding all weedy rice origins is necessary to create more effective weed management strategies. The origins of weedy rice in Spain and Portugal, where there are no native Oryza species are unknown. We used genotyping-by-sequencing (GBS) to understand the origin of Iberian weedy rice and its relationship to other weedy, wild, and cultivated rice groups worldwide. This is the variant call format (vcf) file for all 481 accessions including weedy, wild, and cultivated rice. We used this dataset to understand the phylogenetic relationships and population structure among these different populations, especially the Iberian weedy rice. We find that weedy rice in the Iberian Peninsula has primarily evolved through de-domestication of temperate japonica cultivars, with minor origins from exotic weedy rice.

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