Fig. 1: Morphotypes and genomic classification of Japanese weedy rice.

a Hull colour of two major morphotypes of Japanese weedy rice and cultivated rice (Koshihikari): BH weedy rice (top); SH weedy rice (centre); and Koshihikari (bottom). b BH (left) and SH (right) weedy rice in a paddy rice field (red arrows indicate spikelets of SH weedy rice). c Spikelets of BH weedy rice with a red-pigmented apiculus (left), SH weedy rice with a red-pigmented apiculus (centre), and SH weedy rice with a non-pigmented apiculus (right). d PCA plot of 174 rice strains, including weedy rice from Japan, China and the US and landrace and modern cultivated rice from Japan; the first and second eigenvectors were obtained using genotype likelihoods estimated by ANGSD using the aligned and mapped reads of whole-genome sequencing data. PCA plot of 129 TEJ rice strains including BH, SH_TEJ, modern_TEJ, landrace_TEJ and China_TEJ, showing the first and second eigenvectors in a subplot (top right corner). e Phylogenetic tree based on 1,936,292 homozygous SNPs. TEJ, temperate japonica; TRJ, tropical japonica; IND, indica; AUS, aus; BH, TEJ-derived BH weedy rice; SH1_TEJ, TEJ-derived SH weedy rice with a red-pigmented apiculus; SH2_TEJ, TEJ-derived SH weedy rice with a non-pigmented apiculus; SH_TRJ, TRJ-derived SH weedy rice; 1970s_W, weedy rice collected in the 1970s in Japan, China_TEJ and China_IND, Chinese TEJ- or IND-derived weedy rice; US_IND and US_AUS, US IND- or AUS-derived weedy rice.