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Table S1 Accessions included in the study. Accession numbers, species names, variety and cultivar designations, country of origin, and pericarp colour for samples included in the study. Unless otherwise noted, white-pericarp accessions carry the common rc domestication allele. Shaded samples were not sequenced completely and were excluded from data analysis.

Table S2 Genomic context of sequenced loci. Names of sequenced loci, name of gene where sequenced locus is located, description of gene function, location and length of locus based on Nipponbare reference sequence and approximate distance from Rc.

Table S3 Primer sequences used to amplify and sequence the Rc locus, including upstream and downstream regions and flanking fragments. Primers are named starting at the 5′ end of the sequence (rc_001) and ending at the 3′ end of the sequence (rc_019). Locations based on the Nipponbare reference genome are listed for the original forward and reverse sequence for each fragment and redesigned/optimized primers listed below original primers are located in roughly the same regions.

Table S4 Values of π, θW, and Tajima’s D for total sites and silent sites at flanking fragments.

Fig. S1 Nucleotide diversity across the Rc genomic region. Values of π for silent sites at Rc and sequenced flanking loci for O. rufipogon, cultivated O. sativa (all accessions), cultivated O. sativa (rc allele class) and US weedy rice. The white-pericarp hybrid weed accession is excluded from all calculations.

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