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Table S1 List of accessions used for this study. Accessions are grouped by type (weed, wild or cultivar). Identification numbers as well as genotypes at qsh1 and sh4 are listed along with phenotypic values for seed shattering

Table S2 List of primer sequences and their location. Primers are grouped by gene (sh4 and qsh1) as well as genetic vs. flanking region. Additionally, the enzyme used in the qsh1 CAPS study is identified and the cut site is listed

Fig. S1 Neighbour Joining Tree of sh4 haplotypes. Numbers below branches represent bootstrap support in percentages; only clades with over 50% support are labelled. The black star denotes the G to T substitution associated with loss of shattering in domesticated rice. Colour key at left of the tree identifies Oryza groups represented by the observed haplotypes. The O. sativa group contains accessions of the five recognized domesticated rice populations: aus, indica, aromatic, tropical japonica and temperate japonica. Labels on the right side the tree identify the number of individuals sharing a haplotype. A triangle is placed anywhere more than ten individuals share an identical haplotype. Four haplotypes unique to weedy rice are numbered (I, II, III, and IV) while haplotypes unique to O. rufipogon are not labelled or numbered. Three of the unique weedy rice haplotypes contain mutations that alter amino acids: Glutamic Acid to Lysine in exon 1 in haplotype II, Arginine to Leucine in exon 2 in haplotype III, and Arginine to Tryptophan in exon 2 in haplotype I.

Fig. S2 Graphical view of unique sh4 haplotypes. The top haplotype represents the common shared cultivated haplotype found in 90 individuals from cultivated, weedy, and wild groups. Of the three unique cultivar haplotypes, only the aromatic individual (2B01) contains a nonsynonymous SNP. Four unique weedy haplotypes (I–IV) are displayed where three of the four contain nonsynonymous SNPs. Haplotype numbers match those of Fig. 2. Additionally, three wild individuals are shown. 2E01 and 2C03 contain the nonshattering T nucleotide plus additional coding and noncoding SNPs. 2C05 was chosen to represent one of the many wild haplotypes containing a shattering G nucleotide for comparison.

Fig. S3 Ratios of silent site nucleotide diversity at sh4 and surrounding loci. The ratio of the average pairwise nucleotide diversity (θπ) per kb is shown (A) for three cultivated groups (indica, aus and tropical Japonica) against wild O. rufipogon and (B) for the three major weed groups (SH, BHA1 and BHA2) against their putative progenitors (Indica or Aus). Overall diversity is low across the entire region in cultivated and weedy rice groups.

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