Table S5
To assess the relatedness of weedy rice populations to otherOryza categories, the proportion of private alleles shared among the weedy rice group, the cultivated rice group, and the wild rice group was determined. A Venn diagram was employed to graphically illustrate the shared proportion of private alleles among the groups (Fig. S2). A total of 214 private alleles were identified among all rice groups. The cultivated rice group shared 22 alleles, which represented 10.3% of the private allele portion. The three rice groups collectively shared 139 private alleles, which represented 65% of the total. Conversely, the weedy rice populations shared only 1.9% of the private alleles. Specifically, 79% (169 alleles) of private alleles were shared between the weedy and cultivated groups, while 65.9% (141 alleles) were shared between the weedy and wild rice groups. We also observed that approximately 71.1% (152 alleles) of the private alleles were shared between the wild and cultivated Oryza groups, indicating the existence of multi-way allele transfer in the DWWC.
Fig. S2
Coalescent-based Bayesian estimates by MIGRATE indicated that the sixOryza groups have relatively large effective population sizes, with Ne >1,000 (Table 1, μ=10-4) (Jamieson and Allendorf, 2012). The long-term gene flows among the sixOryza types are shown in Table 1. The gene flow from weedy rice to O. rufipogon (M=7.299) was much higher than from O. rufipogon to weedy rice (M=4.334). The gene flow from weedy rice toO. nivara (M=4.2966) was marginally lower in comparison to the flow from O. nivara to weedy rice (M=4.9654). The gene flow from landraces to weedy rice was moderately high (M=5.9470), while gene flow from inbred rice varieties to weedy rice has reported at a high rate (M=6.1028). There were relatively high gene flows between feral rice and two cultivated rice types (inbred rice varieties and landraces). The highest gene flow was from inbred rice to feral rice (M=8.1597). Gene flow between wild species was recorded in moderate values (Table 1).