Plant Materials, Growth Conditions and Reference Genomes

Fourteen cultivated and 16 wild soybean germplasms were taken from a previously re-sequenced collection (Supplementary Table S1) (Lam et al., 2010). A RI population originating from reciprocal crosses of W05 (wild) and C08 (cultivated) was adopted from a previous study (Qi et al., 2014). In brief, lines were propagated on a single-seed descendant basis from F2 to F7. All seeds of each line were bulked up since F8. Seeds for analyses were collected from open fields (22°25′7′′ N, 114°12′26′′ E) and (38°35′0 ′′ N, 116°48′0′′E) from 2010 to 2012.