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Soybean is a source of edible oil for humans and provides a third of the vegetable oil consumed worldwide. Increasing seed oil content in seeds is thus a key objective in soybean breeding. In the present study, a four-way recombinant inbred line (FW-RIL) population comprising 144 lines, planted in 10 environments, and a germplasm panel of 455 accessions, planted in two environments, were used to collect oil-content phenotypes. First, 59 quantitative trait loci (QTL) were detected in the FW-RIL population by inclusive complete interval mapping on a linkage map consisting of 2232 single-nucleotide polymorphism (SNP) markers. Also in the FW-RILs, 44 quantitative trait nucleotides (QTNs) were detected by association analysis using 109,676 SNP markers and five methods of multi-locus genome-wide association study. Second, 77 QTN were detected by association analysis in the germplasm panel using 63,306 markers. Comparison of the QTL and QTN suggested four QTN controlling oil content. Pathway analysis was performed on genes in attenuation regions of these four QTN, and two candidate genes involved in the synthesis or metabolism of soybean oil were identified. These findings provide useful information about the genetics of oil content and may contribute to its genetic improvement by marker-assisted selection.