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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.

Although the main stem node number of soybean [Glycine max (L.) Merr. ] is an important yield-related trait, there have been limited studies on the effect of plant density on the identification of quantitative trait loci (QTL) for main stem node number (MSNN). To address this issue, here, 144 four-way recombinant inbred lines (FW-RILs) derived from Kenfeng 14, Kenfeng 15, Heinong 48, and Kenfeng 19 were used to identify QTL for MSNN with densities of 2.2 × 105 (D1) and 3 × 105 (D2) plants/ha in five environments by linkage and association studies. As a result, the linkage and association studies identified 40 and 28 QTL in D1 and D2, respectively, indicating the difference in QTL in various densities. Among these QTL, five were common in the two densities; 36 were singly identified for response to density; 12 were repeatedly identified by both response to density and phenotype of two densities. Thirty-one were repeatedly detected across various methods, densities, and environments in the linkage and association studies. Among the 24 common QTL in the linkage and association studies, 15 explained a phenotypic variation of more than 10%. Finally, Glyma.06G094400, Glyma.06G147600, Glyma.19G160800.1, and Glyma.19G161100 were predicted to be associated with MSNN. These findings will help to elucidate the genetic basis of MSNN and improve molecular assistant selection in high-yield soybean breeding.

Pod number is an important component of yield in soybean (Glycine max (L.) Merr.), and pods are unevenly distributed in the upper, middle and lower parts of the plant. Here, linkage analysis combined with genome-wide association study (GWAS) was used to identify 20 pod number-related traits in four-way recombinant inbred lines (FW-RILs) derived from crosses between the four soybean varieties (Kenfeng 14 × Kenfeng 15) × (Heinong 48 × Kenfeng 19). The results show that pod number-related traits are highly influenced by genetic factors, while the environment plays only a minor role. A total of 602 QTLs were identified, of which 52 were detected in multiple environments (over two environments). In addition, GWAS detected 26 common QTNs (identified by multiple methods or environments) in the QTL intervals. Based on gene ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, 11 potential candidate genes were identified that likely involved the growth and development of soybean pods. These findings will help elucidate the genetic basis of pod number traits.