Pods are unevenly distributed on soybean (Glycine max L. Merr.) plants, with significantly fewer pods in the lower regions, which limits overall yield. Elucidating the genetic basis of pod formation in the lower part of the plant holds substantial theoretical and practical significance for breeding efforts aimed at increasing seed yield. In this study, we evaluated a four-way recombinant inbred line (FW-RIL) population and a germplasm population (GP) of soybean across seven and five environments, respectively, to assess pod number in the lower part (PNL) of the soybean plant. We identified quantitative trait loci (QTL) and quantitative trait nucleotides (QTN) associated with PNL. We systematically screened candidate genes potentially involved in regulating PNL within linkage disequilibrium (LD) blocks of QTN that colocalized with QTL. Finally, we developed a molecular-assisted selection (MAS) model based on QTN derived from the GP and identified the optimal breeding schemes using the B4L (breeding for pure lines) ISB (in silico breeding) model. We identified 25 QTL in the FW-RIL population and 93 QTN in the GP, including 5 QTN that colocalized with the QTL. In LD blocks surrounding the QTN AX-90477863, we identified Glyma.09G040000 as a candidate gene associated with PNL. Using a MAS model, the 93 QTN accounted for 52.5% of the standing phenotypic variation in PNL in the GP. Using this model, we selected 16 hybrid combinations with PNL genotypic values exceeding the breeding target of 16. Our findings enhance our understanding of the genetic basis of soybean pod number and provide technical support for the molecular breeding of high-yielding soybean varieties.

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.

Number of pods per plant and number of seeds per pod are quantitative, multigenic traits and important components of yield in soybean [Glycine max (L.) Merr.]. Pods are distributed unevenly in the upper, middle, and lower segments of the plant and this distribution is affected by sowing date (SD). A population of four-way recombinant inbred lines (FW-RIL), containing 160 F_2:8 individuals, was generated from the cross (Kenfeng 14 × Kenfeng 15) × (Heinong 48 × Kenfeng 19). A linkage map consisting of 275 simple sequence repeat (SSR) markers was used to map quantitative trait loci (QTL) associated with the production of one, two, three, and four seeds per pod in the upper, middle, and lower segments of plants at two SDs, totaling 12 measurements per SD. A wide range of variation in the twelve characteristics was observed among the four parental lines and the FW-RIL population at the two SDs. The effect of SD2 (May 17, 2016) on pod number was stronger than that of SD1 (May 7, 2016) because the heritability of each trait in the SD1 experiment was generally greater than that of SD2. The study identified 76 QTL controlling pod number, with the phenotypic variation explained by each QTL ranging from 1.86% to 13.71%. The numbers of QTL controlling one, two, three, and four seeds per pod were 28, 23, 23, and 23, respectively. There were 30, 28, and 28 QTL controlling the pod number in the upper, middle, and lower segments of the plant, respectively. Forty-five QTL were identified at SD1 and 38 QTL were identified at SD2. Seventeen QTL were associated with pod-number traits. The QTL qPN-A1–3 was associated with the number of pods containing one seed in the middle segment of the plant at both SDs. Sixty-three QTL were published QTL (common areas existed when integrating on a map GmComposite2003 of Wm82 based on left and right markers). and 13 QTL related to pod number were newly discovered. These results provide a reference for breeders to improve soybean yield by combining advantageous alleles for these QTL. Future studies may reveal candidate genes for these QTL and identify causal alleles for marker-assisted selection.