Fine-mapping of a gene associated with pod number in the lower parts of soybean plants and evaluating molecular-design breeding schemes

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.