Genetic Dissection of Image-Derived Pod-Related Traits in an Interspecific Soybean RIL Population

Soybean pod-related traits are important agronomic characteristics associated with seed development, domestication, cultivar identification, and breeding improvement. However, conventional phenotyping methods mainly rely on manual measurements, which are time-consuming and labor-intensive and capture only limited dimensions of pod variation, while the genetic basis of skeleton- and curvature-based pod descriptors remains insufficiently characterized in biparental populations. In this study, eight quantitative traits representing pod size, shape, and color components were extracted from an existing mature pod image dataset of an interspecific soybean recombinant inbred line (RIL) population using the established deep learning-based image phenotyping framework. These traits exhibited substantial phenotypic variation, with across-year entry-mean broad-sense heritability (H²) estimates ranging from 0.30 to 0.80. Composite interval mapping (CIM) based on a high-density genetic linkage map identified 54 quantitative trait loci (QTLs), which were integrated into 39 non-redundant loci, including six cross-year stable QTLs and three QTLs supported by best linear unbiased prediction (BLUP) analysis. Candidate genes within selected focal QTL regions were prioritized through functional annotation and pod and seed developmental expression analyses. Among them, Glyma.17G109100 (GmSW17) was prioritized as a positional candidate gene for pod size-related variation, whereas Glyma.19G120400 (L1), a previously validated causal gene for pod color, was located within qV19. These findings demonstrate the effectiveness of combining deep learning-based phenotyping with genetic analysis for dissecting the genetic architecture of complex soybean pod-related traits and provide valuable stable QTLs and candidate genes for future functional studies and soybean molecular breeding.