Pod and seed weight per plant (PSW) is one of the most important components of soybean yield. We analysed 147 recombinant inbred lines (RILs) of soybean. Using a combination of simple sequence repeat (SSR) and specific-length amplified fragment (SLAF) high-density maps, we applied composite interval mapping (CIM) and multiple interval mapping (MIM) to map quantitative trait loci (QTLs) for PSW across multiple years (2006–10 and 2013). We mapped 24 QTLs for PSW, with 10 QTLs identified by SSR genetic map and 14 by SLAF genetic map. Five consensus QTLs were integrated, and they were validated by a chromosome segment substitution line (CSSL) population. Furthermore, the functions of all genes located in consensus QTL intervals were predicted; nine candidate genes function directly or indirectly in regulating seed development as well as seed size and weight. Our results lay a foundation for the cloning of candidate genes related to PSW and marker-assisted breeding in soybean.

Long-term continuous monocropping of foxtail millet (Setaria italica) in China has increased crop vulnerability to emerging diseases and threatens yield stability and grain quality. This practice may also influence inoculum carryover and host–pathogen interactions, making foxtail millet health a central issue for sustainable production. This study reports the first occurrence in China of a previously undescribed bacterial leaf disease of foxtail millet. Early symptoms are characterized by water-soaked lesions at leaf tips that spread basipetally along the veins and gradually desiccate as the tissue dehydrates. Koch’s postulates were fulfilled to isolate and identify the causal agent. Multilocus sequence analysis of three concatenated housekeeping genes (gyrB, infB, and rpoB) classified the pathogen as Pantoea ananatis. The isolate was further characterized for metabolic profile; its colonization pattern and spatial distribution within foxtail millet tissues were elucidated, revealing features of host–pathogen interaction. A high-quality de novo whole-genome assembly was generated, and candidate virulence determinants were identified by integrated genome annotation and cell wall hydrolase activity assays. This genomic resource is intended as a supporting tool for plant protection research, including disease surveillance, resistance breeding, and management. Collectively, this study represents the first report of P. ananatis causing bacterial leaf disease on foxtail millet in China. It clarifies the colonization and distribution of the pathogen in host tissues, reveales reveals its interaction characteristics with foxtail millet, and provided genomic resources to support research on foxtail millet health protection and plant protection under continuous cropping conditions.