The study was conducted from June 2018 to June 2019 at the Institute of Sustainable Agro-ecosystem Services (ISAS), the University of Tokyo, Japan (35°43′N, 139°32′E). Soybeans were grown during the summer (June to October), followed by winter wheat in the winter (November to June). The soil was derived from a volcanic ash, classified as a Typic Melanudand (USDA Soil Taxonomy). Climatic data during the soybean and wheat growing seasons are summarized in Supplementary Table 1.

Fourteen soybean cultivars (Supplementary Table 2) with different plant types and yield potentials were used (Kaga et al., 2011). Seeds of the GmWMC (Glycine max world mini core-collection) line were obtained from the current Genetic Resource Center, National Agriculture and Food Research Organization, Tsukuba, Japan. There were 70 experimental plots: 56 plots for soybean cultivar testing, 4 plots where the natural weed community was allowed to develop (weedy), 4 plots where the soil was covered with an anti-weed covering (sheet), and 6 plots for destructive sampling of soybean plants (Figure 2A and Supplementary Table 3). Each plot was 10.08 m2 (2.4 m × 4.2 m). The cultivars were assigned to the plots in a randomized design, with 2–6 replicates (Supplementary Table 3). Three soybean seeds were sown per hill, on 20 June or 20 July 2018, with a row spacing of 60 cm and a hill spacing of 30 cm. Hills were thinned to one seedling at 3 weeks after sowing. A basal fertilizer (N:P:K, 3:10:10) was applied at a rate of 1,000 kg ha–1 for soybean cultivation.

Experimental field P1–70 used in the work reported here. (A) Soybean (Glycine max) cultivation plots; (B) subsequent wheat (Triticum aestivum) cultivation, with locations of preceding soybean plots superimposed on the image; (C) the field divided into 25-cm × 25-cm cells, using the UAV aerial surveillance data.

The above-ground parts of the soybean plants were manually harvested at physiological maturity during October 2018 and dried completely at 80°C. The whole-plant above-ground dry weight, stem dry weight, seed dry weight, and 100-seed weight were measured. The below-ground parts were left in the soil. The field was tilled twice to a depth of 15 cm using a rotovator at 2 weeks after the soybean harvest. In November 2018, wheat (“Satonosora”) was uniformly sown over the entire area (40 m × 50 m), including both the location of the 70 soybean plots and the adjacent field area (Figure 2B), at 80 kg ha–1. No fertilizer was applied for wheat cultivation. Standard crop protection practices for soybean (manual weeding, pesticide application, intertillage, and molding) and wheat (herbicide application, manual weeding, and fungicide application) were followed.

During 5 to 10 June 2019, the above-ground parts of the wheat plants were manually harvested from 154 sampling points (1 m × 1 m; Supplementary Figure 1) by cutting at the soil surface and placed in a mesh bag. The 154 sampling points comprised one each in the 70 soybean plots and 84 in the adjacent area of the field. A local area RTK-GPS (Real-Time Kinematic Global Positioning System) that was conducted with Hemisphere GNSS devices (Hemisphere GNSS, Scottsdale, AZ, United States) was used to determine the locations of the sampling points. After drying completely at 80°C, the harvested wheat samples were weighed and sorted into immature ears, mature ears, and straw. The dry weights of mature ears and straw were measured separately. The number of mature ears was counted.

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