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Soil-surface roots (SORs) in rice are primary roots that elongate over or near the soil surface. SORs help avoid excessive reduction of stress that occurs in paddy, such as in saline conditions. SORs may also be beneficial for rice growth in phosphorus-deficient paddy fields. Thus, SOR is a useful trait for crop adaptation to certain environmental stresses. To identify a promising genetic material showing SOR, we established methods for evaluating SOR under different growth conditions. We introduced procedures to evaluate the genetic diversity of SOR in various growth stages and conditions: the Cup method allowed us to quantify SOR at the seedling stage, and the Basket method, using a basket buried in a pot or field, is useful in quantifying SOR at the adult stage. These protocols are expected to contribute not only to the evaluation of the genetic diversity of SOR, but also the isolation of related genes in rice.

Additional file 1. Procedure to examine soil substrates for X-ray CT scanning. Five types of soil substrates—calcined clay, volcanic ash soil, andosol, alluvial soil, and sand—were used.

Additional file 9. Representative images of the wired basket method, using 16 cm diameter pots. CT image: vertical projection of processed X-ray CT volume; basket: image taken from directly above the basket; trace: CT image with trace lines of roots observed from the result of using the wired basket method. Lateral roots were not traced. Solid and dashed lines indicate detectable and undetectable roots in the processed X-ray CT volume, respectively. Green, blue, and red lines indicate the roots present in the soil layer between 0–1 cm, 1–3 cm, and 3–5 cm from the soil surface, respectively.

Additional file 6. Visualization of RSA development over 3 weeks. Kinandang Patong was cultivated for 1 week and subjected to daily X-ray CT scanning. Horizontal projections of the processed CT volume are shown, with numbers above the images indicating the number of days after sowing.

Additional file 2. Representative CT images of rice roots in five types of soil substrates. To remove CT image noise, a minimum intensity was calculated for a 120 mm-deep CT slice, using the “thick slab” option in the VG Studio MAX software. The scale bar represented 2 cm.

Additional file 8. Representative images of the wired basket method, using 20 cm-diameter pots. CT image: vertical projection of processed X-ray CT volume; basket: image taken from directly above the basket; trace: CT image with trace lines of roots observed from the result of using the wired basket method. Lateral roots were not traced. Solid and dashed lines indicate detectable and undetectable roots in the processed X-ray CT volume, respectively. Green, blue, and red lines indicate the roots present in the soil layer between 0–1 cm, 1–3 cm, and 3–5 cm from the soil surface, respectively.