Background

A subset of Indonesian lowland rice belonging to the ecotype Bulu develops thick crown roots above the soil surface (soil-surface roots; SORs) from the seedling stage, although such development is not observed in other commonly cultivated rice worldwide (Ueno and Sato, 1989, 1992). Lafitte et al. (2001) described that the occurrence of SORs is caused by selection pressure within the Bulu ecotype for adapting to anaerobic environments. The ecological and physiological functions of SORs in rice have not yet been understood in detail.

Recently, we demonstrated that SORs contribute to the prevention of excessive stress reduction in saline paddy through the cloning and characterization of a quantitative trait locus (QTL) for SOIL SURFACE ROOTING 1(SOR1) called qSOR1 (Kitomi et al., 2020). We also reported that SOR is a useful root trait for phosphorous uptake in phosphorus-deficient conditions (Oo et al., 2021). Therefore, the SOR phenotype is a valuable breeding target for the development of rice cultivars adapted to such abiotic stresses.

Several previous studies have investigated the genetic diversity of root system architecture in various rice cultivars. Accordingly, various root phenotyping methods, such as soil-core, soil-block, and soil-monolith around rice plants have been developed to date (Pavlychenko, 1937; Abe and Morita, 1994; Uga et al., 2013; Teramoto et al., 2019). These primarily field-based methods are suitable for investigating root biomass and length, but not for quantifying SOR.

Because SORs grow on the ground surface, the common root sampling method in a soil block cannot quantify the degree of SOR occurrence relative to the total roots. Therefore, a phenotyping method specific for SOR quantification is required, to evaluate the genetic diversity of the SOR phenotype in cultivated rice.

We developed a Cup method to quantify the SOR in a large number of samples for QTL mapping (Uga et al., 2012). The Cup method has been effective in identifying an SOR QTL on rice chromosome 7, by using recombinant inbred lines derived from a cross between a representative rice cultivar with SOR (cv. Gemdjah Beton), and without SOR (Sasanishiki) (Uga et al., 2012). A novel mutant gene SOR1, involved in soil-surface rooting, was also identified on rice chromosome 4, using the Cup method (Hanzawa et al., 2013). Furthermore, the Cup method was useful for phenotyping the QTL cloning of SOR (Kitomi et al., 2020).

The Basket method for plants grown in pots was originally developed to quantify the root growth angle of wheat seedlings (Oyanagi et al., 1993). This method was modified, and used to quantify the root growth angle of adult rice plants in the field (Uga et al., 2009). We modified the Basket method to quantify the SORs of rice grown in pots or flooded paddy fields (Uga et al., 2011, 2012; Kitomi et al., 2020). Here, we describe the protocols to quantify SOR in rice.