The root is the sole organ taking up water and nutrients from soils. Hence, root system architecture (RSA) is important for enhancing high-level and stable rice (Oryza sativa L.) production. However, the genetic improvement of RSA has received less attention than yield and yield components. Here, we aimed to identify and characterize quantitative trait loci (QTLs) for RSA by determining the maximum root length (MRL) of seedlings grown hydroponically under various concentrations of NH4 +. We used a total of 280 introgression lines (ILs) with an Indica-type variety IR64 genetic background, consisting of ten sibling ILs groups, to detect the QTLs. Greater variation of MRL was found in three sibling ILs groups. In total, five QTLs were detected by single marker analyses: two each on chromosomes 5 and 6 and one on chromosome 7. Among them, the most effective QTL was detected on a segment derived from IR69093-41-2-3-2 (YP5), which was localized to the long-arm of chromosome 6. The QTL, designated as qRL6.4-YP5, concerned in root elongation. MRL and total root length of a near-isogenic line (NIL) for qRL6.4-YP5 were significantly (15.2-24.6 %) higher than those of IR64 over a wide range of NH4 + concentrations. Root number and weight of the NIL were the same as those of IR64. These results indicated that qRL6.4-YP5 was a constitutive QTL for root length in response to change in nitrogen concentrations. To enhance yield potential by improving RSA, qRL6.4-YP5 might help to improve root development in rice molecular breeding programs with marker-assisted selection.
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