Root development in rice (Oryza sativa L.) plays a key role in water uptake (WU) and water use efficiency (WUE) in water-saving technologies such as aerobic cultivation. Traits that contribute to root development are controlled by many complex quantitative trait loci (QTLs). Understanding the genetic mechanisms of root traits related to WUE is strategic in breeding for aerobic cultivation. Here, we mapped QTLs for root traits in double haploid lines derived from a cross between a japonica paddy rice, Koshihikari, and a japonica upland rice, Sensho. Under aerobic conditions, we detected 22 QTLs for various root and shoot traits in 2015, and 8 in 2017. WU and WUE QTLs derived from Sensho with high additive effects were detected on chromosomes 1, 6 and 10. QTLs for traits associated with WU were mapped in the same regions, forming clusters. The QTL clustering suggests inheritance as a unit and combined overall effect on plant growth, root architecture and WU, which consequently influences WUE. Evaluation of selected lines for phenotypic performance based on genotype in the QTL clusters showed that WUE of DH3, with the Sensho genotype in all cluster regions, was not significantly reduced under aerobic conditions. These results found increased WUE with increased WU by enhanced root traits, such as root length (RL), root surface area (RSA) and root volume (RV), can be obtained without incurring biomass trade-offs. Co-localization of identified QTLs for these traits may be exploited in marker-assisted breeding to develop novel high yielding varieties for aerobic cultivation.
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