Mapping of quantitative trait loci for root elongation in rice (Oryza sativa L.) treated with various nitrogen sources and concentrations

ABSTRACT Roots are important plant organs that absorb water and nutrients. Root length responses are influenced by the plants’ sources of nitrogen (N), such as ammonium (NH4 +) and nitrate (NO3 −) ions and their concentrations. Here, to determine the genetic resources with the potential to improve the root system of rice (Oryza sativa L.), the root development traits of a core set of 334 introgression lines (ILs) were assessed in plants grown in hydroponic culture medium containing low (5 μM) or high (500 μM) concentrations of N in the form of NH4 + or NO3 −. ILs were classified into three clusters. The mean value of maximum root length (MRL) in cluster I was significantly higher than that in the other two clusters under all conditions. Root number (RN) differed significantly between clusters IIa and IIb, with the mean RN being higher in cluster IIa. In addition, the order of the mean total root length of the clusters was cluster I > IIa > IIb. Therefore, ILs in cluster I are considered genetic resources for improving root development traits under all tested N conditions. Among the ILs, YTH187 – which is derived from YP5 as a donor – had a longer MRL under all conditions. Quantitative trait loci (QTL) analyses, performed using recombinant inbred lines derived from a cross between IR 64 and YTH187, revealed that qRL5.3-YP5 and qRL6.5-YP5 were detected under all N conditions. In contrast, qRL4.1-YP5 was detected only under low KNO3 concentrations, whereas qRL8.1-YP5 was detected under high concentrations of NH4Cl and KNO3. YP5 alleles at these QTLs increased MRL. QTLs for root length in rice grown in hydroponic culture have not previously been detected in the vicinity of qRL8.1-YP5; thus, this may be a novel QTL that controls root length in rice. Moreover, qRL8.1-YP5 and qRL4.1-YP5 could be useful QTLs to determine the mechanism of root elongation under KNO3 conditions because such QTLs have not yet been detected under these conditions in rice. In future studies, further fine-mapping and characterization of qRL8.1-YP5 could reveal the mechanism of root elongation under high KNO3 concentration conditions.