Improving nitrogen use efficiency of japonica rice by molecular marker-assisted selection of the NRT1.1B gene

The gene NRT1.1B enhances nitrogen use efficiency (NUE) in rice. The aim of this study was to improve the NUE of the major japonica variety Huaidao 5 by introgressing the indica NRT1.1B allele using molecular marker-assisted selection.

A functional marker, NRT1.1B-KASP, was developed from indica-japonica NRT1.1B variations and validated using F₂ populations from 22 crosses. It introgressed the beneficial allele from donor AR56 into Huaidao 5. Nitrate uptake capacity and chlorate sensitivity were assessed, and the expression of key nitrogen metabolism genes was analyzed. Chlorate resistance assays were conducted to evaluate the NUE of Huaidao 5 and the improved line Xinhuai 5, measuring seedling growth inhibition. Field trials at multiple nitrogen levels (0-330 kg N hm^-²) were used to analyze agronomic traits, yield, and various NUE parameters. Rice quality and blast resistance were assessed according to national industry standards.

Xinhuai 5 exhibited significantly enhanced nitrogen absorption and utilization, with increases in nitrogen accumulation, harvest index, agronomic efficiency, physiological efficiency, and partial factor productivity. Increased shoot ¹⁵N accumulation, great chlorate sensitivity, and upregulated expression of nitrate transporter and assimilation genes were also observed in Xinhuai 5. Its yield under 30% nitrogen reduction matched that of Huaidao 5 under normal conditions. Agronomic traits, including more effective tillers, higher seed setting rate, shortened growth period, and reduced plant height, improved. Furthermore, Xinhuai 5 demonstrated superior eating quality and enhanced blast resistance than Huaidao 5, with no significant difference in processing or appearance quality.

The developed NRT1.1B-KASP marker enabled efficient introgression of the NRT1.1B gene into japonica rice, significantly improving the NUE. Our results provide a scientific basis and germplasm resources for improving NUE of japonica rice.