BSA-seq and fine linkage mapping for the identification of a novel locus (qNUE6) for nitrogen use efficiency in rice

Effective panicle number (EPN) is a major determinant of rice yield and is strongly influenced by nitrogen (N) availability. Identifying genes that maintain EPN under low-N conditions is therefore important for improving nitrogen use efficiency (NUE) in rice. In this study, bulked segregant analysis by sequencing (BSA-seq) of a recombinant inbred line (RIL) population comprising 1128 individuals identified a novel NUE-related quantitative trait locus, qNUE6. The locus was initially mapped to a 1.93 Mb interval on chromosome 6 and was subsequently narrowed to a 61.8 kb region through fine mapping of backcross-derived populations. Among the four annotated genes within the final interval, OsNRT1.2, which encodes a nitrate transporter, exhibited the strongest response to low-N treatment and was identified as the most likely candidate gene. Sequence comparison between the parental lines revealed one InDel and several SNPs, including promoter polymorphisms that may contribute to differential responses to low-N conditions. Functional analyses of overexpression and knockout lines demonstrated that OsNRT1.2 positively regulates nitrogen uptake, effective panicle number, grain yield, and overall NUE. Taken together, these results identify OsNRT1.2 as a strong candidate gene underlying qNUE6 and provide a useful molecular target for improving NUE in rice. However, broader validation across diverse germplasm and direct testing of the causal promoter variants is necessary to fully resolve the underlying mechanism.