Genome-wide association study, linkage mapping and transcriptomic analysis reveal candidate genes associated with nitrogen use efficiency in wheat.

key messageGenome‑wide association studies, linkage mapping and transcriptomic analysis reveal TraesCS1B02G308200 as a candidate gene associated with nitrogen use efficiency in wheat. Enhancing nitrogen use efficiency (NUE) in wheat production can substantially increase crop productivity while minimizing nitrogen application. In this study, QTLs for NUE-related agronomic traits were detected in two populations: (1) a natural population of 243 wheat accessions from the Yellow and Huai River Valleys in China (CH population) and (2) a recombinant inbred line (RIL) population derived from a cross between Avocet and Chilero (AC population). Nine agronomic traits were evaluated under two nitrogen regimes, namely, normal and low-nitrogen stress, at two experimental sites during two growing seasons. A total of 836 and 154 QTLs were identified through association and linkage analyses, respectively, based on the low-nitrogen tolerance index of the nine traits across all environments. By further transcriptome analysis of Chilero at the jointing, anthesis and grain-filling stages, a total of 48 differentially expressed genes were identified within the colocalization interval of the two populations. A stable QTL, QYSI1B.2 (chr1B: 501.04-508.02 Mb), was successfully validated in both populations. By examining local linkage disequilibrium, QYSI1B.2 was refined to a smaller physical region spanning 506.02-507.19 Mb. A possible candidate gene, TraesCS1B02G308200, which encodes a WRKY transcription factor, was identified through evaluation of its expression levels. These findings provide a foundation for exploring the molecular targets underlying wheat NUE.