Genome-wide association study, linkage mapping and transcriptomic analysis revealed candidate genes with the flag leaf traits associated with nitrogen use efficiency in wheat.

Background: Enhancing flag leaf nitrogen use efficiency (NUE) in wheat production can substantially increase crop productivity while minimizing nitrogen application. Quantitative trait loci (QTLs) for NUE-related have been rarely reported in wheat flag leaf traits.

Results: In this study, a natural population of 243 varieties and an RIL population of 123 F₇ recombinants were subjected to different nitrogen treatments. A genome-wide association study (GWAS) and linkage analysis were performed for four agronomic traits in terms of flag leaf length, flag leaf width, flag leaf area, and SPAD (chlorophyll content) under low and normal nitrogen conditions. Through GWAS, 1,016 significant SNP loci were identified and clustered into 290 QTLs, including 11 stably mapped QTLs (stable detection in multiple environments). Additionally, an AC population was established to verify the GWAS results and identify reliable QTL intervals. Three stable loci, namely, QFLLR6D.3 QFLWR6A.6, and QSPADR5B.3, were validated in the AC population, located 1.34 Mb, 2.84 Mb, and 5 Mb away from linkage mapping significant QTL, respectively. Through further transcriptome analysis of Chilero leaves at the jointing, anthesis and grain filling stages, four DEGs were identified within QSPADR5B.3. Among them, TraesCS5B02G394300, TraesCS5B02G394200, and TraesCS5B02G39390 encode beta-glucosidases, and TraesCS5B02G396400 encodes a potassium channel.

Conclusions: These findings offer potential candidate genes for wheat breeding, and provide a foundation for exploring the molecular targets underlying wheat NUE.