Genome-wide association study of seedling nitrogen-use efficiency-associated traits in common wheat (Triticum aestivum L.)

Nitrogen (N) fertilizer application is essential for crop-plant growth and development. Identifying genetic loci associated with N-use efficiency (NUE) could increase wheat yields and reduce environmental pollution caused by overfertilization. We subjected a panel of 389 wheat accessions to N and chlorate (a nitrate analog) treatments to identify quantitative trait loci (QTL) controlling NUE-associated traits at the wheat seedling stage. Genotyping the panel with a 660K single-nucleotide polymorphism (SNP) array, we identified 397 SNPs associated with N-sensitivity index and chlorate inhibition rate. These SNPs were merged into 49 QTL, of which eight were multi-environment stable QTL and 27 were located near previously reported QTL. A set of 135 candidate genes near the 49 QTL included TaBOX (F-box family protein) and TaERF (ethylene-responsive transcription factor). A Tabox mutant was more sensitive to low-N stress than the wild-type plant. We developed two functional markers for Hap 1, the favorable allele of TaBOX.