GWAS reveals genetic interplay between root architecture and nitrogen uptake in Aegilops tauschii

Wheat productivity and sustainability are constrained by low nitrogen use efficiency (NUE), while the genetic basis of NUE-related root traits in its wild progenitor Aegilops tauschii remains poorly explored. We hypothesized that natural allelic variation in Ae. tauschii can reveal loci controlling root architecture and nitrogen acquisition for wheat improvement. A panel of 123 sequence-characterized accessions was evaluated under field conditions at two nitrogen levels (recommended N120 and reduced N60) for root traits, flowering time, leaf morphology, kernel weight, and tissue nitrogen content. Genome-wide association analysis using 3.6 million SNPs identified 69 and 51 significant marker–trait associations under N60 and N120, respectively, including stable loci on chromosome 6D and novel regions on chromosomes 1D and 2D associated with root length, root volume, and shoot and grain nitrogen content. Quantitative RT-PCR provided preliminary functional evidence, revealing nitrogen-responsive expression of three candidate genes in roots (AET6Gv20610400, AET3Gv20907900, AET5Gv20603200) and two in shoots (AET3Gv20717100, AET6Gv20605200) during nitrogen starvation and recovery. These findings identify novel genomic regions and candidate genes for improving NUE through marker-assisted wheat breeding.