GWAS identifies genetic loci underlying nitrogen responsiveness in the climate resilient C4 model Setaria italica (L.)

•Evaluating nitrogen(N) responsiveness in crops has many commercial/environmental advantages.•Current lack of knowledge on its physio-genetic basis is a major bottleneck.•We demonstrated that N dependent yield increase is driven by grain number (GN) in S.italica.•GN has strong genetic basis –22 unique SNPs; six exhibiting haplotypes in natural population.•Based on this, we define N responsive and non-responsive accessions with distinct panicle types.•Few genes lying between SNPs with haplotypes show distinct transcript levels in two genotypes.