<jats:title>Abstract</jats:title><jats:sec> <jats:title>Key message</jats:title> <jats:p>Genetic modification of spike architecture is essential for improving wheat yield. Newly identified loci for the ‘Miracle wheat’ phenotype on chromosomes 1AS and 2BS have significant effects on spike traits.</jats:p> </jats:sec><jats:sec> <jats:title>Abstract</jats:title> <jats:p>The wheat (<jats:italic>Triticum</jats:italic> ssp.) inflorescence, also known as a spike, forms an unbranched inflorescence in which the inflorescence meristem generates axillary spikelet meristems (SMs) destined to become sessile spikelets. Previously, we identified the putatively causative mutation in the <jats:italic>branched head</jats:italic><jats:sup><jats:italic>t</jats:italic></jats:sup> (<jats:italic>bh</jats:italic><jats:sup><jats:italic>t</jats:italic></jats:sup>) gene (<jats:italic>TtBH</jats:italic>-<jats:italic>A1</jats:italic>) of tetraploid wheat (<jats:italic>T. turgidum</jats:italic> convar. <jats:italic>compositum</jats:italic> (L.f.) Filat.) responsible for the loss of SM identity, converting the non-branching spike to a branched wheat spike. In the current study, we performed whole-genome quantitative trait loci (QTL) analysis using 146 recombinant inbred lines (RILs) derived from a cross between spike-branching wheat (‘Miracle wheat’) and an elite durum wheat cultivar showing broad phenotypic variation for spike architecture. Besides the previously found gene at the <jats:italic>bh</jats:italic><jats:sup><jats:italic>t</jats:italic></jats:sup>-<jats:italic>A1</jats:italic> locus on the short arm of chromosome 2A, we also mapped two new modifier QTL for spike-branching on the short arm of chromosome 1A, termed <jats:italic>bh</jats:italic><jats:sup><jats:italic>t</jats:italic></jats:sup>-<jats:italic>A2</jats:italic>, and 2BS. Using biparental mapping population and GWAS in 302 diverse accessions, the 2BS locus was highly associated with coding sequence variation found at the homoeo-allele of <jats:italic>TtBH</jats:italic>-<jats:italic>B1</jats:italic> (<jats:italic>bh</jats:italic><jats:sup><jats:italic>t</jats:italic></jats:sup>-<jats:italic>B1</jats:italic>). Thus, RILs that combined both <jats:italic>bh</jats:italic><jats:sup><jats:italic>t</jats:italic></jats:sup>-<jats:italic>A1</jats:italic> and <jats:italic>bh</jats:italic><jats:sup><jats:italic>t</jats:italic></jats:sup>-<jats:italic>B1</jats:italic> alleles showed additive genetic effects leading to increased penetrance and expressivity of the supernumerary spikelet and/or mini-spike formation.</jats:p> </jats:sec>