Spike architecture influences both grain weight and grain number per spike,which are the two major components of grain yield in bread wheat (Triticumaestivum L.). However, the complex wheat genome and the influence of variousenvironmental factors pose challenges in mapping the causal genes that affectspike traits. Here, we systematically identified genes involved in spike traitformation by integrating information on genomic variation and gene regulatorynetworks controlling young spike development in wheat. We identified 170 locithat are responsible for variations in spike length, spikelet number per spike,and grain number per spike through genome-wide association study and meta-QTLanalyses. We constructed gene regulatory networks for young inflorescences atthe double ridge stage and the floret primordium stage, in which the spikeletmeristem and the floret meristem are predominant, respectively, by integratingtranscriptome, histone modification, chromatin accessibility, eQTL, andprotein-protein interactome data. From these networks, we identified 169 hubgenes located in 76 of the 170 QTL regions whose polymorphisms are significantlyassociated with variation in spike traits. The functions of TaZF-B1, VRT-B2, andTaSPL15-A/D in establishment of wheat spike architecture were verified. Thisstudy provides valuable molecular resources for understanding spike traits anddemonstrates that combining genetic analysis and developmental regulatorynetworks is a robust approach for dissection of complex traits.