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Plants photoreceptors perceive changes in light quality and intensity and thereby regulate plant vegetative growth and reproductive development. By screening a γ irradiation-induced mutant library of the soybean (<i>Glycine max</i>) cultivar “Dongsheng 7”, we identified <i>Gmeny</i>, a mutant with elongated nodes, yellowed leaves, decreased chlorophyll contents, altered photosynthetic performance, and early maturation. An analysis of bulked DNA and RNA data sampled from a population segregating for <i>Gmeny</i>, using the BVF-IGV pipeline established in our laboratory, identified a 10 bp deletion in the first exon of the candidate gene <i>Glyma.02G304700</i>. The causative mutation was verified by a variation analysis of over 500 genes in the candidate gene region and an association analysis, performed using two populations segregating for <i>Gmeny</i>. <i>Glyma.02G304700</i> (<i>GmHY2a</i>) is a homolog of <i>AtHY2a</i> in <i>Arabidopsis thaliana</i>, which encodes a PΦB synthase involved in the biosynthesis of phytochrome. A transcriptome analysis of <i>Gmeny</i> using the Kyoto Encyclopedia of Genes and Genomes (KEGG) revealed changes in multiple functional pathways, including photosynthesis, gibberellic acid (GA) signaling, and flowering time, which may explain the observed mutant phenotypes. Further studies on the function of GmHY2a and its homologs will help us to understand its profound regulatory effects on photosynthesis, photomorphogenesis, and flowering time.