Narrow leaflet cultivars tend to have more seeds per pod than ovate leaflet cultivars in soybean [Glycine max (L.) Merr.], suggesting that the leaflet-shape trait locus is tightly linked to or cosegregates with the trait locus controlling the number of seeds per pod (NSPP), one of yield components that determine the productivity of many crop plants. In this study, a high-resolution map delimited the genomic region controlling both the leaflet shape and NSPP traits to a sequence length of 12 kb. Only one gene was annotated in this 12 kb region. The gene is 47.8% homologous to the zinc finger (C2H2 type) family protein encoded for by the JAGGED gene, which is necessary for the proper shaping of lateral organs and is sufficient to induce the proliferation of lateral organ tissue in Arabidopsis. The transition from dominant Ln (‘V94-5152’ cultivar) to recessive ln (‘Sowon’ cultivar) phenotypes in soybean is associated with a single nucleotide substitution, which led to a single amino acid change in Sowon and V94-5152. Based on these results, we performed map-based cloning for ln gene and transformation to Arabidopsis mutant jag. We are analyzing phenotypes in the ln-transgenic Arabidopsis including leaf-, slique- and flower-morphology with an aim to identify relationships among leaf shape, NSPP and yield. These map-based cloning, transformation and functional elucidation of this yield-regulating locus is expected to provide fundamental knowledge useful in efforts to improve the yields of soybean and other crops.