c Symbioses between leguminous plants and soil bacteria known as rhizobia are of great importance to agricultural production and nitrogen cycling. While these mutualistic symbioses can involve a wide range of rhizobia, some legumes exhibit incompatibility with specific strains, resulting in ineffective nodulation. The formation of nodules in soybean plants (Glycine max) is controlled by several host genes, which are referred to as Rj genes. The soybean cultivar BARC2 carries the Rj4 gene, which restricts nodulation by specific strains, including Bradyrhizobium elkanii USDA61. Here we employed transposon mutagenesis to identify the genetic locus in USDA61 that determines incompatibility with soybean varieties carrying the Rj4 allele. Introduction of the Tn5 transposon into USDA61 resulted in the formation of nitrogen fixation nodules on the roots of soybean cultivar BARC2 (Rj4 Rj4). Sequencing analysis of the sequence flanking the Tn5 insertion revealed that six genes encoding a putative histidine kinase, transcriptional regulator, DNA-binding transcriptional activator, helix-turn-helix-type transcriptional regulator, phage shock protein, and cysteine protease were disrupted. The cysteine protease mutant had a high degree of similarity with the type 3 effector protein XopD of Xanthomonas campestris. Our findings shed light on the diverse and complicated mechanisms that underlie these highly host-specific interactions and indicate the involvement of a type 3 effector in Rj4 nodulation restriction, suggesting that Rj4 incompatibility is partly mediated by effector-triggered immunity. P lants of the legume family can effectively make their own fertilizers by forming symbioses with a diverse group of nitrogen-fixing soil bacteria known as rhizobia. This cross-kingdom collaboration is characterized by the formation of the root nodule, a specialized plant organ that provides an optimized environment in which the bacteria convert atmospheric nitrogen into ammonia. The symbiotic interactions between leguminous plants and Rhizobium bacteria show high species specificity, which is determined by the exchange of signal molecules. The best-known determinants of host specificity derived from rhizobia are the so-called Nod factors (NFs), which comprise a family of lipochitooligosaccharides with various strain-specific chemical decorations (1). Legume roots excrete flavonoid compounds that can interact specifically with the rhizobial transcriptional factor NodD. Activation of NodD induces the expression of nodulation genes in rhizobia, which are required for the synthesis of NFs (2, 3). NFs are received by host NF receptors (NFRs) and activate host signal transduction pathways that lead to root hair infection and nodule organogenesis (2, 3). A recent study showed that introduction of the putative NFRs NFR1 and NFR5 of Lotus japonicus into Medicago truncatula initiated nodulation of the transgenic roots by the L. japonicus symbiont Mesorhizobium loti (4, 5). Thus, NFs and their receptor proteins contribute significantly to the de...