The legume-rhizobial symbiosis results in the formation of root nodules that provide an ecological niche for nitrogen-fixing bacteria. However, plant-bacteria genotypic interactions can lead to wide variation in nitrogen fixation efficiency, and it is not uncommon that a bacterial strain forms functional (Fix + ) nodules on one plant genotype but nonfunctional (Fix − ) nodules on another. Host genetic control of this specificity is unknown. We herein report the cloning of the Medicago truncatula NFS1 gene that regulates the fixation-level incompatibility with the microsymbiont Sinorhizobium meliloti Rm41. We show that NFS1 encodes a nodulespecific cysteine-rich (NCR) peptide. In contrast to the known role of NCR peptides as effectors of endosymbionts' differentiation to nitrogen-fixing bacteroids, we demonstrate that specific NCRs control discrimination against incompatible microsymbionts. NFS1 provokes bacterial cell death and early nodule senescence in an allele-specific and rhizobial strain-specific manner, and its function is dependent on host genetic background.legumes | nodulation | nitrogen fixation specificity | symbiosis persistence | NCR peptides P lants of the legume family can supply their own nitrogen needs through symbioses with nitrogen-fixing soil bacteria called rhizobia. This symbiotic interaction commences when the host perceives rhizobial lipo-chitooligosaccharides known as nodulation (Nod) factors and initiates development of nodule primordia that become infected by the rhizobia (1). Infection of most legumes, including the model legume Medicago truncatula, starts in root hairs and involves formation of plant-made tubular structures known as infection threads (2). Infection threads direct bacteria to these primordia, where the rhizobia are released into the cytoplasm of host cells. During this process, the bacteria become surrounded by a host membrane, and these membrane compartments containing rhizobium are named symbiosomes. Subsequently, the rhizobia differentiate into nitrogen-fixing bacteroids (3).The legume-rhizobial symbiosis shows a high level of specificity, occurring at both species and genotypic levels (4, 5). Incompatible interactions at initial stages of the association can block bacterial infection and nodule organogenesis. This incompatibility can be caused by failed Nod factor or exopolysaccharide recognition (6-9) or by induced plant immune responses (9-11). Symbiotic incompatibility also takes place at later stages of nodule development, resulting in the formation of infected but nonfunctional nodules (12,13). This latter situation is well-documented in the Medicago-Sinorhizobium symbiosis, in which the bacteria undergo terminal differentiation (14). We previously screened a core collection of Medicago accessions using multiple Sinorhizobium meliloti strains, evaluating many host-strain combinations (13). In that experiment, ∼40% of the plant-strain combinations produced small, white infected nodules that were defective in nitrogen fixation (Fix − ) whereas only ∼2% resulte...