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Fusarium oxysporumf. sp. pisi(Fop) is a major soil‐borne pathogen and the causal agent of Fusarium wilt of pea (Pisum sativumL.), resulting in significant yield losses. Resistant cultivars have become the most effective method for controlling this fungal disease. The gene controlling resistance to F. oxysporumrace 1 in pea, Fw, is located on linkage group (LG) III and widely used in breeding programs. Although this locus is routinely used for developing resistant cultivars, a robust codominant DNA marker for selection of the Fwgene is not currently available. We developed a breeder‐friendly functional codominant cleaved amplified polymorphic sequence (CAPS) marker, THO, which can be used in pea breeding programs for selection of resistance to F. oxysporumrace 1. Using this marker, we were able to select pea lines with 96 to 98% accuracy in mapping populations and 94% accuracy in advanced pea breeding lines. This marker, in combination with other gene based markers (AnMtL6, Mt5_56, and PRX1TRAP13) developed from conserved sequences of closely related legume species, lays the foundation for candidate gene identification through comparative mapping.

Pea enation mosaic virus (PEMV) causes an important disease of cool‐season food legumes, resulting in significant yield loss worldwide. The present investigation was carried out to study the inheritance and identify the molecular markers linked with the PEMV resistance gene (En) in field pea (Pisum sativumL.) using an F7–derived mapping population developed from the cross ‘Lifter’ (resistant)/‘Radley’ (susceptible). Three hundred ninety‐three recombinant inbred lines (RILs) were phenotyped for reaction to PEMV in the field under natural inoculation and in the greenhouse using artificial inoculation. The RILs segregated in the expected 1:1 ratio for resistance and susceptibility in the field and greenhouse evaluations. Sequence tagged site markers were developed through an intron targeted amplified polymorphism approach based on comparative mapping with Medicago truncatulaGaertn. and a targeted region amplified polymorphism approach was also used to enrich the genomic region segregating for the Engene. Our results demonstrate that resistance to PEMV in pea is governed by a single gene, En, located on linkage group III between markers CNGC (2.5 cM) and tRNAMet2 (1.3 cM) with many other closely associated markers. These two markers in combination predict the presence of Enwith 99.4% accuracy in the Lifter/Radley mapping population and have implications for marker‐assisted selection for PEMV resistance in pea improvement breeding programs.