Although aphids are worldwide crop pests, little is known about aphid effector genes underlying virulence and avirulence. Here we show that controlling the genetics of both aphid and host can reveal novel recombinant genotypes with previously undetected allelic variation in both virulence and avirulence functions. Clonal F 1 progeny populations were derived from reciprocal crosses and self-matings between two parental genotypes of pea aphid (Acyrthosiphon pisum) differing in virulence on a Medicago truncatula host carrying the RAP1 and RAP2 resistance genes. These populations showed Mendelian segregation consistent with aphid performance being controlled largely by a dominant virulence allele derived from only one parent. Altered segregation ratios on near-isogenic host genotypes differing in the region carrying RAP1 were indicative of additional heritable functions likely related to avirulence genes originating from both parents. Unexpectedly, some virulent F 1 progeny were recovered from selfing of an avirulent parent, suggesting a reservoir of cryptic alleles. Host chlorosis was associated with virulence, whereas necrotic hypersensitive-like response was not. No maternal inheritance was found for any of these characteristics, ruling out sex-linked, cytoplasmic, and endosymbiotic factors. Our results demonstrate the tractability of dissecting the genetic basis of pest-host resistance mechanisms and indicate that the annual sexual cycle in aphids may lead to frequent novel genotypes with both increased and decreased virulence. Availability of genomes for both pest and host can facilitate definition of cognate gene-for-gene relationships, potentially leading to selection of crop genotypes with multiple resistance traits. KEYWORDS aphid; virulence; avirulence; F 1 hybrid; near-isogenic line; R gene; gene-for-gene interaction; effector A BOUT 250 of the 4400 known species of aphids feed on agricultural crops (Oerke et al. 1994;Blackman and Eastop 2000). Given their wide host ranges and high fecundity, aphids can have dramatic negative impacts on host plants (Dixon 1987). Aphids feed specifically from phloem sieve elements, causing damage directly by ingestion of plant nutrients and by acting as vectors of many major plant viruses (Ng and Perry 2004). In many instances, aphids may manipulate or evade host defenses by secretion of saliva into phloem sieve elements and by minimizing cellular damage by moving their stylets along intercellular paths (Miles 1999;Will et al. 2007).Aphids have unusual reproductive cycles, typically with numerous asexual parthenogenetic generations followed by one sexual phase in winter (Via 1992). Novel genetic diversity may be subsequently stably propagated through asexual parthenogenetic lineages (Blackman 1985). Aphid populations harbor a considerable amount of genetic variability (Via 1989(Via , 1991aBlack et al. 1992), and cyclic parthenogens can evolve nearly as fast as species with sexual reproduction each generation (Lynch and Gabriel 1983). The genetic variation arising ...