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In spite of its widespread cultivation and nutritional and economic importance, the eggplant (Solanum melongena L.) genome has not been extensively explored. A lack of knowledge of the patterns of inheritance of key agronomic traits has hindered the exploitation of marker technologies to accelerate its genetic improvement. An already established F2 intraspecific population of eggplant bred from the cross '305E40' x '67/3' was phenotyped for 20 agronomically relevant traits at two sites. Up to seven quantitative trait loci (QTL) per trait were identified and the percentage of the phenotypic variance (PV) explained per QTL ranged from 4 to 93%. Not all the QTL were detectable at both sites, but for each trait at least one major QTL (PV explained ≥ 10%) was identified. Although no detectable QTL x environment interaction was found, some QTL identified were location-specific. Many of the fruit-related QTL clustered within specific chromosomal regions, reflecting either linkage and/or pleiotropy. Evidence for putative tomato orthologous QTL/genes was obtained for several of the eggplant QTL. Information regarding the inheritance of key agronomic traits was obtained. Some of the QTL, along with their respective linked markers, may be useful in the context of marker-assisted breeding.

Both inter- and intra-specific maps have been developed in eggplant (Solanum melongena L.). The former benefit from an enhanced frequency of marker polymorphism, but their relevance to marker-assisted crop breeding is limited. Combining the restriction-site associated DNA strategy with high throughput sequencing has facilitated the discovery of a large number of functional single nucleotide polymorphism (SNP) markers discriminating between the two eggplant mapping population parental lines '305E40' and '67/3'. A set of 347 de novo SNPs, together with 84 anchoring markers, were applied to the F(2) mapping population bred from the cross '305E40' x '67/3' to construct a linkage map. In all, 415 of the 431 markers were assembled into twelve major and one minor linkage group, spanning 1,390 cM, and the inclusion of established markers allowed each linkage group to be assigned to one of the 12 eggplant chromosomes. The map was then used to discover the genetic basis of seven traits associated with anthocyanin content. Each of the traits proved to be controlled by between one and six quantitative trait loci (QTL), of which at least one was a major QTL. Exploitation of syntenic relationships between the eggplant and tomato genomes facilitated the identification of potential candidate genes for the eggplant QTLs related to anthocyanin accumulation. The intra-specific linkage map should have utility for elucidating the genetic basis of other phenotypic traits in eggplant.