5 Molecular Mapping, QTL Identification, and GWA Analysis Lorenzo Barchi, Ezio Portis, Laura Toppino and Giuseppe Leonardo Rotino Abstract Both inter- and intraspecific maps have been developed in eggplant. The former benefit from an enhanced frequency of marker polymor- phism, but their relevance to marker-assisted crop breeding is limited. The first maps devel- oped could be defined as ‘first generation,’ built up by means of pre-NGS (next-generation sequencing) molecular biology techniques (AFLP, RAPD, SSR, etc.). Unfortunately, the reduced polymorphism detected in intraspecific mapping populations in the ‘first-generation’ maps, along with the relatively low commercial importance in the ‘seed market’ of the species, hampered the construction of dense eggplant genetic maps. Recently, thanks to NGS-derived molecular markers, new marker-rich maps (‘second-generation maps’) were constructed. To assist selection in breeding programs, in particular to identify QTLs underlying key agronomic traits, biparental approaches as well as genome-wide association (GWA) mapping studies were conducted in this species, using the available linkage maps. Among the traits studied, great importance was given to the identification of QTLs linked to morphological and biological traits, including leaf, flower, plant, and fruit characteristics, as well as QTLs associated with parthenocarpy and to resis- tances to fungal (Fusarium oxysporum f. sp. melongenae and Verticillium dahliae) and bacterial (Ralstonia solanacearum) wilts. QTL studies to elucidate the genetic basis of bio- chemical composition, content in bioactive and antinutritional compounds, as well as other fruit quality traits were also carried out. 5.1 Linkage Map Construction Genetic linkage maps are key tools routinely used in plant genetics and breeding to carry out genome analysis as well as to identify genomic regions associated with agronomic and qualitative traits by means of quantitative trait loci (QTL) mapping. The construction of linkage maps in eggplant can be divided into two main groups: the ones con- structed by means of pre-NGS (next-generation sequencing) molecular biology techniques (AFLP, RAPD, SSR, etc.), later referred to as ‘first-generation maps,’ and the ones constructed by means of NGS-derived molecular markers (‘second-generation maps’). In that respect, genetic maps for Solanum melongena (eggplant) were constructed using plant populations from both intra- and inter-specific hybridizations. L. Barchi (&) Á E. Portis Department of Agricultural, Forestry and Food Science (DISAFA), University of Turin, Turin, Italy e-mail: lorenzo.barchi@unito.it L. Toppino Á G. L. Rotino CREA-GB, Research Centre for Genomics and Bioinformatics, Montanaso Lombardo, LO, Italy © Springer Nature Switzerland AG 2019 M. A. Chapman (ed.), The Eggplant Genome, Compendium of Plant Genomes, https://doi.org/10.1007/978-3-319-99208-2_5 41