Molecular Mapping, QTL Identification, and GWA Analysis

Abstract

Both inter- and intraspecific maps have been developed in eggplant. The former benefit from an enhanced frequency of marker polymorphism, but their relevance to marker-assisted crop breeding is limited. The first maps developed 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 resistances to fungal (Fusarium oxysporum f. sp. melongenae and Verticillium dahliae) and bacterial (Ralstonia solanacearum) wilts. QTL studies to elucidate the genetic basis of biochemical composition, content in bioactive and antinutritional compounds, as well as other fruit quality traits were also carried out.