SNP mapping and identification of QTL for horticultural key breeding traits in eggplant (Solanum melongena L.)

Eggplant genome is relatively unexplored, especially compared to those of the other major Solanaceae crops tomato, pepper and potato. We recently combined the developed Restriction-site Associated DNA (RAD) approach with Illumina DNA sequencing to effect the rapid and mass discovery of both SNP and SSR markers in eggplant for mapping as well as QTL analysis. A subset of 384 SNPs was used to genotype an F2 intraspecific mapping population and integrated into a previously developed genetic linkage map encompassing a total of 415 markers. The framework map includes 12 linkage groups spanning 1,390 cM with an average map distance of 3.8 cM. The newly developed map was used for identifying quantitative trait loci (QTL) for the traits fruit weight, maximum fruit diameter, fruit shape (length max/diameter max) and adaxial leaf lamina anthocyanin in two locations. On the whole 18 and 17 QTLs were identified in both environments, and at least one major QTL for each trait was identified on the basis of both LOD threshold and coefficient of determination (R2) values.