E-QTL is based on the gene expression data as phentoype. For e-QTL analysis this expression data is associated with SNP, genotype data in order to find linked SNP to the expressional variation among the genotypes. E-QTL analysis is a high resolution mapping and hence trait can be evaluated precisely which are advantegous for selection in plant breeding.

Just to add to Peter and Ali clear and straight answer, for breeders selection based on expression QTL adds to precision breeding ,and less influenced by environment hence most sought methodology to estimate the direction of selection and reap best genetic gain.