Peach and nectarine quality traits such as flavor, texture, and juiciness are important for consumer acceptance. Maturity date (MD) also plays a role in the fruit-ripening process and is an important factor for marketing fresh fruit. On the other hand, cold storage produces a physiological disorder known as chilling injury where the most important symptom is a lack of juice in the flesh or mealiness (M). In this study, we analyzed an F2 population obtained from a self-pollination of “Venus” nectarine that segregates for MD and M. We built a linkage map with 1,830 SNPs, 7 SSRs and two slow-ripening (SR) morphological markers, spanning 389.2 cM distributed over eight linkage groups (LGs). The SR trait was mapped to LG4 and we compared the whole genome sequences of a SR individual and “Venus” and identified a deletion of 26.6 kb containing ppa008301m (ANAC072) co-localized with the SR trait. Three Quantitative Trait Loci (QTL) for MD were detected; they all co-localize on LG4 between 31.0 and 42.0 cM. Four co-localizing QTLs on LG4 between 33.3 and 40.3 cM were detected for M, explaining 34 % of the phenotypic variation. We identified five and nine candidate genes (CGs) for MD and M from the QTL regions, respectively. Our results suggest that the transcription factors (TFs) ANAC072 and ppa010982m (ERF4) are CGs for both traits. LG4 contains a cluster for genetic factors that possibly regulate M and MD, but functional validation is necessary to unravel the complexity of genetic control responsible for fruit traits.