This work describes genomics research and applied breeding in pepper and squash towards improvement in fruit quality and disease resistance. A major factor in pepper fruit quality is the presence or absence of pungency, caused by the presence of capsaicinoid molecules and controlled by the major gene Pun1. Three mutant alleles of Pun1 have been identified that cause the production of little to no capsaicinoids. A suite of PCR-based molecular markers are presented that differentiate the four Pun1 alleles, which will be useful for pepper breeding, seed purity testing, and characterization of new germplasm. Disease resistance is also important for pepper production, and Phytophthora capsici is an oomycete pathogen that can cause total yield loss in pepper. Nine bell pepper inbred lines were developed that are resistant to P. capsici. They have yields comparable to commercial cultivars, but have smaller fruit. They provide a high level of resistance to F1 progeny and are therefore suitable for use as both inbred lines and hybrid parents. To study fruit quality in winter squash, an acorn squash fruit and seed transcriptome was sequenced from the cultivar Sweet REBA at five developmental stages. A total of 55,949 unigenes were assembled, and 85% of the unigenes with predicted open reading frames had homology with previously identified genes. Building on this transcriptome, comparative fruit and seed transcriptome sequencing was conducted to compare 'Sweet REBA' with the oilseed pumpkin 'Lady Godiva', developed for seed consumption. Pathways for carotenoid, starch, and sucrose biosynthesis in winter squash fruit were assembled from the literature and homologs were identified for all of the structural genes involved. Differential gene expression between the two cultivars was consistent with their observed phenotypes for these three metabolites of interest, indicating that transcriptional regulation of metabolic genes is an important determinant of winter squash fruit quality. Overall, this research supports vegetable breeding through molecular marker development, the evaluation of improved diseaseresistant lines, and the investigation of the genetic basis of traits of interest.