Analysis of the Genetic Basis of Fruit Quality in Winter Squash (Cucurbita pepo) through Comparative Transcriptome Sequencing

Squash is a highly nutritious vegetable crop that is popular both in the United States and worldwide.  To increase the nutrient density and consumption of winter squash, fruit quality is an important target for improvement through breeding.  Squash fruit quality is determined by several factors, including nutrient content, color, flavor, sweetness, and texture.  RNA-sequencing was used to investigate the metabolic basis of fruit quality in two winter squash cultivars with contrasting carotenoid and carbohydrate phenotypes.   Fruit mesocarp tissue and seed tissue were collected at five developmental time points and the mRNA was sequenced to generate a fruit and seed transcriptome consisting of 51,978 unigenes.  Fruit samples were also phenotyped for fruit quality traits including percent soluble solids, percent dry matter, and beta-carotene and lutein levels.  We have identified in the transcriptome the putative genes involved in simple sugar metabolism, starch metabolism, and carotenoid metabolism.  By comparing expression levels throughout fruit development of these two contrasting cultivars, we have identified potential genes underlying these important fruit quality traits.