Comparative RNA-seq analysis reveals candidate genes associated with fruit set in pumpkin

Abstract Fruit set is a complex biological process, which determines fruit development and production. Little information is available on the fruit set and regulatory mechanism in pumpkin. In an attempt to obtain the candidate genes involved in fruit set and elucidate the regulatory networks, early growth properties of pumpkin fruit were evaluated from anthesis until 4 days post anthesis (DPA) between pollination and non-pollination treatment. The results showed that non-pollinated ovary delayed its growth and suffered the aborting process from 2 DPA, while, pollinated fruit showed an exponential growth from anthesis until 4 DPA, with notable changes in fruit length and diameter. Furthermore, RNA-seq was carried out aimed at identifying differentially expressed genes (DEGs) responsible for fruit set in pumpkin after pollination. The results revealed that a total of 7536 DEGs were screened during pumpkin fruit set after pollination, including 3406 up-regulated and 4130 down-regulated. Of these DEGs, 5180, 1594 and 762 were differentially expressed in PF_2 vs UF_2, PF_2 vs UF_0 and UF_2 vs UF_0, respectively. 644 DEGs related to cell growth, cell division, cell cycle (28), photosynthesis (15), glycometabolism (71), transcription factors (405) and plant hormone signal transduction (125) were analyzed based on functional annotation, which might play a crucial role during pumpkin fruit set. In addition, quantitative real-time PCR (qRT-PCR) analysis of 9 DEGs selected randomly indicated that RNA-seq data was reliable. Taken together, our results will provide useful gene resources for genetic improvement, and lay a theoretical foundation for understanding the molecular mechanism of pumpkin fruit set.