Pecan [Carya illinoinensis (Wangenh.) K. Koch] is a famous high grade dry fruit, oil tree species and excellent tree species for both timber and fruit. Pecan is a monoecious plant, and the formation and number of female flowers directly determine the pecan yield. In this work, to illuminate the molecular mechanism of floral formation in pecan, scanning electron microscopy was employed to distinguish the developmental stages of female flower. Three flower buds and two flowering stages were collected for high throughput RNA sequencing. 65,680 unigenes were generated with 41, 806 differentially expressed genes annotated. The plant hormones and sucrose metabolic pathways play important roles in flowering transition stage. 40 MADS-box genes were identified and differentially expressed during flower development.These findings are of great significance for further understanding of the molecular basis for reproductive development in Carya Nutt species.
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