Morphological characterization and transcriptome analysis of pistillate flowering in pecan (Carya illinoinensis)

Abstract

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. Genes involved in hormone signaling, carbon and nitrogen metabolism showed significant differential expression during the floral developmental process. The MADS-box gene family was analyzed in depth, the six type-I genes were not expressed in the FL2 stage, while most type-II genes were highly expressed in the late flower stages. In order to explore the regulation mechanism of pecan flowering, we selected 299 floral-related genes to construct gene co-expression network. The photoperiod pathway genes LHY, PHYA, ELF3 and the gibberellin metabolic pathway gene DELLA proteins function as key roles in floral pathways. We also identified four hormone metabolic pathway genes correlated (SAUR15, IPT1, IAA29, and ARF2) with CiMADS5, CiMADS8, CiMADS9, CiMADS20, and CiMADS39. Furthermore, the expression patterns of 16 unigenes involved in flower development were validated using quantitative real time PCR. These findings are of great significance for further understanding of the molecular basis for reproductive development in Carya Nutt species.