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Use of transcriptome sequencing to understand the pistillate flowering in hickory (Carya cathayensis Sarg.)

You-Jun Huang1, Li-Li Liu2, Jian-Qin Huang1, Zheng-Jia Wang1, Fang-Fang Chen1, Qi-Xiang Zhang1, Bing-Song Zheng1* and Ming Chen2*

Author Affiliations

1 The Nurturing Station for the State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin’an, Zhejiang 311300, China

2 Department of Bioinformatics, State Key Laboratory of Plant Physiology and Biochemistry, College of life Science, Zhejiang University, Hangzhou, Zhejiang 310058, China

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BMC Genomics 2013, 14:691  doi:10.1186/1471-2164-14-691

Published: 10 October 2013



Different from herbaceous plants, the woody plants undergo a long-period vegetative stage to achieve floral transition. They then turn into seasonal plants, flowering annually. In this study, a preliminary model of gene regulations for seasonal pistillate flowering in hickory (Carya cathayensis) was proposed. The genome-wide dynamic transcriptome was characterized via the joint-approach of RNA sequencing and microarray analysis.


Differential transcript abundance analysis uncovered the dynamic transcript abundance patterns of flowering correlated genes and their major functions based on Gene Ontology (GO) analysis. To explore pistillate flowering mechanism in hickory, a comprehensive flowering gene regulatory network based on Arabidopsis thaliana was constructed by additional literature mining. A total of 114 putative flowering or floral genes including 31 with differential transcript abundance were identified in hickory. The locations, functions and dynamic transcript abundances were analyzed in the gene regulatory networks. A genome-wide co-expression network for the putative flowering or floral genes shows three flowering regulatory modules corresponding to response to light abiotic stimulus, cold stress, and reproductive development process, respectively. Totally 27 potential flowering or floral genes were recruited which are meaningful to understand the hickory specific seasonal flowering mechanism better.


Flowering event of pistillate flower bud in hickory is triggered by several pathways synchronously including the photoperiod, autonomous, vernalization, gibberellin, and sucrose pathway. Totally 27 potential flowering or floral genes were recruited from the genome-wide co-expression network function module analysis. Moreover, the analysis provides a potential FLC-like gene based vernalization pathway and an 'AC’ model for pistillate flower development in hickory. This work provides an available framework for pistillate flower development in hickory, which is significant for insight into regulation of flowering and floral development of woody plants.

Co-expression network; Carya cathayensis Sarg; Floral development; Seasonal flowering; Hickory; High-throughput data analysis