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

Abstract

BackgroundDifferent 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.ResultsDifferential 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.ConclusionsFlowering 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.

Transcriptome Analysis and Identification of Genes Associated with Floral Transition and Flower Development in Sugar Apple (Annona squamosa L.)

“…Woody plants undergo a long vegetative period to achieve transition to the reproductive stage (Rottmann et al, 2000; Huang et al, 2013). After this transition, woody plants start to form flower buds in the spring (Hsu et al, 2011).…”

“…In our study, many CK signaling related genes and MADS-box genes were identified as differential expressed genes in sugar apple (Figures 7, 5H), suggesting an involvement of CK-MADS pathway in the regulation of floral transition. In classical flowering network, ABC model genes AP and AG genes are possibly activated by some floral integrators and consequently floral development (Huang et al, 2013). AP1 and AP2 genes belong to “class A” and specify sepal identify.…”

“…Some of these genes encode regulators involved in flowering integrator or floral meristem identification, while others are related to flower development (Huang et al, 2013). These flowering-related genes were identified in our study, suggesting that all six of the flowering pathways may also be present in sugar apple (Table S4).…”

“…As an intricate biological and morphological process, flower development is regulated by a large number of genes (Huang et al, 2013). Flowering is the first step of sexual reproduction, and the timing of the transition from vegetative growth to flowering is an important characteristic in agriculture and horticulture (Bernier et al, 1993; Zhang et al, 2013).…”

SVP-like MADS-box protein from Carya cathayensis forms higher-order complexes

“…The PCR primers were designed base on the full length CcSVP sequence that was obtained from our Transcriptome 454 sequencing (Huang et al, 2013). The RNA was first transcribed into ssDNA, the complementary DNA was synthesized and amplified by reverse transcription, and cloned into a pMD19T vector to serve as a template which was verified through DNA sequencing (Sangon Biotech, Shanghai).…”