Genome-wide identification and characterization of the NF-Y gene family in grape (vitis vinifera L.).

Chong Ren,Zhenchang Liang,Shaohua Li,Zhan Zhang,Yi Wang

doi:10.1186/s12864-016-2989-3

Chong Ren, Zhenchang Liang + Show 3 more

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https://doi.org/10.1186/s12864-016-2989-3

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Abstract

BackgroundNuclear factor Y (NF-Y) transcription factor is composed of three distinct subunits: NF-YA, NF-YB and NF-YC. Many members of NF-Y family have been reported to be key regulators in plant development, phytohormone signaling and drought tolerance. However, the function of the NF-Y family is less known in grape (Vitis vinifera L.).ResultsA total of 34 grape NF-Y genes that distributed unevenly on grape (V. vinifera) chromosomes were identified in this study. Phylogenetic analysis was performed to predict functional similarities between Arabidopsis thaliana and grape NF-Y genes. Comparison of the structures of grape NF-Y genes (VvNF-Ys) revealed their functional conservation and alteration. Furthermore, we investigated the expression profiles of VvNF-Ys in response to various stresses, phytohormone treatments, and in leaves and grape berries with various sugar contents at different developmental stages. The relationship between VvNF-Y transcript levels and sugar content was examined to select candidates for exogenous sugar treatments. Quantitative real-time PCR (qPCR) indicated that many VvNF-Ys responded to different sugar stimuli with variations in transcript abundance. qPCR and publicly available microarray data suggest that VvNF-Ys exhibit distinct expression patterns in different grape organs and developmental stages, and a number of VvNF-Ys may participate in responses to multiple abiotic and biotic stresses, phytohormone treatments and sugar accumulation or metabolism.ConclusionsIn this study, we characterized 34 VvNF-Ys based on their distributions on chromosomes, gene structures, phylogenetic relationship with Arabidopsis NF-Y genes, and their expression patterns. The potential roles of VvNF-Ys in sugar accumulation or metabolism were also investigated. Altogether, the data provide significant insights on VvNF-Ys, and lay foundations for further functional studies of NF-Y genes in grape.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2989-3) contains supplementary material, which is available to authorized users.

Highlights

Nuclear factor Y (NF-Y) transcription factor is composed of three distinct subunits: NF-YA, NF-YB and NF-YC
Identification and characterization of grape NF-Y genes NF-Y proteins were identified by searching the Plant Transcription Factor Database (PlantTFDB, http:// planttfdb.cbi.pku.edu.cn/) and the UniProt database using the PFAM and KOG IDs of conserved domains
It is notable that the transcript abundance of most VvNFYs exhibited no much difference in berries with the exception being VvNF-YC5, which had a higher expression level (P < 0.05) in FR rather than in FV (Fig. 6a). All these results suggested that some of VvNF-Ys may be associated with grape development, which is consistent with the results of RNA-seq. Quantitative real-time PCR (qPCR) was conducted to further demonstrate the expression patterns of VvNF-Ys in grape berries at three different developmental stages

Summary

Introduction

Nuclear factor Y (NF-Y) transcription factor is composed of three distinct subunits: NF-YA, NF-YB and NF-YC. NF-Y (for Nuclear factor Y) transcription factors (TFs) are almost found in all eukaryotes, and they are involved in regulation of gene expression by binding the CCAAT element [1, 2]. The NF-Y complex known as CCAAT binding factor (CBF) or heme activator protein (HAP) consists of three distinct subunits: NF-YA ( known as CBF-B or HAP2), NF-YB (CBF-A or HAP3) and NF-. Despite the ubiquity of NF-Y proteins in eukaryotes, there is only one or two genes encoding each NF-Y subunit in animals and yeast [9, 10]. 10 NF-YAs, 13 NF-YBs, and 13 NF-YCs are encoded by the Arabidopsis thaliana

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