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

Abstract

Background: Nuclear 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.).

Results: A 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.

Conclusions: In 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.

Keywords: Expression profiles; Grape (Vitis vinifera L.); NF-Y transcription factor; Phylogenetic analysis; Quantitative real-time PCR.

Fig. 1

Phylogenetic analysis of NF-Y proteins from grape and Arabidopsis thaliana. Thirty-four NF-Y proteins from grape and 36 NF-Y proteins from Arabidopsis were divided into four branches according to subunit type. Red branch indicates NF-YAs, blue branch represents NF-YBs, and two yellow branches denote NF-YCs

Fig. 2

Alignments of grape NF-Y domains. The sequences of grape NF-YAs (a) NF-YBs (b) and NF-YCs (c) were aligned with corresponding referred sequences from Arabidopsis thaliana (At), human (Hs), mouse (Rn) and yeast (Sc), respectively. The actual amino acid numbers of the end of the domains are shown on the right of the figure. Functionality required amino acids (Required AA) that are verified in rat [44] and yeast [45] are given below the sequences. The residual clusters located in the blue boxes are essential for nuclear targeting [64]

Fig. 3

Expression profiles of VvNF-Ys in response to abiotic stress treatments. a Expression patterns of VvNF-Ys in response to salt, drought (PEG) and cold (5 °C) treatments. b Expression patterns of VvNF-Ys under heat stress treatment. HT represents high temperature and RC means recovery process. The color scale indicates fold-change values (log2 values) with red representing increased transcript abundance and green indicating decreased transcript abundance. A red box indicates up-regulation and blue box indicates down-regulation

Fig. 4

Expression patterns of VvNF-Ys during downy mildew infection. Plants of different genotypes were used in the experiment: susceptible plants without resistance loci Rpv1 and Rpv2 (Rpv1 (−) Rpv2 (−)) and incompatible plants bearing the resistance gene Rpv1 (Rpv1 (+) Rpv2 (−)) or Rpv2 (Rpv1 (−) Rpv2 (+)). PI means Plasmopara viticola inoculation. The color scale indicates fold-change values (log2 values) with red representing increased transcript abundance and green indicating decreased transcript abundance. A red box indicates up-regulation and blue box indicates down-regulation

Fig. 5

Expression patterns of VvNF-Ys in response to phytohormone and elicitor treatment. a Expression patterns of VvNF-Ys in response to methyl jasmonate (MJ) and cyclodextrin elicitor (CD). b Expression patterns of VvNF-Ys under ABA treatment. Dav represents days after veraison. The color scale indicates fold-change values (log2 values) with red representing increased transcript abundance and green indicating decreased transcript abundance. A red box indicates up-regulation and blue box indicates down-regulation

Fig. 6

Expression profiles of VvNF-Ys in grape leaves and berries at different developmental stages. a Detailed expression levels of VvNF-Ys in grape leaves and berries. LV and LR denote leaves at veraison (V) and fully ripe (R) while FV and FR represent berries at V and R, respectively. b Detailed expression levels of VvNF-Ys in grape berries at three different developmental stages: fruit set (FS), V and R. c Expression patterns of VvNF-Ys in different berry tissues. WW and WD mean well-watered and water-deficit conditions, respectively. Grape Actin1and UBC were used as internal controls of quantitative real-time PCR analysis. The data are presented as mean values ± SD. * and ** represent statistically significant (P < 0.05) and highly significant (P < 0.01) differences, respectively. Significance of values in (a) was based on comparison of expression levels in leaves and berries at different stages with expression levels in leaves at V while in (b) was based on comparison of expression levels in berries at V and R with expression levels in berries at FS

Fig. 7

Expression levels of VvNF-Ys and fructose content in different grape varieties. VvNF-YAs (a) VvNF-YBs (b) and VvNF-YCs (c) are divided into three groups. Soluble sugars were extracted from five grape varieties (S1-S5) and then analyzed by HPLC with water as eluent. The fructose content was relatively stable in three successive years (unpublished data), so values for 1 year are given as reference. Black broken lines denote transcript levels of NF-Y genes, and green broken lines indicate fructose content in grape berries

Fig. 8

Detailed expression levels of VvNF-Ys in response to exogenous sugar treatments. VvNF-YAs (a) VvNF-YBs (b) and VvNF-YCs (c) are divided into three groups. Relative expression levels were measured by quantitative real-time PCR, and grape Actin1 and UBC were used as internal controls. The data were showed as mean values ± SD. * and ** represent significant (P < 0.05) and highly significant (P < 0.01) differences, respectively. Significance of values was based on comparison of expression levels at 0.5, 1.0, or 2.0 % (v/v) sugar with expression levels at 0.0 % (v/v) sugar in ‘Chardonnay’ suspension cells. The experiment was repeated three times