The common transcriptional subnetworks of the grape berry skin in the late stages of ripening

BMC Plant Biology

Research Article

Aaron Fait¹  Ryan Ghan²  Grant R. Cramer²  Karen A. Schlauch³  Juli Petereit⁴  Richard L. Tillett⁴  David Toubiana⁵ 

[1] Ben-Gurion University of the Negev, Jacob Blaustein Institutes for Desert Research, 84990, Midreshet Ben-Gurion, Israel;Department of Biochemistry and Molecular Biology, University of Nevada, 89557, Reno, NV, USA;Department of Biochemistry and Molecular Biology, University of Nevada, 89557, Reno, NV, USA;Nevada INBRE Bioinformatics Core, University of Nevada, 89557, Reno, NV, USA;Nevada INBRE Bioinformatics Core, University of Nevada, 89557, Reno, NV, USA;Telekom Innovation, Laboratories and Cyber Security Research Center, Department of Information, Systems Engineering, Ben Gurion University, Beer Sheva, Israel;

关键词: Circadian clock;    Chromosome organization;    Epigenetic modification;    Fruit development;    Grape berry;    Network analysis;    RNA-seq;    Transcriptomics;    Vitis vinifera;   

DOI  :  10.1186/s12870-017-1043-1

 received in 2016-09-20, accepted in 2017-05-22,  发布年份 2017

来源: Springer

【 摘 要 】

BackgroundWine grapes are important economically in many countries around the world. Defining the optimum time for grape harvest is a major challenge to the grower and winemaker. Berry skins are an important source of flavor, color and other quality traits in the ripening stage. Senescent-like processes such as chloroplast disorganization and cell death characterize the late ripening stage.ResultsTo better understand the molecular and physiological processes involved in the late stages of berry ripening, RNA-seq analysis of the skins of seven wine grape cultivars (Cabernet Franc, Cabernet Sauvignon, Merlot, Pinot Noir, Chardonnay, Sauvignon Blanc and Semillon) was performed. RNA-seq analysis identified approximately 2000 common differentially expressed genes for all seven cultivars across four different berry sugar levels (20 to 26 °Brix). Network analyses, both a posteriori (standard) and a priori (gene co-expression network analysis), were used to elucidate transcriptional subnetworks and hub genes associated with traits in the berry skins of the late stages of berry ripening. These independent approaches revealed genes involved in photosynthesis, catabolism, and nucleotide metabolism. The transcript abundance of most photosynthetic genes declined with increasing sugar levels in the berries. The transcript abundance of other processes increased such as nucleic acid metabolism, chromosome organization and lipid catabolism. Weighted gene co-expression network analysis (WGCNA) identified 64 gene modules that were organized into 12 subnetworks of three modules or more and six higher order gene subnetworks. Some gene subnetworks were highly correlated with sugar levels and some subnetworks were highly enriched in the chloroplast and nucleus. The petal R package was utilized independently to construct a true small-world and scale-free complex gene co-expression network model. A subnetwork of 216 genes with the highest connectivity was elucidated, consistent with the module results from WGCNA. Hub genes in these subnetworks were identified including numerous members of the core circadian clock, RNA splicing, proteolysis and chromosome organization. An integrated model was constructed linking light sensing with alternative splicing, chromosome remodeling and the circadian clock.ConclusionsA common set of differentially expressed genes and gene subnetworks from seven different cultivars were examined in the skin of the late stages of grapevine berry ripening. A densely connected gene subnetwork was elucidated involving a complex interaction of berry senescent processes (autophagy), catabolism, the circadian clock, RNA splicing, proteolysis and epigenetic regulation. Hypotheses were induced from these data sets involving sugar accumulation, light, autophagy, epigenetic regulation, and fruit development. This work provides a better understanding of berry development and the transcriptional processes involved in the late stages of ripening.

【 授权许可】

CC BY   
© The Author(s). 2017