Abstract
Grapevine berry development is a complex and genetically controlled process, with many morphological, biochemical and physiological changes occurring during the maturation process. Research carried out on grapevine berry development has been mainly concerned with wine grape, while barely focusing on table grape. ‘Fujiminori’ is an important table grapevine cultivar, which is cultivated in most provinces of China. In order to uncover the dynamic networks involved in anthocyanin biosynthesis, cell wall development, lipid metabolism and starch-sugar metabolism in ‘Fujiminori’ fruit, we employed RNA-sequencing (RNA-seq) and analyzed the whole transcriptome of grape berry during development at the expanding period (40 days after full bloom, 40DAF), véraison period (65DAF), and mature period (90DAF). The sequencing depth in each sample was greater than 12×, and the expression level of nearly half of the expressed genes were greater than 1. Moreover, greater than 64% of the clean reads were aligned to the Vitis vinifera reference genome, and 5,620, 3,381, and 5,196 differentially expressed genes (DEGs) were identified between different fruit stages, respectively. Results of the analysis of DEGs showed that the most significant changes in various processes occurred from the expanding stage to the véraison stage. The expression patterns of F3’H and F3’5’H were crucial in determining red or blue color of the fruit skin. The dynamic networks of cell wall development, lipid metabolism and starch-sugar metabolism were also constructed. A total of 4,934 SSR loci were also identified from 4,337 grapevine genes, which may be helpful for the development of phylogenetic analysis in grapevine and other fruit trees. Our work provides the foundation for developmental research of grapevine fruit as well as other non-climacteric fruits.
Highlights
Grapevine is one of the most economically important and globally cultivated fruit crops, producing about 77.2 million tons of grape berries in (FAO, 2013), which can either be consumedPLOS ONE | DOI:10.1371/journal.pone.0170571 January 24, 2017Transcriptome Analysis of Table Grapevine Fruit Development
The sequencing depth in each sample was larger than 12×, and the expression values of nearly half of the expressed genes were greater than 1 (Fig 1B, S1 and S2 Tables). These results indicated a good representation of the grapevine fruit RNA-seq data
We found that 5,620 transcripts were significantly differentially expressed in DAF65/DAF40 (|log2 fold-change| ! 1 and false discovery rate (FDR) < 0.001), including 957 (17.03%) up-regulated and 4,663 (82.97%) down-regulated transcripts (Fig 2D, S5 Table)
Summary
Grape berry sampling and developmentGrapevine trees were grown in the fruit experiment station in Nanjing (N32 ̊02’12.77”, E118 ̊ 37’33.25”), and the experiments were carried out under the supervision and permission of the deans of College of Horticulture. Berries from three year old ‘Fujiminori’ grapevine trees were sampled at the fruit expanding (40DAF or DAF40), veraison (65DAF or DAF65), and ripe (90DAF or DAF90) stages throughout the growing season. In order to capture a representative biological selection of transcripts at each time-point, RNA for Illumina sequencing was purified from tissues of 40 berries sampled from 20 bunches. Total RNA extraction and purification, construction of cDNA library and Illumina deep sequencing. Total RNA was extracted from grape fruit samples using TRIzol reagent (Invitrogen, Carlsbad, CA, USA), and the processed RNA was checked for purity and integrity using Nanodrop-2000 spectrophotometer (Thermo Scientific, Wilmington, DE, USA) and Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA). Sequencing was performed by the Shanghai Hanyu Biotechnology Company (Shanghai, China)
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