Research Article: RNA-Sequencing Reveals Biological Networks during Table Grapevine (‘Fujiminori’) Fruit Development

Date Published: January 24, 2017

Publisher: Public Library of Science

Author(s): Lingfei Shangguan, Qian Mu, Xiang Fang, Kekun Zhang, Haifeng Jia, Xiaoying Li, Yiqun Bao, Jinggui Fang, Yuepeng Han.

http://doi.org/10.1371/journal.pone.0170571

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.

Partial Text

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 consumed fresh or processed into juices and liquors [1]. Grape berry growth and development is a complex process displaying a dual sigmoidal pattern with three distinct phases, including two periods of growth intervened by a lag phase characterized by slowing of fruit expansion and maturation of seeds [2]. Phase I is also known as the hard green stage, and is characterized by general cell division and cell enlargement in berries, with a massive concomitant accumulation of amino acids, tannins, and organic acids [3–7]. During phase II, growth of berries slows markedly, organic acid concentration reaches its highest level and sugar accumulation commences [4]. Phase III starts after véraison. During this phase, the growth rate of berries increases rapidly along with their softening, and fundamental changes in metabolites, such as accumulation of sugar and pigments, loss of chlorophyll, etc. [3, 4].

To date, many experiments have focused on grape fruit development using RNA-seq technology or complemented with other technologies [32, 33, 50, 51, 54, 58–60]. In this study, RNA-seq analysis of transcript abundances during berry development enabled us to carry out a global investigation of gene expression at three time-points during table grape maturation. More than 25 million reads were obtained in each sample, and 5,620, 3,381, and 5,196 transcripts were found to be differentially expressed in DAF65/DAF40, DAF90/DAF65, DAF90/DAF40 respectively. Most of the DEGs were found to be involved in cell wall, lipid, starch-sucrose, and secondary metabolism and light reaction categories.

This work describes a comprehensive analysis of the transcriptome during table grapevine fruit ripening (‘Fujiminori’). RNA-seq results indicated that most significant changes in the processes occurred from the expanding stage to the véraison stage. The expression patterns of F3’H and F3’5’H were the key determinants of red or blue grapevine fruit skin color. DEGs involved in cell wall development, lipid metabolism, and starch-sugar metabolism were also identified. This study provides a foundation for the investigation of fruit quality, fruit softening and cracking, and skin color formation in grapevine.

 

Source:

http://doi.org/10.1371/journal.pone.0170571

 

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