title: RNA-Sequencing Reveals Biological Networks during Table Grapevine ('Fujiminori') Fruit Development.
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.
authors.affiliation: College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, PR China.
authors.forename: Lingfei
authors.initials: L
authors.lastname: Shangguan
authors.affiliation: College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, PR China.|Shandong Academy of Grape, Jinan, Shandong, PR. China.
authors.forename: Qian
authors.initials: Q
authors.lastname: Mu
authors.affiliation: College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, PR China.
authors.forename: Xiang
authors.initials: X
authors.lastname: Fang
authors.affiliation: College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, PR China.
authors.forename: Kekun
authors.initials: K
authors.lastname: Zhang
authors.affiliation: College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, PR China.
authors.forename: Haifeng
authors.initials: H
authors.lastname: Jia
authors.affiliation: Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, PR China.
authors.forename: Xiaoying
authors.initials: X
authors.lastname: Li
authors.affiliation: College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, PR China.
authors.forename: Yiqun
authors.initials: Y
authors.lastname: Bao
authors.affiliation: College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, PR China.
authors.forename: Jinggui
authors.initials: J
authors.lastname: Fang
mesh_terms: D000872:Anthocyanins / Q000378:metabolism; D050260:Carbohydrate Metabolism / Q000235:genetics; D002473:Cell Wall / Q000378:metabolism; D018076:DNA, Complementary / Q000235:genetics; D005638:Fruit / Q000254:growth & development* / Q000378:metabolism; D020869:Gene Expression Profiling; D018507:Gene Expression Regulation, Developmental; D018506:Gene Expression Regulation, Plant; D053263:Gene Regulatory Networks; D017343:Genes, Plant; D006824:Hybridization, Genetic; D050356:Lipid Metabolism / Q000235:genetics; D010802:Phylogeny; D010940:Plant Proteins / Q000096:biosynthesis / Q000235:genetics; D012333:RNA, Messenger / Q000096:biosynthesis / Q000235:genetics; D018749:RNA, Plant / Q000032:analysis / Q000235:genetics*; D060888:Real-Time Polymerase Chain Reaction; D017423:Sequence Analysis, RNA; D059467:Transcriptome; D027843:Vitis / Q000235:genetics* / Q000254:growth & development
chemical_list: D000872:Anthocyanins; D018076:DNA, Complementary; D010940:Plant Proteins; D012333:RNA, Messenger; D018749:RNA, Plant