Scientia Agricultura Sinica ›› 2011, Vol. 44 ›› Issue (13): 2748-2759 .doi: 10.3864/j.issn.0578-1752.2011.13.013

• HORTICULTURE • Previous Articles     Next Articles

Isolation of Effective Genes with Digital Northern Platform of NCBI Grapevine (Vitis vinifera L.) EST Sequences

SHANGGUAN Ling-fei; WANG Chen; FANG Jing-gui; LI Xiao-ying; WANG Xi-cheng; SONG Chang-nian   

  1. 南京农业大学园艺学院
  • Received:2010-12-27 Revised:2011-03-14 Online:2011-07-01 Published:2011-07-01
  • Contact: Jinggui Fang

Abstract: 【Objective】The objective of the study is to take full advantage of mass grapevine (Vitis vinifera L.) expression sequence tags (ESTs) from NCBI database, establish localization digital platform for grapevine genes, and achieve the purpose of rapid large-scale gene expression analysis.【Method】A total of 362 193 grapevine ESTs were downloaded from GenBank, processed further by bioinformatics methods, and used to build the digital Northern platform. The verification of the accuracy of the electronic analysis was done by quantitative RT-PCR technique.【Result】The digital northern platform for eleven tissues and those under five stress conditions were effectively established. The comparison of the results from qRT-PCR of four grape genes (VvAG, VvCHS, VvF3H, VvLDOX) and the corresponding electronic expression analysis data indicated that the predictive efficiency of this platform was high. The efficiency of expression prediction in the organs and tissues (berry, inflorescense, and flower) with more ESTs from them available was good, and the prediction in the tissues which has less ESTs deposited needs more experimental analysis. The predictive result will be closer to the true gene expression situation with more ESTs from various tissues are sequenced and deposited in the NCBI database.【Conclusion】The grape gene digital Northern platform has relatively high efficiency of predicting result, and can provide a useful analysis tool for rapid large-scale analysis of the grapevine gene expression and mining of the related important data.

Key words: Grape, in silico Expression Analysis, Expression Sequence Tag (EST), Bioinformatics

[1] ZHANG KeKun,CHEN KeQin,LI WanPing,QIAO HaoRong,ZHANG JunXia,LIU FengZhi,FANG YuLin,WANG HaiBo. Effects of Irrigation Amount on Berry Development and Aroma Components Accumulation of Shine Muscat Grape in Root-Restricted Cultivation [J]. Scientia Agricultura Sinica, 2023, 56(1): 129-143.
[2] LÜ XinNing,WANG Yue,JIA RunPu,WANG ShengNan,YAO YuXin. Effects of Melatonin Treatment on Quality of Stored Shine Muscat Grapes Under Different Storage Temperatures [J]. Scientia Agricultura Sinica, 2022, 55(7): 1411-1422.
[3] GUO ZeXi,SUN DaYun,QU JunJie,PAN FengYing,LIU LuLu,YIN Ling. The Role of Chalcone Synthase Gene in Grape Resistance to Gray Mold and Downy Mildew [J]. Scientia Agricultura Sinica, 2022, 55(6): 1139-1148.
[4] LI ShiJia,LÜ ZiJing,ZHAO Jin. Identification of R2R3-MYB Subfamily in Chinese Jujube and Their Expression Pattern During the Fruit Development [J]. Scientia Agricultura Sinica, 2022, 55(6): 1199-1212.
[5] WANG HuiLing, YAN AiLing, SUN Lei, ZHANG GuoJun, WANG XiaoYue, REN JianCheng, XU HaiYing. eQTL Analysis of Key Monoterpene Biosynthesis Genes in Table Grape [J]. Scientia Agricultura Sinica, 2022, 55(5): 977-990.
[6] WANG Bo,QIN FuQiang,DENG FengYing,LUO HuiGe,CHEN XiangFei,CHENG Guo,BAI Yang,HUANG XiaoYun,HAN JiaYu,CAO XiongJun,BAI XianJin. Difference in Flavonoid Composition and Content Between Summer and Winter Grape Berries of Shine Muscat Under Two-Crop-a-Year Cultivation [J]. Scientia Agricultura Sinica, 2022, 55(22): 4473-4486.
[7] LIU Xin,ZHANG YaHong,YUAN Miao,DANG ShiZhuo,ZHOU Juan. Transcriptome Analysis During Flower Bud Differentiation of Red Globe Grape [J]. Scientia Agricultura Sinica, 2022, 55(20): 4020-4035.
[8] CHEN FengQiong, CHEN QiuSen, LIN JiaXin, WANG YaTing, LIU HanLin, LIANG BingRuoShi, DENG YiRu, REN ChunYuan, ZHANG YuXian, YANG FengJun, YU GaoBo, WEI JinPeng, WANG MengXue. Genome-Wide Identification of DIR Family Genes in Tomato and Response to Abiotic Stress [J]. Scientia Agricultura Sinica, 2022, 55(19): 3807-3821.
[9] MA YuQuan,WANG XiaoLong,LI YuMei,WANG XiaoDi,LIU FengZhi,WANG HaiBo. Differences in Nutrient Absorption and Utilization of 87-1 Grape Variety Under Different Rootstock Facilities [J]. Scientia Agricultura Sinica, 2022, 55(19): 3822-3830.
[10] JI XiaoHao,LIU FengZhi,WANG BaoLiang,LIU PeiPei,WANG HaiBo. Genetic Variation of Alcohol Acyltransferase Encoding Gene in Grape [J]. Scientia Agricultura Sinica, 2022, 55(14): 2797-2811.
[11] YANG ShengDi,MENG XiangXuan,GUO DaLong,PEI MaoSong,LIU HaiNan,WEI TongLu,YU YiHe. Co-Expression Network and Transcriptional Regulation Analysis of Sulfur Dioxide-Induced Postharvest Abscission of Kyoho Grape [J]. Scientia Agricultura Sinica, 2022, 55(11): 2214-2226.
[12] HAN Xiao, YANG HangYu, CHEN WeiKai, WANG Jun, HE Fei. Effects of Different Rootstocks on Flavonoids of Vitis vinifera L. cv. Tannat Grape Fruits [J]. Scientia Agricultura Sinica, 2022, 55(10): 2013-2025.
[13] XU XianBin,GENG XiaoYue,LI Hui,SUN LiJuan,ZHENG Huan,TAO JianMin. Transcriptome Analysis of Genes Involved in ABA-Induced Anthocyanin Accumulation in Grape [J]. Scientia Agricultura Sinica, 2022, 55(1): 134-151.
[14] LIU Chuang,GAO Zhen,YAO YuXin,DU YuanPeng. Functional Identification of Grape Potassium Ion Transporter VviHKT1;7 Under Salt Stress [J]. Scientia Agricultura Sinica, 2021, 54(9): 1952-1963.
[15] XuXian XUAN,ZiLu SHENG,ZhenQiang XIE,YuQing HUANG,PeiJie GONG,Chuan ZHANG,Ting ZHENG,Chen WANG,JingGui FANG. Function Analysis of vvi-miR172s and Their Target Genes Response to Gibberellin Regulation of Grape Berry Development [J]. Scientia Agricultura Sinica, 2021, 54(6): 1199-1217.
Viewed
Full text


Abstract

Cited

  Shared   
  Discussed   
No Suggested Reading articles found!