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Microarray analysis of differentially expressed genes engaged in fruit development between table and wine grape

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Abstract

Microarray analysis of genes can provide individual gene-expression profiles and new insights for elucidating biological mechanisms responsible for fruit development. To obtain an overall view on expression profiles of metabolism-related genes involved in fruit development of table and wine grapes, a microarray system comprising 15,403 ESTs was used to compare the expressed genes. The expression patterns from the microarray analysis were validated with quantitative real-time polymerase chain reaction analysis of 18 selected genes of interest. During the entire fruit development stage, 2,493 genes exhibited at least 2.0-fold differences in expression levels with 1,244 genes being up-regulated and 1,249 being down-regulated. Following gene ontology analysis, only 929 differentially expressed (including 403 up-regulated and 526 down-regulated) genes were annotated in table and wine grapes. These differentially expressed genes were found to be mainly involved in carbohydrate metabolism, biosynthesis of secondary metabolites as well as energy, lipid and amino acid metabolism via KEGG. Our results provide new insights into the molecular mechanisms and expression profiles of genes in the fruit development stage of table and wine grapes.

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Abbreviations

GO:

Gene ontology

KEGG:

Kyoto encyclopedia of genes and genomes

qRT-PCR:

Quantitative reverse transcription-polymerase chain reaction

MDH:

Malate dehydrogenase

TCA cycle:

Tricarboxylic acid cycle

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Acknowledgments

This project was supported by the Fundamental Research Funds for the Central Universities (No. KYJ200909) and the Program of NCET (No. NCET08-0796).

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Authors and Affiliations

  1. College of Horticulture, Nanjing Agricultural University, No. 1 Weigang Road, Nanjing, 210095, Jiangsu, People’s Republic of China

    Xicheng Wang, Emrul Kayesh, Jian Han, Chen Wang, Changnian Song & Jinggui Fang

  2. Zhengzhou Institute of Pomology, Chinese Academy of Agricultural Sciences, 11 Hanghai East Road, Zhengzhou, 450009, People’s Republic of China

    Chonghuai Liu

  3. Plant Science and Technology College, Beijing University of Agriculture, 7 Beinong Road, Beijing, 102206, People’s Republic of China

    Anjing Ge

  4. Institute of Horticulture, Jiangsu Academy of Agricultural Sciences, 50 Zhongling Street, Nanjing, 210014, People’s Republic of China

    Xicheng Wang

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  1. Xicheng Wang
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Correspondence to Jinggui Fang.

Electronic supplementary material

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11033_2014_3311_MOESM1_ESM.doc

Additional File 1. Percentage distribution of up/down-regulated differentially expressed genes involved in biological process, molecular functions and cellular component annotation. (DOC 441 kb)

11033_2014_3311_MOESM2_ESM.cdt

Additional File 2. 2,493 differentially expressed genes with two fold increase or decrease detected by microarray between fruits of table and wine grape. This file can be recognized via Tree View 1.6 software. The clustering diagram shows that the up- or down regulated genes between table and wine grape were divided into two groups, with genes having similar expression profile were clustered into the sub-groups. (CDT 299 kb)

11033_2014_3311_MOESM3_ESM.pdf

Additional File 3. The metabolic pathways map corresponding to up/down-regulated differentially expressed genes encoding enzymes. The red lines shown in metabolic pathway figure represent the up-regulated differentially expressed genes, which were with high expression in table grape, the green ones represent the down-regulated genes, which were with high expression in wine grape. (PDF 189 kb)

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Wang, X., Kayesh, E., Han, J. et al. Microarray analysis of differentially expressed genes engaged in fruit development between table and wine grape. Mol Biol Rep 41, 4397–4412 (2014). https://doi.org/10.1007/s11033-014-3311-6

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