Open Access Highly Accessed Research article

Global gene expression analysis of apple fruit development from the floral bud to ripe fruit

Bart J Janssen1*, Kate Thodey2, Robert J Schaffer1, Rob Alba38, Lena Balakrishnan4, Rebecca Bishop5, Judith H Bowen1, Ross N Crowhurst1, Andrew P Gleave1, Susan Ledger1, Steve McArtney6, Franz B Pichler7, Kimberley C Snowden1 and Shayna Ward1

Author Affiliations

1 The Horticulture and Food Research Institute of New Zealand Ltd., Mt Albert, Private Bag 92169, Auckland Mail Centre, Auckland 1142, New Zealand

2 John Innes Centre, Colney Lane, Norwich NR4 7UH, UK

3 Boyce Thompson Institute for Plant Research, Tower Road, Cornell University Campus, Ithaca, NY 14853, USA

4 22 Ramphal Terrace, Khandallah, Wellington, New Zealand

5 4 La Trobe Track, RD2 New Lynn, Karekare, Auckland, New Zealand

6 Department of Horticultural Science, North Carolina State University, Mountain Horticultural Crops Research and Extension Centre, 455 Research Drive, Fletcher, NC 28732-9244, USA

7 Microbial Ecology & Genomics Lab, School of Biological Sciences, University of Auckland, Auckland, New Zealand

8 Monsanto Company – O3D, Product Safety Center, 800 North Lindbergh Blvd., St. Louis, MO 63167, USA

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BMC Plant Biology 2008, 8:16  doi:10.1186/1471-2229-8-16

Published: 17 February 2008



Apple fruit develop over a period of 150 days from anthesis to fully ripe. An array representing approximately 13000 genes (15726 oligonucleotides of 45–55 bases) designed from apple ESTs has been used to study gene expression over eight time points during fruit development. This analysis of gene expression lays the groundwork for a molecular understanding of fruit growth and development in apple.


Using ANOVA analysis of the microarray data, 1955 genes showed significant changes in expression over this time course. Expression of genes is coordinated with four major patterns of expression observed: high in floral buds; high during cell division; high when starch levels and cell expansion rates peak; and high during ripening. Functional analysis associated cell cycle genes with early fruit development and three core cell cycle genes are significantly up-regulated in the early stages of fruit development. Starch metabolic genes were associated with changes in starch levels during fruit development. Comparison with microarrays of ethylene-treated apple fruit identified a group of ethylene induced genes also induced in normal fruit ripening. Comparison with fruit development microarrays in tomato has been used to identify 16 genes for which expression patterns are similar in apple and tomato and these genes may play fundamental roles in fruit development. The early phase of cell division and tissue specification that occurs in the first 35 days after pollination has been associated with up-regulation of a cluster of genes that includes core cell cycle genes.


Gene expression in apple fruit is coordinated with specific developmental stages. The array results are reproducible and comparisons with experiments in other species has been used to identify genes that may play a fundamental role in fruit development.