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

Bart J Janssen,Judith H Bowen,Ross N Crowhurst,Robert J Schaffer,Rob Alba,Franz B Pichler,Andrew P Gleave,Kate Thodey,Rebecca Bishop,Kimberley C Snowden,Steve Mcartney,Lena Balakrishnan,Susan Ledger,Shayna Ward

doi:10.1186/1471-2229-8-16

Abstract

BackgroundApple 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.ResultsUsing 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.ConclusionGene 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.

Highlights

Apple fruit develop over a period of 150 days from anthesis to fully ripe
Microarray analysis of apple fruit development When apple trees (Malus domestica 'Royal Gala') were at full bloom individual fully open flowers were tagged and trees separated into two biological replicates (Rep1 and Rep2)
The 14 and 25 Days After Anthesis (DAA) sampling time points coincide with the period of cell division that occurs after pollination

Summary

Introduction

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. At early stages during development (both before and after successful fertilization, and sometimes in the absence of fertilization) the fruit tissue undergoes several rounds of cell division, followed (usually) by cell expansion during which the fruit stores metabolites and energy, in the form of starch or sugars (e.g. tomato development [2,3,4]). Usually after the seeds mature, the fruit undergoes a series of biochemical changes that convert starches into more available and attractive compounds, such as sugars, as well as producing volatile secondary metabolites that are thought to function as attractants for animals or insects which disperse the seed

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