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


RESULTS
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.


CONCLUSIONS
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.
Janssen
Bart J
BJ
The Horticulture and Food Research Institute of New Zealand Ltd,, Mt Albert, Private Bag 92169, Auckland Mail Centre, Auckland 1142, New Zealand. bjanssen@hortresearch.co.nz
Thodey
Kate
K
Schaffer
Robert J
RJ
Alba
Rob
R
Balakrishnan
Lena
L
Bishop
Rebecca
R
Bowen
Judith H
JH
Crowhurst
Ross N
RN
Gleave
Andrew P
AP
Ledger
Susan
S
McArtney
Steve
S
Pichler
Franz B
FB
Snowden
Kimberley C
KC
Ward
Shayna
S
D035264:Flowers / Q000235:genetics / Q000254:growth & development* / Q000378:metabolism; D005638:Fruit / Q000235:genetics / Q000254:growth & development* / Q000378:metabolism; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D018551:Solanum lycopersicum / Q000235:genetics / Q000378:metabolism; D027845:Malus / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism*; D020411:Oligonucleotide Array Sequence Analysis; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism; D018749:RNA, Plant / Q000235:genetics / Q000378:metabolism; D020133:Reverse Transcriptase Polymerase Chain Reaction; D013213:Starch / Q000378:metabolism; D013997:Time Factors
D010940:Plant Proteins; D018749:RNA, Plant; D013213:Starch