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Open Access Research article

Transcriptome analyses of early cucumber fruit growth identifies distinct gene modules associated with phases of development

Kaori Ando14, Kevin M Carr2 and Rebecca Grumet3*

Author affiliations

1 Program in Plant Breeding, Genetics and Biotechnology, Michigan State University, East Lansing, MI, 48824, USA

2 Research Technology Support Facility, Michigan State University, East Lansing, MI, 48824, USA

3 Department of Horticulture and Program in Plant Breeding, Genetics and Biotechnology, Michigan State University, East Lansing, MI, 48824, USA

4 Present address: Department of Crop and Soil Science, Washington State University, Pullman, WA, 99164, USA

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Citation and License

BMC Genomics 2012, 13:518  doi:10.1186/1471-2164-13-518

Published: 2 October 2012



Early stages of fruit development from initial set through exponential growth are critical determinants of size and yield, however, there has been little detailed analysis of this phase of development. In this study we combined morphological analysis with 454 pyrosequencing to study transcript level changes occurring in young cucumber fruit at five ages from anthesis through the end of exponential growth.


The fruit samples produced 1.13 million ESTs which were assembled into 27,859 contigs with a mean length of 834 base pairs and a mean of 67 reads per contig. All contigs were mapped to the cucumber genome. Principal component analysis separated the fruit ages into three groups corresponding with cell division/pre-exponential growth (0 and 4 days post pollination (dpp)), peak exponential expansion (8dpp), and late/post-exponential expansion stages of growth (12 and 16 dpp). Transcripts predominantly expressed at 0 and 4 dpp included homologs of histones, cyclins, and plastid and photosynthesis related genes. The group of genes with peak transcript levels at 8dpp included cytoskeleton, cell wall, lipid metabolism and phloem related proteins. This group was also dominated by genes with unknown function or without known homologs outside of cucurbits. A second shift in transcript profile was observed at 12-16dpp, which was characterized by abiotic and biotic stress related genes and significant enrichment for transcription factor gene homologs, including many associated with stress response and development.


The transcriptome data coupled with morphological analyses provide an informative picture of early fruit development. Progressive waves of transcript abundance were associated with cell division, development of photosynthetic capacity, cell expansion and fruit growth, phloem activity, protection of the fruit surface, and finally transition away from fruit growth toward a stage of enhanced stress responses. These results suggest that the interval between expansive growth and ripening includes further developmental differentiation with an emphasis on defense. The increased transcript levels of cucurbit-specific genes during the exponential growth stage may indicate unique factors contributing to rapid growth in cucurbits.

Cucumis sativus; Exponential fruit growth; Fruit maturation; Fruit set; Fruit surface; Gene expression