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Bart J. Janssen studies the molecular control of plant development. A 2008 study led by Janssen followed gene expression as apple fruits developed, linking molecular measurements to recognizable changes in anatomy and growth.

The investigators collected samples at eight developmental times and used a DNA microarray representing approximately 13000 genes. Four broad temporal patterns distinguished flower stages, early cell division, growth with starch accumulation, and ripening. Selected measurements were checked using Quantitative PCR.^[ref]

An apple is a pome, with both an ovary-derived core and surrounding hypanthium tissue. Comparing stages therefore asks how growth of a composite fruit is coordinated. A gene whose expression peaks during cell division becomes a candidate for further investigation; matching the timing does not alone demonstrate that the gene causes that developmental change.^[ref]

By Bart J. Janssen and colleagues. BMC Plant Biology 8, article 16 (17 February 2008); DOI doi.org/10.1186/1471-2229-8-16

Background distinguishes the expanding core (ovary) from the cortex (hypanthium). Results, Microarray analysis of apple fruit development: eight time points, approximately 13000 genes, and two biological replicates; four major temporal expression patterns associated with floral buds, cell division, mid-development and ripening.

A pome is a fleshy accessory fruit developing from an inferior ovary, with an enlarged hypanthium surrounding the central fruit tissues. An apple is a familiar example. Much of its edible flesh comes from tissue around the ovary, whereas the central core corresponds to the developed ovary. Thus the fleshy part of a pome cannot simply be identified with the pericarp, the wall derived from the ovary.^[ref]

To see the distinction, cut an apple lengthwise through its stalk and centre: locate the seeds, the enclosing core and the surrounding flesh. The fruit integrates structures with different developmental origins.

In a 2008 study, Bart J. Janssen and colleagues sampled developing apple fruits at eight times and used a DNA microarray representing roughly 13000 genes. They identified coordinated gene expression patterns associated with early cell division, later growth and starch accumulation, and ripening. The experiment illustrates how the anatomy of a pome motivates a molecular question: how are growth and maturation of its different tissues coordinated?^[ref]