The Tomato/GFP-FLP/FRT method can be used to study the effect of a mutation or of ectopic expression on the development and survival of PRs in the Drosophila retina. It is rapid, making it ideal for screening purposes, as recently demonstrated 20. The presence of mutant PRs next to wild-type PRs in the same eye makes it easy to detect defects associated with mutant PRs and to address the cell autonomy issue.
The developmental defects observed in our analysis affected various processes, including PR recruitment, morphogenesis and planar cell polarity (PCP) establishment (Figure 5). Seven in absentia is required for PR recruitment, particularly for R7 one of the inner PR. The loss of Seven in absentia results in the loss of the inner PR and some outer PRs (Figure 5A). Grainy head (grh) is involved in PCP establishment and some ommatidia are inverted in grh mutant clones (Figure 5B). This method makes it possible to identify the mutant PRs in mosaic ommatidia, facilitating identification of the PRs in which the gene is required for the correct acquisition of PCP. We have shown that grh is required for the correct acquisition of PCP in R3 precursors 20. Indeed, we observed that, in the inverted ommatidia, R4, which originates abnormally from the R3 precursor, was always mutant. Crumbs (Crbs) is an apical membrane protein required for rhabdomere morphogenesis 23. The loss of Crbs in the Crbs11A22 mutant results in irregular, larger or smaller PRs (Figure 5C).
This method can also be used to follow the fate of single PRs during adulthood (Figure 6). It is ideal for neurodegeneration studies, because a group of homozygous mutant PRs can be viewed and the same group can be found in the same eye of the same fly over a period of days or weeks. It is therefore possible to determine which PRs survive and which are doomed to die, because each clone has a unique shape that can be recognized when the eye is positioned under the fluorescence microscope. As the retina is polarized, it is possible to orient the retina to find the same clone again, on the basis of its shape. We used this method to show that fatpk10307 mutation induces progressive PR degeneration in adulthood (Figure 6, 24). This visualization method can also be used to analyze cell autonomy. In fatpk10307 mosaic retina, PR loss was restricted to fatp mutant PRs, the wild-type PRs being unaffected. The requirement of fatp for PR viability is therefore cell autonomous. We were also able to rescue the fatp mutant PR by reexpressing wild-type fatp with a rh1-Gal4 driver and a UAS-fatp construct (Figure 7). The possibility of carrying out such rescue experiments is one of the advantages of the Tomato/GFP-FLP/FRT method over clonal analysis based on histological sections of resin-embedded retina. Indeed, clonal detection with the Tomato/GFP-FLP/FRT method is not affected by the use of P(UAS, w+) transgenic constructs, whereas the red pigmentation associated with the mini-white gene (w+) covers the eye with red pigment, masking mosaic clones in histological sections.

Figure 1. Organization of the Drosophila eye. (A) Photograph of a Drosophila eye taken with a stereomicroscope. The Drosophila eye is composed of approximately 800 ommatidia. (B) Schematic diagram of a field of 64 ommatidia in the middle of the eye. The six outer photoreceptor neurons (PRs) of each ommatidium, shown in green, are organized into a stereotypical trapezoid that points to the nearest poles of the eye. They consequently point in opposite directions in the ventral and the dorsal part of the eye and are mirror image according to the border between the two parts, which is called the equator. (C) Schematic diagram of an ommatidium. Each ommatidium contains eight PRs. PRs R1 to R6, shown in green, are the outer PRs. They express the photosensitive molecule rhodopsin1 (Rh1) and are the equivalent of mammalian rod cells. The inner PRs, R7 and R8, are shown in gray (R7 sits on top of R8). The inner PRs express rhodopsin 3, 4, 5 or 6 and are the equivalent of mammalian cone cells. For simplicity, only the rhabdomere, the light-sensitive part of the PR, is shown for each PR. Click here to view larger figure.

Figure 2. Generating and visualizing mosaic PR clones in the Drosophila eye with the Tomato/GFP-FLP/FRT method. (A) Schematic diagram of the generation of mosaic clones in the Tomato/GFP-FLP/FRT method. Mosaic clones are generated by mitotic recombination, due to the expression of the flipase (under control of the eyeless promoter) during eye development and the FRT sequences. After recombination of the FRT sequence and cell division, homozygous mutant, homozygous wild-type and heterozygous cells can be generated from a heterozygous cell. These cells divide again to form mosaic clones of PRs in the adult eye. The identification of mutant cells is facilitated by inserting a construct expressing the red fluorescent protein tdTomato into the wild-type chromosome, to label wild-type and heterozygous cells. (B-B'') Visualization of mosaic PR clones with the Tomato/GFP-FLP/FRT method. The Tomato/GFP-FLP/FRT method combines mitotic recombination, cornea neutralization and confocal microscopy. All PRs express the green fluorescent protein GFP, which facilitate the visualization of the PRs using cornea neutralization and confocal microscopy (B). PRs can be visualized at a single-cell level. Mutant mosaic clones are generated by mitotic recombination and can be identified by the absence of the red fluorescent protein tdTomato (B'). Consequently, on merged images, homozygous PRs appear in green, whereas wild-type and heterozygous PRs are yellow (B''). Click here to view larger figure.

Figure 3. Setting up the Drosophila for visualization by cornea neutralization. (A-A'''') Photographs of a Drosophila immobilized on a plate filled with agarose. In panel A'''', a piece of agarose containing the fly has been cut to take a profile photograph. The Drosophila is half-embedded in the agarose, with the right wing within the agarose and the left wing stuck on the agarose surface (A, A'', A''''). When the Drosophila is embedded in the agarose, its head is frequently poorly positioned for the visualization of the eye (A, A'). The head must therefore be reorientated with forceps such that the middle of the eye is pointing upwards (A'', A'''). (B-B') Schematic diagram showing a Drosophila immobilized on an agarose plate and the positioning of the Drosophila under the objective of the microscope. (C-C') Photographs of the setting of the Drosophila on the stage of the microscope under its objective. Click here to view larger figure.

Figure 4. Orientation of the eye for time-course analysis. The figure shows photographs of a Drosophila head in two different orientations and the corresponding fields of ommatidia viewed by cornea neutralization, represented as schematic diagrams. (A) During the first observation, the eye is placed such that a clone of heterozygous or wild-type PRs (in yellow) is viewed in the middle of the field, at the level of the equator (red line). (B) During the second observation, the eye is often not in exactly the same orientation. Thus, the same group of PRs can be found again, but it is not possible to view the exact same field (on the left). The eye must be reoriented for the same field to be viewed again. The position of the equator can be used as a guide. In this example, we know that the observed field is too ventral and that the eye must therefore be turned ventrally to place the equator in the middle of the observed field again, as in the first observation.

Figure 5. Examples of PR development defects detected by the Tomato/GFP-FLP/FRT method. (A) Visualization of mosaic sina[BG02648] mutant PRs, showing the loss of inner PRs. In the mutant ommatidia, outer PRs are clustered together due to the absence of the inner PR R7. Indeed, sina is known to be required for inner PR recruitment. (B) Visualization of mosaic grh[s2140] mutant PRs showing polarity defects. The mosaic mutant ommatidia, surrounded by a circle, are pointing in the opposite direction from wild-type ommatidia, indicating a dorso-ventral inversion. A detailed study with the Tomato/GFP-FLP/FRT method showed that grh was required in the R3 precursor for the correct acquisition of ommatidium polarity 20. (C) Visualization of mosaic crb[j1B5] mutant PRs, showing deformed homozygous mutant PRs. Crb is known to be required for rhabdomere morphogenesis.

Figure 6. Time-course analysis of mosaic fatp[k10307] mutant PRs with the Tomato/GFP-FLP/FRT method, over 14 days. A mosaic fatp[k10307] mutant retina is observed on day 1 (A, A'), day 4 (B, B'), day 8 (C, C') and day 14 (D, D') after hatching. The same group of mosaic PRs can be found at each time point, in the observed field (white rectangle, A, B, C, D). In this field of PRs (A', B', C', D'), homozygous mutant PRs are labeled in green, whereas heterozygous and homozygous wild-type PRs are labeled in yellow. From day 4 (B') onwards, the homozygous mutant PRs begin to disappear, indicating that the fatp[k10307] mutation induces a progressive degeneration of these PRs. Click here to view larger figure.

Figure 7. Rescue of fatp[k10307] mutant PRs with a mini-white-carrying fatp-expressing construct. The mosaic PRs are visualized with the Tomato/GFP-FLP/FRT method in 15-day-old flies. (A) Visualization of mosaic control PRs. (B) Visualization of mosaic fatp mutant PRs, showing the loss of mutant PRs. (C) Visualization of mosaic fatp mutant PRs in a fly reexpressing fatp in outer PR (rh1>fatp). The mutant PRs are rescued. The presence of a mini-white gene and the associated red eye pigmentation in rh1>fatp conditions does not alter Tomato or GFP fluorescence or clonal detection.