The protocol presented here is mainly based on a previously published protocol6. However, since A. mexicanus spawns during night hours, we designed a housing rack for fish breeding that can change the photoperiod independent of working hours (Figure 1). The fish light cycle is altered within a fully enclosed, flow-through aquaculture system containing three rows of tanks (Figure 1). Each tank contains an independent heating element that is used to manually increase the temperature during the priming process. Individual shelves can be put on separate photoperiods and can be closed to prevent light from entering or escaping. All photoperiods can be manipulated by way of an automated controller positioned on the side of the light cycle rack. For access during dark hours, the rack is equipped with a red work light and blackout curtains. A. mexicanus spawns after an increase in temperature from 23 - 26 °C with an increment of 1.5 °C per day16. To achieve this in our dark cabinets, we used submersible aquarium heaters in each tank (Figure 1).
The key factor for a successful IVF procedure in A. mexicanus is the quality of the collected ova. Gravid, female fish with large, protruding abdomens are most likely to release viable ova, which appear clear and even in appearance (Figure 2a-d). Adding the collected milt to such ova results in the development of fertilized embryos usually within 20-30 min (Figure 2e). Viable fertilized embryos will become slightly more translucent before entering the one cell stage of the developmental cycle while unfertilized ova will appear more uneven and opaque (Figure 2e). Resulting embryos are held in Petri dishes in ZIRC E2 Embryo Media and incubated at 23 °C in a 14/10 light/dark cycle. Embryos are then transferred to the main recirculating housing system at 5 days post fertilization for rearing.
To demonstrate the importance of the technique, we show how the phenotyping of hybrids for specific traits such as eye size and body pigmentation can help in deciphering their genetic basis. Cavefish clearly differ from surface fish in their eye size and body pigmentation. To understand the genetic basis of these traits, we crossed surface and cavefish (F0) and generated hybrid F1 and F2 populations using IVF to observe the phenotypic variation obtained (Figure 3). The size of the eyes is smaller in the F1 generation indicating that the presence of eyes is a partially dominant trait (Figure 3). In surface-cave F2 hybrids, we obtain a broad range of eye sizes, indicating that there are multiple loci that control eye size in A. mexicanus, making it a quantitative trait (Figure 3). Another example is pigmentation. Observing the F1 hybrid of surface and cavefish, it can be concluded that body pigmentation is a dominant trait as the fish are fully pigmented (Figure 3). In the F2 generation, the variation in body pigmentation again points towards a quantitative trait. Combination of this phenotypic data with sequencing data can reveal underlying genetic loci responsible for these phenotypes. These F2 populations are a good resource for understanding the genetic basis of various traits and such populations have been used previously for studying these traits17,18,19. A standardized IVF technique can greatly streamline the generation of hybrids, enabling genetic mapping of the loci controlling such traits and helping us understand how certain phenotypes are disadvantageous in some habitats and adaptive in others.

Figure 1: Design of racks to shift day/ night cycles of A. mexicanus. (a) The general setup of this rack system allows photoperiod manipulation, giving a simulation of night time during the day hours when doors are closed, and the shelf lights are turned off. (b) Priming the fish to stimulate ova maturation is achieved by using submersible heaters (see Table of Materials) installed in individual tanks that can be adjusted separately (red arrows). Please click here to view a larger version of this figure.

Figure 2: Examples of suitable females for ova collection and representative illustration of viable and unviable ova. (a) Gravid, female fish with large, protruding abdomens are more suitable for manual ova collection than (b) females with a streamlined shaped abdomen. (c) Viable ova (i.e., ova producing viable embryos when fertilized) can be identified by their clear, even appearance, while unviable ova (i.e., ova not producing viable embryos when fertilized), as shown in (d), have a cloudy, uneven appearance. (e) After successful fertilization, viable embryos become more translucent and enter the one cell stage while unfertilized ova (red arrows) will slowly decay. Please click here to view a larger version of this figure.

Figure 3: Genetic analysis of eye size and body pigmentation traits. Pedigree showing pictures of parental (F0) surface fish (top left) and cavefish (top right), F1 hybrids (second row) and the F2 hybrids. The F1 fish have intermediate eye size and are fully pigmented while F2 fish show a broad variation in the two morphological traits: eye size and pigmentation. All original data underlying this figure can be accessed from the Stowers Original Data Repository at http://www.stowers.org/research/publications/libpb-1365. Please click here to view a larger version of this figure.