A Look at Genetics

Summary: A look at genetics was written with particular regard to the selective breeding of guppies, this authoritative article applies to other species of fish too.

Genes. What are they?

A gene is a unit in a chromosome that determines the hereditary outcome of the offspring. Take a new born baby, and the expressions.. “Oh, he’s got his father’s eyes” or “Doesn’t he look like his mum?” These factors are the “noticeable” features that have derived from the parents, both father and mother. Basically it is the same with fish, and just like the human adult we can spot certain features that may be passed down to the offspring. These features may be in fin shape, or tail shape, or certain colourings that the fish may have – but just because you start off with a fish with all the desired features, it is no guarantee that the resulting fry will retain these features.

Few of us would have the desire and dedication to develop a new type or strain of guppy, as these things take a lifetime of dedication, but most of us would like to understand more on the subject of what makes these little fish look so beautiful, and how we can make an effort to improve the present strains available and share the results with others.

There are two types of genes that will concern us, and those are the “Recessive” gene, and the “Dominant” gene. As the names imply, one type is stronger than the other, but unless we know what we are doing, finding out the dominant and recessive genes is a task in itself, and often can only be established by selective breeding over an extended period of time. Fortunately there are also some of the recessive and dominant genes that breeders have already discovered and have made this knowledge available to other breeders. We can learn about these established findings as we delve into the world of breeding. We may choose the best looking male, with all the right colours and features, along with the best coloured female with the correct body shape, but again, these pairings may not give us the results we expect. Many times the choice of a good sound female of good body and fin shape, but lack of any obvious colour will often give better results. Some of the terminology used in guppy breeding follows below:

Selective Breeding

This sounds obvious, as it is referring to the correct selection of a pair that you are proposing to breed, but the question here of course is “which pair” you should select, as this is the confusing part.

Line Breeding

Here we have a selective line of fish that we are working on that has begun to throw some good results, and we do our best to keep that line going by selective selection of the offspring from within that line.


Once the above has started to take place, we now become involved with Interbreeding, which is the process of breeding the fish within a fixed family. Usually the females from your selected trio of breeders are kept separated so that you can form two distinct lines of fish. The fry from these fish can also be bred back to the parents, (Back Crossing) or to following generations in order to continue the line. This can only be done up to a point, as defects may begin to show such as loss of colour, size and vigour, virility, or fin shape, so then we may have to resort to other means, which may involve the introduction of new blood. Some reports have said that they have had no defects whatsoever over eighteen generations of fish, so this should give the breeder a chance to obtain some favourable results before there is need to introduce some new blood.

Out Or In Crossing

A move that few breeding enthusiasts care to take, as this involves the introduction of new blood into the line that you have spent so long in perfecting. Often this is done either in the very early stages (while you are still trying to find a decent match), or as a last resort, as your line has started to decline in some way and has begun to show defects. It is wise at this point to restrict the activities of the newly introduced blood that you have acquired to a very restricted number of fish, so that you have full control over the outcome and your main line is not compromised in any way. Allowing an unknown male to run loose in your stock could destroy the direction of your main line.

The Recessive Gene

In simple terms, these are the genes that can be pushed away, or “dominated” by the more Dominant genes that the parent holds. When we look at the details of the fish being used in a breeding pair, we often see upper and lower case letters being used. The upper case letter signifies the “Dominant” gene, and the lower case letter signifies the “Recessive” gene. So we may see something like this.. CC Cc or Aa aa.. as there is no restriction on what letters are used. This only applies to the gene pool, but when signifying the male and female, the letters are “always” the same, and XY is used for the male, while XX is used for the female.

The Dominant Gene

These are the genes that can override the Recessive genes, and are usually the ones that stand out in the appearance of the fish, but sometimes only a “slight” hint of a dominant gene is showing through, and in some cases this may take several breedings to show itself in the upcoming broods. By very careful selective breeding, these dominant genes can be made stronger, as can the Recessive genes in many cases. Mention above was made that the best looking females of good colour will not often give the results we require, and that a female of sound body, but with no obvious colour will often give better results. This is true in many cases, but if you acquired say a trio of quality stock from a breeder, then the chances are that these fish will be from the same line, and so many of the genes will be either fixed, or available in your existing trio, so using a different female from an unknown line would not be the thing to do in this situation. The female is the one that is going to carry the combined gene pool onto the next brood of fish, so the less she has in the way of a mixed gene structure, the better. Females of good colour and fancy coloured tails can in some cases prevent the progress of the dominant factors that we are trying to pass on through the male, so often a non-coloured female is used to avoid this hindrance, but as above, if your trio is of good breeding and your females have already produced fixed or semi-fixed results, then they would be the ones to use, and not one of unknown origin.

The Virgin Female

The above is one reason why the breeder often uses the virgin female to extend or start the line, but things are not quite that easy, as even the virgin females can carry traits that we don’t want, and therefore these unwanted traits have to be bred out of the fish. The important factor here is to try to obtain your virgin females from a recognised line of fish of the type you are wanting to breed. It is pointless getting females that have come from say Half Blacks if you want to have say all red fish, so try to obtain the virgin females from a breeder that can show you the line the fish have derived from, as this could save you a great deal of time. Find out from your supplier all the details you possibly can about the fish you are getting… what strains they have come from and what generation they are, or if they are F1 F2 F3 hybrids, or are they from a fixed line of no outcrossing.

Once the line is running of course, then your selected female breeders are normally used, but many breeders isolate their female fry at the earliest possible time to avoid unwanted results further down the line. We must remember that the passing on of genes is all a bit “hit and miss” in some cases, and that just because your male may show a certain feature that you want, it is no guarantee that those particular features will be passed down to future generations, but “some” of the features may be carried on, and this is where we have to carefully isolate the ones showing promise from the ones that are void of the things we are looking for.

Having the tank space to house these fish is also a problem, and if we were to keep “every” fish from our lines, we would soon find ourselves overrun with not only fish, but with fish carrying traits that we don’t want, so separation and culling is the preferred method.

Back to the Genes

Pretty confusing stuff all this, but let’s try to look at it in simple terms. Imagine we have two jars of marbles of all different colours. Now imagine that each of these marbles is a gene. We have one jar for the male, and one for the female. Now looking at all these pretty colours we might not like some of them, but there may be a few we do like, and many will look alike in both jars, but the problem is, how do we sort them out? Now if the two jars represented fish that came from a fixed line of fish, we would see a distinct pattern, where most of the marbles in both jars were of a similar colour, but if the fish were not related, or from different lines, then the colours would be all random, with no sequence. Don’t confuse the reference to the marble colour with the colour of the fish, as each gene (marble) represents a certain feature that the fish may hold… eg: Size, Vigour, Tail size, Dorsal size, Colour variation and so forth. If we now mix the two jars together.. (breed the fish).. then we have scrambled all the genes up and made the task of sorting them out even harder. However, if the fish were related or from a fixed line, we would possibly get more of the colours we are looking for, rather than a completely scattered gene pool.

We can see by the above that starting off with fish of a known background will give you a better start, than two randomly selected unrelated fish. Selecting a couple of fish from a local shop fish tank and hoping they will breed true will just not happen, so obtain your starting stock from a reputable breeder if possible. By having two similar jars of marbles (fish) in the beginning, then the gene pool is not so mixed up, and we have a better chance of seeing the genes that we want to appear in our future broods. If we reach a point where the only option is to use another un-related fish from another line because we are not getting the results we want after extensive trials and breedings, then you should only select the new blood (outcross) from a line of fish that most closely resembles the one you are working on. Failure in doing this will be like taking your two jars of marbles and mixing them all together once more… in other words, you “could” be back to square one.

A crossing from another unrelated source will produce what are termed as a Hybrid, and the first generation of this brood will be known as F1, with subsequent generations being F2, F3 and so on. Before selecting an outcross, ensure that all your present options are not going to give you the results you want. Take the jars of marbles once more as an example. All the colours are there representing the different genes, but some of the results that may be obtained could be hidden, so only careful selective breeding over time will tell you this. Now if you have a feature that is “obviously” missing in your breeding results, and you want to attempt to introduce that feature into your line, then you will need to find a fish that has the feature that you seek, plus one that is as close in appearance as the line you are working on, plus has a proven record that the offspring it has produced are true to form.. eg: that it carries the feature (gene) you are looking for. The offspring from this fish “may” have the gene you are looking for but it may have been passed on by the female, but if all the male fish from this brood show the feature you want, then it might be better to select some promising stock from them.

Again it must be stressed that you must keep all breeding from this un-related fish isolated from your main breeding line, until such times that you have favourable results that you again want to backcross into selected females from your original line.


Not exactly a genetic term, but one that you will be deeply involved with if you seek favourable results. This is a sore point with many non-hardened breeders, but is something that “must” be done, and “done early” if your line is to be protected. Careful continuous separation is needed to sort the males and females at the earliest possible time, and any fish that show up that do not have the qualities you are seeking, should be disposed of quickly. These can become the feeders for your other fish stocks, or even sold off at a later date if no obvious defects are apparent, but whatever you decide to do, you should endeavour to keep these fish away from your main stock or lines you are producing. Many hard decisions will have to be made, and often the temptation to ignore the risks can ruin a great deal of work, but if you want to perfect your goals, then the culling or separation will need to be done on a regular basis. There are many other terms that you may come across, but we will just mention them briefly here as these are terms that the geneticist will use more than the average breeder.


These are where the genes can be found.
Alleles – Genes are known to do certain things, and occupy certain locations on the chromosomes where they are held, and it is these that control the outcome of certain traits that we are trying to achieve, but if there is a variation in this pattern they are called alleles.
Polygenes – Quite often more than one pair of genes influences a certain feature we are trying to obtain, and in this case they are called polygenes.
Genotype – This is a method of describing the genetic makeup of something, and is usually signified by the use of letters.
Phenotype – This is when something caused by the genetic makeup appears. Fish with different genotypes could still have the same phenotype, or appear to have the same phenotype. Beyond here gets very complicated, so we will leave it at that for now.
Homozygous – This basically means that all the offspring will look like the parents.

First publication: Bill’s web site: Fishy Types Aquarium, august 2005
Source: Aquarticles (no longer available)

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