WFR Genetics

Contents

1. An Introduction to the Warm Fuzzies Rat Genetics Calculator

2. Instructions for use

3. Reading the results

4. Explanation of ' ? '

5. A note on Blues

6. Naming Conventions

1. An Introduction to the Warm Fuzzies Rat Genetics Calculator

For those who have not seen or used a rat genetics calculator before; the basic purpose of such a program is to determine the most probable litter that will be produced by the mating of two specific rats, based of the known information about these rats. Calculations are based on genetic probabilities, and though the results will seldom be perfect, they will be accurate within reason (provided the calculator is given accurate information).

Though our Calculator is not the first of its kind it differs from other Calculators in two main ways: firstly in appearance, secondly and most importantly in convention of naming. This is due to various clubs and/or ratteries having different names for the same colour. The naming convention used in the Calculator is based on the accepted names used by our club, in other parts of Vic and NSW and possibly elsewhere within Australia. For a list and explanation of various naming conventions, including our own, click here.

If there is sufficient interest, the next update to the Calculator will provide the added function of choosing your preferred naming convention.

2. Instructions for use

Most if not all of the Rat Genetics Calculators in the world are currently designed specifically for use in regards to colours; the colours of the parents help determine the colours of the pups. This is partly due to the popularity of various colours and the complexity of combining various colours. Though there plans to expand our Calculator, it too is currently designed for use solely with regards to colours.

Colours

From the Main Menu you will see two options in the colours section: Basic & Advanced. These represent the two methods of input for the Calculator. Here follows a brief description of each, followed by more specific detail about their separate layouts:

Basic:

For anyone unfamiliar with either genetics or genetic Calculators, this method is designed to allow easy composition of your parents' genetic make-up.

The components on this page include:

One drop-down menu for each parent to select their respective colours.

A series of checkboxes for describing the parents' carried traits.

A Main Menu button which will return you to the Main Menu.

A Calculate button for when you are ready to proceed with the calculation.

This method can be completed by following these steps:

1. Select each parents colour from the drop-down menu. For a full list and explanation of colour conventions click here.

2. Indicate each parents carried traits using the checkboxes; for each trait, one of these checkboxes should be checked: Y - indicating that yes the trait is carried, N - the trait is not carried, or ? where you are unsure if the trait is carried or not. Note that with certain colours some traits are always present and so cannot be considered to be carried, if you choose one of these colours the relevant checkboxes will become inactive.

3. Press the Calculate button.

And that's it, if you wish to make use of the advanced input method read on, otherwise skip down to Reading the Results.

Another thing to mention here is with regards to pink-eyed rats; due to the fact that if your rat is pink-eyed it is difficult to determine whether said rat is also mink or ruby-eyed. If you have a pink-eyed colour chosen (but not Albino) and check ' ? ' for carrying mink or ruby-eyes, then a ? will occur in both positions for that trait.

Advanced:

For those who are familiar with genetics and/or genetics Calculators, this method is designed to allow a more direct manipulation of your parents' genotypes.

The components on this page include:

Six drop-down menus for each parent representing the six loci relevant to the Calculator, which can be used to directly compose the genotypes of the parents.

Three buttons (All Carried, None Carried, All Unknown) for each parent which can be used to instantly switch all possible loci to the relevant state (carried, not carried, or ? ). Note that any locus with two recessive traits or two unknowns ( ? / ? ) will not be affected by these buttons.

A drop-down menu and activating button for each parent for loading preset colours. When a colour is selected from the menu and the Load Preset button is pressed, the genotype of that parent is changed to reflect the colour chosen. Note that any carried traits or unknowns that have no effect on the new colour will be left as they are.

A Main Menu button which will return you to the Main Menu.

A Calculate button for when you are ready to proceed with the calculation.

3. Reading the Results

Once the calculation is complete, the type of pups that could be produced from that mating are displayed, along with a probability for each type.

It should be remembered that the calculations are dependant on exact knowledge of the parents genotype, which can be quite difficult to determine, and also that genetics can be extremely unpredictable, with colours often appearing or not appearing against all probabilities.

Having said that, the results can be interpreted in the following way:

The types shown in the results should reflect the types produced in the litter, and the probability of each type (when multiplied by the total number of pups) should reflect the number of pups produced of each type.

Example 1: Lets say the results tell you that the pups will be %50 Agouti and %50 Black, and your dam gives birth to exactly ten pups, then with any luck you will have exactly 5 Agoutis and 5 Blacks.

Example 2: Lets say the results tell you that the pups will be %75 Agouti and %25 Black, and your dam has exactly ten pups, then with any luck you will have 7 / 8 Agoutis and 2 / 3 Blacks.

This won't happen every time but it is the most probable outcome.

There are some differences between the results screens of the Basic and Advanced methods, here follows a brief description of the layouts of each:

Basic:

The Basic Results screen displays the phenotypes then the genotypes in order. Two buttons are also available; a Back button to return to the Basic Input screen, and an Advanced Results button which will switch to the Advanced Results screen.

Advanced:

The Advanced Results screen initially displays the results in order of genotype in this order of category; phenotype, genotype, haploid. The haploid lists represent the possible genotypes carried by each parents sex cells, which combine to make the list of possible pups, this is why haploids contain only one gene from each allele. At the top of the screen there are two buttons; A Back button to return to the Advanced Input screen, and a Basic Results button which will switch to the Basic Results screen. The Advanced screen also has various components for affecting the way the results are displayed;

The Show All button, which is selected as the default, shows all three categories.

The 'Show Phenotypes', 'Show Genotypes' & 'Show Haploids' buttons, when pressed, show only each specific category in the results.

The Buttons labeled '%Probability', 'Colour', 'Phenotype' & 'Genotype', which indicate what each column represents in the results, can be pressed to sort the results in order of that category. Pressing twice will sort the results in reverse order of that category.

The Adjust Feature

If the genotype of either parent contain a ? , then the Adjust button will also be available; Pressing the Adjust button will open a new window which contains controls for temporarily changing the genotypes of your parents with regards to any unknown genes. The purpose of this is to be able to change uncertain genes between possibilities and instantly see what effect this change has a the results. For example, if you are not sure whether your rat carries mink or not, give it a mink locus that shows M / ? (non-mink, unknown carrying). Then when viewing the results, open the Adjust window and change the mink locus to M / M, then change it to M / m, so that you can see for yourself what effect/s this change could have on your litters.

Closing the Adjust window will revert the parents genotypes to their original state.

4. Explanation of '?'

The basic Calculator design is useful providing that you know the exact genotype of your intended parents, but most of the time this is not the case. Even slight changes can have an effect on results so it is advisable to take the unknowns into consideration when planning your litter. One method would be to re-do the calculation for every possible genotype of the parents, changing the parts your unsure of, to see what effect this has on the results. However there is also an alternative, simply by placing a ' ? ' in any position on the genotype that you're unsure of, the results will be affected in the following ways:

If the ? occupies both positions at one locus, each ? will be replaced (at calculation time) with an equal probability by each mutation occurring at that locus.

Example: If the Agouti locus of a parent is set to ? / ?, each ? will be replaced with a %50 probability of 'A' (Agouti) and a %50 probability of 'a' (Black). And so the results will show an equal possibility of 'A/A', 'A/a', 'a/A' and 'a/a'. Then, 'A/a' and 'a/A' (being the same) will be combined and the final results will be %25 pure Agouti, %50 Agouti carrying Black, and %25 Black.

If the ? occupies only one position at a locus it will be replaced (at calculation time) by each mutation occurring at that locus with these probabilities: %66.6 probability for the recessive trait and %33.3 probability for the dominant trait. This is due to the fact the rats carrying such traits are generally more common than non-carrying rats.

Example: If the Agouti locus of a parent is set to A / ?, this will be replaced with a %33.3 probability of A / A (pure Agouti) and a %66.6 probability of A / a (Agouti carrying Black).

Another function of ? in this Calculator is to make use of the Adjust feature in the Advanced Results page. Some more info about this can be found here.

5. A note on Blues

Internationally, the blue genes are generally represented symbolically by the letters D and G. However, due to the fact that Australian blues are still relatively new and that there is a great lack of evidence about the genetic background of Australian blues, blue will be represented in this Calculator by the letter X. This is not to say that Australian blue is necessarily different to overseas varieties but simply that enough evidence has not been seen to justify labeling blues as D or G, which in itself could cause confusing.

There are also many different names for the various shades of blue, to avoid confusion the Calculator refers to blues in the following ways;

A Non-Agouti blue with no other mutations (a/a x/x) is referred to simply as Blue.

An Agouti blue with no other mutations (A/- x/x) is referred to as Blue Agouti.

A Pink-eyed Non-Agouti blue (regardless of other mutatations) is referred to as Silver.

A Pink-eyed Agouti blue (regardless of other mutatations) is referred to as Silver Agouti.

All other blue colours are referred to as a blue version of their non-blue counterparts. Example; While a mink-Agouti is called Cinnamon, a blue-mink-Agouti shall be referred to as Blue Cinnamon.

It has also been said that carrying blue can have an slight affect on non-blue colours, this is not taken into account in the Calculator however it may be worth keeping in mind for anyone who intends to breed Australian blues.

6. Naming Conventions

The following table shows the names of various colours, based on genotype, as they differ between various clubs and/or ratteries, and between Australia, the UK and the USA. Due to a lack of response to permission requests I am unable to show the names of these sources, however should anyone from any country wish to submit there own convention, I will be happy to include you in this list.

GENOTYPE	WFR	(UK)	(USA)	(USA)	(USA)
A- D- G- M- P- R-	Agouti	Agouti	Agouti	Agouti	Agouti
A- D- G- M- P- rr	Argente	Fawn / Topaz	Fawn	Fawn / Topaz	Fawn / Topaz
A- D- G- M- pp R-	SilverFawn	Amber	Amber / Silver Fawn	Amber	Amber / Silver Fawn
A- D- G- mm P- R-	Cinnamon	Cinnamon	Cinnamon	Golden Agouti / Cinnamon	Cinnamon Agouti
aa D- G- M- P- R-	Black	Black	Black	Black	Black
aa D- G- M- P- rr	Buff	Beige / Buff	Beige	Beige / Buff	Beige / Buff
aa D- G- M- pp R-	Champagne	Champagne	Champagne	Champagne	Champagne
aa D- G- mm P- R-	Mink	Mink		Mink / Dove	Mink
aa D- G- mm P- rr	Dove	Beige / Buff	Dark-Eyed Champagne	Lilac	Mocha
aa D- G- mm pp R-			Pale Champagne
A- dd G- M- P- R-		Blue Agouti		Russian Blue Agouti	Russian Blue Agouti
A- dd G- M- P- rr					Russian Fawn
A- dd G- M- pp R-		Apricot Agouti / Silver Agouti
A- dd G- mm P- R-		Platinum Agouti
aa dd G- M- P- R-		(American / English / Slate) Blue		Russian Blue	Russian Blue
aa dd G- M- P- rr				Blue Beige	Russian Beige
aa dd G- M- pp R-		Silver
aa dd G- mm P- R-		Platinum / Quicksilver		Lilac	Russian Dove
A- D- gg M- P- R-		Russian Blue Agouti	Blue Agouti	Blue Agouti / Opal	Blue Agouti / Opal
A- D- gg M- P- rr					Platinum Agouti
A- D- gg M- pp R-					Silver Agouti
A- D- gg mm P- R-		Russian Cinnamon
aa D- gg M- P- R-		Russian Blue	Blue	American Blue	American Blue / Slate
aa D- gg M- P- rr				Platinum
aa D- gg M- pp R-			Silver	Silver	Silver
aa D- gg mm P- R-		Dove	Powder Blue		Platinum
A- dd gg M- P- R-		Russian Silver Agouti			Russian Silver Agouti
aa dd gg M- P- R-		Russian Silver			Russian Silver
c/c -/- -/- -/- -/- -/- -/-	Albino	Albino		Albino	Albino