Reports - Mate Recommendations

To view this report, choose Mate Recommendations from the report selector (at the top of the report pane) in the main window.

PedScope makes breeding recommendations by studying potential pairings and ordering them according to a single value reflecting the respective merit of the pairing. In this way it can be used as a tool to guide population management decisions. It provides various ways of calculating the merit for each pairing.

As with the Gene Diversity Metrics report, to use this feature you first need to define a group of animals that represents the available sires and dams. You do this by tagging the sires and dams in the main record table.

If you want to include all the living members of the population it can help if you first sort the main record table by the Age if Living or Living columns, if available. This will bring all the living animals together so you can tag them with a range-tagging operation.

Next, you choose the depth of ancestry to be considered in the calculation using the Ancestry to pulldown. This includes the option of using all known ancestry.

Finally, you choose the method by which the pairings are to be ordered using Rank by pulldown. The following table describes the different rankings in detail, and gives some of advantages and disadvantages of each.

Ranking Method Description
Inbreeding
Prospective Offspring Inbreeding Matrix - Showing the inbreeding for every sire/dam combination within a chosen group of males and females
Prospective Offspring Inbreeding Matrix - Showing the inbreeding for every sire/dam combination within a chosen group of males and females

 

Prospective Offspring Inbreeding List - Ranking list of prospective pairings, ordered by offspring inbreeding
Prospective Offspring Inbreeding List - Ranking list of prospective pairings, ordered by offspring inbreeding

Breeders of fancy animals such as dogs and cats are often particularly interested in limiting the inbreeding of the offspring of a prospective mating.

To help with this one of the available ranking methods is simply the coefficient of inbreeding of the potential offspring.

The results can be listed either in a table, ordered by ranking, or as a color-coded matrix of inbreeding coefficients with the sires in columns and the dams in rows.

If your aim in using the mate recommendations report is to maximize genetic diversity over the longer term, simply minimizing the inbreeding in immediate breeding decisions is not necessarily the best way to go.

Better results will be obtained by using a ranking method that uses Kinship Value (KV), such as the Parental KV or Composite rankings (see below).

Gene Diversity Delta (GD)

Gene diversity (GD) is a measure applied to a whole population that expresses the diversity of genes present. Gene diversity Delta is the change in gene diversity of the population as a result of the addition of a single offspring from the prospective mating.

If every animal in a population is unrelated, then by definition you would have the maximum genetic diversity possible for a population of that size.

A common goal of population management programmes for threatened species is to maximize the genetic diversity of the available population.

When ranking by GD Delta what PedScope does is this: for each possible pairing, it computes the GD that would result by addition of a single animal with given parents to the current population, and then compares this to the GD of the 'old' (i.e. current) population. An increase in GD as a result of the pairing is a good thing, a decrease is a bad thing.

Gene Value Delta (GV)

This is the change in gene value of the population as a result of the addition of a single offspring from the prospective mating. GV is a function of the average kinship value of the population. GV is to KV what GD is to MK.

It should be preferred over GD when kinship values are available because it takes into account the age structure of the current population.

This method requires that you have 'Vx' data set up, in order to compute the kinship values. For further information see Vx Data.

Parental MK

This is the mean of the parental mean kinships. I.e. PedScope computes the mean kinship of both sire and dam (with respect to the current population) and then ranks the prospective matings according to the mean of these two values for each pairing.

A lower value is better (because, lower values prioritize mating of animals that share fewer of their genes with the rest of the population).

Parental MK Delta

This is the difference in the mean kinships of the sire and the dam.

It can be detrimental to pair animals with widely differing mean kinships because this has the effect of combining rare gene lines with over-represented lines. A lower MK delta is better, and ranks higher.

Parental Genome Uniqueness

This is the average of the genome uniqueness of the sire and the dam.

It is the total probability, for all founders, that the animal is the only one (normally) in the current population containing genes from any one founder.

Therefore the higher an animal's 'genome uniqueness', the greater the chance that if that animal is not bred from, then under-represented gene lines will disappear forever from the current population.

Parental KV

This is the mean of the parental kinship values. The kinship value of an animal is related to the MK, but is weighted according to the age structure of the current population.

This can be a better metric upon which to base breeding decisions than the mean kinship, but requires that you also have reproductive values for the different age classes of the current population ('Vx data'), and - obviously - you have the age data of the current population.

E.g. the current population may include animals that are past reproductive age. Clearly such animals can never be bred from, so it is better if the genetic diversity contributed by those animals to the current population be discounted when making breeding decisions. Use of KV values enables this.

This method requires that you have 'Vx' data set up, in order to compute the kinship values. For further information see Vx Data.

Composite
Mate Recommendations Report - Pairings ranked by composite breeding value
Mate Recommendations Report - Pairings ranked by composite breeding value

This is where a weighted combination of any of the other breeding metrics above, alongside the offspring inbreeding coefficient, is used. This is probably the most ranking powerful method.

It lets you combine the various measures in whichever way you like, weighted according to the values you wish to prioritize. You can also set a limit threshold for the offspring inbreeding, so as to remove from the rankings any pairings that would result in excessively highly inbred animals, irrespective of the other merits of the pairing.

To customize the weightings used by the composite ranking, use the KV Weights tab of the Document Settings window.

For further information see Population Genetics.


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