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
Mate Recommendations Report - Pairings ranked by composite breeding value
PedScope can make breeding (mating) recommendations by analyzing 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.
Breeders of fancy animals such as dogs and cats are often particularly interested in limiting the inbreeding of the potential offspring. To help with this one of the available measures is simply the coefficient of inbreeding of the 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. You can immediately see which matings give rise to low or high inbreeding.
In addition to the ranking values it is also possible to list the kinship between each of the prospective parents with a specific known ancestor. For example, breeders of fancy animals are sometimes interested in seeking matings that maximize the influence of particular prized individuals from the past whose influences they are trying to promote in their own breeding lines. I.e. it lets you easily answer the question: against which sire from a group of potential sires should I mate my female against in order to get offspring with the greatest influence from a particular significant ancestor? You simply sort the mate recommendations according to the sire's KC with the significant ancestor and read off the top result.
As with the measures of genetic diversity (above), you use the breeding prediction feature by first defining a group of individuals that represents the available sires and dams, and then you choose the depth of ancestry to be considered in the calculations (including the option of all known ancestry).
The following methods of ranking potential breedings are provided:
- Gene Diversity Delta (GD delta) - this is the change in GD of the population as a result of the addition of a single offspring from the prospective mating. GD is a function of the average mean kinship of the population.
- Gene Value Delta (GV delta) - this is the change in GV 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.
- Parental MK - this is the average of the parental mean kinships. I.e. the software 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 individuals that share less of their genome in common 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 individuals with widely differing mean kinships because this has the effect of combining rare gene lines with over-represented lines.
- Parental Genome Uniqueness - this is the average of the 'genome uniqueness' of the sire and the dam. The 'genome uniqueness' is the total probability, for all founders, that the individual is the only one in the current population containing genes from any one founder. Therefore the higher an individual's 'genome uniqueness', the greater the chance that if that individual 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 individual 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, and - obviously - you have the age data of the current population. E.g. the current population may include individuals 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.
- Offspring Inbreeding - the inbreeding of the offspring of the prospective mating.
- Composite - this is where a weighted combination of any of the other breeding metrics above, including the offspring inbreeding coefficient, is used. This lets you combine the various measures in whichever way you like, weighted according to the values you wish to prioritize. You can also apply a limit threshold for the offspring inbreeding, so as to remove from the rankings any pairings that would result in excessively highly inbred individuals, irrespective of the other merits of the pairing.
For further information please see the Reports - Mate Recommendations section of the User Guide.