Tenset - Breeders Assistant Pedigree Software

The Extended Edition of Breeders Assistant can rank prospective matings according to the extent to which the offspring would be inbred. This is one of a number of advanced population genetics tools.

The prospective matings can be shown either as matrix, such as that shown below, or an ordered list.

See video

The matrix shows the inbreeding that would result from each different mating between a chosen set of sires and a given set of dams. The columns represent the sires, and the rows the dams. The value in any cell shows both the inbreeding that would result from the given mating (the F value), and a rank which varies from 0-100 where 100 means 'best' (i.e., lowest F).

E.g. the 5th row in the 2nd column shows the inbreeding that would result from mating 'Robbie' against 'Hyacinth'. In this case the inbreeding of the resultant offspring would be 36.22% and the rank value would be 22.3.

The results can be exported to text/CSV.

A demonstration of this feature can be found in the 'Mate Selection, Kinship And Population Analysis' tutorial included with the product.

Figure: Mate Selection Matrix With Inbreeding Minimization

The rank values are assigned by first working out the range of inbreeding that would result from all the matings, then scaling them from 0 to 100, where 0 represents the worst outcome (i.e. highest F) and 100 the best.

The matrix cells are color coded according to the inbreeding, with lighter colors representing lower inbreeding. This helps you see at a glance which matings are best/worst.

© 1996-2024 Tenset Technologies Ltd.
"Tenset", "PedPro", "GedWiz", "Breeders Assistant" and "Pedigree Assistant" are registered trademarks of Tenset Technologies Ltd in the United Kingdom. Microsoft and Windows are registered trademarks of Microsoft Corporation in the U.S. and/or other countries. Apple, Mac and Macintosh are trademarks of Apple Inc., registered in the U.S. and other countries.

The Extended Edition of Breeders Assistant provides a 'key metrics' analysis which computes various population genetics metrics for a group of animals, such as inbreeding coefficients, pedigree completeness indices and genome completeness coefficients. This is one of a number of advanced population genetics tools.

For a video demonstration see this video

The group of animals can be the entire database, or it can be a subset, such as all the animals in the current view (for a selective index). Additional filter conditions can also be set e.g. to only include animals less than a given age, or meet other customized conditions.

To access this select Population Analysis from the Tools menu, then choose Key Metrics.

Once the animals to be studied and the depth of ancestry have been selected, the key metrics can be computed.

A demonstration of this feature can be found in the 'Mate Selection, Kinship And Population Analysis' tutorial included with the product.

Displayed Columns

The columns displayed by default include:

Inbreeding Coefficient (symbol F) - computed using all the ancestry that was specified.
Ancestral Inbreeding (symbol AF) - the cumulative proportion of the animal's genome that has been previously exposed to inbreeding in its ancestors. E.g. an animal may not be inbred itself but there can be extensive inbreeding present in its ancestry. This value is computed using the method of Ballou, (see "Ancestral Inbreeding Only Minimally Affects Inbreeding Depression in Mammalian Populations", Journal of Heredity 1997, 8:169-178).
Genome Uniqueness (symbol GU) - an estimation of the probability that an animal contains founder alleles not present in any other single (normally) animal within the set of animals for which the table has been compiled. This latter point is crucial to understand - the whole purpose of the GU measure is to identify animals within the breeding population that are likely to carry genes from founders where there is little or no representation of those genes in other members of the breeding population. GU can be factored into mate selection decisions when prioritizing prospective matings using gene diversity metrics. Informally, if an animal is the only one carrying a particular founder's genes, then you'd likely want to breed from that individual so as not to lose those genes from the population forever.
Full Generations (symbol GF) - the number of generations of ancestors that are 'full' - i.e. all ancestors given (within the depth of ancestry under consideration).
Max Generations (symbol GM) - the maximum depth of ancestry at which ancestors were found - (within the depth of ancestry under consideration). It is possible for this to exceed the #generations chosen if the group of animals for which it is compiled also includes some of their ancestors. E.g. if you have two animals in your database called, say 'Fred' and 'Bert', where 'Bert' is the sire of 'Fred', and you chose to do the analysis for just 2 generations, then because 2 generations of Bert's ancestors are traced, it means that ancestors will have been seen for 'Fred' 3 generations back.
Equivalent Complete Generations (symbol ECG) - a measure of the completeness of the pedigree. It is the sum total of the proportion of the ancestors that were traced at every generation at which ancestors were found (including, possibly, ancestor generations beyond those requested, for the same reasoning as given for Max Generations). E.g. if both parents are present that contributes 1 to the ECG value. If 2 grandparents are present that would add 0.5 to the ECG (i.e. 2/4). If 3 great-grandparents are present that would add 0.375 to the ECG (i.e. 3/8). Etc.
Pedigree Completeness (symbol PC) - another measure of the completeness of the pedigree. It is the sum total of the proportion of the ancestors that were traced at each generation, divided by that number of generations, shown as a percentage. E.g. if you were to request 3 generations of ancestors be included, then for an animal where both parents are present (i.e. proportion 1.0), 2 grandparents are present (proportion 0.5), and 3 great-grandparents (proportion 0.375) then the PC value would be (1.0 + 0.5 + 0.375) ie 1.875 divided by 3 which is 0.625 or 62.5%.
Pedigree Completeness Index (symbol PCI) - this is yet another measure of the completeness of the pedigree, and probably the most useful. It is the harmonic mean of the PC values for the parents of an animal, so long as both parents are present, otherwise it is zero. Because it is the harmonic mean it weights the result to the lower of the parent PC values. This value is computed using the method of MacCluer et al ("Inbreeding and Pedigree Structure in Standardbreed Horses", Journal of Heredity 1983, 74:394-399). PCI can be useful when deciding how much importance to give to an inbreeding value. Informally, if insufficient ancestry is available then a low inbreeding coefficient is not a reliable guide to the true level of inbreeding. When selecting prospective matings by inbreeding Breeders Assistant can use weightings for the sire and dam PCI values in the overall ranking. A threshold can also be specified to exclude prospective matings which have a PCI value below a given value.

© 1996-2024 Tenset Technologies Ltd.
"Tenset", "PedPro", "GedWiz", "Breeders Assistant" and "Pedigree Assistant" are registered trademarks of Tenset Technologies Ltd in the United Kingdom. Microsoft and Windows are registered trademarks of Microsoft Corporation in the U.S. and/or other countries. Apple, Mac and Macintosh are trademarks of Apple Inc., registered in the U.S. and other countries.

The Extended Edition of Breeders Assistant provides a 'gene diversity metrics' report which computes mean kinship for a group of breeding sires and dams, along with other values such as inbreeding coefficients and pedigree completeness indexes. This is one of a number of advanced population genetics tools.

For a video demonstration see this video

The sires and dams are typically specified using a selective index (view) into the full set of records in your database. Additional filter conditions can also be set e.g. to only include animals less than a given age, or meet other customized conditions.

To access this select Population Analysis from the Tools menu, then choose Gene Diversity Metrics.

A demonstration of this feature can also be found in the 'Mate Selection, Kinship And Population Analysis' tutorial included with the product.

Displayed Columns

The columns displayed by default include:

Mean Kinship (symbol MK) - the mean of the kinship of the individual with every other individual in the breeding group, including itself, for which the report was compiled.
Inbreeding Coefficient (symbol F) - computed using all the ancestry that was specified.
Genome Uniqueness (symbol GU) - an estimation of the probability that an animal contains founder alleles not present in any other single (normally) animal within the group for which the report has been compiled. This latter point is crucial to understand - the whole purpose of the GU measure is to identify animals within the breeding population that are likely to carry genes from founders where there is little or no representation of those genes in other members of the breeding population. GU can be factored into mate selection decisions when prioritizing prospective matings using gene diversity metrics. Informally, if an animal is the only one carrying a particular founder's genes, then you'd likely want to breed from that individual so as not to lose those genes from the population forever.
Full Generations (symbol GF) - the number of generations of ancestors that are 'full' - i.e. all ancestors given (within the depth of ancestry under consideration).
Max Generations (symbol GM) - the maximum depth of ancestry at which ancestors were found - (within the depth of ancestry under consideration). It is possible for this to exceed the #generations chosen if the group of animals for which it is compiled also includes some of their ancestors. E.g. if you have two animals in your database called, say 'Fred' and 'Bert', where 'Bert' is the sire of 'Fred', and you chose to do the analysis for just 2 generations, then because 2 generations of Bert's ancestors are traced, it means that ancestors will have been seen for 'Fred' 3 generations back.
Equivalent Complete Generations (symbol ECG) - a measure of the completeness of the pedigree. It is the sum total of the proportion of the ancestors that were traced at every generation at which ancestors were found (including, possibly, ancestor generations beyond those requested, for the same reasoning as given for Max Generations). E.g. if both parents are present that contributes 1 to the ECG value. If 2 grandparents are present that would add 0.5 to the ECG (i.e. 2/4). If 3 great-grandparents are present that would add 0.375 to the ECG (i.e. 3/8). Etc.
Pedigree Completeness (symbol PC) - another measure of the completeness of the pedigree. It is the sum total of the proportion of the ancestors that were traced at each generation, divided by that number of generations, shown as a percentage. E.g. if you were to request 3 generations of ancestors be included, then for an animal where both parents are present (i.e. proportion 1.0), 2 grandparents are present (proportion 0.5), and 3 great-grandparents (proportion 0.375) then the PC value would be (1.0 + 0.5 + 0.375) ie 1.875 divided by 3 which is 0.625 or 62.5%.
Pedigree Completeness Index (symbol PCI) - this is yet another measure of the completeness of the pedigree, and probably the most useful. It is the harmonic mean of the PC values for the parents of an animal, so long as both parents are present, otherwise it is zero. Because it is the harmonic mean it weights the result to the lower of the parent PC values. This value is computed using the method of MacCluer et al ("Inbreeding and Pedigree Structure in Standardbreed Horses", Journal of Heredity 1983, 74:394-399). PCI can be useful when deciding how much importance to give to an inbreeding value. Informally, if insufficient ancestry is available then a low inbreeding coefficient is not a reliable guide to the true level of inbreeding. When selecting prospective matings by inbreeding Breeders Assistant can use weightings for the sire and dam PCI values in the overall ranking. A threshold can also be specified to exclude prospective matings which have a PCI value below a given value.

© 1996-2024 Tenset Technologies Ltd.
"Tenset", "PedPro", "GedWiz", "Breeders Assistant" and "Pedigree Assistant" are registered trademarks of Tenset Technologies Ltd in the United Kingdom. Microsoft and Windows are registered trademarks of Microsoft Corporation in the U.S. and/or other countries. Apple, Mac and Macintosh are trademarks of Apple Inc., registered in the U.S. and other countries.

The Extended Edition of Breeders Assistant can rank prospective matings according to various measures of gene diversity of the breeding pool and/or the prospective parents. This is one of a number of advanced population genetics tools.

For a video demonstration see this video

One way to rank potential matings is by the 'average genome uniqueness' of the parents, but several others are possible, such as changes in mean kinship (of a breeding pool) that different matings would cause.

The following screenshot shows potential matings ranked according to the average genome uniqueness of the parents, weighted according to their reproductive value.

The genome uniqueness (symbol: GU) of an individual with respect to a current population of which it is part is the probability that it contains founder alleles not present in any other single (normally) individual in that current population. Informally, if an individual is the only one carrying a particular founders genes, then you'd likely want to breed from that individual so as not to lose those genes from the population forever. So, it might be considered desirable to be able to prioritize matings involving parents with higher GU than others.

Another factor that can be helpful to take into account is the reproductive value of the parents. E.g. if there are two potential dams with the same GU, but one is older than the other, then - and ignoring any other factors - it may be desirable to give a greater priority to breeding from the older dam first, to lessen the risk that its genes are lost for good. And yet calculations based on pure GU do not take this into account.

In order to allow for such considerations to contribute to the mating selection, the software can use the reproductive value for each individual in conjunction with the ranking factors (average parental GU in this case). The reproductive value varies from 0 to 1 where 0 means the individual is entirely unreproductive and 1 means 'fully reproductive'. Thus an older individual might have a lower reproductive value.

In the following screenshot the prospective matings have been ranked according to the average GU of the parents, but weighted according to reproductive values. E.g. the first 3 results all involve parents both of which have 100% GU. But the reproductive values of the dams (in this case) differ. The matings involving dams with lower reproductive value are ranked higher.

A demonstration of this feature can be found in the 'Mate Selection, Kinship And Population Analysis' tutorial included with the product.

Figure: Prospective Matings Ranked By Gene Diversity Metrics

Setting Reproductive Values

Reproductive values can be set in 2 ways.

One way is to define default reproductive values using the Extended Edition preference settings. These defaults are set by age and sex. Which means, in practice, you need to have the date of birth recorded for each individual in the breeding pool. E.g. you might define that up to age 5 years, say, females have reproductive value 1.0, then moving to 0.5 for age 5-8 years, then 0.2 for 8 years and older. Etc.

Alternatively you can optionally assign one of the user defined fields to hold the reproductive value. If you do this, any value stored in this field in the individual's record will override the default. This allows reproductive values to be customized for certain individuals, if that's appropriate to your situation.

Note that there is an option to entirely exclude prospective matings where either parent has a reproductive value of zero (i.e, entirely unavailable for breeding). In a real world situation there is little benefit to ranking such matings because they cannot actually happen. This option was disabled when the above screenshot was produced, which is why you see dams with zero reproductive value in the ranking list. Normally you would wish to remove these.

© 1996-2024 Tenset Technologies Ltd.
"Tenset", "PedPro", "GedWiz", "Breeders Assistant" and "Pedigree Assistant" are registered trademarks of Tenset Technologies Ltd in the United Kingdom. Microsoft and Windows are registered trademarks of Microsoft Corporation in the U.S. and/or other countries. Apple, Mac and Macintosh are trademarks of Apple Inc., registered in the U.S. and other countries.