Diversity coefficient

Comparison of genetic profiles – determination of inbreeding/diversity coefficient – selection of optimum breeding pair

Diversity or inbreeding coefficient = a number that shows the genetic similarity of the given breeding pair. The smaller the number, the greater is the difference between the male and the female. The coefficient can be determined for dogs and cats from their DNA profiles.

At present, by testing genetic profiles the breeder gains a lot of benefits. Besides the possibility to determine the paternity and the clear identification of an individual it is also possible to use the genetic profile for selection of a breeding pair. The inbreeding coefficient is determined by comparing the variability of genetic profiles of the chosen individuals and according to this the breeder can choose the most suitable breeding pair from the genetic point of view.

Obviously, the selection of an optimum breeding animal is based on many factors. The most important are the breeding standard, health, temperament, working abilities, appearance or coat colour and length....

However, today the breeder can choose from a great variety of top individuals of a given breed from all over the world. How to decide between two or more selected breeding animals?

Just this comparison of genetic profiles of a breeding female and of some potential partners or of a breeding male and several potential females can make the choice of the correct partner easier. For ideal crossing it is suitable to choose genetically most variable individuals who will keep the highest level of genetic diversity of the offsprings.

Thanks to the specialized breeding of individual canine and feline breeds the genetic variability (heterozygozity) of many breeds has been substantially reduced. The reduced genetic variability of the given breed often results in occurrence of genetic diseases and reduced number of healthy young animals in a litter. In general, the risk of occurrence of genetic diseases reduces with higher genetic diversity in the breed population. Therefore the current breeding practices are focused on keeping or gradual increasing the genetic variability of the given breed.

The genetic profiles of the potential breeding pair can be compared by calculation of so-called inbreeding coefficient of the given pair. The inbreeding coefficient of an ideal breeding pair is as low as possible – such a pair produces most probably a litter with high level of genetic variability.

Genomia laboratory determines the genetic profiles of individuals according to ISAG.


Overview of canine DNA-profiles and chromosomes tested

In dogs, 22 markers with high informative power localized on many key chromosomes are analysed. The inbreeding coefficient is calculated from 21 markers (Amelogenin has no informative power for the coefficient calculation; it only determines the sex of the animal).

Marker Chromozom Marker Chromozom
INRA21 21 REN54P11 18
AHT137 11 INU030 12
REN169D01 14 Amelogenin X
AHTh260 16 AHT121 13
AHTk253 23 FH2054 12
INU005 33 REN162C04 7
REN169O18 29 AHTh171 6
INU055 10 REN247M23 15
FH2848 2 AHTH130 36
AHTk211 26 REN105L03 11
CXX279 22 REN64E19 34


Example of the inbreeding coefficient calculation for a canine breeding pair

F = a genetic profile of a female dog we are looking an ideal partner for; the genetic variability of the breeding pair shall be as high as possible, i.e. the inbreeding coefficient shall be as low as possible

P1 = genetic profile of the first potential partner

P2 = genetic profile of the second potential partner

Marker Value (F) Value (P1) Value (P2)
[INRA21] 97/99 97/99 97/97
[AHT137] 133/133 133/149 137/149
[REN169D01] 202/216 210/212 202/216
[AHTh260] 246/250 246/250 244/252
[AHTk253] 286/286 286/286 288/290
[INU005] 110/126 110/126 110/126
[REN169O18] 160/160 162/162 160/166
[INU055] 210/210 210/210 210/210
[FH2848] 234/242 238/238 240/244
[AHTk211] 89/97 89/95 89/89
[CXX279] 120/128 118/124 120/126
[INU030] 150/150 150/150 144/150
[Amelogenin] X/X X/Y X/X
[REN54P11] 226/226 232/232 232/232
[AHT121] 92/94 92/92 92/102
[FH2054] 156/160 152/152 156/156
[REN162C04] 202/204 202/204 204/204
[AHTh171] 225/235 221/235 221/235
[REN247M23] 268/268 268/268 268/270
[AHTH130] 127/129 127/129 129/133
[REN105L03] 231/235 235/235 235/235
[REN64E19] 145/153 145/153 145/155

Calculation of the inbreeding coefficients of potential canine breeding pairs:

Marker F versus P1 F versus P2
[INRA21] 0,5 0,5
[AHT137] 0,5 0
[REN169D01] 0 0,5
[AHTh260] 0,5 0
[AHTk253] 1 0
[INU005] 0,5 0,5
[REN169O18] 0 0,5
[INU055] 1 1
[FH2848] 0 0
[AHTk211] 0,25 0,5
[CXX279] 0 0,25
[INU030] 1 0,5
[Amelogenin] - -
[REN54P11] 0 0
[AHT121] 0,5 0,25
[FH2054] 0 0,5
[REN162C04] 0,5 0,5
[AHTh171] 0,5 0,25
[REN247M23] 1 0,5
[AHTH130] 0,5 0,25
[REN105L03] 0,5 0,5
[REN64E19] 0,5 0,25
Diversity coefficient 9 7,25

The table shows individual inbreeding coefficients at 21 determined markers of a female genetic profile and of two potential partners. If the values at a given marker differ between the female and the male, so the inbreeding coefficient is 0. If the value of inbreeding coefficient is 0.25, it means that there is 25% probability that the offspring will be homozygous with regard to this marker. If the inbreeding coefficient equals 0.5, the probability of the homozygosity at this marker is 50%. If the inbreeding coefficient equals 1, so the homozygosity of the offspring at this marker is 100%. The total inbreeding coefficient is a sum of the individual coefficients at all markers. The maximum value is 21 and the minimum value is 0. The lower the value of the inbreeding coefficient is the better.

In the above example, we would choose the partner no. 2 from the two potential breeding mates, whose inbreeding coefficient equals 7.25 on contrary to the partner no. 2 whose total inbreeding coefficient after comparing with the female is 9.

The diversity of the individual markers differs among various breeds and depends on the genetic basis of the given breed.