Coefficient of Inbreeding
We are now in the 21st Century with an educated population able to utilise modern science and technology, it is on this basis that this article has been written. We need to construct policies and proper breeding strategies in order that Exmoor Ponies survive into the next millennium. This can only be done with a general understanding of Modern Animal Breeding based upon the science of Genetics, which may be defined as "the science which seeks to account for the resemblences and differences exhibited among organisms related by descent"(12).
A specific study was carried out at the Roslin Institute in 1999 on the Exmoor Pony Breed (13). Now a computer programme exists which can print out not only the pedigree and progeny of every individual pony but has also the capacity to carry out some sixteen separate analyses all useful to the practical breeder.
The terms utilised in animal production, effective population size (Ne), true-breeding, cross-breeding, homozygous, heterozygous and inbreeding degeneration have been defined and discussed at length elsewhere. (3, 3a, 4, 11, 12)
True-breeding preserves the breed and the strains within that breed, and involves a high degree of "inbreeding". Inbreeding is the mating of related individuals. Not only is this necessary to maintain the purity of the strain but the very basis for cross-breeding production is destroyed as soon as the original breeds or strains cease to exist.
The statement, “It is generally accepted in the field of animal breeding that populations where animals are highly inbred are likely to produce problems” (1), reflects the fears often expressed about inbreeding which are based upon human mating taboos and complex proscriptions that arise from social and religious reasons rather than genetic ones. The view of modern animal breeding states “As a system, inbreeding arouses a great deal of anxiety in the lay person and some practical breeders. Inbreeding does not create defects, but, because many defects tend to be recessive in nature, the mating of close relations increases the chance of such deleterious genes coming together and giving rise to abnormal progeny. Undesirable though this may be it is not a major disaster. – Those who become emotionally involved in such issues must realise that all stock carry defects and there is currently no way they can all be eliminated without ceasing to breed altogether”(19).
Inbreeding degeneration may be observed after continued inbreeding, and is caused by the increasing homozygosity of deleterious genes, such genes are generally recessives. The degree of this problem depends upon the skill of the stockman in his selections, and the abundance of undesired genes in the stock with which he begins.
Articles actually published by the EPS advocated “he could get the box to score his mares against all the stallions and the lowest numbers would give him a selection to choose from. If any had a score of zero, they would be the best choice, but if not, he could go for any with really low numbers.” (7) This "Out-breeding" is the crossing of animals within the same breed but as distantly related as possible. It is the last resort of those whose choice of parental stock was poor and whose selection of offspring has been faulty.
A computer programme was written for the EPS designed to find the relationships between ponies. This was actually used to find the stallion least related to a potential brood mare. It was not understood or appreciated that using this as a breeding strategy within three to four generations all animals would be equally closely related allowing for no genetic leverage.
Among other articles published by EPS members, it is clear that there has been much confused thinking about genetic advice “important if herd owners wish to breed true to a specific line. Inbreeding will inevitable be higher than using a different bloodline, so it can be crucial to know which colt would produce the lowest level of inbreeding in the offspring.” (1) The author did not understand that to “breed true” is to inbreed. Also there has been the mistaken idea that "Linebreeding" is different from inbreeding. “When this linebreeding is carried out for a long time, sometimes it involves too much inbreeding. – Linebred stallions sometimes end up mating with their aunts, sisters, even mothers and daughters.” (7), By definition linebreeding is a form of inbreeding directed toward offspring being closely related to one ancestor. It is the most intensive form of inbreeding, being equalled by full brother/sister matings in the early generations, and becoming more extreme in later generations. (8, 9, 10, 12)
The Coefficient of Inbreeding (F) expresses the degree of relationship between an individuals parents, and is the probability that two genes at any locus on a chromosome are identical by descent. The relationship expressed in the coefficient is a comparison between the population examined and an implied base population, which by definition has a Coefficient of Inbreeding of zero.
Without this point of reference calculations are meaningless. (8, 18)
All ponies alive on a given date are regarded as Founder Stock, regardless of their inter-relationships, that is they are treated as 'wild' with parentage unknown in order to "level the playing field". It must be ensured that the sires of foals carried by in-foal mares on that date are included as Founders. All Founder Stock must by definition have a Coefficient of Inbreeding of zero.
The EPS Stud Book was closed on the 2nd May 1962, we could use this date as the base for zero Inbreeding Coefficient. Objections to this date are:-
1. It would give only three to four generations to compute the Coefficient
of Inbreeding to the present. Realistically this is insufficient.
2. Many well known ponies which survived the losses during the Second
World War would be excluded.
Careful perusal of the Stud Book (15) indicates that if we use a date post branding in 1949, say 1st January 1950`, we solve the above objections since only 17 progeny of unregistered parents were registered between 1948 and 1962. These were mainly non-breeders, and the descendants of only five registered between these dates survive at present. Special provision can be made for demographic calculations regarding their descendants. We thus define Founder Date as 1st January 1950.
It will probably be argued that earlier records of pedigrees should be included. It does not follow that an animal was better because it was registered, unidentified and unregistered progeny survived and prospered as well. We cannot assume a foal was "less good" because the parents names were not written down.
The early Stud Book records are of historical rather than genetic value. We must be more concerned about recent Exmoor Pony Breeding and not confuse the present by seeking insignificant relationships from the past.
The Inbreeding Coefficient may be expressed as a percentage, F=12%, or as a fraction of one, F=0.12. It is constant throughout an individual animal’s life. (8, 16) It should not be confused with the Rate of Inbreeding (dF), this is usually calculated on a herd basis and relates to the change in Inbreeding Coefficients of animals within a herd from generation to generation, again this can be expressed as a percentage or a fraction. e.g. dF=6% or dF=0.06. The Rate of Inbreeding is the increase of the coefficient of inbreeding in one generation. (8, 16)
Inbreeding should be regarded as the process that converts genetic variation within a random population into differences between groups of that population by making each strain breed true for chosen characteristics. We should endeavour to keep the different Exmoor types by managing them within inbred lines, ideally in separate herds.
With continued inbreeding, every new generation becomes more homozygous, and the population breaks up into a number of lines, the individuals within each line becoming progressively more similar genetically. It preserves the breed and the strains within that breed, and involves a high degree of inbreeding.
Stock which is homozygous for a genetic character breeds true for that character, and as homozygosiyy increases then animals become more prepotent, that is it is more likely to pass on characteristics to their offspring than average parents.
Recent genetic studies (2, 17) have shown that wild species of garden birds can have coefficients of inbreeding in excess of 10%. In certain strains of laboratory mice F% may be in excess of 99%. By the mid-1950’s the poultry industry was producing F2 hybrids from four highly inbred strains with F% in excess of 95%. These figures should help to allay the fears of the less informed among pony breeders. “The level of inbreeding where problems occur depends upon the species and the population being studied. Some populations can withstand high levels of inbreeding with no apparent ill effects.” (19)
Establishment of Coefficients of Inbreeding:
Using ASCII file information, which agrees completely with EPS records, from our Studbook © programme written in Mallard Basic and the algorithm written in Fortran by Sneha Maroo (13, 20) we can now evaluate the coefficients of inbreeding of all ponies born since Founder Date. Results can be summarised as follows:-
F% Males Females
0 745 953
1 – 5 344 409
6 – 10 218 300
11 – 15 160 205
16 – 20 83 113
21 – 25 64 92
26 – 30 25 36
31 – 35 21 37
36 – 40 10 13
41 – 99 5 10
The highest recorded is an F of 56%, a female born in 1998, 243/12, Feline. The herd with the greatest number of high F% is Herd 23, this is clearly due to the continued use of the stallion Golden Gorse 23/69.
However within the EPS there is the belief that “Once values rise over 25% the negative effects begin to emerge and after about 40% in some cases lines can die out altogether.”(1) The evidence shows that this is certainly not the case.
We now know from the results of blood protein and DNA analysis (5) that Exmoor heterozygosity is extremely high in spite of relatively close inbreeding. This condition is well known in quantitative genetics and is the consequence of a phenomenon called overdominance.
Overdominance is the result of selection favouring heterozygotes. A constant balance is created by the heterozygote having a greater fitness than either homozygote. No matter how little the heterozygote is superior to both homozygotes, the equilibrium point is at an intermediate gene frequency.
A feature of this stability is that the actual gene frequency depends not on the degree of superiority of the heterozygote but of the relative disadvantage of one homozygote over the other.
There has been uneasiness expressed about inbreeding, this fear is groundless. In non-inbred populations, statistically, not more than 50% of the population can be heterozygous for a particular pair of alleles. In an inbred herd, genes that are overdominant, are at intermediate frequencies and thus contribute more variation than genes at low frequencies. This is an important factor in maintaining genetic variation within a population. In addition genetic variation in the breed is the result of not only segregation of single loci but also segments of chromosomes. These segments can show overdominance even though separate loci do not. This overdominance with respect to fitness probably accounts for much of the stable polymorphism found in natural populations.
“Inbreeding does not, on average, change gene frequency; the effect of the decrease in heterozygosity is simply to relocate genes from heterozygosity to homozygosiyy.”(14)
The most important practical result of overdominance is its utilisation by inbreeding a population. The occasional crossing of the resultant inbred strains in later generations is a better means of maintaining heterosis than even rigorous selection without inbreeding. In effect most Exmoor ponies have bred by this method.
Computer software now in existence can store information on registered progeny, failures, and coefficients of inbreeding in such a way that a studbook entry would contain:
Number Name Sex Sire Dam Born Live M F R F%
100 B F P Q 1990 L 3 3 0 2
101 C F R S 1990 L 3 3 0 25
102 D M T U 1990 L 8 8 4 10
103 E M V W 1990 L 7 8 5 25
104 F M Y Z 1990 L 7 7 6 37
Pony Number: Each pony has an unique studbook number based upon the present branding system and its sex.
Name: As in present studbook.
Sex: F = female, M = male
Sire / Dam: Studbook numbers for sire and dam.
Year Born: As in present studbook.
Dead / Live: D = dead, L = live.
Foals Born: M = registered males, F = registered females, R = rejected at inspection.
F% : represents Coefficient of Inbreeding, a high F% represents greater prepotency, i.e. the ability to pass on characteristics.
99, 100, 101 are brood mares, each has had 6 progeny. Which mare would you wish? Clearly 99 has had most progeny rejected. 100 and 101 appear the same but 101 will have the greater prepotency to pass to her offspring.
102, 103, 104 are stallions, each has sired 20 progeny. 102 has had least progeny rejected but has the lowest prepotency. 104 has more rejects but the greatest prepotency. Which of the three stallions would you choose?
References:
1. BAKER, S. Survival of the Fittest. 1993.
Exmoor Books.
2. CHESSER, R. K. et al. Effective Sizes for Subdivided Populations.
Genetics 135: 1993. pp.1221-1232.
3. COPLAND, A. N. 1999. Exmoor Pony Breeding
Dartmoor Diary. Dartmoor Pony Society.
3a. COPLAND, A. N. 1999. Exmoor Biometrics
Dartmoor Diary. Dartmoor Pony Society
4. COPLAND, A. N. 2000. Breeding Strategies.
http://users.quista.net/epic. Epicentre Issue 3.
5. COTHRAN, E. G. 1994 - 2000. Personal Communications
Department of Veterinary Science. University of Kentucky.
6. EXMOOR PONY SOCIETY. 1992. Stud Book 4th. Ed.
7. EXMOOR PONY SOCIETY. 1994. The Great Debate. E.P.S. Newsletter
8. FALCONER, D.S. 1960. Introduction to Quantative Genetics.
Oliver & Boyd. Edinburgh.
9. HILL, W.G. 1994. Personal Communications.
Institute of Cell Animal and Population Biology. University of Edinburgh.
10. INSTITUTE OF ANIMAL GENETICS. 1957. Notes for Courses.
Oliver & Boyd. Edinburgh.
11. JONES, W.E. & BOGART, R. 1973. Genetics of the Horse.
Caballus Publishers. U.S.A.
12. LUSH, J.L. 1945. Animal Breeding Plans.
Iowa State College Press. U.S.A.
13. MAROO, SNEHA. 1999. A Genetic Analysis of the Exmoor Pony Population.
MSc. Thesis. University of Edinburgh
14. NICHOLAS, F. W. 1996. Introduction to Veterinary Genetics
Oxford University Press.
15. STEVENSON, M. 1994. Personal Communication, Computer Time to Optimise
Base Zero for Coefficients of Inbreeding on Sparks Programme
Royal Zoological Society of Scotland. Corstorphin, Edinburgh.
16. SUZUKI, D.T., et al. 1986. An Introduction to Genetic Analysis.
W.H. Freeman & Co. New York.
17. THORNHILL, N. W. 1993. The Natural History of Inbreeding and Outbreeding. University of Chicago Press.
18. WILLIAMS, J. 1994. Personal Communications.
Department of Immunogenetics. Roslin Institute. Edinburgh.
19. WILLIS, Malcom B. 1998. Dalton’s Introduction to Practical Animal Breeding.
Blackwell Scientific.
20. WOOLLIAMS, J. 2000. Personal Communications
Department of Quantitative Genetics. Roslin Institute. Edinburgh.
26 February 2001
A.N.Copland, P. Dean, and A. Downing.