Here is the link to the presentation given by Dr Andy Dell & Libby Henson launching SPARKS for the Highland Pony Society and an update on how the information will be available, in the future, via Grassroots.
Q&A
See responses to questions raised after the seminar:
1. Where a Sire or Dam have common parentage how far back in the pedigree would you need to go before it would no longer be considered inbreeding? Or is it always inbreeding no matter how far back?And how will this affect Line breeding? Many breeders follow particular lines.
Where does line breeding stop and when does it become inbreeding – probably at about second cousin level i.e. 0.0625 We have set the SPARKS red line at 0.10 or 10% for the Highland Pony – i.e. quite a lot higher than 6.25%. Line breeding was what fixed the breed type, but eventually it can have negative effects by the accumulation of homozygosity and an increasing probability of deleterious traits manifesting themselves which outweigh the phenotypic benefits of continued linebreeding/inbreeding. Deleterious alleles can be purged under random mating but that is atypical of breeding practice in the highland pony.
2. Is there anything for stallion owners to look at see what there stallion are good with without searching all mares etc
The tables can be produced this way but are not available and would be very large documents and unwieldy to work with - this functionality maybe available via Grassroots when the SPARKS module is launched.
3. There are some matings that show as red but when I look at the pedigree there are not common ancestors in the recent pedigree. What else comes into the "red" calculation and how far back in a pedigree will result in a red?
The algorithm sums all repeats on both sides of a pedigree right back to the start of the electronic data – that could easily be 12 or more generations back - and maybe not visible in the 4 generations available in a Grassroots view of a pedigree.
4. What if my pony is "Red"
If foals are red that is not a problem – just more important that if they go on to breed themselves to try to avoid future red matings – i.e. break the chain. There will be green matings for animals that themselves were red matings. Foals that are the product of a red mating are not inferior or any less valuable than those of a green mating - remember - this is no reflection on the quality of the pony itself or the result of "irresponsible breeding"- this is an assessment of the ponies genetic make up in the context of the overall breed.
The below sections give an overview of the aims of SPARKS and guidance that should be used when viewing SPARKS data sheets.
Data sheets for your own mare can be requested by emailing
SPARKS PROJECT OVERVIEW
THE AIMS AND SUCCESS OF THE PROJECT
Maximizing the retentions of genetic diversity across the whole population
The avoidance of mixing of rare and more common alleles
A sustainable reduction of the rate of increase in inbreeding
Increase in Effective Population Size (assessed from rate of increase in inbreeding)
By adopting these strategies, we hope to prevent the loss of genetic diversity and increasing levels of inbreeding that are becoming apparent in the HIGHLAND Pony population. This in turn should help avoid future problems brought about by increasing homozygosity and manifestation of deleterious alleles such as increasing infertility, foal mortality, osteochondritis dissecans (OCD)) and other genetically linked phenomena.
PopRep analysis shows that inbreeding in the HIGHLAND Pony population is accumulating at a rate that is detrimental for the long-term survival of the breed (Fig. 1). Without control there will be continued loss of genetic diversity and an increasing probability that deleterious alleles will manifest themselves.
This problem is common in other endangered equine breeds but can be managed with breeder cooperation and the use of breeding advice such as that provided by the SPARKS data sheets.
The SPARKS breeder’s guidance scheme has now run for 18 years with the Cleveland Bay Horse Society. Over the period of the scheme there has been a significant and sustained decrease in the rate of increase in inbreeding (Fig 2) and an increase in Effective Population Size.
Figure 1:Average inbreeding in the HIGHLAND Pony 1900 to 2020(Source PopRep)
Figure 2:Average inbreeding in the Cleveland Bay Horse 1900 to 2020
MEAN KINSHIP OF PROGENY
The use of datasheets with other equine breeds has highlighted the subtle difference between Mean Kinship of parents and Co-ancestry Coefficient of progeny. Until new animals are registered and entered onto the system we cannot calculate their Mean Kinship or Kinship Band. This highlights the importance of prompt registration of pure-bred foals. Owners are advised to follow the above guidelines in making breeding choices, as they continue to be the most robust and scientifically validated method of ensuring the genetic wellbeing of the HIGHLAND Pony population.
ANOMALIES
If when studying the datasheets for your mares you recognize information that is not or might not be correct, please let the Society know. The programme can only be as good as the data it contains, so please let us know if, for example, mares with identical breeding do not have identical datasheets.
NB The data provided in this set of sheets is highly filtered from the SPARKS database and should not be taken as a true representation of the current HIGHLAND Pony population. As such it is not suitable for research purposes.
Andy Dell. Endmoor. April 2024
2024 GUIDANCE NOTES ON THE USE OF SPARKS KINSHIP TABLES
Please read the Guidance Notes. Individual mare data sheets can be requested for your own mare by emailing
1. INTRODUCTION
The Highland Pony Society (‘the Society’) is adopting SPARKS to raise awareness and address inbreeding in the Highland Pony population. This is needed because inbreeding leads to loss of genetic diversity in the population. In turn, this threatens the health of individual horses and the health and sustainability of the breed as a whole, because it has the following consequences:
· Increased infertility
· Increased foal mortality (deaths)
· Increased likelihood of harmful genes accumulating in the breed
· Increases risk of inherited diseases and deformities
· Reduced overall fitness of the breed and resistance to diseases
A powerful way of doing this is by managing ‘Mean Kinship’ through selection of mare/stallion pairings.
2. WHAT IS SPARKS?
SPARKS is an advisory scheme that helps manage Mean Kinship and inbreeding. It is a computer programme that calculates Mean Kinships for every living pure-bred Highland Pony on the Highland Pony Grassroots Database, measuring how related any one pony is to all others. SPARKS also calculates the potential inbreeding of foals resulting from specific mare/stallion pairings. Based on this analysis, SPARKS produces Kinship Tables for mares.
3. WHAT ARE KINSHIP TABLES?
The Kinship Tables are a tool to help breeders manage Mean Kinship and inbreeding via their decisions on which stallions to put to which mares.
There is a Kinship Table for every living pure bred Highland Pony mare of up to 20 years old, as recorded on Grassroots (individual sheets for older mares that are still breeding can be provided on request).
Note:
· Each Kinship Table is specific to a named mare
· Each Table has more than one page
· Each page gives the mare’s name, date of birth, registration number and Mean Kinship Coefficient
· Based on the Mean Kinship Coefficient, the mare is assigned to a Mean Kinship Band
· Mares in Band A are of lowest Mean Kinship, i.e. are least related to the rest of the population; those in Band H are the most related
The mare information also gives the mare’s Inbreeding Coefficient. This is a measure of how related an individual animal is to itself through common ancestors that appear on both sides of its pedigree, whether in recent or distant generations.
Each Kinship Table includes a list of pure-bred, licenced Highland Pony stallions in the UK.
Stallions have been included in the data tables using the following criteria:
· Stallions whose owners responded to survey
· Stallions who have sired foals in 2019-2023 and are identified on Grassroots as alive & entire
· Stallions born 2019 onwards
For each stallion, there is information on their kinship figures and band, location. Where a stallion owner has confirmed that a stallion may be available for public stud or AI, this is denoted by “Contact Owner”.
4. HOW ARE KINSHIP TABLES USED?
The Kinship Tables give the ‘Co-ancestry Coefficient of Progeny’ for each stallion/mare pairing. This is the level of inbreeding that the resulting foal would have. The lower this coefficient, the less inbred the foal would be.
The Kinship Tables are on the Society’s website for download free of charge.
Using SPARKS is voluntary and intended to help mare owners to select a stallion. The Tables do not relate to the physical attributes of any mares, stallions or potential foals. Breeders should continue to use their own best judgement on this. The Tables are an additional tool to add genetic health to dam/sire pairing decisions.
To help interpretation of the Kinship Tables, the potential matings between mares and stallions are ranked into four Tiers. Tier 1 represents the genetic pairings that are encouraged while Tier 4 matings are those that should be avoided because of potential impact on the genetic health of the whole population.
It should be noted that the “tiering” is an assessment of the merit of pairing of two animals and is not an endorsement or criticism of the genetic makeup or quality of either of the individuals.
The Tiers are “traffic light” colour coded as follows:
TIER 1: The mare and stallion are from the same or an adjacent Kinship Band AND the mating would produce a foal of lower co-ancestry coefficient than the Mean Kinship of the Mare. These matings are said to be ‘SPARKS compliant’ and are coloured green in the Kinship Tables. THESE MATINGS ARE ENCOURAGED
TIER 2: The mare and stallion are from the same or an adjacent Kinship Band BUT the mating would result in a foal of higher co-ancestry coefficient than the Mean Kinship of the mare but still less than 0.1. These matings represent ‘The Best of the Rest’ and are coloured yellow in the Kinship Tables. THESE MATINGS ARE THE PREFERRED ALTERNATIVE IF A SPARKS COMPLIANT OR ‘GREEN’ MATING DOES NOT EXIST OR IS NOT DESIRABLE.
TIER 3: The mare and stallion are from widely differing Kinship Bands and Kinship Coefficients less than 0.1. These matings bring together genes in a way that puts less common genes at greater risk of loss. They are coloured orange in the Kinship Tables and ARE DISCOURAGED.
TIER 4: These matings, coloured red in the Kinship Tables, are highly inbred (resultant foal with a coefficient of 0.1 or above) and increase the probability of deleterious genes / harmful traits being expressed in future generations as well as accelerating the loss of genetic diversity. THESE MATINGS SHOULD BE AVOIDED.
Please note:
· The traffic light colours are shown on the names of the stallions, but do not represent the level of inbreeding of the stallions themselves. They represent the level of inbreeding that the foal would have if the stallion was mated with the named mare.
· The RED traffic light colour is highlighted on the Co-Ancestry Coefficient of Progeny figure as well as on the stallion’s name. This is to help distinguish between orange and red matings, given that the two colours may look similar on some computer screens.
5. IMPORTANT NOTES ON USING THE KINSHIP TABLES
Kinship Tables are valid for one year only because the Highland Pony population, and therefore the kinship relationships within it, change each year. Tables are therefore only valid for the year shown at the top of each sheet.
New tables are produced each year.
6. CORRECTIONS AND ANOMALIES
The information in the Kinship Tables is only as good as the information in the Society’s Database (Grassroots), so the more up to date we can get Grassroots, the better the SPARKS data will be. Therefore, if you see a pony registered to you, in the Kinship Tables, that has died or identify a stallion who has been gelded, please follow the guidelines on the Society website regarding notification of Death of a Pony and Transfer to Gelding. Likewise, if you see information that is not or might not be correct about any pony, please let the office know.
7. CONTACT DETAILS AND HELP
Mrs S Keron, Secretary
Garbh Allt House
Maidenplain Place
Aberuthven
Perthshire PH3 1 EL
Tel: 01764 664000
www.highlandponysociety.com
NB The data provided in this set of sheets is highly filtered from the SPARKS database and should not be taken as a true representation of the current HIGHLAND Pony population. As such it is not suitable for research purposes.
