Genetic Conditions and Responsible Reactions to Them

Other breeds of horses and ponies have genetic issues which they have addressed.  These have been mentioned in prior blogs.

HYPP    -    Quarter Horses and derivatives from the 'Impressive' line

HERDA -     Appaloosa and derivatives from Poco Bueno

SCID
CA        -      Arabs
Lavender Foal

OLWS     -    mainly Paints and Pintos

FIS        -      Fell and Dales ponies

Friesian Horses - Multiple issues

However horse breeders are not alone in dealing with such issues; all other species have their own problems. It is how these problems are dealt with by the 'custodians' of the breed/s which separates the 'men from the boys'.

Open acknowledgement that a problem exists is the first requirement.

Informed decision making is the second.

Acting upon the informed decision made, is the third.

The following post and illustration is about Dairy Cattle.  For those who take the time to read this you will find it very informative and helpful as it is very relevant to the HWSS issue.  

LIC (short for Livestock Improvement Corporation) is an international artificial breeding company which supplies and trades frozen bull semen throughout the world.  They are an industry leader in the area of genetic research in dairy cattle.

LIC is a player in the dairy industry in Ireland supplying semen and expertise to farmers in this country.  This small calf syndrome 'problem' will be present in Ireland.  

"The average herd of 400 cows could expect to have 60 cows which are carriers.  If this herd was mated to a cross-section of Holstein Friesian bulls in New Zealand, LIC expects one to two calves would result. 

Putting this into perspective, since the 1960's a quarter of one percent (0.25%) of calves bred from Holstein Friesian or crossbred type animals each season are likely to have been affected by the Small Calf Syndrome."

Present research would suggest that in some countries, HWSS has a similar if not higher level of carriers, in the population as a direct result of the overuse of certain sires, to the level seen for small calf syndrome in Holstein-Freisian cattle and their cross-breds.

 LIC discovers small calf gene : the full text for the graphic below.

General News Updates

Those readers of the blog who also follow the HWSS Facebook page will already know that last month the number of hits on the blog reached 20,000 - this total has been reached in 19 months of operation.  As of right now the hits are 20,570.  There has been big upsurge in traffic, especially from Ireland.  As the number of hits from Ireland does not even register in the top ten source countries, which is deemed to indicate a low internet presence, this increase in traffic may be in part due to the following:

 DoneDeal advertisement

To whomsoever paid for and listed this advertisement the Irish Connemara Pony breeders should be grateful. From the perspective of the global community the significance of the HWSS issue does not seem to be understood in the heartland of Connemara pony breeding.  

It is a proven fact that continuing to ignore the existence of a genetic disease will do far more harm to the sales market than accepting that there is indeed a problem and doing something positive about it.  This has been proven in the past in the case of both HYPP and HERDA.

Linked to the incidence of  the expression of genetic disease in any population is the level of inbreeding in that population.    Deirdre Feely in her 2003 paper Characterisation of the Connemara Pony Population in Ireland states the following - the highlights are those of this blog editor:

"Following the analysis, it appears that the Connemara Pony breed is being confronted with two problems. Firstly, the survival of the traditional type of breed is under threat, and secondly, the genetic diversity of the breed is diminishing.

Today, the riding industry is an important outlet for Connemara Ponies. However, there is concern that this industry is instigating a shift from the traditional type of pony, to a taller, ‘modern’ type. The traditional type of Connemara Pony is perfectly adapted to the environment in which it developed and is completely distinct from other equine breeds. It may be necessary to safeguard against market forces inciting the disappearance of the traditional type of pony, which is a valuable national resource, and once lost can never be recovered.

The results generated from the characterisation of the Connemara Pony population indicate that past breeding practices have caused a significant loss in the breeds’ genetic diversity. To ensure that the genetic variation in the breed does not recede to a detrimental level, breeding policies need to be altered.

In future, it is vital that sire family sizes become more balanced, giving all stallions a better opportunity to breed their own replacements in the next generation. This would help to control the level of inbreeding and genetic diversity within the population.

The stallions used for breeding are closely related to each other and tend to be of similar ancestry or breeding lines. From a genetic diversity perspective it may be advantageous to have a pool of breeding stallions that are less related to each other to bestow a variety of genes to the proceeding generations.

As relationships among animals in the present population is high the mating of related animals is inevitable. Breeders must be very vigilant in respect to the stallions that they use for breeding to ensure that a minimal amount of inbreeding is practised.

There are 16 different countries, outside Ireland, that have formed their own Breeders’ Societies and maintain their own stud books. A study is presently being undertaken to characterise the Connemara Pony populations in a number of these countries. It is hoped that these animals may be a source of genetic variability that could be used to widen the gene pool of the Irish Connemara Pony population.

Adequate genetic diversity is vital for the long term health and viability of any population. Thus, it is vital that breeding practices are altered in order to secure the future prosperity of the Connemara Pony breed.'

Sadly this advice does not appear to have been taken on board by the majority of the ruling elite within the pony breeding community worldwide, not just in Ireland.  

Analysis of the genetics of the Connemara pony in all of the countries where the ponies are bred is presently underway.  If the issue of  over used bloodlines and stallions is not addressed then we can expect to see the incidence of new emerging genetic disorders to rise.   

HWSS is potentially the 'canary in the mine' - an indicator of what is to come for the breed if fundamental changes are not made now, about the selection of breeding stock to reduce the level of in-breeding.  Over use of popular or fashionable stallions is the leading cause in-breeding and subsequent population decline.  

There has to be a shift in outlook from just breeding the next generation, to looking as to what will happen in three to five generations, if this breed is to survive in a healthy state for future pony owners and breeders to enjoy.

The results of this work to date can be read on the new website Connemara Pony Genetics International  Comments and questions on the presented papers is encouraged and contributions for publication are invited.

Another new site has also recently been started Connemara Pony Breeders/Producers of Ireland, Chat & Debate where hopefully discussions of importance will not be censored as has happened in the past on other sites.

Thought for the day

"Entrenched belief is never altered by the facts".   

So true, so true; strongly held beliefs, however nonfactual they may be, rarely (if ever) are changed as the result of being exposed to the facts.  It is human nature to cling to what one believes in, for to challenge such beliefs can cause psychological harm in susceptible individuals.  

Sometimes it is considered more expedient to just accept what one is told, without challenging the status quo or the teller/s of the tale.  After all challenging one's beliefs requires introspection into many facets of the life one leads and that is way too scary for many people.

There is now much mis-information being spread 'out there' over the HWSS research.  Where people or organisations have a history of  distributing mis-information, do not expect them to be truthful in what they tell you with regards to their involvement in and support for the HWSS research project.  It was to be expected but still regretable; anything which challenges groups or individuals which exposes them to the risk of having their authority undermined, invariably results in shooting the messenger/s whilst at the same time trying to gain control over the message being delivered.  

To re-iterate once again the Connemara Pony Research Group is made up from a group of individuals who have been working together for just over one year now to get the scientific evidence to support:

1. That there is a developmental problem in the hooves of some Connemara ponies, and,
2. that this condition has a genetic cause
3. Both of these points have now been incontrovertibly proven. As regular readers of this blog will be aware the laboratory is now awaiting the data analysis from the further series of arrays which have narrowed down the area of the genome, that needs to be studied in greater detail.

The Connemara Pony Research Group is not aligned with any breed society in anyway.  The research has been independently funded by donations sent directly to the Centre for Equine Health at the University of California (Davis) by many groups and individuals.  The research at the Bannasch Laboratory (UC Davis)  has received support, both moral and financial, from societies in North America and Northern Ireland only and the group publically acknowledges our thanks to them.

Interestingly enough, when the blog author went to attribute "Entrenched belief is never altered by the facts" researches failed to find an historical context in which this was used.   Perusal of various hard copy books of quotations to no avail and thence having to resort to google (and the ubiquitous wikipedia) linked this homily only to the authorship of one Dick Francis in his novel 'Straight'.  One has to wonder from whence he learnt this very salient truth, or whether he came to this conclusion himself  and just used it as a one-liner in his book.  Either way, the truth revealed by this statement is real.

For any of the blog readers 'out there' who are not acquainted with the novels of Dick Francis then dip your toes in the water.  Rip snorting good yarns based loosely around National Hunt Racing in the UK.  Of course they are formulaeic and I swear the heroes must all have 'superman' embroidered on their underpants as they always succeed in righting wrongs against terrible odds, but they are good reads.

Wish to know more about HWSS? Book a presentation.

The research on HWSS has more depth to it than what is shown in this blog.  Only the basics have been put on the internet because the internet is not a secure medium.  Anyone can lift  files off the net and use these for what ever they choose; although unlikely people with an 'agenda' could be tempted to use such information to their own advantage and not for the greater good which is the aim of this research group.

Jocelyn Garneau-Davies was invited to a meeting of the American Connemara Pony Society to talk about HWSS which happened on Friday 13.  For this meeting the group put together a Power Point Presentation with a much greater degree of information.   The people present at the meeting found that the information which they saw greatly helped them in their understanding of the whole HWSS issue. 

The group has repesentatives in most countries.  If your Breed Society, farrier/podiatry or equine group is interested in hosting such a presentation then email us.   Translations still have to be made into other languages, so please do not try and book a presentation for 'next week' :)

The results from the Genome Wide Association Study

This morning the results from the GWAS arrived in the inbox of the Connemara Pony Research Group; much earlier than was expected.  The reason they came in early is because there is no questioning the results. There is no doubt that the DNA of affected ponies and their close relations (parents, full or half siblings) is very different from both  the 'control' Connemara ponies and the Horse Genome Map.

This area of difference is call a 'candidate region'.  The candidate region which has been determined by the GWAS is in the area where the genes for keratin metabolism have been mapped.

Keratin metabolism controls how hoof, hair and horn grows in all mammals.

We now know definitely that there is something different happening in the genes of  HWSS affected ponies.   The area where this difference occurs supports the working hypothesis for HWSS.

Where to now?

The next stage requires the candidate region of all the 'positive' ponies in the GWAS to be investigated at a more refined level.  We now know where to look and now need to look much more closely to find out what is actually happening in the genes in the candidate region.
To conduct this research, of course requires more funding.  The Centre for Equine Health already holds the balance of the donated funds, not used to pay for the initial GWAS.
With this money already in-hand, the next stage of the research requires another US$8000.    The research group and the Bannasch Laboratory are hopeful that people will support this next stage of the research by making donations to pay for the sequencing of  the candidate genes.

You can make your donations here http://www.vetmed.ucdavis.edu/ceh/give_online.cfm

Bannasch Laboratory also wishes to let pony owners worldwide know that they now want more samples from HWSS affected ponies and control ponies.  The first point of contact for pony owners who wish to become actively involved in this research by submitting blood samples to the laboratory is the Connemara Pony Research Group       connemara.pony.research.group@gmail.com

Preliminary Results on the Genome Wide Association Study, for HWSS in the Connemara Pony

The official word from the Bannasch Laboratory at UC Davis is that the first results from the study are expected to be available in the first week of February 2012.

We have come a long way in a very short space of time.
The acceptance that HWSS is a distinct hoof condition has increasing support from equine professionals worldwide.  Input from farriers especially has been superb; these people are the ones who have been dealing with the problem at the 'coal-face'.   These professionals are themselves relieved that  others in their profession worldwide have been challenged by such an intractable hoof problem.  Reports have now come in informing the research group that a very similar hoof condition is noted as occurring with another minority native breed.

However to be successful in obtaining a diagnostic screening test for HWSS requires that Stage Two of the project can flow seamlessly from the results of Stage One.   Stage Two still requires more funds to make this happen.   The link to the donation page is here. http://connemara-pony.blogspot.com/2011/11/how-to-make-donation-to-support-hwss.html

Further information is also coming to the research group from owners and breeders around the world about their own experiences with attempting to treat the hooves of HWSS afflicted ponies.   The aim is to get a list posted on the blog of what people have found helps in keeping their ponies as sound as possible.

A 'don't try this it made things worse/made no difference and cost mega-bucks' scenarios will be included.  Owners can then make up their own minds as to what may just help for ponies in their situation.

How to Make a Donation to Support HWSS Research

Readers of this blog will already know that the Bannasch Laboratory at UC Davis has already commenced the SNP arrays to find the genetic mutation which causes HWSS.     This is but the first stage in the process required to develop a diagnostic test for HWSS.

The array has for the most part, been financed from private donations.  There has been a small funding grant received but this was not as much money as what had already been received from donors.   To carry on with the second stage of the research a further $US5000 is needed.
The research group has had many requests asking what is the best method to donate funds.
The Centre for Equine Health (which the Bannasch Laboratory is part of) has the giving page.



One of the research group members tried the system out, and it works.
UC Davis donation page

On the above page you will see a link to a secure page.  Follow this link and you will see the following:

You need to specify where the money is to go:

CONNEMARA DNA RESEARCH

and the person who is to be notified that a donation has been made:
DR CARRIE FINNO


The information above needs goes in the boxes on the far left of this screen (sorry cannot put arrows in to show you where).
The long thin field is where the Connemara DNA Research Fund goes.
The smaller box below: Dr Carrie Finno.















If credit card transfers are not your preferred method to make a donation  then you can send a cheque to the Center for Equine Health, One Shields Ave, Davis, Ca 95616. 
Send a letter accompanying the cheque stating that the donation should be directed to Connemara DNA research.


THANK YOU.

Exciting Exciting NEWS. SNP Arrays to commence

Today I have received confirmation that there has been sufficient donations received by the Centre for Equine Health (UC Davis) (CEH) combined with a small grant, that the first stage of the Genome Wide Association Study (GWAS) is ready to start at the Bannasch Laboratory.
This is such exciting news that we have progressed so far, so quickly.
From the researchers at Bannasch Lab I received this today:

"We are still interested in donations for the 2nd stage of the project (either SNP genotyping additional samples or sequencing a candidate gene/region).
I am waiting on 9 more unaffected distantly related control samples to come in this week and then we plan to send out the DNA. We should have the results before the holidays and some preliminary information by the end of the year."

The next stage of the project requires $5000.

The research group has no idea who has donated money via CEH for this work to commence so promptly, but we thank you from the bottom of our collective hearts.

For those of you who wish to know more and to understand what is about to happen


The whole process involves looking for areas on a gene (or genes) which are different from what the reference genotype shows.   There are breed differences so that it why the genome of non-related ponies are needed to compare the genes of the affected ponies too.  In other words there can be specific genes which are not on the reference (library copy) of the horse genome, but which are in fact totally normal in another breed.

Because we already know what the problem is at a functional level, then the genes influencing lipid metabolism in hoof (keratin) structure is a an area for possible candidate gene(s) or a region within one of the keratin coding genes.