Tuesday, August 11, 2020

Inbreeding and Genomics

Photo from the Equine Science Review

Inbreeding has played a key role in the improvement of livestock breeds, resulting in more uniform populations with highly specialized performance traits. Selection for desirable traits entails identifying individuals with superior performance and often mating them to relatives (inbreeding) who possess the same superior traits. The goal of this practice is to increase the frequency of the desired characteristics and thus of the beneficial genes in the offspring. At the same time, negative consequences of inbreeding are well known. In small populations such as captive bred species, the loss of diversity associated with inbreeding is a major concern, and significant losses of diversity may lead to extinction. The increased expression of recessive deleterious genotypes can also lead to embryonic loss or other defects, some of which can be fatal. Furthermore, inbreeding can lead to a phenomenon called inbreeding depression.
Inbreeding depression is commonly manifest in poor performance of traits that are complex (due to contributions of many different genes), such as fertility and athleticism. Mindful of the dangers inherent with inbreeding, breeders traditionally balance the benefits and dangers of inbreeding by monitoring their breeding stock, culling poor performers and avoiding matings of closely related individuals.
Recently, genetic tools have become available that provide an alternative approach to unambiguously quantify and manage inbreeding relative to the traditional use of pedigrees. Today, a genomic survey of a horse’s DNA may cost $70 to $180. A comprehensive whole genome sequence, including analyses, may cost $1,000 to $2,500. So far, over 1,000 horses have had their entire DNA sequenced in connection with research projects. Those genome sequences have been used to identify the genetic bases of diseases, coat colors and even some performance traits. Nevertheless, the overall performance of horses is complex, involving over 20,000 genes and probably millions of other functional elements. Studying genes one at a time is unlikely to be effective to significantly improve performance. Genomic tools, however, make it possible to identify associations between the genome and traits that contribute to success or which may cause problems.
One of the areas in which genomics excels is in determining levels of inbreeding. An animal’s inbreeding coefficient is the likelihood that both parents transmitted the same piece of DNA to their offspring that they each inherited from a common ancestor. Traditionally, we measured inbreeding by identifying all common ancestors – those that appear in the paternal and maternal sides of an individual’s pedigree. After common ancestors are identified, the relationship between the parents of the individual in question can be calculated. Using this method, on average, pedigree-based inbreeding coefficients for Thoroughbred horses are reported to be between 12.5%-13.5%, however individual horses may have values that range from less than 5% to over 20%. When genomic measures have been made in other species, geneticists discovered that inbreeding levels calculated from pedigrees are poorly correlated (50%-80%) with genomic measures of inbreeding. This is not surprising since pedigrees inaccurately assume a random and equal transmission of genes each generation.
Which variant of each gene is inherited, however, is not predictable. For example, full-siblings share, on average, 50% of their genes; however, at any particular part of the genome they may share 0, 50 or 100%. Further, genes are not randomly distributed in a breed since selection practices are applied in mating horses. If we are good breeders, the genetic constitution of our current generation is not a random representation of the ancestors, but rather, a selection of the genes contributing to their success.
There are other ways to apply genomics to horse breeding. As noted above, both the genome and the traits we value are complex. Our genomic tools are powerful, and we can begin to seek genetic patterns correlated with measures valued by horse owners. The limitation for such studies is the quality and availability of data for traits related to fertility, conformation, durability and athleticism. Collecting these data and using genomics to identify genes associated with these complex traits would be a more sensible way to improve performance rather than simply seeking to limit inbreeding.

Ernest Bailey, PhD, professor, and Ted Kalbfleisch, PhD, associate professor, both in the Department of Veterinary Science at the Gluck Equine Research Center, and Jessica Peterson, PHD, University of Nebraska-Lincoln, provided this information. Source: January 2020 Equine Disease Quarterly.
The Equine Disease Quarterly is published in January, April, July, and October each year by the Department of Veterinary Science. It is funded by Underwriters at Lloyd’s, London. Material published in the Equine Disease Quarterly is not subject to copyright. Permission is therefore granted to reproduce articles, although acknowledgement of the source and author is requested. 
This article appeared in the Equine Science Review, a new monthly newsletter from the University of Kentucky College of Agriculture, Food and Environment.

Saturday, August 8, 2020

USEA: Top 10 Tips for Handling Babies

When does a professional start halter training a foal? What about weaning, or trailering?

The US Eventing Association's new article recognizes that, "From the moment they hit the ground to the day they take their first steps under saddle, everything you do with your young horse is setting them up for success in their future career." The article, "Top 10 Tips for Handling Babies" is written with Sue Clarke, who is the stable manager at Stonehall Farm in Virginia. Her tips for setting youngsters up for success are gleaned from many years' experience managing a breeding operation with many young horses.

Click here to read the Top Ten Tips.


Thursday, August 6, 2020

USEA: Producing a Young Horse

For a humane and extremely successful approach to starting young horses, check out the USEA podcast Producing a Young Horse, with guests Lauren (Kieffer) Nicholson and Max Corcoran, hosted by Nicole Brown. Since Lauren and Max have been involved with all aspects of producing young horses, the topics range from breeding and the initial evaluation of a young horse to the under saddle work and beginning competition.

Lauren Nicholson works for David and Karen O'Connor, and "has spent the last 15 years bringing hundreds of horses along in their barn and for Jacqueline Mars’ program which breeds and produces horses from the ground up." Max Corcoran, now president of the US Eventing Association, "also spent over a decade on the O'Connor Eventing Team grooming and working with the young horses." The O'Connor team has been known for decades for their dedication to starting young horses using low-stress, humane methods.

Early on in the podcast, Lauren made some very interesting comments about what she looks for in a young horse. Knowing she's looking for a horse with the potential to become a 5* eventer, what is her top priority for selection? Conformation? Precocious jumping ability? Nope. Her top priority is trainability. Tune in to the podcast to hear her reasons - and listen also for Lauren's deep understanding of how young horses think. Her decisions and advice are rooted in that, which explains her success over many years.

This podcast is worth a listen by anyone involved with horses, especially youngsters.

Click here to listen to "Producing a Young Horse."

Tuesday, August 4, 2020

UK Launches New Equine Research and Outreach Newsletter

The Equine Science Review gives horse owners, members of the equine industry and the general public the opportunity to learn more about the cutting-edge equine research going on at UK.

July 29, 2020 | By: Holly Wiemers

Lexington, Ky., - The University of Kentucky Ag Equine Programs has launched a new monthly newsletter, the Equine Science Review, highlighting UK equine research and outreach efforts.

The free newsletter comes out mid-month from the UK College of Agriculture, Food and Environment, which is home to world-class research and service excellence in equine health, safety, nutrition, pasture and forages, economics, engineering, environmental compliance and many other areas of interest. Programs at UK offer the depth and breadth of scope that is fitting of its location in the heart of horse country.
“Reporting completed projects and exciting new knowledge is obviously important, but the Equine Science Review also enables new ideas and 'work-in-progress' stories to be shared,” said James MacLeod, UK Ag Equine Programs director and faculty member in the Gluck Equine Research Center. “Awareness of efforts at these earlier stages also has value, providing information on new and innovative approaches being used by students and faculty to address critical challenges. We might not have the answer yet, but such stories convey reasons for the equine world to look to the future with hope.”
The July issue of the Equine Science Review can be read via Issuu at https://issuu.com/ukagequineprograms/docs/equine_science_review_july2020_final or as a downloadable PDF at https://equine.ca.uky.edu/content/july-2020-equine-science-review. Contents in the July issue include a story about promising developments in the quest to prevent catastrophic racehorse injuries through an mRNA study; a look at equine markets during the COVID-19 pandemic; an exciting report regarding an absence of any equine lepto abortion cases at the UK Veterinary Diagnostic Lab for first time in 30 years, which is likely linked to use of a new vaccine; pasture renovation information; advice about whether or not rained hay is any good and much more.
“I am very pleased to see the successful launch of the Equine Science Review,” said David Horohov, chair of the Department of Veterinary Science, director and Jes E. and Clementine M. Schlaikjer Endowed Chair and professor in the Gluck Center. “The ESR provides an excellent opportunity for faculty and staff in our college to reach out to our equine stakeholders, both professionals and horse enthusiasts, and inform them of our important work.”
Subscribe to the publication at https://mailchi.mp/uky/equinesciencereview. Past issues can be found at https://equine.ca.uky.edu/equinesciencereview.
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We will be reprinting some of the UK articles in this news and info blog, selecting ones of interest to breeders.

Saturday, August 1, 2020

World Breeding News August Posted


A new issue of World Breeding News has been posted, with news of interest to breeders around the world.

Its centerpiece is the final installment of Celia Clarke's three-part series on the breeding industry. This series looked at sport horse breeding in the past, present - and in this article the future. Where is the sport horse breeding industry headed? What are the challenges? Where will we be in 5, 10, 15 years? Celia Clarke asked for responses from six experts from six different countries. The United States can be proud of being represented by Jos Mottershead in this discussion, whose knowledge and experience are deep, and whose opinions are informed and outspoken. Jos and Kathy St. Martin own Equine-Reproduction.com and Avalon Equine.

All in all a very interesting issue, with features on breeders and breeding the truly span the world. Check out the current issue here.

Subscribe to WBNSH

theHorse.com: Small-Scale Success: Responsible Boutique Horse Breeders

theHorse.com posted an article late in 2019 on small, boutique horse breeders. I'm not sure what they considered to be "small," but I'm guessing most sport horse breeders probably fit into that category.

One of the two breeders featured is Tricia Veley of First Flight Farm in Boerne, Texas, a breeder of dressage and hunter/jumper prospects. Breeding ten to twelve mares a year, First Flight Farm is probably a little larger than the median for sport horse breeders.

This is a sympathetic look at what the life of a small breeder is like, with practical issues addressed by the featured breeders.

Check out the article from theHorse.com