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Inbreeding Study By Sydney Uni. Student

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Gay3 View Drop Down
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    Posted: 22 Apr 2018 at 4:52pm
https://www.nature.com/articles/s41598-018-24663-x

Founder-specific inbreeding depression affects racing performance in Thoroughbred horses


Abstract

The Thoroughbred horse has played an important role in both sporting and economic aspects of society since the establishment of the breed in the 1700s. The extensive pedigree and phenotypic information available for the Thoroughbred horse population provides a unique opportunity to examine the effects of 300 years of selective breeding on genetic load. By analysing the relationship between inbreeding and racing performance of 135,572 individuals, we found that selective breeding has not efficiently alleviated the Australian Thoroughbred population of its genetic load. However, we found evidence for purging in the population that might have improved racing performance over time. Over 80% of inbreeding in the contemporary population is accounted for by a small number of ancestors from the foundation of the breed. Inbreeding to these ancestors has variable effects on fitness, demonstrating that an understanding of the distribution of genetic load is important in improving the phenotypic value of a population in the future. Our findings hold value not only for Thoroughbred and other domestic breeds, but also for small and endangered populations where such comprehensive information is not available.

Introduction

The Thoroughbred horse population is one of the largest closed populations of animals in the world. Thoroughbreds are extremely valuable because of the large amount of prizemoney on offer and the high residual value of superior athletes. All Thoroughbred horses trace their ancestry back to three paternal lines, due to the narrow bottleneck at the foundation of the population1,2,3. More than 300 years of breeding practices have produced signatures of selection in the 21st century Thoroughbred population, contributing to the superior athleticism of the breed4,5. At the same time, these practices have increased levels of inbreeding and reduced the genetic diversity of Thoroughbreds compared with other domestic horse breeds3,6,7.

To our knowledge, there has been no detailed examination of the effects of inbreeding on the racing performance of Thoroughbred horses and the genetic load of the population. Genetic load, the presence of unfavourable genetic material, is a reflection of a population’s fitness because a higher genetic load leads to a lower mean fitness level8. A large proportion of genetic load consists of recessive deleterious mutations, known as mutational load. Inbreeding can expose mutational load because it increases an individual’s chance of inheriting two copies of recessive deleterious alleles from a common ancestor8,9. The subsequent decrease in fitness caused by these expressed recessive deleterious mutations is thought to be a major cause of inbreeding depression10. Other mechanisms believed to contribute to inbreeding depression include epistatic interactions and reductions in favourable heterozygosity10,11.

The inevitable effect of selection in a closed population is an increase in the level of inbreeding12,13. There is some evidence that continued inbreeding for selection can purge a population of some or all of its genetic load, such that new inbreeding events have negligible or even positive effects on phenotype9. Although some domestic and wild populations show signs of purging14,15,16, others still show strong signs of inbreeding depression even after multiple population bottlenecks and inbreeding events17,18,19. Purging is most likely to occur in populations under strong selection and slow rates of inbreeding, allowing deleterious alleles to be effectively eliminated rather than fixed by genetic drift11,20. Additionally, inbreeding for favourable phenotypic characteristics can have unexpected negative implications through deleterious alleles hitchhiking on regions of the genome under positive selection, thereby increasing their frequency in the population21,22,23.

Understanding the effects of selection is further complicated by the uneven distribution of genetic load in a population. Inbreeding to different ancestors can have varying effects on fitness, such that the total proportion of alleles identical by descent (IBD) might not be an accurate reflection of mutational load24,25,26. This raises the possibility that inbreeding in different pedigree lines has variable effects on genetic load in the Thoroughbred population.

The availability of extensive phenotypic and pedigree records, dating back to the late 18th century, makes the Thoroughbred population ideal for studying the long-term, population-wide effects of selection on performance and genetic load. Here, we examine the effects of inbreeding on racing performance and mutational load in the Australian Thoroughbred population. Australia has the second-largest racing and breeding population in the world, containing approximately 15% of all Thoroughbreds27.

We analyse a sample of 135,572 individuals, representing all Thoroughbred horses that had one or more race starts in Australia between 2000 and 2011. A genealogy of these individuals, dating back to the founders of the population (n = 257,249), is also included in our analyses. Although some lines of pedigree are incomplete, we have comprehensive pedigree information for all individuals in the racing performance data set, making our inbreeding estimates highly accurate. The availability of extensive pedigree records not only allows us to study broad population trends over time, but also to determine whether the selection for optimal racing performance has alleviated mutational load. We use these data to measure inbreeding and ancestral coefficients for all individuals. We also identify the ancestors that have made the greatest genetic contributions, in order to understand better the distribution of mutational load in the population. For a representative subset of individuals, we perform high-density genotyping to determine whether inbreeding load is reflected at the genomic level.

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brogers View Drop Down
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Post Options Post Options   Thanks (1) Thanks(1)   Quote brogers Quote  Post ReplyReply Direct Link To This Post Posted: 25 Apr 2018 at 2:18am
I'd written a summary of what I thought were the more interesting findings of the paper.....

https://www.performancegenetics.com/single-post/2018/04/24/How-inbreeeding-affects-racing-performance-in-Thoroughbreds
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Post Options Post Options   Thanks (0) Thanks(0)   Quote Gay3 Quote  Post ReplyReply Direct Link To This Post Posted: 25 Apr 2018 at 7:52am
Many thanks for summarising as I wouldn't otherwise have read it LOL & looking forward to the results of your 'next step' suggestion Thumbs Up
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Post Options Post Options   Thanks (1) Thanks(1)   Quote diomed Quote  Post ReplyReply Direct Link To This Post Posted: 26 Apr 2018 at 2:22pm
Many thanks for that summary. 
I was in a fog reading the original.
One good thing is they took a large data sample.
I was not too happy with some of their selections.

"we have comprehensive pedigree information for all individuals in the racing performance data set, making our inbreeding estimates highly accurate. " 
..... they are assuming a lot here.  Other (DNA) research points out major errors in pedigree recording.

"These included two measures that are based on the assumption that more successful individuals earn more prizemoney: cumulative prizemoney earnings and prizemoney earnings per start." 
.... again an experienced racegoer might quibble with this. 
More prizemoney might also come from a longer career from a lesser horse.
Better individuals will be rushed to stud. 
Prizemoney per start is also tricky - a Derby winner will be retired to stud, and an unbeaten horse retired early (Epsom Derby almost never run as 4-y-o, Winx and Black Caviar exceptions).
I would prefer ratings to money won.  In my work I used 160,000 ratings, the best 3-y-o or older rating achieved.

"We also included two measures of constitutional soundness: total number of race starts and career length. Finally, we accounted for consistency of performance with the measure winning strike rate."
.... again poor horses run more races and more years.
A winning strike rate can also be dodgy. 
A horse that ran once and won has 100%, a horse that ran 110 times and won 20 has "only" a 20% win rate.

What saves the study imo is the large data sample as it would even out the oddities.

I have written programs to produce 12 generation pedigrees, only 8,190 ancestors.
To count the number of times Herod appears in my mare I think I need a pedigree that goes to 26 generations or more - 26 generations is 134,217,726 ancestors.
It could probably be done with a two step process - do a 12 gen pedigree for each of the 4,096 ancestors in her 12th gen and count the Herod there.

I think a study like that needs to be tested.
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Post Options Post Options   Thanks (0) Thanks(0)   Quote furious Quote  Post ReplyReply Direct Link To This Post Posted: 26 Apr 2018 at 3:13pm
To be truthful could depend on prevalent sireline in that period of time.  Given a different time frame the result might reverse.  Just guessing here but that is the way I read things.  Every 30 years or so a new line emerges to take over the top mantle.  Then some female lines recede for a period of time as that line doesn't cross well etc.  With all the crossing to Northern Dancer that would of certainly pushed up the percentage rate for whatever his extended pedigree carries.
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Post Options Post Options   Thanks (1) Thanks(1)   Quote brogers Quote  Post ReplyReply Direct Link To This Post Posted: 27 Apr 2018 at 12:54am
I was going to raise similar in my post.

If they are looking at horses that raced between 2001 and 2011 they were born between 1995 and 2005 (roughly). What occurred during that period

1) The number of stallions in Australia reduced significantly in that time period. It went from over 100 to closer to 800. 

2) An inbred stallion (Danehill) and his sons were serving a high proportion of the commerical broodmare population. Every farm in Australia it seemed at that time either got a hold of a local son of Danehill or brought one in from Europe. 


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Post Options Post Options   Thanks (0) Thanks(0)   Quote diomed Quote  Post ReplyReply Direct Link To This Post Posted: 27 Apr 2018 at 4:38pm
sorry about the type font above. Embarrassed
Although I questioned the results (without any evidence) I think it is great that people are working on pedigrees.
kincsem
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