A Horse of a Different Hue: The Suffolk Horse 1880-2022, Part 2: Epigenetics

Introduction

Figure 1.0 in Part 1 of this series of articles gave a basic definition of the term Phenotype ‘specially for equines’:  here’s a reminder.:

Recall that also that the phenotype ‘is determined by its genotype, which is the set of genes the organism carries, as well as by environmental influences upon these genes…..”  www.nature.com/scitable/definition/phenotype-phenotypes-   35/               

 and

‘Some traits are largely determined by the genotype, while other traits are largely determined by environmental factors.’     https://www.genome.gov/genetics-glossary/Phenotype

The significant phrase here is “…. while other traits are largely determined by environmental factors.’  Another term for this is – Epigenetics 

A useful definition from http://epialliance.org.au/what-is-epigenetics/

Part 2 of A Horse of a Different Hue sets out to explore what  Epigenetics means for the future of  Suffolk Horse.

Appendix 1 gives a small glossary of terms used.   

A little more background to the Definition of Epigenetics

“The term ‘epi-‘ is derived from the Greek prefix meaning upon, on, over, or beside.   

Epigenetics looks at the extra layer of instructions that lie over or on top of DNA that control the way genes are expressed.   All cells in the body contain the same genetic code.   Yet each of these cells have different structures and functions.   A heart cell, for example, is very different from a nerve cell. Epigenetics seeks to understand how this happens.

“It explores how certain chemical tags attached to different parts of DNA and its associated proteins can activate or silence genes. Such chemical changes are known as epigenetic modifications. This process does not alter the underlying genetic code. Instead it controls which genes are turned on or off in individual cells which determines the specific structure and function of the cell. Epigenetic modifications also help explain differences found between identical twins that share the same genetic code.

“The epigenetics mechanism plays an important role in the normal development of the cell and maintaining the body’s equilibrium or homeostasis. Any disturbance of the epigenetic process can have major adverse health and behavioural consequences. This can be affected by internal imbalances within the body itself and wider environmental and lifestyle factors.

“Most epigenetic changes only occur during the lifetime of the individual organism. Such modifications, however, can have long-term effects and be passed on to offspring and subsequent generations.

(Added emphasis using italics by suffolkpunchaustralia.com) https://www.whatisbiotechnology.org/index.php/science/summary/epigenetics

The Implications of Epigenetics for owners and breeders

The questions are no longer:

Is it Nature or Nurture?         Is it Inherent or Acquired?

because the answer is  now:                It’s both.

And as epigenetic research demonstrates, moderation, or a combination of moderations, can ‘switch on’ quiescent genes in the mare and/or stallion which “will be passed on to offspring and subsequent generations”.

 In the article, Epigenetic control of exercise adaptations in the equine athlete: current evidence and future directions, mention is made of epigenetic effects over four generations.

” … Therefore, epigenetic inheritance, including intragenerational¹ and trans-generational² inheritance, underscores the notion that individual phenotype modifications could at least partly result from the environmental effects on founder generations during key developmental stages of germline cells  (Skinner, 2011; Nilsson et al., 2018; Skinner et al., 2018).

1. 1. 1. 1.  change occurring within an individual’s life time                                                 
         2. having an effect on several generations of a family.

See also:  https://en.wikipedia.org/wiki/Transgenerational_epigenetic_inheritance

 Points to bear in mind:

Epigenetic modifications occur from gametes, embryos, the developing foal in the uterus, during foaling, in the neonate, life with its dam, and post weaning. Then throughout all stages of life, in both male and female.

When a young Licensed stallion covers his first mare (and hopefully achieves a successful mating), his genetic and epigenetic inheritance combines with that of the mare in their resultant progeny.

Because epigenetic changes take place through their lives, any subsequent same mating of mare and stallion, will not have identical genetic and epigenetic outcomes.    This is visible with the phenotype, but invisible to the human eye with the  epigenome.   

If a Stallion subsequently becomes an Elite Sire (aka Popular Sire)¹, then  they would be producing several progeny per season.   

 1. See:  Table 1:  Ten Popular Sires with Total Numbers of Progeny in Section;  Genetic Bottlenecks and onwards (published July 2017):  https://suffolkpunchaustralia.com/the-suffolk-punch-draught-horse/the-clock-is-ticking-part-1  

Figure 2.2.0 above shows a theoretical  transgeneration epigenetic inheritance over four generations from 1989 to 2011 on the male side.    This equals 22 years.   But of course the 4th generation Progeny, a Sire, would still be alive and breeding, as might be his Sire foaled in 2006.     If one factors in the Mares, it is 1988 to 2011, 23 years.

And at each generation, there might be the emergence of a new transgenerational epigenetic inheritance.     For any one 4th generation progeny, it has involved 14 other horses.    In the example above, in any one year, that is 7 mares, but the stallions have have contributed to another five or six or more half siblings to the one featured above in Figure 2.2.0

In such a tiny breeding population of the UK Suffolks, the numbers speak for themselves.   

See: suffolkpunchaustralia.com/nine-articles-on-the-status-of-the-suffolk-horse/where-are-we-now-may-2021-part-3-remedial-action-needed-now/

Equine Assisted Reproductive Therapies and Epigenetics

Emerging research is showing that perhaps the lower rate of successful pregnancies relating to AI, is not just to do with the sperm.   An Editorial in the Equine Veterinary Journal in 2021, stated:

‘Nevertheless ARTs are not a panacea for fertility problems and can create issues of their own, not least because in vitro manipulation may introduce epigenetic changes with initially imperceptible, but potential life-long effects of the health of the offspring.”

How small the Effective Population Size  is in any breed, (and for the Suffolk Horse it has continued to be very small),  becomes even more important in considering the continued use of long-term frozen semen, collected many years ago.

(See Figure 2 which compares the Effective Population Size of the three native UK Draught Horses :  suffolkpunchaustralia.com/nine-articles-on-the-status-of-the-suffolk-horse/where-are-we-now-may-2021-part-1-between-a-rock-and-a-hard-place/ ) 

Epigenetic and genetic considerations of long term frozen semen.

Colony Edward 8781 was first Licensed in 1995.  His semen was collected in 2000, and 2003 his death was recorded.  As of April 2022, his legacy has been the production of 45 progeny, throughout 27 years.    

Or of an Elite Sire who has already contributed appreciably to the present gene pool of the UK Suffolks, and will possibly continue to contribute through the next four years.

The Editorial  goes one to say:

”  … the need for ongoing research to optimise results also applies to more hand-off breeding systems, such as intensively managed natural mating programmes, since there is still much that we do not understand about common fertility-limited conditions, such as persistent post-mating endometritis, declining endometrium and oocyte quality in older mares and other factors that predispose to fertilisation failure or early pregnancy loss.”

http://Equine Vet J. 2021:53:1084-1087

A closer look at the frozen semen available from The Suffolk Horse Society in 2022

Table 2.1 is derived from the Suffolk Horse Society’s latest magazine announcement of  an updated list of stallions’ frozen semen for Artificial Insemination  of Suffolk mares is available. NB. this is for domestic use only, and subject to the category ‘Green’ on SPARKS.   (Issue 107, Spring 2022,  p.17).

It may prove helpful to review Table 8.1 Eight Elite Sires Licensed & Listed for 2021 Breeding Season, Plus Eight unproven Stallions Showing Years on Stallion List, under the Section heading:  The significance of individual timespans for Elite Licensed Stallions.    (NB: Table 2.1 has been updated from  Table 8.2 Frozen semen available 2021.  See:  https://suffolkpunchaustralia.com/nine-articles-on-the-status-of-the-suffolk-horse/where-are-we-now-may-2021-part-2-more-rocks-difficult-terrain )

Table 2.2. below, re-tabulates the information above in  Table 2.1, to emphasis, once again,

• • • the potential loss of diversity by the repeated use of Elite Sires, 
    • the inter-relatedness of the first five who, between them have produced 221 progeny from the total of 284 progeny,

Golden Grandchild 8810 (foaled 1994)  and Sire of 68 progeny, is the Grand Sire of Besthorpe Achilles 8961 (foaled 2005) and Great Grand Sire of Colony Eli (foaled 2018).   Besthorpe Achilles is also the Grand Sire of Colony Eli on the maternal line.    Golden Grandchild is also the Grand Sire of Tinglestone Cyclone James (foaled 2015, Licensed 2017).   Readers with access to the e-Stud Book of the Suffolk Horse Society may wish to  explore further  these Elite Sires ancestry and inter-relatedness.

Some important questions for the Uk Suffolk Horse Society

As at 9th April 2022, the UK Rare Breeds Survival Trust, is still only showing seven separate Suffolk Horse frozen semen collections as reported in February 2022 – an increase of four collections to add to only three collections since 2017.  (see: https://suffolkpunchaustralia.com/nine-articles-on-the-status-of-the-suffolk-horse/where-are-we-now-february-2022/)

1. 1. How many of the 15 named Sires’ collected frozen semen in Table 2.1 are  with the RBST Gene Bank?
   2. If not already in process to donate more, why the delay?
   3. If there are no plans to donate more, how does this comply with:

‘The Suffolk Horse Society defines its Objectives in its report to the Charities Commission, and usually includes the same material in the Preface to its yearly Stud Books:

The Society identifies two major areas:

• • • maintaining the purity of the breed and
    • maintaining a genetic reservoir of the breed, that adheres to the DEFRA conservation strategy’

(from:  https://suffolkpunchaustralia.com/clock-ticking-part-2/)

Why is epigenetic modification important for the UK Suffolk Horse Population?

With such a limited gene pool in the UK’s tiny population of Suffolk Horses, any increases overall of ‘negative’ transgeneration epigenetic inheritance (and/or epigenetic modifications), may:

• • • • • • • • interfere with attempts to increase population size, 
              •  affect overall and ongoing health, 
              • facilitate the changing Phenotype.   

As increasingly wider research in both humans and animals is showing, epigenetics may have profound effects on the genome and phenotype.

In the French article Gametes, Embryos, and Their Epigenome: Considerations for Equine Embryo Technologies, 2016, the authors state clearly their points:

• • • • • • • • Major epigenetic programming occurs during gametogenesis and embryonic development.
              • Epigenetic marks can be modified by the maternal or paternal environment.
              • Reproductive technologies are known to affect epigenetic marks.
              • The memory of these events can lead to long-term effects in offspring.

“The preconceptional and/or periconceptional periods (before and just after fertilisation until the embryo blastocyst stage) are critical for the developmental origins of health and disease. Major epigenetic modifications occur during gametogenesis, fertilisation, and the early stages of embryonic development. These modifications can be altered by the environment in vivo, particularly through maternal and/or paternal nutrition, but also in vitro, including during procedures such as assisted reproduction.

“Female gametes, but also male, are involved as targets of the epigenetic modifications and also as vectors of modified epigenetic marks, leading to long-term effects on the offspring. Physiological and epigenetic effects observed vary depending on fetal gender. Although this review focuses on new developments in epigenomics in the horse, most of the mechanism information was derived from mice, men, and cattle.

Indeed, although the long-term impact of equine embryo technologies is yet to be evaluated, data from other species already indicate that the nutritional status of both gamete donors and of the recipient mare should not be overlooked.

“Finally, as opposed to most other domestic species, and closer to the situation in humans, older horses are used for reproduction, and this may also affect the quality of gametes and subsequently offspring to be born.”  (Emphasis added using italics by suffolkpunchaustralia.com)

Not surprisingly, research in epigenetics for humans and animals has expanded dramatically over the past few years, with the human research showing implications which are often applicable to animals.   

The   race horse industry investing large sums in actively pursuing several lines of enquiry.

“Domestication has changed the natural evolutionary trajectory of horses by favouring the reproduction of a limited number of animals showing traits of interest. Reduced breeding stocks hampered the elimination of deleterious variants by means of negative selection, ultimately inflating mutational loads. However, ancient genomics revealed that mutational loads remained steady during most of the domestication history until a sudden burst took place some 250 years ago.

To identify the factors underlying this trajectory, we gather an extensive dataset consisting of 175 modern and 153 ancient genomes previously published, and carry out the most comprehensive characterisation of deleterious mutations in horses.

We confirm that deleterious variants segregated at low frequencies during the last 3500 years, and only spread and incremented their occurrence in the homozygous state during modern times, owing to inbreeding.

This independently happened in multiple breeds, following both the development of closed studs and purebred lines, and the deprecation of horsepower in the 20th century, which brought many draft breeds close to extinction. Our work illustrates the paradoxical effect of some conservation and improvement programs, which reduced the overall genomic fitness and viability.”

Origin and Evolution of Deleterious Mutations in Horses Ludovic Orlando & Pablo Librado, Genes (Basel). 2019 Sep; 10(9): 649.   Published online 2019 Aug 28. doi: 10.3390/genes10090649

Does epigenetic diversity have a positive role to play?

Yes.   And although nothing to do with equines or mammals, a 2020 paper, published by the Annals of Botany Plants (AoBP) by Medrano, Alonso & Herrera: unambiguously  states at the beginning of the paper 

“Genetic diversity defines the evolutionary potential of a species, yet mounting evidence suggests that epigenetic diversity could also contribute to adaptation.   Elucidating the complex interplay between genetic and epigenetic variation in wild populations remains a challenger for evolutionary biologists and the intriguing possibility that epigenetic diversity could compensate for the loss of genetic diversity is one aspect that remains basically unexplored in wild plants. 

The Journal of Evolutionary Biology‘s recently published article, The Adaptive Value of Epigenetic Mutation:  Limited in large but high in small peripheral populations (December 2019), reports:

The fate of populations during range expansions, invasions and environmental changes is largely influenced by their ability to adapt to peripheral habitats. Recent models demonstrate that stable epigenetic modifications of gene expression that occur more frequently than genetic mutations can both help and hinder adaptation in panmictic ¹ populations.

However, these models do not consider interactions between epimutations  and evolutionary forces in peripheral populations. Here, we use mainland-island mathematical models and simulations to explore how the faster rate of epigenetic mutation compared to genetic mutations interacts with migration, selection and genetic drift to affect adaptation in peripheral populations. Our model focuses on cases where epigenetic marks are stably inherited.

In a large peripheral population, where the effect of genetic drift is negligible, our analyses suggest that epimutations with random fitness impacts that occur at rates as high as 10^-3 increase local adaptation when migration is strong enough to overwhelm divergent selection.

When migration is weak relative to selection and epimutations with random fitness impacts decrease adaptation, we find epigenetic modifications must be highly adaptively biased to enhance adaptation.

Finally, in small peripheral populations, where genetic drift is strong, epimutations contribute to adaptation under a wider range of evolutionary conditions. Overall, our results suggest that epimutations can change outcomes of adaptation in peripheral populations, which has implications for understanding conservation and range expansions and contractions, especially of small populations.

1. 1. 1. panmictic: characterised by random mating within a breeding population

A serious question to consider:

Isn’t it time to scientifically  examine (and fund) the benefits of using the North American Suffolk herd to stave off the projected genetic extinction now four years and eight months away?

Research, and just as importantly, funding for equine research, is usually aimed at exploring the whys and hows of problems:  why they are happening and how to fix them.   Often this is economically driven. 

Unfortunately, the draught horse sector is too small  to attract good quality research from outside the sector.  Good quality research needs to come from within the sector.  The UK Suffolk Horse Society could be an instigator and driver of this research.

This suggestion was made some five years ago in the article  The Clock is ticking … … … Part 2.  https://suffolkpunchaustralia.com/clock-ticking-part-2/ See section:  Potential Areas for a Conservation Committee to Examine:

1. 1. 1. …. genetics of the Suffolk Horse in the UK
      2. … identification  of areas of genetic research which could be carried out   by graduates for higher degrees …
      3. … liaise with other geneticists both within the UK and internationally to  explore sucesses such as that in the Canadian Horse.
      4. …  grading up through the male line.

etc.

Surely, this area of research could, and should, be undertaken by  the Breed Society charged with the preservation and healthy continuance of the Suffolk Horse breed.

Part 3 of this Article ‘A Horse of a Different Hue’ – coming shortly:

continues this examination of the effects of potential epigenetic changes for the Suffolk Horse. It looks at the possibility of how one might possibly ameliorate them, through  husbandry and use.

Appendix 1:   EPIGENETICS – some definitions associated with the term

Genetics

Genetics is the branch of science concerned with genes, heredity, and variation in living organisms. It seeks to understand the process of trait inheritance from parents to offspring, including the molecular structure and function of genes, gene behaviour in the context of a cell or organism (e.g. dominance and epigenetics), gene distribution, and variation and change in populations.

http://www.nature.com/subjects/genetics

Genome

The genome is the full genetic complement of an organism, encoded in either DNA or, in many viruses, RNA. It includes both the genes and non-coding sequences.

https://www.nature.com/subjects/genome

Epigenomics

Epigenomics is the systematic analysis of the global state of gene expression not attributable to mutational changes in the underlying DNA genome. An organism has multiple, cell type-specific, epigenomes comprising epigenetic marks such as DNA methylation, histone modification and specifically positioned nucleosomes.

https://www.nature.com/subjects/epigenomics

Epigenome

The term epigenome is derived from the Greek word epi which literally means “above” the genome. The epigenome consists of chemical compounds that modify, or mark, the genome in a way that tells it what to do, where to do it, and when to do it. Different cells have different epigenetic marks. These epigenetic marks, which are not part of the DNA itself, can be passed on from cell to cell as cells divide, and from one generation to the next.

https://www.genome.gov/genetics-glossary/Epigenome

Mitochondrial genome

The mitochondrial genome is the full genetic complement of a mitochondrion. Mitochondrial DNA is only a small portion of the total DNA of a eukaryotic cell and in most species is solely inherited from the mother. In humans mitochondrial DNA contains approximately 16,600 base pairs encoding 37 genes.

https://www.nature.com/subjects/epigenomics

 

© Eleanor Yvonne Hatch, Australian Suffolk Punch Registry & Grading Up Registry  2022