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Archive for Epigenomics

During the recent “Advancing Dairy Cattle Genetics: Genomics and Beyond”,  Paul VanRaden with USDA’s Animal Improvement Programs Laboratory pointed out that “If we took the best haplotypes (genes) from all the cows genomic tested to date, we would have a cow at $7515 Net Merit”.  That’s pretty spectacular considering the current top Sire on the $NM list is DE VOLMER DG SUPERSHOT at 1000 $NM.

Now to put that into perspective the current rate of gain is $80 per year.  So in order to breed that $7515 animal it would take us 81 years to actually breed that animal.  Therefore it raises the question whether such an animal is actually achievable and is there technology out there that could accelerate the process of getting that Super Cow.


The interesting fact here is the greatly accelerated rate of genetic gain since the introduction of genomics.  This results for the most part from the greatly shortened generation interval.  Females are now being used as bull mothers 18 months sooner than in the past (as yearlings vs mid 1st lactation), and sires of sons are now being used 24 and sometime 36 months sooner than they were in the past.  (Genomic indexes vs waiting for proven sires).  The almost 40% increase in reliability of estimated transmitting ability has breeders and AI companies contracting and working with these elite animals at a significantly younger age.

An interesting comparison is found by taking the top 8 proven sires from April 2010 and comparing them to the top 8 genomic sires from April 2010 with their current daughter proofs.  You see that the genomic sires are 99 $NM (704 vs 605) higher than the proven sires.  These top genomic sires, that have been heavily used as sires of sons, are 16% higher than if we had used their proven counterparts from the same time.



This reminded me of a discussion stemming from an article we wrote over a year ago, “Are You Ready For Genetically Modified Cattle?”.  We discussed about how many larger and larger corporations are entering the dairy genetics marketplace and the fact that technology is advancing at such a rate that some time in the not so distant future it will be possible to take the best haplotypes in the Holstein population and produce progeny that would have an estimated breeding value of $7515 as VanRaden proposes.  But at this point it’s just like the “Perfect” Holstein Cow picture, it does not exist at this time.  (Read more: The Perfect Holstein Cow)

Not only does the potential exists to produce high $NM progeny, but what about creating or developing traits that are not yet available in nature.  Things like Epigenomics, Nutrigenomics and Transgenics will make this possible.  (Read more: Forget Genomics – Epigenomics & Nutrigenomics are the Future)

The Bullvine Bottom Line

There is no question that great breeding has always been part art and part science.  However as technology grows and new discoveries seem to happen almost monthly as opposed to yearly, the balance between art and science is starting to shift drastically.  I often hear many breeders comment about the failures of genetic predictions in the past.  That was when reliabilities were in the 30% and 40% range.  As the systems are refined and biases removed, these rates are now approaching the 70% and 80% range.  Given more time, there will come a point where we have over 90% reliable information for animals on the day that they are genomically tested.  Add to this the ability to genetically preselect or even manipulate the embryo and there is no question that, before long, numbers like 7515 $NM will not seem to be so astronomical.  They will be the expected.

The Dairy Breeders No BS Guide to Genomics


Not sure what all this hype about genomics is all about?

Want to learn what it is and what it means to your breeding program?

Download this free guide.





Two months ago I had one of those conversations. A friend said to me “you know Murray I am moving on from just simple genomics”. That perked my ears up and I listened more intently. “Yep I am now thinking about epigenomics”, he said. Well that was enough to set me off investigating what is out there that is beyond what our industry is currently considering and using when it comes to genomic.  Relax a little, this may seem like rocket science today, but it is in tune with what our industry has always done in the past.  We look to find more accurate ways of indentifying the elite animals. Then we figure out how knowing that information gives us ways to make dairy breeders and dairy farming more profitable.

Already Many Steps Too Far?

So now ‘epigenomics’ was pinned to my clipboard. But I didn’t get any further before I had a Master Breeder husband and wife corner me for half an hour and ‘inform’ me that “The Bullvine was leading the industry astray”. They stated to me that “they were from Missouri” and perhaps we should “still only be using the actually officially authenticated information – DHIR records and breed classification results – when it comes to selecting bulls and marketing females.  They asked how can we know that the hair pulled and submitted for DNA testing actually came from said animal.” I have known this couple for almost forty years so I took the discussion on to a review great cows of the past and how they would not compare to the great show and brood cows of today. As we started to conclude our conversation the lady, who had been somewhat quiet during our sharing, commented “You (Murray) have a good point about how the genetic evaluation results over our lifetimes have resulted in the fact that we have far superior cows for both conformation and production, but our herd’s current biggest genetic problem is cows not getting back in calf. We just do not now get to have very many ten year old and older cows in our herd, liked we used to.” That gave me the opportunity to talk to them about genomics and having fairly reliable information, early in an animal’s life, on its genetic merit for reproductive traits.

The husband’s concluding comment warmed my heart. “Our grandson plans to come home to our family farm and he tells us that at university his professors are saying the information we have today on genomics is just the start. So don’t give up on us old guys. You folks at The Bullvine just keep giving us the facts and helping the industry do an even better job of breeding dairy cattle. We don’t own a computer but our family keep us quite up-to-date on what The Bullvine is writing about.”  Obviously this couple are not as set in their ways as they led me to understand at the start of the conversation.

So if we have just scratched the surface, let’s delve a little deeper.

Epigenomics – What’s That?

By definition, epigenomics is the study of modification of the expression of the genetic material in a cell. Sounds rather out of the norm. Something can alter what the DNA says is the genetic merit of an animal? Let’s think that through a bit more.

As cattle breeders we can all think of times when three full sisters all had very similar performance. And I expect many of us can also remember situations where two of the sisters were very similar but the third sister just did not measure up to the other two.  The question that breeders always ask is did the third one not get the good genes, or did she get the good genes but something inhibited her from being able to express them.  I have even heard very knowledgeable breeders say that the third one will breed just a good as the other two.  How they arrived at that conclusion I am not really certain. But I have seen it happen as they predicted.

Research in mice has shown that the diet of a sire can influence the gene expression of their progeny. So that fits under the definition of epigenomics. Dr. Jacques Chesnais of Semex feels that “there is a definite possibility that epigenomics plays as important role in adaption to the environment. In particular, in our industry, the way we feed and treat a cow in the early stage of pregnancy could affect the calf for a lifetime and therefore affect the future productivity of the herd.” Hearing that made me wonder if the recipient dams of ET calves may have an influence on how those calves pass on their genetics.

Leaders in the study of epigenomics in livestock Dr Marc-Andre Sirard and Dr Claude Robert, Laval University, are currently  investigating how epigenomics applies to the bovine and in particular to female reproduction and embryo development. It will be interesting to follow their reports.

There is obviously much to be studied and learned about epigenomics in the bovine. Definitely traits like reproduction, health and immunity are ones that dairy breeders wish to know more about as they relates to inheritance.

So then – What is Nutrigenomics?

The second new kid-on-the-block, so to speak, is nutrigenomics. The study of the effects of foods and food constituents on gene expression. By definition “Nutrigenomics can be described as the influence of genetic variation on nutrition, by correlating gene expression or SNPs with a nutrient’s absorption, metabolism, elimination or biological effects.” Think about it. If we know the genetic make-up of our dairy cows we would be able to design their diets accordingly. Are there cows out there that can make better use of lower quality forages? Wouldn’t that be a boon for the economics of dairy farming. Especially given that feed costs are 52-58% of total dairy enterprise costs and low quality forages are less costly.

I asked two nutritional consultants about this. I got two very different responses. The first one said – “don’t bring that on too quickly I still have another ten to fifteen years in my working career”. The other consultant said “Well it would change my job but if it means dairy farming can be profitable and sustainable and if we can feed the hungry world – well bring it on”.

Expect Genetics to Play an Even Bigger Role in the Future

Investigation by Canadian Dairy Network (CDN) has predicted that, in stable milk pricing times and on milk production focused farms, half of the increased on-farm profits comes from increasing the genetic merit of sires and cows used to produce the next generation of females.  With a better understanding and more definitive knowledge of epigenomics and nutrigenomics it could possibly be that 60+% of on-farm profits could be as a result of the genetics used.

From the DNA analysis using hair follicles, breeders now know with 50-70% accuracy the genetic merit of their animals for a host of important traits. Think what might be possible if by including epigenomics and nutrigenomics information. The accuracy levels could rise to 70-80%.

The Bullvine Bottom Line

The research phase of studying how epigenomics and nutrigenomics relate to the dairy cow is well underway. We can expect refinements to our genetic evaluation procedures based on what the research tells us.  And in time breeders will have information so they can better breed, feed and manage their herds. Stay tuned to the Bullvine for more great insight into these two future changing technologies.

The Dairy Breeders No BS Guide to Genomics


Not sure what all this hype about genomics is all about?

Want to learn what it is and what it means to your breeding program?

Download this free guide.





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