Results: Hereford Breed Research Project

[woodford]

     
     Dr. Matt Hegarty has finished his report of the latest findings in the ongoing project researching the genetics of the Hereford breed, and has made the report available to the public.

   
     This is the link to download your free copy of the paper:


     hdl.handle.net/2160/7ae993bf-83d8-47da-a2a3-768cae47744b

     Scroll down to this and click on: HOP report final 11-10-2020PDF


     This project has had several delays, some of which were in the UK, and unavoidable. However, a significant amount of the delay is the result of the very excellent, candid and sometimes heated discussion on this Forum. Many of the ideas, theories, and general comments about the issue of whether or not the Hereford breed is corrupted by other breed genetics, were followed and researched as new data came in. The interest in the issue by the Forum Membership was instrumental and invaluable as a source of support, information and genetic samples that could not have been found anywhere else. Just as important were the discussion and information that gave the researchers a lot to think about. Before, if the results were being checked for errors five times, the forum discussions caused the same checks to occur ten times. The process was slow, but has resulted in a 39 page paper that represents a portion of what is probably the most comprehensive research project ever done on the Hereford breed.


     It would be more accurate to say: Hereford breeds, plural, because there are two separate breeds in the Hereford family. They are related, somewhat, but very much apart from each other. Many people reading this Report will be upset, but I think unsurprised, by the results in it.


     Another thing that the research was able to do, was to be able to offer breed percentages. This is a win to breeders of North American Derived (NAD) cattle, because even if they aren’t interested in using Original Population (OP) Hereford genetics, the breed percentage test also tests for the category of Unexplained genetics which is a polite name for crossbred, or genetics from breeds other than Hereford (OP or NAD). If the test shows more than 9.9% Unexplained, then the chart automatically shows that the animal is possibly a crossbred.


     I can tell you that many of the data results that I have seen have NAD cattle that are under less than 9.9% Unexplained, regardless of the percentages of OP, or NAD in those animals. I can also tell you that many of the NAD cattle also show more than 9.9% Unexplained, including animals that were born after the 2010 requirement by the AHA to have very walking herd bull parent verified in order for the breeder to be able to register calves from that bull. Parent verification does NOT guarantee breed purity. Breed percentage testing will.



     Not only are NAD cattle that were born in North America having difficulties with high percentages of Unexplained, but there are modern day animals that have been imported into North America that have high percentages of Unexplained as well. What makes this interesting is the fact that some of the imported animals don’t necessarily have a lot of actual North American breeding in their pedigrees. This means that not only are breeders in North America vulnerable to Unexplained genetics from breeders at home, but also from the Unexplained genetics of imported cattle.



     I hope that every Hereford Breeder, and every Hereford Breed Association/Society reads the Report, and takes it seriously. I also hope that Breeders decide to make use of the HTOPP test. Regardless of everyone’s difference of opinion of what type or combination of Hereford they want to raise, the test is an important and useful tool that will instantly tell the Breeder where their herd is going genetically.



     herefordhbi.com will be offering the test to breeders from North America, the UK, and Australia through HHBI and the labs of Neogen. It may be that it will also be possible to send samples from South America by way of Neogen in Brazil, but this has not yet been tried, or set up. The test is now being offered on the HHBI website, and the main components are now in place. There may be some delay at the beginning, as details such as payment options and a few other small details are being attended to at this time, so if you are interested in trying the test please be patient, it is a new system.


     Have a good day,


     Woodford

[mj]

Fascinating, as is the company mentioned, Illumina (ILMN)

[alex]

The report is incorrect about how the first polled Herefords started, where it says that "Ornduff does not record how or where these animals were found". He specifically wrote in his book, The Hereford in America, how and where they were found and how Gammon came up with the idea of hornless cattle by studying Charles Darwin's writings describing "freaks of nature". He recorded which herds they came from spread throughout the US along with their registration numbers. Some had strong Anxiety 4th influence and Lord Wilton among others.

[Glenn]

Regardless where they came from as the report says and many have said before “it strains credibility that the US population happened to have 16 “freak” polled Herefords existing simultaneously with which to form a genetic base”.

[rockmillsherefords]

The 2 dimensional pics are kinda useless after you've seen the 3D. The polled guys have an excuse, the horned guys have some explaining to do beings it looks like they're riding in the same boat. Interesting that despite all the supposed crossbreeding we are still fairly well separated from the other breeds. I want the names/reg. of what they chose has the reference population for the North American Hereford. If North American Herefords are as they say genetically distinct from OP Herefords why would I want to use OP Hereford genetics essentially crossbreeding.

[kph]

Since they include very little "idiot-explanation" about the jumble of dots and lines, here's my take on what I just saw. Horns and Polled are exactly the same shooting down that theory.
Lent's cattle ( true "OP" )are light years away from UK OP in every picture as are Aus "OP" even if it was UK embryos imported to Aus. That disproves the idea that environment and geography have no influence which is what they have used to argue against separation of "OP" and US genetics.
Interesting that 7777 and 15G are separate from the main Hereford cluster since most Hereford bloodlines are heavy in both.
They're using great-great grandprogeny to try to track individuals??
Didn't know they had gone around and milked the sample animals to test milk differences.
Obviously put together by anti-Polled people since they couldn't resist an opinionated rant on Polled origin, even though they show no separation of horned and polled samples.
I look forward to seeing a better explanation of what the different graphs mean. Maybe someday they will have something that can be used to destroy confidence in the Hereford breed in North America, I just don't know if they are there yet.

[soherf]

Do we have registration numbers for the samples used in this experiment? I seriously doubt any mini Hereford lines were tested but wouldn't be surprised if they were the most pure because they were almost completely skipped over back when cattle got tall in no time at all.

It would be nice to see the horned vs polled genetics head to head along with a comparison of American cattle vs cattle that have Canadian blood.

[George]

Nov 12, 2020 14:05:42 GMT -6 kph said:

Since they include very little "idiot-explanation" about the jumble of dots and lines, here's my take on what I just saw. Horns and Polled are exactly the same shooting down that theory.
Lent's cattle ( true "OP" )are light years away from UK OP in every picture as are Aus "OP" even if it was UK embryos imported to Aus. That disproves the idea that environment and geography have no influence which is what they have used to argue against separation of "OP" and US genetics.
Interesting that 7777 and 15G are separate from the main Hereford cluster since most Hereford bloodlines are heavy in both.
They're using great-great grandprogeny to try to track individuals??
Didn't know they had gone around and milked the sample animals to test milk differences.
Obviously put together by anti-Polled people since they couldn't resist an opinionated rant on Polled origin, even though they show no separation of horned and polled samples.
I look forward to seeing a better explanation of what the different graphs mean. Maybe someday they will have something that can be used to destroy confidence in the Hereford breed in North America, I just don't know if they are there yet.

I agree with most of what you have said. I think 15G and 7777 are more separate because they contain a higher % of outside blood and their influence has been diluted in the cattle that trace back to them, so descendants would plot more toward/in the cluster. I have the test results on 7777, since I supplied the semen sample and hope to post it on this thread.

[George]

Nov 12, 2020 11:46:39 GMT -6 rockmillsherefords said:

The 2 dimensional pics are kinda useless after you've seen the 3D. The polled guys have an excuse, the horned guys have some explaining to do beings it looks like they're riding in the same boat. Interesting that despite all the supposed crossbreeding we are still fairly well separated from the other breeds. I want the names/reg. of what they chose has the reference population for the North American Hereford. If North American Herefords are as they say genetically distinct from OP Herefords why would I want to use OP Hereford genetics essentially crossbreeding.

Paul, I haven't read the report in detail yet, but my first impression is that it isn't as bad as I thought, at least in terms of the NA population. Let's see if someone can convince me otherwise. Like you, I certainly see no need to "purify" my cattle by breeding to OP cattle. And if I had OP cattle, I wouldn't want to use NAD cattle either. It would still be pretty interesting to see how some of these CURRENT "goggle eyed wonders" would test!

[Glenn]

I’m still digesting the report so not much at this point that I already wasn’t doing. Luckily I’m 23D (7777) free in my herd as well as free of 15G and Perfection. I do have genetics that I wonder about in about 1/3rd of my herd but if that bull was tested he wasn’t a named bull. I sure am not going to be running out and using any HOP bulls. The ones I see on FB don’t appeal to me in the least bit. I do think there may be some value in keeping your herd where it is or moving it closer to NAD (if that’s important to you) in having a commercial test available. It will also serve as a de facto tool to keep others more honest if they know the stuff they are selling can be tested by buyers or potential buyers.

[woodford]

     Good Morning,



    Now that some here have had a little time to digest the paper by Hegarty, Broadbent, and MacMahon, I am glad to see that some discussion of it has begun.


     There isn’t one breeder of OP cattle that I have ever met, or communicated with, that is on a mission to get all breeders of NAD cattle to either quit using NAD altogether, or even use OP genetics at all. Mostly, they are wanting to identify and protect the existing OP cattle populations both in and out of the UK. The fact that NAD cattle are crossed with non-Hereford genetics should be reason enough for that.



     However my concern is for the NAD breed itself, which I fully intend to continue to breed, raise and hopefully improve, all without using non-Hereford genetics levels of over 10%, if possible. The point that I am trying to make plain is the fact that NAD cattle are actually more vulnerable than OP cattle in one simple fact. NAD is continuing to cycle to non-Hereford genetics , which is dangerous to the Hereford breed because once the NAD Hereford genome becomes diluted enough, the breed will become more and more chaotic, and unpredictable.


     For breeders that want to try it, the use of the HTOPP test makes it possible to stabilize the NAD at the level it is now. It should be possible to utilize OP genetics to create a useful OP/NAD hybrid as well, since it would actually be as much of a hybrid as using non-Hereford genetics. So far, the experiments that I have seen and tried myself, say that this is indeed possible.



     We won’t be able to give out the identities of the animals that were used in the study for the exact same reason the AHA wouldn’t give us the identity of the samples that they allowed to be used by Taylor in about 2015. How many of you out there would like it if we have profiles of your cattle and made the individual animal results public without your permission, or knowledge? What if your animals had been published with results showing upwards to 30% Unexplained, and several hundred registered progeny, and included at least one genetic defect?



     Because that is what we have people. We have a little of everything, we have the good, we have the bad, and we have the downright ugly and are finding more every day. Our genetic reach runs from 1962 to present day, from three continents of this world.


     Some of the data we are seeing now isn’t in the Report. Let me give you a taste. I have to add the provision that these are my own statistics and are not official, however some of you will know me enough to know that these are reasonably accurate figures.



     Of the NAD qualifying samples that were sent from North America:

Approximately 100 Polled and Horned profiles were of animals born after the year 2000.


11% of these animals are over 9.9 % Unexplained (Crossbred) and range up to at least 20% Unexplained.



Of this 11%, two were imported into North America and have presence in the UK and Australia.



Of the 11%, at least two are defect carriers.



Of the 11% that were born in North America, at least three have presence outside of North America. It might be more, I didn’t think to check them all for that, but I remember the three.



As of today the total count of progeny, no grandchildren, and not great grandchildren, of this 11%, in the United States (AHA) stands at 14,682 head.



     My friends, the time has come for breeders decide if they want a stabilized NAD breed, or an honest open herd book. The implementation and use of HTOPP by breeders and breed associations will stabilize NAD. I have ideas on how this can be done as painlessly as possible, but I am just too damn angry to talk about it just now.


     Woodford

[soherf]

Woodford, the easy way to stabilize would be require parentage verification on every calf born after _______. Thus requiring samples from the Sire and Dam (sire is likely already on file) prior to calf registration. This is how I manage our herd and the herds I consult. Other breeds have moved this direction and I suspect that over time the AHA will move toward complete DNA sampling. It's been a slow move from AI sires to all sires to ET donors, etc. It wouldn't be a far fetched idea that the next steps could be ET calves, AI sired calves and then all calves.

I would be concerned that taking these results too literally could lead folks to think that Anxiety 4th samples could also be construed as their own breed due to their tight cluster from intense linebreeding practices as stated in the article.

I spent an hour this morning reading it for errors and biases and have several questions about the selection criteria for NAD cattle.

The article states that on page 6, "NAD cattle are on average longer legged, larger framed and 200kg heavier." Did anyone seek out NAD cattle that were not from this phenotype? They are out there and in growing numbers inside the AHA and have DNA on file.

The next line states that OP and NAD cattle produce, "completely different types of milk." Were milk types of other breeds analyzed to make a speculation as to the origin of this change?

Were the samples split into white faced vs brockle faced? The speculation is that cattle aren't pure so it would be a logical thing to label these samples so they could be potentially used as their own subgroup.

Page 6 paragraph 4 has the most damaging statement for all results in this study, "Ogden's test was focused on affordability and thus used a very small SNP set, LEADING TO THE POSSIBILITY OF MIS-ASSIGNMENT BETWEEN HEREFORD (NAD) AND HEREFORD (OP.)" I'm fairly certain this would be the target of any subsequent research/peer review on this matter, including but not limited to the selection bias of such a small SNP set when larger HD arrays were available.

Page 7 also states that dataset for some individuals were in the wrong format and not included in the sample set. Did anyone scrub the data that was converted for any anomalies? Data conversion is a known source for systemic errors but must be applied to all data sets to wash out, which in this case it seems it was not applied to all sets.

Was the OP sample set really only 19 animals? That would by your accounting above make that sample very narrow comparted to the NAD sample set. If a narrow sample set is used it can greatly skew the outcome. Let's say that the Anxiety 4th samples were used as the NAD samples...you see where I'm going here? What if only L (Perfection) cattle were used as the NAD sample? What if only small frame cattle were used as the NAD sample? What if Wonder calves were used as the NAD sample? All used as an illustration to show you how much of a potential problem the sample size and selection criteria can be when selection bias occurs and it does occur.

And I'm only 1/3 of the way through the second reading of the report with my pencil in hand. I'm sure there will be more questions to come.

It should be noted that we have verifiable proof that genetic mutation/change/shift occurs in a single generation. So are we also compounding our NAD defect mutations into the mix? If so it along with selection pressure could well account for the genetic drift away from the OP.

Some terms I'd encourage folks to read up on are:
Founder effect
Serial founder effect
Population bottleneck
Selective breeding
Popular sire effect
Small population size
Genetic drift
Sampling error

It should also be noted that if any mathematical models were applied to the data set it's common practice to name them and their application.

Is this report being peer reviewed and by whom?

[Glenn]

Nov 13, 2020 12:04:03 GMT -6 soherf said:

Woodford, the easy way to stabilize would be require parentage verification on every calf born after _______. Thus requiring samples from the Sire and Dam (sire is likely already on file) prior to calf registration.

Many way have been calling for complete sire AND dam parentage verification as a requirement for registration. This would in EFFECT close the herd book at the date chosen. But don't hold your breath waiting for it to happen.

[rockmillsherefords]

I don't believe requiring all to be parentage verified is enough anymore, there also needs to a breed standard. They need to resemble a Hereford. I don't think it would take much, say, has to have 90% white face and a white underbelly. The AHA have shown the really don't care, maybe some new leadership will have the balls to take a stand.

[soherf]

Nov 13, 2020 12:19:54 GMT -6 Glenn said:

Nov 13, 2020 12:04:03 GMT -6 soherf said:

Woodford, the easy way to stabilize would be require parentage verification on every calf born after _______. Thus requiring samples from the Sire and Dam (sire is likely already on file) prior to calf registration.

Many way have been calling for complete sire AND dam parentage verification as a requirement for registration. This would in EFFECT close the herd book at the date chosen. But don't hold your breath waiting for it to happen.

Well based on the current wording of the AHA registration qualification we already have a closed herd book, don't we?  

[soherf]

Another idea to help break the data down would be to label AI sired calves. I know of a situation that happened a few years back with a MAJOR bull stud that incorrectly labeled semen straws and sold them for their techs to use with customer cattle. Those customers then wound up with calves that DID NOT VERIFY TO THE AI SIRE. Making seedstock producers furious!

Errors occur and data must be scrubbed of any potential error sources especially in cases like this.

[redgem]

It says/shows what I expected. Most are in a group with a few that are separated some more than others.
Not sure it will make much difference unless breeders start testing and showing results. Or it's a requirement for registration. If I've spent $8000 on a bull I'm not sure I'd ship him after testing and finding out he's only 60-70% hereford. Probably not even going to pay for the test. So unless breeders test before the sale and post the results I don't think it's going to change much for most.

[strojanherefords]

I have read through the study a couple of times. And I am reserving final judgment until I see which animals made up the North American reference sample.
My initial thought about the study is that it is designed to bring out the differences between that are unique to HOP cattle and was not an assay of how related the current North American Hereford is to the original animals imported from England in the 1880's. I am suspicious of the scatter plots because they don't show the trail between the Anxiety 4th population and the rest of the breed. Station Line 1 cattle are by pedigree 50% Gudgell and Simpson breeding yet I see no sign of that information in the results.

[soherf]

Nov 13, 2020 23:27:01 GMT -6 strojanherefords said:

I have read through the study a couple of times. And I am reserving final judgment until I see which animals made up the North American reference sample.
My initial thought about the study is that it is designed to bring out the differences between that are unique to HOP cattle and was not an assay of how related the current North American Hereford is to the original animals imported from England in the 1880's. I am suspicious of the scatter plots because they don't show the trail between the Anxiety 4th population and the rest of the breed. Station Line 1 cattle are by pedigree 50% Gudgell and Simpson breeding yet I see no sign of that information in the results.

Had the exact same conversation prior to falling asleep.  (All except the last sentence.)

[franklinridgefarms]

I didn’t read the project information, not sure I could understand or stay focused on a lot of scientific lingo. We are a commercial cattle farm with only a few registered animals. Both my wife and I were raised up around commercial Herefords, and appreciate several traits that Herefords have brought to the table. I had tried to utilize Angus for several years and finally got so disgusted with that septic tank of issues that started using Hereford bulls then moved towards a Hereford based cowherd, half of our cows are now Hereford. The straight Hereford calves are better growing and by far better disposition than Angus calves, the stupid Hereford dock at the sales is the biggest problem facing the breed. That being said, we have used 5 different Hereford bulls, and 2 of them sired calves that definitely were not what one would expect out of registered bulls and purebred and or registered cows. One bull had a large frame and really liked his calves however his calves had a lot of white, two had a white stripe running down their shoulder on calf had it on both sides. It was sold for a four h show steer and someone saw a picture of it on another forum and posted the picture on this forum. The disposition of that bull and several of his calves was also not what one would expect from Herefords. Another bull we used sired some much lighter colored calves than we like, some were light as a light colored Gelbvieh or Limousin. That bull in spite of supposed to be being polled, sired several horned calves. That bull was definitely misrepresented. We really like Herefords and would prefer to use them for bulls, but this year we replaced our Hereford bulls with a home raised 3/4 Angus 1/4 Hereford, BWF bull, and purchased a black Simmental bull,

[Glenn]

George asked me to post this for him.

[Glenn]

Nov 14, 2020 12:27:48 GMT -6 Glenn said:

George asked me to post this for him.

Just some back of the envelope math puts 23D (sire of 7777) at about a half blood. Assuming the dam wasn’t too “crossbred” herself, since 7777 is showing at over 28% unexplained.

[timbernt]

Many years ago there was a paternal brother to 23D in the Canadian Digest. There would be no question in anyone's mind that he would be anything but an old time Canadian Horned Hereford bull. The contrast with 23D was unbelievable.

[lcc]

I will leave interpretation of the academic paper to people smarter than myself.

But, I know that I have always been told that the Hereford white face is dominant. Earlier this fall, I bought a group of fall calving crossbred cows (to be used as recips), bred to registered Hereford bulls. After calving them out in Sept and Oct, the amount of brockle faces on those supposed-to-be half Hereford calves is depressing.

So much for crossbred baldies.

[rockmillsherefords]

Strojans post on the other thread reminded me that a few months back I was reading some old threads here where Dr Beever was participating in them. Some good threads back there if you take the time to look. Anyway I remembered this one, thought it was relevant to this thread, especially where he writes about losing ancestors DNA in just a few generations.


old thread