Why Genomics Will Be the Future of EPDs

[Bright Raven]

Genomics can eliminate many of the problems of current EPDs. EPDs are generated by models. As I mentioned previously, there are three components to the database that are used to calculate EPDs:

1. Parentage (this is pedigree or knowledge/data from ancestors)
2. Performance Data (this is raw numeric data, collected and reported by members)
3. Genomics (this is where DNA information utilizing markers is converted to numerical data).

Performance Data is the area which depends on an honor system. If all members reported accurate data, there would not be a problem. The "human factor" creates an environment where data may be bad because of user error and/or because of deliberate fraud such as shaving birth weights.

With advances in genomics and research, the correlation of markers to performance, function and traits is going to be discovered and tested.

For example, if the markers for claw set are located. The bull with the best claw set can be tested. The bull can be taken to a farm, bred to a 100 heifers and the results studied. This kind of research is going to take time.

It is the only way to eliminate the "human factor".

The trouble with Genomics is that there is a lot of mistrust. There is a lot of information that many feel threatened by especially if the numbers of their favorite cow/bull goes down and they think that there is a conspiracy going on against them.

 

[sstterry]

But isn't genetics the future of just about everything, from humans to soybeans?

 

[Bright Raven]

But isn't genetics the future of just about everything, from humans to soybeans?

That and money.

 

[Cornfed01]

So genomics are the EPD's of fake meat?

 

[Red Bull Breeder]

From my small amount of DNA testing they still have a ways to go.

 

[Bright Raven]

But isn't genetics the future of just about everything, from humans to soybeans?

That is a very broad statement. Genetics already influences almost everything we do.

 

[Bright Raven]

From my small amount of DNA testing they still have a ways to go.

Speculation on my part but I think 20 years.

 

[True Grit Farms]

DNA is the the future. It sure is nice to be left behind till you need something.

 

[Red Bull Breeder]

Who is being left behind TG? If DNA is the future why plug it into EPD'S. Why can't it stand alone?

 

[True Grit Farms]

Who is being left behind TG? If DNA is the future why plug it into EPD'S. Why can't it stand alone?

Expected Progeny Differences. DNA isn't expected, it's exactly what it is. RB, I don't think technology has caught up with how to properly use DNA yet. We all know that even if you have the same DNA, the results won't be the same. But once they figure out how to line the genes up we're in trouble.

 

[Ebenezer]

For example, if the markers for claw set are located.

Fly in the ointment is the word "If" and the other implied message here is "If all of the markers". The problem now is that just some of the markers are known and folks act like it is the whole deal. It is not "garbage in/garbage out" it is merely an incomplete data system right now.

And I think we can say that all DNA is not inherited equally (50/50) to offspring, we need to remember gestational programming and epigentics so that knowing some on sire and dam do not fully paint the whole future.

Indiscriminate use of genomics will be used to narrow the genepool unless gene altering is also used. Just like the chase for AAA $B has already done for the Angus. So all that glitters is not gold.

For now, I live in and deal with the present.

 

[Bright Raven]

For example, if the markers for claw set are located.

Fly in the ointment is the word "If" and the other implied message here is "If all of the markers". The problem now is that just some of the markers are known and folks act like it is the whole deal. It is not "garbage in/garbage out" it is merely an incomplete data system right now.

And I think we can say that all DNA is not inherited equally (50/50) to offspring, we need to remember gestational programming and epigentics so that knowing some on sire and dam do not fully paint the whole future.

Indiscriminate use of genomics will be used to narrow the genepool unless gene altering is also used. Just like the chase for AAA $B has already done for the Angus. So all that glitters is not gold.

For now, I live in and deal with the present.

The geneticist and modelers are aware of the challenges. The genome of the cow has been mapped but the identification of all the genes and what they influence is ongoing.

Regarding inheritance. Geneticist the world over are involved. They understand the mechanisms of meiosis, crossing over, mutation, etc. There are a plethora of mechanisms that influence inheritance. Nevertheless, within the sphere of knowledge being gained and the testing through research, these challenges will be met.

Edited to add: the scope is much broader than Angus and the AAA.

 

[Red Bull Breeder]

Who is being left behind TG? If DNA is the future why plug it into EPD'S. Why can't it stand alone?

Expected Progeny Differences. DNA isn't expected, it's exactly what it is. RB, I don't think technology has caught up with how to properly use DNA yet. We all know that even if you have the same DNA, the results won't be the same. But once they figure out how to line the genes up we're in trouble.

It becomes expected progeny differences as soon as its incorperated into EPD's Grit. I would agree that dna is what it is. But there is sure enough is some things that i see that don't match the dna.

 

[True Grit Farms]

Who is being left behind TG? If DNA is the future why plug it into EPD'S. Why can't it stand alone?

Expected Progeny Differences. DNA isn't expected, it's exactly what it is. RB, I don't think technology has caught up with how to properly use DNA yet. We all know that even if you have the same DNA, the results won't be the same. But once they figure out how to line the genes up we're in trouble.

It becomes expected progeny differences as soon as its incorperated into EPD's Grit. I would agree that dna is what it is. But there is sure enough is some things that i see that don't match the dna.

I see that when I look at my brothers and kids. Had my oldest tested to make sure he was mine.

 

[SPH]

Been trying to stay out of some of the hot button EPD threads here lately but I'm glad you broke it down like you did Raven. It's such a divisive hot button topic with some because you have people who rely too much on EPDs, those who think they are worthless and hate them, and then everyone else pretty much falls in the middle somewhere with them.

I can't stress enough that EPDs are just ONE of many tools you have available to make selection decisions. I can show you animals with great EPDs that come no where near performing like them and some that have poor EPDs that outperform animals with much better EPDs. Also a big thing to factor into EPDs are the accuracies. You may be able to trust that an animal is more true to their EPD if the accuracy is say .80 and not .20 The only way you'll get those accuracies higher is to report as much raw data on your cattle as possible so they factor into the EPD calculations. DNA testing also affects that but when I go through our cattle's EPDs I see the biggest changes each time we submit stuff like birth, weaning, yearling, and carcass scan data to the association. I don't know how other associations EPDs are weighted and calculated but I know with the Herefords I've seen EPDs change more on raw data submission than when we had a DNA test done on them. And the older animals it seems like their EPDs hardly move much because there is enough production data reported on them they probably have been pretty consistent over time and another calf on say an 8 year old cow probably isn't going to sway the data much on them or another set of calves out of a heavily used AI sire too. I've also seen new or less proven AI sires that once there is a calf crop or 2 out of them have their EPDs go to pot once people start submitting their weights -seen a few bulls over the years look OK for calving ease and BW initially then their EPDs get hurt badly once the actual weights start being reported.

I won't lie, it is nice to tie some good EPDs to your cattle as it makes them more marketable, but a good set of EPD numbers isn't going too fool anyone when they do the eye test or look through their production records. A good cattleman is not going to buy a bull or female that has a flawed phenotype or structure issues or has had poor calves just because they have a nice looking set of EPDs. Especially those who sell bulls to commercial cattlemen, if that high EPD bull isn't putting pounds on their calves they probably aren't going to come back to buy another bull from you.

As much as we all try to understand EPDs many of us probably will never fully understand everything that goes into them. I'm not going to tell a guy how to run his operation as there is no "cookie cutter" way of doing things across the board for everyone so there will always be a spectrum of guys out there who don't care to use EPDs at all to those who maybe rely too heavily on them.

 

[cow pollinater]

The dairy side of the cattle industry jumped on genomics a few years before beef did. I've seen a few very fine herds really struggle with the results of going all in on genomic young sires. A few of the better herds did okay by balancing high genomic young sires and highly proven bulls. The safest and far away most productive herds stuck with progeny proven sires.
After a few years of it's introduction it was decided that a genomic proof is equal to twelve milking daughters. That's a great start but it's miles away from being progeny proven. Progeny proven works. It takes a while but it works.
I do believe that the technology will continue to improve but to date the best answer for commercial cattlemen is to buy bulls from seedstock producers that run their herds like commercial cattleman so that the consistency is bred in. If they make excuses for problems and sell you a bull, plan on making excuses for your cattle. If they treat every cow the same and you like what you see from their herd then you can expect the same from the calves. It's not rocket science unless you insist on turning it into that.

 

[sstterry]

I see that when I look at my brothers and kids. Had my oldest tested to make sure he was mine.

That begs the question, whose do you think he was? :lol: :hide:

 

[Jeanne - Simme Valley]

Cowpol - that is how ASA explains it.
"The traits show how many progeny records it takes for an animal without genomics to have the same BIF accuracy as the young animal with genomics (but no progeny). In other words, EPD on a genotyped 1-month-old calf will be as accurate as an animal with birth weights on 21 calves, weaning weights on 22 calves, etc."
ASA gives us all the traits & how many calves a DNA is equal to. I had that info in my last newsletter.

 

[NEFarmwife]

Cowpol - that is how ASA explains it.
"The traits show how many progeny records it takes for an animal without genomics to have the same BIF accuracy as the young animal with genomics (but no progeny). In other words, EPD on a genotyped 1-month-old calf will be as accurate as an animal with birth weights on 21 calves, weaning weights on 22 calves, etc."
ASA gives us all the traits & how many calves a DNA is equal to. I had that info in my last newsletter.

You talk about your newsletter occasionally. Is there a place to subscribe to that? Yes, you're sim but we are all cattlemen and women and I do enjoy your educated responses.

 

[wbvs58]

I'm no geneticist or genomics guru but the way I see it these markers for traits are not found by just scanning the markers and saying hey that one has a big bump there so that must be for big balls so we will call that a marker for scrotals. The way I see it they get the DNA from an animal with high accuracy EPD's and look for something that lines up with is common in another high accuracy animal for that trait and another and another and of course with the massive computing power they have now this is easy to do. But the whole backbone of this process is the recording of raw data. RAW DATA IS KING for checking on what they have already found and for looking ahead to find more markers and to improve the accuracy. We have only just started on the process but the information is growing at an exponential rate.

Angus Australia has a benchmark programme that has been going for about a decade now. 100 straws from a bull are used on heifers from cooperative herds and progeny followed through to slaughter or calving. This data is used to help prove the genomics as well as individual EBV's of an animal however the amount of research that is feeding off this data is incredible. The CSIRO, many universities, Meat and Livestock Australia, drug companies are using the data to complement their own research and are contributing to the cost of the programme as well. I am sure the use far exceeds the original intention of the programme of improving accuracy of EBV's of future sires.

RAW DATA is king.

Ken