Understanding Genotype info

[cotton1]

Hello folks, its been a while but I need some info. I am a small scale Registered Charolais breeder and have been looking at the 50k deal. AICA has started taking DNA test for 50k so I am having some donors tested. I was looking at some cattle results and just dont understand what the abbreviations stand for(ex. bld, dna, 50k, snp, and karyo). These test can be viewed under lab results on the AICA website.The results have only a few letters like pv,po,kt,or just a y. Im trying to figure out what these results mean,and what they will mean for my calfs EPDs, as well as how to use this info for breeding decisions. I have searched the web for geonotype definitions but cant seem to find what I am looking for. Hoping some of you might help. Also wondering if these test are breed specific so that what I am looking at on Charolais might be different from Hereford or Angus? Thanks in advance

 

[UG]

The DNA profiles offered by each breed association are breed specific. I would encourage you to give the folks at the Charolais association a call, and have them explain each of the abbreviations to you.

 

[cotton1]

Thanks for your reply. I have tried the AICA and still do not understand. Looks like no one here does either. I was hoping that somebody on here had some info. Nice to know its breed specific, I thought that may be the case. Thanks anyway...

 

[VirginiaCattle]

I'm more familiar with the Angus process but I'll take a stab at it. The abbreviations you put are the types of lab results the association has on the animal. I don't know what karyo is but bld would most likely be blood. The dna, 50k, and snp would all be variants of dna tests. With Angus they can have either a Igenity or Pfizer test and there are the older versions and newer versions of both. SNP's used to be used for parentage a lot in Angus so you'll see them on a lot of older donors and bulls. 50k tests are more of the current model. The letters under results appear to be just codes for the type of results on file. They aren't the results themselves. There is a lot of data not being shown to you. So if you get your own 50k test done you'll get access to your data. The data usually comes as percentile rankings. There should be an area where you can see your actual results if you purchased them and not just the summary under the LAB results tab. You probably have to log in to view it or it might have been sent to you. So the actual results are traits with numbers, not the pv, po etc you are seeing.

The results are breed specific so you can't really compare them across breeds. As to how to use them, it's better if your association incorporates them into your EPDs because that would give you a more complete picture of their importance. In general they just enhance the accuracy of traits on animals without much data. Some traits it is about like having 15 progeny records turned in on Angus.

 

[cotton1]

Thanks VirginiaCattle, I think you have helped me some.I am starting to think that because we have been collecting data for a short while that I may see more info in the future. Right now its just as I explained earlier even on my cows that I paid for testing on. The majority of the prominent A.I. bulls were done early on and some donors.Because the bulls I have flushed with were done I am hoping that if I have donor dams tested there will be results on the ET calves from those matings.What I am looking for in these ET calves are accuracy values that are similar to an animal that has several progeny.Right now our ET calves may only get parental averaging until they have actual progeny data reported. So does this mean the acc value for any given trait is still the tool for breeding? Only with the 50k acc values will be higher earlier on in that animals life? I envisioned being able to test a calf crop and sort out which ones are suitable for breeding stock and which ones should go to beef. The time between weaning and 14-24 mo when we market is where we spend inputs here. Would be nice to get things sorted out at weaning time. Is that how it works for you in Angus?

 

[VirginiaCattle]

So when I get my bulls tested I get a report on the percentiles they rank for each category there is a test for. Then when the next EPD run is done (every Friday for Angus) the info is incorporated into their EPDs. It can change the value of the EPD itself but more importantly it changes the accuracy. So you could make early selection decisions based on genomic tests. It'd be better to use them once they are incorporated into the EPD though. For example if you had a calf rank in the top 1% of marbling according to his genomics that'd be great. If you find out the genomic test for marbling in Charolais only explains 5% of the variance it might not mean much. So the effect on the EPD will vary by how much each trait can be explained by genetics.

Here is an info sheet on genomic testing Angus. Most of the basics remain the same. Obviously the parts about which companies etc could be different for Charolais. http://www.angus.org/AGI/GE_EPDs_GenomicTraitTests.pdf

This info sheet is about how they use the results to put it into EPDs: http://www.angus.org/AGI/GenomicEnhancedEPDs.pdf

Somewhere I've seen the equivalent numbers of progeny reports each genomic test can replace in increased accuracy. I can't find it right now. If I run across it again I'll try to send a link.

 

[UG]

As Virginiacattle pointed out, when an Angus producer submits a DNA sample through the Angus association for either a Zoetis (formerly Pfizer) or GeneSeek (formerly Igenity) Angus profile, they not only get genomic enhanced EPDs, but they also get the percentile rankings for each trait. Of all the breeds that I am aware of that offer a breed specific profile, only the Angus association provides the percentile rankings. The other breed associations only provide genomic enhanced EPDs. I'm not familiar with what the Charolais association will provide in regards to DNA information.

 

[cotton1]

Those links were good, thanks. I am pretty sure we use geneseek on our test and the runs are done quarterly. So now the next run would be winter EPDs. As of today I have had animals tested 50k at my cost and only have the info I posted earlier. I am not trying to complain about the way things are , just trying to understand what I do have. I hope that the next run will indicated geo epds.I still would like to know what the results mean. Should Geneseek send me a report? I believe that next year things will be eaisier to understand. So do you test each calf for the 50k, or does it matter if the sire and dam have been tested? That is one thing I dont understand, If my donor is tested and the bull I flush with is tested will there be any benifit of EPD, or EPD accuracy on the ET calfs or will I still have to test each calf. If I do have to test each calf would it matter if the parents have been tested? We do get percentile rankings on our calfs even without 50k. There is a ranking for virgin animals and a ranking for producing cows and bulls each I believe.

 

[VirginiaCattle]

I would ask the lab you sent the samples to if they have any kind of results that they can share. It'll be up to your own situation whether you find the cost of the test economically feasible. I don't raise registered cattle. I mostly do it so I can test the commercial replacements with the cheap test to verify parentage and give an indication of growth and carcass merit. It's becoming more popular every year to DNA test animals for sale. I think there will come a time where it is pretty much expected.

To your question about whether just testing the parents is good enough, it really isn't. The question you are trying to answer is which half of the genes did each parent contribute. Did they give more of their "good" genes or more of their "bad" genes for a given trait. If your bull is AaBbCc for three traits where the capital letters are dominant. You will want to find out whether he contributed ABC or abc or something in the middle to the calf. Same thing from the female side.

 

[robert]

To your question about whether just testing the parents is good enough, it really isn't. The question you are trying to answer is which half of the genes did each parent contribute. Did they give more of their "good" genes or more of their "bad" genes for a given trait. If your bull is AaBbCc for three traits where the capital letters are dominant. You will want to find out whether he contributed ABC or abc or something in the middle to the calf. Same thing from the female side.

Ideally that would be the goal for DNA testing however the current tests, either Geneseek or Zoetis, do not give you that information so there is no way to 'stack' traits per se as there was with the older star system test which relayed whether an animal carried one, two or no copies of the gene identified. Current genomic testing only measures the number of markers which are more indicator traits than specific genes, so using the system as currently enabled means that you could breed two animals that rank in the top 10% for a trait and end up with progeny that rank in the bottom 50% simply due to random recombination of genes.

 

[cotton1]

Robert, I wasnt sure that there was any reports available. Looks like we will still just have EPDs from the 50k just maybe more accurate EPDs. There are so many genetic possibilitys in a calf, makes me think of full sibs to the great AI sires. Full sibs might be close or not good at all.So it looks like I will make my mind up to test the calves or not.I do feel like this will be expected in the future to sell stock. Virginia cattle- I dont know if I can get a report from the lab or not.If I did get one will I get some definition to what all the test are and what the results mean? I am going to ask AICA again.Maybe as time rolls on there will be more info.We are paying about 85 bucks for these test, is that what other breeds are paying.I can get parentage test without 50k.That is a requirement for donors and I think that is a great idea. I would like this 50k to be something I could stack traits with beyond EPDs. Maybe in the future

 

[UG]

We currently have registered cattle of four breeds; three of which provide genomic enhanced EPDS (AN, GV, SM). Because we are purchasing the genomic tests from the breed associations, we are basically a their customer and not the direct customer of the DNA lab (Zoetis,GeneSeek). Consequently, the labs do not provide reports direct to the producer, only back to the breed association. The associations then incorporate the DNA information into the EPD calculations to create more accurate genomic enhanced EPDs. I would guess that this is the same situation with the Charolais profile available from the Charolais association.

We pay between $75 and 85 for the larger panel tests (50K, GGP). However, a few breeds including SM and GV are now offering a lower density profile which is nearly as predictive as the higher density product for $45 to 50. ASA and AGA encourage producers to use the Lower Density profile (GGP-LD) for most animals, and just use the higher density test (GGP-HD) for AI sires and donor cows. This is a big cost savings for us.

In regard to your question about profiling animals out of sires and dams that that have been profiled, yes I think it is a good idea, especially if your bull customers pay attention to EPDs. We have seen flush brothers that varied greatly in their GGP genomic percentile rankings from the Angus association and their genomic enhanced EPDs.

 

[cotton1]

well it sounds like the EPDS will be my report on this. I agree it is worth it on donors and stud bulls but at 85 bucks a test is it worth it to test every calf? The lower density test sounds like a great idea. The pricing you mentioned on that is about what parentage only test are costing us.I also feel EPDs make a difference in both bulls and cows when they sale.Thats my trial and error experience.