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venerdì, 06 gennaio 2012

7K Chip Q & A

The 7K SNP test; an economical and more reliable genomic test is now available to the industry. Given this development, a question often asked by producers is should I genomic test my females with the 7K chip? Of course this question inspires a rather extensive list of questions, so what awaits readers is a list of those most frequently asked:

What happened to the 3K chip test?

The 7K chip was designed as a replacement for the former 3K SNP test as it measures almost 7,000 SNPs, had better readability, and boosts reliability of by up to 5% over the 3K test. It also provides an increase in reliability over Parent Average, and more importantly is very accurate at 'parental discovery' meaning that if an animals is misidentified, or NOT identified, the test will be able to tell you the Sire and Maternal Grandsire of that animal – provided they are both sires that have been genotyped themselves.

Should I genomic test my females with the 7K chip?

To properly answer this question, you must first ask yourself what you are going to do with the results. If you are going to use the results to manage, sort or breed your animals differently, then you should consider testing if that information will help you make a better decision. If you can't see how it makes a better decision, and creates more bottom line for your dairy today or in the future, then the investment is not worth it. Although the cost of the genomic test is now much more economical, it is still a substantial investment when multiplied over many animals! Investments have to pay off, and not only should the cost of the investment be considered, but also the opportunity cost, and potential return of investing those resources in other places.

How can I evaluate if genomic testing my females is correct for me?

Genomic testing your females offers the opportunity to more accurately predict and rank animals within your herd on their genetic potential. Ranking your herd can have some real advantages when it comes to a number of management decisions: 1) If you want to use sexed semen on the top portion of your herd, 2) If you want to cull the bottom end of your herd, 3) If you want to do embryo transfer work on extreme genetic outliers within the herd.

What is the accuracy gain between unknown animals (UNK), parent average, 7K, 50K? How does this new technology compare to that currently used for AI bulls?

With UNK, we have to assume each animal is "average" with basically 0% reliability. With parent average, we can assume ~38% reliability and with a 7K test we generally get ~65% reliability for an index like Net Merit, TPI, or one you create for your own dairy. The 50K test (which is currently used for all AI bulls) has a reliability of ~72% for indexes.

What does that accuracy gain mean for genetic progress in my herd?

Most farms breed every available animal back for a replacement – if this is your practice, and you plan to continue this practice, then genomic testing will have no value for your dairy. If you plan to use the results to focus on generating replacements from the upper end of your herd, then genomic testing can have a positive impact in some situations – especially if you have missing or inaccurate identification.

What will the genomic results look like if I do decide to test my animals?

The results will look just like a bull "proof". Animals will get predictions for traits like PTAM, PTAF, PTAP, PL, DPR, SCS, PTAT, UDC, FLC and all linear type traits. If you test a group of animals, you can put the results in a spreadsheet and sort them on an index such as TPI or Net Merit, a practice often done with bull evaluations.

Can I rank my animals on their genetic potential without genomic testing them?

YES! Although it is not often considered, a commercial dairy that has complete and accurate identification can create a ranking on genetic potential based on parent average, with a considerable amount of reliability (~38%). In fact, a parent average can be constructed for each trait in a bull's "proof" and will look very similar to genomic results with a lower level of accuracy. This is very important because for a herd with complete and accurate identification of sires and maternal grandsires, the choice to genome test heifers or not is a decision about the accuracy of the ranking based on parent average vs. the accuracy of the ranking with genomics.

What is a parent average?

Parent average is the average genetics of the sire and dam of the animal. Often times a parent average is estimated with the Sire and Maternal Grandsire (MGS) of the animal when performance data of the dam does not exist.

I record Sire x MGS, is my parent average accurate?

That depends on the accuracy of your identification. If you do a good job recording breedings, and identifying calves, making both the sire and MGS accurate, then a parent average will have enough accuracy to begin ranking your animals for some basic purposes.

Who can do the work on parent average/index ranking?

You should work with a trusted genetic advisor – often your AI Company. It is very important to remember that before ranking your animals – you first have to determine what you are ranking them for! This means that you first need to have a developed genetic plan so you focus on the traits important to you.

What if I do not have accurate or complete identification in my herd?

Without complete and accurate ID, the ranking of heifers based on parent average alone becomes much more difficult, and likely an impossible task. Often times the accuracy of ID within individual herds is overestimated, and the real miss-id rate in the industry is >25%. If you question your ID accuracy, genomic testing provides an opportunity to determine the accuracy of your identification, in addition to accurately ranking your animals.

If I have accurate and complete identification in my herd, in what situations does it make sense for me to genome test my females?

The answer will again depend on what you are going to do with the information. If you are simply going to use it to see how you rank genetically among other farms, it clearly will not pay off. If you are going to use it to cull the bottom animals in your herd, it is unlikely to pay off, as they can also be selected based on parent average. If you are going to use the results for selection of which animals should get sexed semen, it is also unlikely to pay off. However, if you want to select the most extreme animals to do embryo transfer work on, it is likely a good strategy to first genome test a pre-selected group to ensure only the very best are flushed.

I'm surprised that using this technology to select my bottom animals for culling and my top animals for sexed semen will not pay off?

In some extreme situations it may, but if your herd performs as expected, and you have complete and accurate ID, then your virgin heifers will have a parent average reliability of around 38% for Net Merit or TPI. That reliability will increase to about 65% reliability with the genomic test. Using statistics, we can assume that the probability of an animal increasing by more than 100 NM or 150 TPI points is only about 15%, and likewise, an animal decreasing by those amounts is only about 15%. Using a more extreme example, the probability of an individual animal changing by at least 200 NM or 300 TPI points is only 2%.

If 15% of my animals will go up by 100 $NM or 150 TPI and another 15% will go down by the same amount, won't that make a considerable difference in the ranking of my animals?

It will make a substantial difference in the ranking of a few individual animals, but most farms are dealing with groups of animals. For example, the genetically highest group could be destined for insemination with sexed semen, while the poorest group in terms of genetics would be destined to be culled. When dealing with groups, we need to consider how much the average of the group would change if we genomic test the heifers vs. if we used only a parent average to rank them. If your herd is normal, about 95% of animals will be between +/-400 NM and the average of your virgin heifers might be 100 NM. If you wanted to select the top 25% for sexed semen usage, the group of heifers selected for sexed semen would likely be those heifers >250NM. The bottom 10% (which would be culled) would be <-150NM. In this situation, what is the probability that a heifer selected for sexed semen based on parent average (top 25%) would fall into the group to be culled (bottom 10%) after genome testing? Referring back to the last answer, there is only a 2% chance that an animal will change by 200NM points, so the likelihood of an animal going from a sexed semen candidate to a cull, (or vice versa) is nearly zero as she would have to change by at least 400NM.

Figure 1: The graph represents a herd situation where the top 25% of animals based on parent average would be selected for sexed semen, and the bottom 10% would be sold. In a normal situation, there is almost zero opportunity for animals selected for culling based on parent average to ultimately end up in the sexed semen category after genomic testing.

But an animal could still change significantly and therefore the actual animals making up the 10% to be culled would include some different individuals pre and post genomic testing.

This is absolutely true, because the accuracy of the selection of the group increases. However, we need to ask what the effect of this change is. With a normal herd, there is <2% chance that an animal in your top half, based on parent average, will end up in your bottom 10% after genome testing. Therefore the animals crossing the threshold and changing the group to be culled (or be selected for sexed semen usage) do not change the average of the group significantly.

What is "risk" or "error" in the 7K evaluation?

There is not a lot of "risk" in the 7K evaluation. It will always give you more reliable information than simply using parent average (or no information). The real risk is the opportunity cost of investing thousands of dollars when those dollars could have better returns if invested in other ways. Generally using those dollars to simply buy better genetics by way of semen should be considered as an alternative investment.

If I'm expanding, or need to buy replacements, should I only buy heifers with 7K?

This is an interesting question and in some situations it may make sense to pay for testing of unknown heifers. In a normal situation, you will need to test at least 2X the number of heifers you plan to buy to make this a financially sound decision. This decision will be determined by the ratio of replacement cost vs. beef price. At the current low cost of replacements, genome testing these unknown animals is not likely to be an investment that would pay off, however, if we one day experience extremely high prices for replacements and low prices for beef, as has been the case in the past, it would make sense.

If I choose to genomic test Unknown animals, what will the benefits be?

There are two main benefits: 1) "Sire Discovery": This means that we will be able to determine who the sire of the tested animal is – provided it was an AI sire. 2) "Sire Discovery" is the first step in determining accurate genomic predictions. Ultimately you will receive a genomic "proof" just like other animals, or a bull proof, as described earlier.

Can I stop milk recording and classification with a 7K test?

Generally milk recording is done for management, not genetic reasons. We must remember that although the genomic test gives us a lot of valuable information on the genetics of an animal, genetic potential does not answer management questions. For example, an animal with a high cell count on test day still may need to be treated or culled and genomic information will certainly not give us that information.

It is also important that we continue to gather phenotypic data (through milk recording and classification) so our genomic predictions continue to be current, relevant, and accurate for an ever changing dairy economy.

What is the bottom line?

Genomic testing is an excellent technology and is certainly exciting. However, exercise caution when deciding if this is the right investment for you. As with any new information or tool, remember to ask yourself how you will use that information and how the investment will pay off. If you can answer those questions and it is a profitable decision for your dairy then it is right for you. If those questions only inspire more questions, proceed with caution.

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