Does Genomics Really Work? - Decemeber 2011

No concept has been talked about more in the Dairy Cattle Breeding world over the past few years than "Genomics." It is a very compelling science, and has made genetics as popular of a topic as it was following the advent of artificial insemination. But why is genomics such a big deal? Because it really works!

Genomics have been official since January 2009. Back in 2009 when the science was still very new, many of you were hesitant to adopt the technology. However, now that the technology has been around for a few years and results of its use are evident, there's no time like the present to jump on the genetic progress train!

Selection decisions in 2009

Those of you who did adopt the technology in its infancy are truly reaping the benefits today. If in 2009 you chose to breed with the top genomic-proven G-Stars and FutureStars as opposed to the top daughter proven sires for TPI, you would have newly milking daughters of high profile marketing bulls like AltaIOTA, AltaROSS, and AltaR2.

On the other hand, most chose to 'wait and see' back in early 2009, and therefore used the top daughter proven bulls available at that time (Table 1). This is a great group of bulls in its own right, and they have made happy customers around the globe, but the top genomic sires at that time (Table 2) are clearly a superior group genetically.

Proof stability from genomic to 1st crop

What about the risk of these genomic chart toppers dropping? Be not afraid – 911 bulls were genomic tested in August 2010 and have producing daughters now in December 2011. The average drop in TPI is only 28 points (Table 3). Yes, some dropped more, some less, some stayed the same and some increased. What matters here though is the average of the group as this is how genomic bulls should be used – in groups.

Table 3. All bulls (n=911) that were genomic tested in August 2011 and have producing daughters in December 2011

The following graphs further illustrate changes that can be expected from a genomic proof to a first crop proof. The value of the proof change from August 2010 to December 2011 is indicated on the horizontal axis and the number of bulls with a certain change is indicated on the vertical axis. For example, the first graph shows that of the 911 total bulls included in this analysis, about 30 of them had exactly zero change in their TPI. Meanwhile, the largest positive change was +325 TPI points and the largest drop was -350 TPI points. You can therefore infer that the chance of a genomic bull dropping by 350 TPI points is 0.1% (1/911), which is about the same probability of a bull increasing that amount. Likewise we can see that about 95% of bulls are within +/- 200 TPI points from their initial genomic prediction, after they receive their daughter proof.

 *** To see these graphs clearer, download a PDF of the article below under 'Downloads'

These graphs show that the proof changes are normally distributed, and for most traits, the average change is very near zero. An exception is PL, where the average change is -0.6, meaning that genomic predictions are slightly overestimating this trait. That however does not mean that the predictions are invalid or that the trait should not be considered on a genomic sire – only that you can expect to see a small drop on any genomic-proven sire. For PL, 95% of bulls change between -2.1 and +1.0, so the range of change is still relatively tight, and high ranking bulls based on genomics can be expected to continue to be high ranking bulls after they get their milking daughters.

The proof stability graphs also show that a large number of bulls change in the positive direction for all traits, so even though we don't know which bulls will go up or down with daughter proofs, we can't forget the upside! Remember that the reliability of genomic proofs is around 75% for production and type, and a bit lower for health traits – thus contributing to the kind of variation we see in the graphs. The higher the reliability, the narrower the distribution of change.

Change in CE proofs from genomic to 1st crop

A common reason for hesitance to use genomic sires is due to calving ease uncertainty. The graph below shows that a CE proof can change between genomic and 1st crop proofs; however, the majority of change is up by only 1 point. To put exact numbers to the graph, 82% of bulls increased by +1 or less and 97% increased by +2 or less. For this reason we recommend breeding heifers to genomic sires that are 6 or below SCE, until a bull has their own observations for CE.

For those who are extremely risk-adverse to CE, better genetics through genomic sires can be realized with Alta's FutureStar program; a program designed to offer fertility and calving ease assurance on genomic sires, obtained through observations in our Advantage® herds. Often those who are risk-adverse on calving ease believe they must use 'daughter-proven' sires on their heifers, but we must remember that bulls become 'daughter-proven' for CE as soon as their first calves are born, or about 1 year after semen is first released.

Proof Stability from 1st Crop to 2nd Crop

A question often asked is 'are these bulls going to drop again when they get 2nd crop information?' Table 4 shows the average proof changes that occur from 1st to 2nd crop. These changes are much more stable than experienced in the past; showing that the extra 35 daughter equivalents add a significant amount of stability to the proofs. There is basically no expected average change whatsoever for any traits when a bull moves from 1st to 2nd crop.

Table 4. Proofs from bulls that went from 1st to 2nd crop information

Today's Selection Decisions

Since 2009, many improvements have been made to the way genomic proofs are estimated and numerous animals have been added to the reference population. Both of these factors contribute to the accuracy of genomic predictions, and an expectation that the range of change shown in the above tables will continue to narrow. Today, like in 2009, selection options are much the same – you could use the best daughter-proven sires or the best G-Stars (Tables 5 and 6). While AltaIOTA and AltaROSS get a lot of publicity and have made some great daughters, the predictions of the genomic group (Table 6) far exceed the daughter-proven group – showing the extreme genetic progress made because of genomics.

If you decide to breed to today's top 10 genomic proven sires, in three years, you will already be milking daughters of the highest new daughter proven bulls, and effectively get a 1-generation jump on genetic progress! This group of 10 bulls averages over 300 TPI points higher than today's top 10 daughter proven bulls!

Recall the graph above which illustrated the distribution of change in TPI from genomic to 1st crop. Based on this graph, and the expectation that 95% of bulls will be +/- 200 TPI points, each individual genomic sire in Table 6 has >95% chance of being higher TPI than AltaROSS after receiving 1st crop proofs!

If you want to maximize the genetic gain of your entire herd and reach your breeding goal at a faster pace, genomic proven sires are certainly the way to achieve your goals. Much like a stock portfolio, you will need to accept a bit of risk to maximize your expected return. Of course risk can be mitigated in stocks by increasing the number of different companies owned; and with genomics, risk can be reduced by increasing the number of different sires used.

So for those of you who wish to maximize your genetic gain and are willing to accept some risk to do so, make sure you set your genetic plan carefully. Then select a group of at least 5-6 sires that will help you maximize your progress towards your genetic plan!

Article by: Gerbrand van Burgsteden, Nate Zwald and Lynsay Henderson