For years there has been an unspoken awareness that some herds appeared to be able to “work the genetic indexing system.”  These herds clearly understood how genetic indexing systems work in their country and how to manipulate the composition of their herd in order to achieve the highest ranking possible for some top members of the herd.  It was possible to pick these herds out, they had top females and even though they had many sons sampled out of them, seldom were able to produce a top ranking sire, especially for total merit.  This scenario played out in all major countries that use the BLUP (Best Linear Unbiased Prediction) system.  Fast forward to the top total merit rankings since genomic testing has become available.  At first glance it appears there might be a lot less of those animals on the list.  The question is: “Has genomics knocked out all of these animals from the top lists?”

How It Was Done In The Past

First it is necessary to understand what was happening in the past.  Since indexing calculations are based on the variance compared to herd and genetic base, the greater the difference the greater the gain or loss in the result.  Putting that into practice takes two areas: conformation and production evaluations.  The following is a breakdown on how both were done.

Conformation

In order to get maximum results from their genetics programs, many top programs needed to have their top cattle score significantly higher than the other animals scored that same day.  While many people deemed these herds “Hot Houses”, in reality they are just working the BLUP system to get maximum results.  Since the calculations also took into account the genetics of the other animals scored, these “hot house” herds needed to have daughters of high type bulls that would score lower than the selected cattle that were typically sired by bulls with lesser conformation scores.  For example, you have a low value cow sired by a +14 conformation sire that goes 79 points, and a high conformation cow sired by a +6 conformation sire that goes 86 points.  This would provide the selected cow with the greatest difference over the expected value and have significant improvement in their EBV for conformation and thereby in their overall total merit.

It’s in these herds that you may have seen a “good group” and a “bad group” of the herd, with a corresponding difference in management and presentation of the groups.  While it’s normal in any herd to have the high value or “family favorites” get some level of preferential treatment, these herds took it to a new level.  While this sounds bad, in reality it was necessary in order to achieve top rankings.  For the classifier visit the good group was show ready and the bad group was ready to head for beef.  (Though if you read “Tom Byers: It’s Classified” you realize that this really does not make that big a difference for the professional classifier).

In contrast to the “hot house” herds who try to have a high herd average score (for example the average 2yr old score of 83+ points) find it very hard to get high indexing conformation females.  With very little difference in scores from the top to bottom of the herd, there is less herd variance, contributing to a lowering of their overall rankings.  Since these herds where not a cross section representation of the breed population and BLUP treats them as if there were, these cattle actually get somewhat penalized for being a member of a great herd.

In order to have maximum impact, herds wanting to have high index’s needed to have maximum within herd variance. This meant that they have to have a true cross section of the breed present in their herd, as opposed to just the best of the best, like many of these breeders would have liked. It’s also for these reasons why niche type sire sampling programs need to be used in all types of herds not just high conformation breeding programs.

Production

The story is not that different on the production side.  Here the comparisons are for milk, fat and protein yields on a within test day basis.  Adjustments are made for a cow’s age, lactation number, stage of lactation, month / season…etc.

In order to maximize the increase in production genetic evaluations, these “hot house” herds needed to  have underperforming  daughters of high production sires, that were being out produced by the selected females that were typically sired by more balanced sire who’s production index may not be as high.  In Canada, this is where you would see females with very high (i.e. +200 and more) BCA deviations.  Sometimes you would see deviations that were greater than even their herd average BCA.  You ask yourself “How could one cow on the same feed, same treatment, same exact program, produce twice as much milk as another cow?” While it sounds unrealistic, it was necessary in order to gain maximum results.  All breeders have seen cows that can out produce herd mates by 30, 40 even 50%, but when you see them doing more than double (100%) it raises questions in the minds of people with practical cow sense.  Hence why some herds are stamped as “Hot House’s.”

How Genomics Has Changed Things

relative weighting for Direct Genomic Value (DGV) compared to traditional Estimated Breeding Values (EBV)With the introduction of genomic evaluations in August 2009, the effects that any “hot house” efforts can have has been reduced in the genetic indexing systems.  This is because for young cows in first or second lactation, the relative weighting for Direct Genomic Value (DGV) compared to traditional Estimated Breeding Values (EBV) is roughly 55:45 (Source: Canadian Dairy Network).  What that means is that if a “hot house” cow would have had a 300 point jump from these types of efforts, they now would only see a 165 point jump.  While it would still have an effect, genomics has greatly decreased the “hot house” effect. Remember that the female family members of each cow are being re-evaluated as well.  Additionally those females formerly lower on the listings, but that were in herds where practices are normal, could now move up the genetic index rankings.

The other factor that Genomics has brought into play is that, if a particular animal is not gifted with the best genomics her parents had to offer, she will also see a significant drop.  So let’s say that a cow has an EBV-PA of +2500 LPI or TPI, but her genomic panel comes back with a LPI or TPI value of +1500.  That cow would see a drop of about 450 points.  Dropping her  to an LPI or TPI of +2050. This takes her  from being near the top of the list to almost out of consideration.  All this is outside the control of any on-farm practices.  It’s for these reasons I am sure that some owners now get nervous when opening their genomic results letters.  This single test can have the biggest effect on the genetic profitability of any cow.  It can even have a greater effect than the classification.  With GLPI’s and GTPI’s now over 60% reliable, adding animal performance information now has much less influence than in the past.

The Bullvine Bottom Line

The great news is that genetic indexes that contain animal genomic information are not as influenced by preferential treatment or herd variance as traditional genetic indexes are.  Since genomic values are based on evaluations of thousands of cattle in many different herds, in many different environments, and in different countries, the ability of a “hot house” to greatly change results has been significantly diminished.  That is not to say it has been totally removed.  Remember that 45% of the new GLPI formula is still based on an animal’s performance compared to contemporaries.  Therefore, these efforts will still have an effect.  It is for these reasons that you see some previously prominent cows and cow families are now absent from the top female lists.  Am I saying that these cattle may not be great investment?  No, what I am saying is consider these factors when making your purchase decision.  Do your homework before selecting, breeding, merchandising or buying.  GLPI’s, GTPI’s and DVG’s will help you make more informed decisions, but remember they are just a tool.
The Dairy Breeders No BS Guide to Genomics

 

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