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What progressive dairy producers need to know about inbreeding
Concerns associated with inbreeding have recently received more air-time than usual due to genomics.
Read on to have your questions answered about this popular topic.
What is the best way to define inbreeding?
Inbreeding is a measure (or expected measure) of relationship between two individuals. Technically it is
the percentage of genes that are identical by descent, meaning that an animal shares a copy of a gene
from both the sire and the dam, which can be traced back through the pedigree to a common ancestor.
What is the difference between ‘inbreeding’ and ‘line-breeding’?
Technically they are the same thing. “Line-breeding” describes focusing on certain lines (or individual
animals) that have particular traits of interest. “Line-breeding” is a term generally associated with a
planned mating, or a conscious effort to increase the likelihood of particular genes or outcomes. Race
horses are a good example of this. “Inbreeding” is basically the same thing, however, usually has a
negative connotation associated with it because it often happens without planning. “Inbreeding” is a
term commonly used to describe the negative effects of related matings on an entire herd or breed.
Why is there concern about inbreeding?
As animals get more related to each other, inbreeding depression occurs for certain traits, meaning that
performance is lower than expected. While this is not ideal, it must be weighed against genetic gain.
The trend for inbreeding is going up – are we reaching a critical level?
One of the most common misunderstandings about inbreeding is that there is a critical level that we
shouldn’t exceed. There is no research supporting this claim – instead the effects of inbreeding
depression appear to be linear according to the table below.
Table 1. The effects of inbreeding depression on certain traits, (Source: Bennet Cassel, Virginia Tech)
Therefore going from 6% to 7% inbreeding has the same ‘cost’ as going from 1% to 2%.
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So with $23/lifetime of reduced income, should I try to avoid inbreeding?
No – what we need to do is maximize profit. With $23 lifetime cost/% inbreeding, it is easy to over-react
and try to avoid inbreeding at all costs. But remember, one of the reasons breeds are becoming more
related is because there are some really good genes in the population that have a highly favorable
impact on profit as well! Simply put, if we have one cow to breed and three sire options, one being an
‘outcross’ or un-related to the cow, but genetically inferior, and another being highly inbred, but a
genetic standout, it is easy to see how the percent inbreeding is only one factor to consider.
Table 2. NM, Inbreeding and Adjusted NM for level of inbreeding for a particular mating
In the above example, AltaCASCADE and AltaLEO are very close for genetic merit. However, when
considering the mating of this particular cow to each of these two bulls, we must consider how the NM
level will adjust based on the inbreeding of each mating. In this example, AltaCASCADE will ‘re-rank’ to
have a better than expected outcome because the inbreeding level with the cow of interest is 3
percentage points less than that of AltaLEO. Almost never will a far genetically inferior bull, such as
AltaTRIANGLE, re-rank to be higher than the other two sires. This example shows why ‘pedigree mating’
is recommended, as it accounts for these adjustments.
Is the rate of inbreeding going up?
Yes, the rate of inbreeding has been increasing ever since the widespread adoption of AI in the 1950’s
and 1960’s. This isn’t necessarily a bad thing. Very few producers would trade the productive cows of
today for cows they had 25 years ago, even though today’s cows are more inbred. This is because
today’s cows are more efficient, profitable production units due to selection for better and better genes
through the use of AI.
Is the extra attention on inbreeding in the genomic age warranted?
Before genomics, sires were usually 5+ years old before they had widespread usage. However, with
genomics, semen is widely used when a bull is as young is 14-15 months. This change means the
breeding age of daughters of a bull, and the age at which semen is available from sons of that same bull
are much more aligned. Take an example such as AltaMETEOR. Some of the early Advantage® herds
have daughters in their heifer and two-year-old breeding pens right now, and at the same time, the first
AltaMETEOR sons have semen available. This doesn’t change the inbreeding discussion, but it does
mean that it should be a bit more carefully managed, as we certainly don’t want to breed a daughter of
AltaMETEOR to one of his sons!
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Won’t the use of genomic sires speed up the rate of inbreeding?
Yes, on a breed level it will, but we are also increasing the rate of genetic gain in an incredible way! So
our goal should not be a ‘less inbred’ cow, but instead, the most profitable cow. Over the past 25 years,
we have created more inbreeding, but also more profit. The same is true now with genomics, except
that we should now expect both (inbreeding and genetic gain) to increase at a rate of two to three times
what we experienced in the past.
Doesn’t that mean that we can expect to get to 10% inbreeding level on a breed-wide basis soon?
Yes, and while geneticists are working on ways to balance the inbreeding level with genetic gain on a
breed-wide basis, you should really only be concerned with inbreeding vs. genetic-gain in your own
herd.
What do the figures “EFI” and “GFI” mean?
EFI is “expected future inbreeding”. To reach an EFI number, scientists take a random sampling of
animals from the breed and consider that a particular sire is bred to each of those animals – then the
inbreeding level of each theoretical mating is calculated, and averaged across the entire sampling.
Meanwhile, “GFI” (Genomic Future Inbreeding) does the same thing but is more specific because it only
looks at the population that has been genomic tested, and therefore, can look at exactly what genetic
profile an animal has instead of guessing which genes it got from its sire and dam. Neither figure is
particularly useful for an individual herd.
Why are GFI and/or EFI not good indicators for measuring inbreeding for my herd?
A sire that is an ‘outcross’ for your dairy might be highly inbred for another dairy. Take the example
above from Table 1. AltaLEO (6.1% EFI) is a son of AltaMeteor X Nifty, and AltaCASCADE (6.3 EFI) is a
Domain X Ramos. While their EFI is similar when mated to average animals in the breed, it may be highly
different for your dairy and your neighbor’s dairy. If your dairy used AltaMETEOR widely a year ago, but
you never used Domain or Ramos, evidently, AltaCASCADE will be more of an ‘outcross’ for your dairy
than AltaLEO.
What traits does inbreeding have an effect on?
Increases in inbreeding are especially detrimental to health and fitness traits, with some impact on
production traits. If we were not measuring these traits, and selecting for them, we would be much
more concerned about the negative effects of inbreeding. However, as we are selecting for things like
DPR, PL, SCS, CE, and Stillbirths, we are making positive genetic gains for these traits to more than
compensate for the negative effects of inbreeding. 15-20 years ago the situation was much different
because these traits were not being selected for. Genetically, we were headed in the wrong direction in
terms of health and fertility traits due to inbreeding and the genetic correlations between these traits
and the others which were being selected for.
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Has genomics helped find more ‘outcross’ sires in the population?
Genomic selection has helped us find sires from cow families that were previously undiscovered, and
while some less related sires have been found, genomics has not diversified the breed thus far. This is
because, by definition of genomics, we are selecting for parts of the genome that have shown to have a
positive effect on profitability. By doing this we no longer are selecting for animals per say, but instead
for particular genes or SNP’s and genomic selection favors individuals that maximize the number of good
genes.
What knowledge have we gained through genomics to help us with inbreeding?
If two animals look very un-related on paper (through a pedigree analysis), that does not necessarily
mean that they do not share many genes! Likewise, two animals that look very ‘related’ to each other
can be significantly different on the genetic (genomic) level, meaning they actually inherited many
different genes. While an individual animal inherits about 50% of its genes from its dam and 50% from
its sire, the percentages can be FAR different than 25% from each grandparent, because genes are
usually inherited in segments rather than individually. With genomics we can make matings that we
know are unrelated based on the genomic profile instead of matings that we predict to be unrelated,
based on the pedigree.
Does this mean there is a new definition of ‘outcross’?
The word ‘outcross’ is extremely difficult to define. It is an animal that has a low level of relationship to
the population. However, as described above, the population that most producers should be concerned
about is their population of animals, while geneticists generally refer to the worldwide breed as the
population. Therefore, the definition doesn’t change, but the application does.
Are there special mating schemes or programs that can be used to minimize inbreeding?
There are two key factors to minimize inbreeding: 1) Accurate identification, and 2) using a tool like
AltaGPS to assess the impact of inbreeding with each potential mating. No mating scheme will minimize
inbreeding without accurate identification. For example, if you are inseminating a cow that you think
(based on records/eartag/etc) is an AltaBAXTER daughter, but she is actually an AltaESQUIRE daughter,
then you may think you are using a great sire on her with AltaIOTA. But in fact, this mating creates a
substantial amount of inbreeding in the resulting calf because you actually just used AltaIOTA on an
AltaESQUIRE daughter (both Oman sons).
Other programs that want to cross ‘lines’ within the Holstein breed may seem like an easy program to
implement, but will never eliminate inbreeding, and will do no better to prevent it than a traditional
mating scheme. Further, these programs mean that you have to use a bull of a certain ‘line’ each
generation, which can really limit the genetic progress you can make because then you are not using the
best bulls for your breeding goals.
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What tools do we have to prevent inbreeding?
One of the things rarely considered with this discussion is that genetic predictions actually already
account for inbreeding. AIPL considers the average inbreeding of the current daughters of a bull
compared to what the expected future daughter inbreeding level will be, and makes adjustments based
on these figures for the official proof value. So a bull that is expected to be highly unrelated to the
population actually gets a slight increase in his PTA’s, while a bull that is highly related is reduced.
AltaGPS has a couple of great options. First of all, the traditional way of mating with a 1st choice, 2nd
choice, and potentially 3rd choice sire works great because by accounting for the known impacts of
inbreeding listed above, it allows you to set your own inbreeding threshold, and it will not recommend
sires above that level.
The 2nd option is fantastic for larger herds that have a significant number of cows to breed within each
pen. This option, called a “Pen-Mate,” looks at things in the opposite way - Instead of trying to find the
perfect mating for an individual cow, it considers which bull(s) in your tank should NOT be used on a
particular cow. This makes it easy when you have 5 cows in a pen to breed, and would prefer not to use
5 different ‘mated’ sires. Instead, a “Pen-Mate” guides you to a bull that can be safely used on all 5
cows and still ensure the negative effects of inbreeding are minimized. Therefore, you can load 5 guns of
the same bull, and head to the pen without worrying about inseminating the right cow with the right
gun, or recording the proper information. Ask your Alta representative about this unique feature which
helps facilitate efficient breeding and accurate record-keeping while giving you the peace of mind that
inbreeding has been minimized.