I received the following comments and questions from a beef
breeder.
1. From a producer
perspective I experienced the implementation of NCE [National Cattle
Evaluation] from the beginning to the Genomically Enhanced phase we are
experiencing. I saw line breeders with
lifetimes of work begin to outcross in order to keep up. From the stuff I have read from Dr. Wilhelm
two things stuck me. Maybe my
understanding of these is out of context but he felt one of the positives of
numerical breeding was going to be the elimination of line breeding. The second was his statement that creating
some kind of index or indices with the merging the individual traits would be a
mistake. ARE THE UNINTEDED CONSEQUENSES OF ELIMINATION OR DEVALUING OF LEGACY
GENETICS AND LEGACY BREEDING METHODS SOMETHING TO WORRY ABOUT or conversely are
the consequences of a narrowing toward what is bigger and better something to
worry about?
Expected progeny differences (EPDs) from NCE are simply a
tool. The breeder makes the decision about which direction to move the bell
curve, either towards “bigger and better” or in the opposite direction.
The purpose of linebreeding is to increase the frequency of
favorable DNA variants. EPDs accomplish this same purpose. However,
linebreeding has some serious shortcomings, namely that while the frequency
(and homozygosity) of favorable alleles are increased, the frequency (and
homozygosity) of many unfavorable alleles are also increased. This leads to
inbreeding depression, or the reduced fitness of inbred animals. The growth
rates and, most costly, the fertility of linebred cattle is reduced.
Linebreeding requires very strict culling, and in most cases, cattle operations
cannot deal with the economic losses of such high culling levels and decreased performance. Of the more
than 10 inbreeding lines started at the USDA research center in Miles City,
Montana, only 1 has survived the effects of inbreeding depression. EPDs
accomplish these same goals, without the negative consequences.
Selection decisions from pedigree-based EPDs typically
resulted in between family selection, i.e. the same sire families were selected
again and again. If left unchecked, this leads to narrowing the gene pool.
However, genomic prediction allows us to practice within family selection and
identify the genetic merit differences between close relatives, such as full or
half siblings. If the narrowing of genetic diversity is a concern, then genomic
prediction and GE-EPDs are actually a tool to help avoid losing genetic
diversity (pick the best animals from many different families).
Personally, I am not concerned about the “loss” of legacy
genetics. First, we have a cryopreserved genetic bank in Fort Collins, Colorado
that has over 60 years of genetic material (mostly semen). Second, we have lots
of genetic and phenotypic diversity available within breeds, we have tools to
manage and correct consequences of the narrowing of the gene pool, and at the
end of the day, we have crossbreeding to restore genetic variability.
The theory behind selection indexes is even older than that
behind EPDs. Selection indexes are simply the most effective way to make
progress for multiple traits. What is the most important trait? What trait should
be optimized or maximized? In my mind, the answer is quite simple: Profit. Just
as a weaning weight EPD describes progeny performance differences in pounds,
economic selection indexes describe profit differences in dollars.
2. It is obvious I
blame associations, animal science, Genomic companies for being in such a hurry
to introduce this technology very little thought was given to the effects of
training biases. Was the merging of EPDs
and Genomics more about getting ahead than getting it right?
“If you build it, they will come.”
– Cheesy, but applicable
line from Field of Dreams
If you ask breed association leadership, all of them will
attest that increased DNA testing and producing the data needed to create
genomic predictions does not increase until there is a genomic-enhanced EPD
available. I don’t know and won’t speculate on the psychology behind this, but
time and time again, the rate of genomic testing did not increase until after a
genomic-enhanced EPD was released.
Further, this question assumes that breed associations and
research partners got it wrong. I can firmly reject this assumption. The
scientists involved in this process were very careful and conscientious. Further,
the theory behind genomic prediction has been in place since 2001. Although the
method was not used in the beef industry till 2010, the idea was already 9
years old by this time.
3. I think you all
have acted more like cheerleaders/salesmen than responsibly educating
commercial and seed stock producers about the limitations of the
technology. This isn’t a personal you it
is for everyone pushing the technology.
The stated goal of my extension program is “Communication
for Rural Innovation” borrowed from the book by the same name.
Encouraging technology adoption, whether that be 40-year-old EPDs or newer (but
validated) genomic predictions, has been a goal of mine from the first day on
the job. I do not and will not apologize for that.
Why?
Because from my vantage point, the beef industry must more
fully embrace technology to remain competitive. I discuss embracing technology
here, here, and here. The chicken and pork industries are
vertically integrated and a small number of decision makers control the genetic
selection of those production systems. These selection decisions are
data-driven and scientifically based. These industries have seen significant
genetic progress and profit improvement. I think one of the beauties of the
beef industry is the lack of vertical integration, but I fear if there is not
sufficient technology adoption, integration may become inevitable.
Further, I am a proponent of sustainability as defined by NCBA. Sustainability is increased profitability, decreased environmental
impact, and improved social acceptance. In a different definition, the UN Food
and Agriculture Organization (FAO) defines sustainable practices as
environmentally non-degrading, technologically appropriate, economically
viable, and socially acceptable. The adoption of technology, including genomic
technologies, allows beef producers to keep doing what good producers have
always done- raise beef in a sustainable manner. Every time we adopt
technology, agriculture becomes more sustainable.
In my opinion, technology adoption is an American tradition.
I am proud to encourage the survival of this tradition, but I try to help beef
producers think through the decision processes required to make sure the technology
matches their operation.
4. Is there re
evaluation- retraining and third party validation work that could be done to
address some of the concerns?
Over the last 7 years, a person has been hard pressed to
attend an educational event organized by a breed association that did not
discuss training, retraining, and validation of genomic predictions. I have
been to various presentations by Dorian Garrick, Bruce Golden, Mahdi Saatchi, Kent
Anderson, Dan Moser, Ignacy Mistal and others that have discussed in detail
these processes. There have been minor hiccups along the way, but these were
corrected in a matter of weeks, not months or years. Further, the switch to
single-step genomic prediction will better integrate pedigree and genomic data,
and will remove the need to re-calibrate genomic predictions.
Taking Angus for example, employees of Zoetis have trained
genomic predictions. Independently, Angus Genetics Incorportated staff have
validated these predictions. In Simmental, Dorian Garrick and Bruce Golden have
trained genomic predictions and Simmental staff then validate these
predictions. No genomic prediction can be used, unless it is first validated.
I realize that this blog post may not persuade the author of the questions and comments, although I hope it does. Regardless, I hope this post will inform the broader beef community.
Additional
questions or comments? Feel free to contact me.
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