Answering Genomic Prediction Questions
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.
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.
Does the technology have limitations? Yes it does. I discuss those in my article that appeared in the Brangus Journal, “The Dance Steps of Genomics Part I: Understanding Genomic Prediction.”
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.