Introduction to Guided Readings on EPDs
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Introduction to the Use of Statistical Genetics in Animal Breeding.
By Dr Sara Via
University of Maryland
Since animals were first domesticated, breeders have been asking the same fundamental question: “How can I produce the animal that achieves my goal most efficiently and in the least time?” Regardless of whether that goal is to breed dairy cows that give more milk, pigs with leaner muscle, or sheep with finer fleece, the first step in any breeding program is to identify individuals that will pass their superior characteristics to their offspring. This is why EPDs (Expected Progeny Differences) were developed. EPDs are used by all major livestock industries, because they are the most effective tool available for animal breeding. To introduce alpaca breeders to this EPD technology, I have carefully chosen the documents in this annotated set.
Identifying superior individuals for breeding purposes seems like it should be simple—just pick out the ones that have the most desirable characteristics! Indeed, this is how animal breeding was done until the re-discovery of Mendel’s laws of genetics in the 1920s. As breeders embraced the new science of genetics and gained a deeper understanding of why offspring tend to look like their parents, pedigrees took on a greater importance in animal breeding and the idea of “bloodlines” began to guide breeding decisions.
Many animal breeding programs still rely heavily on these two basic methods-- picking animals for breeding that have the most desirable trait values (good conformation, correct behavior, speed, etc.) and using pedigrees to capture information about bloodlines. However, two indisputable facts reduce the accuracy of this approach. First, an individual’s phenotype is affected by both its genotype and the environment in which it is reared. Only the genetic contribution can be passed on to progeny, and an individual’s genetic value cannot be viewed directly. Secondly, only a fraction of an elite ancestor’s genes are passed on to its progeny. The probability that an individual will inherit particular desirable genes from a parent is only 50% , and is only 12.5% from a great-grandparent.
The principles of statistical (quantitative) genetics were first developed and applied to animal breeding in the 1940s. At that time, geneticists linked Mendel’s laws with the analysis of traits that are affected by multiple genes, and that therefore vary continuously (like body weight, fiber diameter). In contrast, Mendel’s laws only apply directly to traits that vary discretely (like round or wrinkled peas) due to the action of a single gene.
The new methods of quantitative genetics were a breakthrough for animal breeders because they allowed the genetic value of an individual to be estimated separately from the effects of the environment. These statistical methods were rapidly adopted by both animal and plant breeders. Between 1940 and the present, livestock and plant breeders have invested millions of dollars on research to improve the accuracy of tools in statistical genetics. With huge sums of money at stake, these industries use statistical genetics because it works!
Developed in the 1980’s, the Expected Progeny Difference (EPD) is the crown jewel of the available genetic tools in animal breeding. EPDs represent an advance over earlier methods for estimating the genetic value of individuals (i.e. progeny testing), because EPDs utilize information from all animals in the herd in the context of the entire pedigree. The data are in and the results are clear. Relative to the time when breeding decisions were based mostly on pedigree analysis and show results, using EPDs to inform breeding decisions has produced dramatic increases in the quality of cattle, swine and sheep. The profitability of these industries have risen in parallel.
Alpaca breeding in the US is a very young industry. We can benefit from the decades of research by geneticists in the cattle and sheep industries, and take immediate advantage of the same cutting-edge genetic methods that they use. Using EPDs as the cornerstone of a breeding program, alpaca breeders can dramatically increase the rate of genetic improvement in their herds. This WILL increase profits. By using EPDs to make breeding decisions, the progeny produced every year will be closer to the elite breeding ideal than their parents, whatever the breeding goal of the individual breeder may be.
Dr. Sara Via, a statistical geneticist at the University of Maryland and an alpaca breeder, has compiled a set of papers for us about EPDs. They are organized into five groups, each of which has a tab above. For each group of readings, Dr. Via has provided a guide with a brief description of each article.
The five folders of documents presented here contain fact sheets and other information from livestock industries that utilize EPD technology.
Folder 1: What EPDs are, and how they are used in animal breeding
Folder 2: How are EPDs Obtained?
Folder 3: Why use EPDs for genetic Improvement?
Folder 4: Advanced EPD use:selecting multiple traits, EPD in the showring.
Folder 5: Who is currently estimating EPDs for alpacas?
The introductory text in each folder, written by Dr Sara Via, contains a list of the documents and a brief description of each one with an informal rating of its level of difficulty.
One star * = simple
Two stars ** = moderate
Three stars *** = technical
The documents are organized by industry (i.e., cattle, swine, sheep). As you read them, you will see a lot of repetition of the basic concepts, underscoring how the same methods can be used to read very different breeding goals. You may want to read only the articles for one industry, then delve into the other articles as needed if you would like to read another rendition of certain explanations, or to see additional examples.