How are EPDs Obtained?
By Dr Sara Via
The articles in this folder concern various aspects of how EPD values are obtained. Fortunately alpaca breeders don't need to know the grisly statistical formulas, because the actual analysis has to be done by card-carrying statisticians. However, it is important to be aware of the factors that affect the quality of the data and the accuracy and precision of the estimates (an "estimate" is statistical jargon for a value that is obtained from a statistical analysis-- it is not a "guess"). Again, the articles are grouped by industry- cattle, swine, and sheep. Many of the articles are fact sheets from the organizations involved in the data collection and analysis. Several are from an excellent book, The Beef Sire Selection Manual, edited by Dr. John Pollack, Department of Animal Science, Cornell University (see www.redangus.com ).
Articles: The following articles are graded according to their complexity.
One star * = simple
Two stars ** = moderate
Three stars *** = technical
General
1- Basic Concepts of Genetic Improvement, Dr. Ronald 0. Bates, University of Missouri-Columbia, and Dr. Erik R. Cleveland, University of Hawaii at Hilo, National Swine Improvement Federation (NSIF) Fact Sheet #2. Dr. Bates introduces the essential genetics needed to understand breeding values. He starts with the familiar one-gene model, where there are two alleles (forms of the gene, i.e., A and a) that produce the genotypes AA, Aa, or aa, which usually correspond to discrete phenotypes (like red, pink or white flowers). These are the only options in this simple model. However, most traits of interest to breeders (like fiber diameter or body weight) are influenced by several to many genes, and this produces a continuous distribution of phenotypes (i.e., fiber diameter can be anything between 10microns and 40microns). Dr. Bullock does a good job of simply introducing this additional aspect of genetics (called "quantitative genetics" because the traits vary in a quantitative rather than qualitative way).*
2- Basic Genetic Principles, Dr. Darrh Bullock, Department of Animal Sciences, University of Kentucky. Beef Sire Selection Manual, Chapter 8. Another introduction to basic genetics, then quantitative genetics, with examples from cattle.**
3- Genetic Parameters and Their Use in Swine Breeding. NSIF Fact Sheet #3. A great continuation of article #1 with essential information about quantitative genetics that is used in EPD estimation. Introduces terms such as breeding value, heritability and genetic correlations among traits.*
4- Estimating Genetic Merit. NSIF Fact Sheet #8. Review of why visual appraisal of phenotype is inadequate for determining genetic merit, discussion of why genetic relatives (i.e. progeny, siblings) are used to estimate genetic value of an individual. Introduction to the method of Best Linear Unbiased Prediction (BLUP), which is the statistical method used to actually get the estimated EPDs. When you say "I used BLUP for this analysis", statisticians will bow down. **
Cattle
5- Expected Progeny Differences, Part I. Background on Breeding Value Estimation, Dr. John Evans, Professor of Animal Breeding, and Dr. Dale Buchanan, Professor of Animal Science, Oklahoma State University. This is a simple and very informative introduction to the history of genetic evaluations in cattle.*
6- Expected Progeny Differences, Part II. Growth Trait EPDs, Dr. John Evans, Professor of Animal Breeding, and Dr. Dale Buchanan, Professor of Animal Science, Oklahoma State University. A simple introduction to EPD estimation in cattle.*
7- Cattle EPD Values, Dr. J.M. Rumph, Department of Animal Science, Montana State University. Beef Sire Selection Manual, Chapter 7. After introducing what EPDs are and why they are useful, Dr. Rumph goes into various important aspects of EPD estimation, including accuracy, adjustment of the data for differences among ages or genders, the importance of the "contemporary group", and then a few more advanced topics. This is a really good article, but it is somewhat technical.***
8- Data Collection and Interpretation, Dr. Jennifer Minick Borman, Department of Animal Science, Kansas State University. Beef Sire Selection Manual, Chapter 9. This is a terrific companion to the previous article from the same book. Dr. Borman discusses why the accurate collection of information on EVERY ANIMAL is so important. The examples are all for cattle, but you can imagine how it would work for traits more relevant to alpaca.**
Swine (all from National Swine Improvement Federation)
9- Performance Records and Their Use in Genetic Improvement. NSIF Fact Sheet #5. Excellent review of data collection for EPDs, review of contemporary groups, and so forth.*
10- Performance Records on Relatives. NSIF Fact Sheet #7. Review of accuracy,precision and excellent discussion of "connectedness", that is to say, the presence and measurement of relatives in different herds. This is what allows the extraneous effects of different environments to be removed from the EPD estimates.*
11- Across Herd Evaluation of Swine. NSIF Fact Sheet #12. Discusses how EPDs are used to compare individuals from different herds. Ideally this is what we as alpaca breeders want (contrast to article #12).*
Sheep (all from National Sheep Improvement Program)
12- What are FEPDs? NSIP Fact Sheet #5. FEPD’s are Flock EPDs, which estimate the relative merit of individuals only within the same flock (contrast to #11).*
13- Accuracy- What is it? NSIP Fact Sheet #1. Another discussion of accuracy and how it is used to interpret EPD estimates.*
14- Contemporary Groups- Overview. NSIP Fact Sheet #2 Further discussion of the definition and use of contemporary groups in EPD estimation.*