By: Joe C. Paschal, Professor Emeritus and Livestock Specialist
Similar to many of the Texas Adapted Genetic Strategies publications, this one has evolved from a presentation at the Texas A&M Beef Cattle Short Course in the early 90s. Dr. Stephen Hammack was asked to give a presentation on “Do Expected Progeny Diff erences Work?” in the General Session. He spent several weeks looking at research reports from all across the US and even internationally on selection results using high and low EPD bulls for various traits proving that EPDs do work in selection. Expected progeny differences (EPD) and now Genomic Enhanced EPD are the result of livestock breeders looking for more accurate ways to compare animals in a breed rather than simply looking at them. Knowing ages and weights improved selection and accounting for differences in the way they were raised improved selection accuracy through the use of adjusted records and ratios.
The forerunner of EPDs were called Estimated Breeding Values (EBV) which used ratios within contemporary groups and added the animals own record to those of its relatives and progeny. It also incorporated heritability (h2), the fraction of each trait under additive genetic control. The main limitation with EBV is that they could not be compared across herds. More improvement in genetic evaluation came with the development of EPD in the late 1970s. EPD has more scope and precision and can be used across contemporary groups.
In 1971 the American Simmental Association published the first National Sire Summary. The ASA Summary only included sires since bulls had more calves and could be widely used through AI. The summary required large numbers of progeny in contemporary groups where at least one widely used sire (reference sire) was included. These types of summaries were conducted for several years, until a model to include ALL the animals in a breed was developed. Any animal with a record could be tied together in a genetic relationship with all other animals. The widespread use of breed registry performance records tied to their pedigree allowed EPD to be calculated for all traits on every animal in the breed. Two things were important to note:
1. The pedigree had to be accurate and
2. Accurate performance records had to be reported.
The first Brahman National Cattle Evaluation was published in 1991. The inclusion of genomic information through SNPs (as done in ABBA) is only used to verify the first point listed earlier, to verify the pedigree is correct so that animal relationships can be accurately characterized. On average, parents pass along 50% of their genes while grandparents pass on only 25% of their genes (50% x 50%) to their grand off spring, but these are only averages. In actuality, some animals are more (or less) related than we expect based on their DNA. More importantly which genes were passed? Genes to improve a trait or to reduce it? That is the real promise of genomics, especially the Brahman breed. To get there though, what is needed is accurate and timely records in correct contemporary groups without selection bias over time due to culling. There are EPD for many traits, some would say perhaps too many. Some traits have no commercial economic value (frame score) others are vitally important (calving ease, longevity).
Now there are even more with EPD for udder, teat and foot size and shape, even hair shedding! That last EPD is targeting the current market that needs Brahman genetics but also wants docility, moderate size, and carcass merit. Many breed associations, including ABBA, have developed indexes of a set of EPD traits that should make selection easier (one value compared to many). For an index to be useful it should include the traits that affect (positively or negatively) profitability because an index should refl ect DOLLARS in income. The American Angus Association has one of the most successful indexes, $BEEF. It was developed for folks raising and feeding Angus cattle, not for those that raise and sell them at weaning although it is used for both very successfully. ABBA has two indices, $Queen (a maternal index) and $Bull (a terminal index). They are not perfect, and more BHIR data is needed so that the indexes can be refined, but they are a beginning. EPDs denote a difference between two animals, not the actual performance of the progeny. All breeds publish a list of EPD for all their traits (you can find it on Digital Beef) along with a listing of EPD by percentile (50% is average) so you can determine if an animal is in the top or bottom half of the breed for an EPD or Index value.
Along with every EPD there is an accuracy value that should be considered. Animals with more progeny will have higher accuracy values as will EPD for traits that are high in heritability. The accuracy is calculated from the amount of information from relatives (progeny are more useful than others) and the heritability of the trait. It provides an indication of how likely an EPD is to change when new records are added. The possible change is greatest with few records and low heritability, highest with large numbers of records and high heritability. Only EPDs have accuracies, Index values do not. However, Index values are calculated from genetic data and are usually very conservative in their estimates. The advent of genomics to improve both EPD and accuracy has been a huge bonus. Some breeds (US Holstein and Jersey) have enough records to assign productive values (with positive or negative impacts) to certain SNPs for yield or milk fat.
Animals with those SNPs that have impacts have them added to or deducted from their EPD. As more beef breeds gather more performance records and tie that performance to SNPs, they will also be able to adjust their EPDs based on SNPs. At present Brahmans are not using this technology in their EPD calculations but Angus and others are. The Brahman breed needs to make a concerted effort to make this happen. Whole Herd Reporting, along with the whole genome sequencing, will make it happen faster. At present, the main benefit of genomic testing to EPD determination is the improvement in accuracy through more precise genetic relationships using SNPs. Beyond a parent off spring relationship, which is 50% (or identical twins or clones which is 100%), relationships between other relatives have usually been estimated as an average (25% for half-sibs, 50% for full sibs) even though in reality, the range could be 0 -50% and 0-100%, respectively.
Most relationships are close to average but many are not and that can change the accuracy, especially with low heritability traits, traits with few records, or little or no progeny data. Using this technology (as in the current Brahman EPD evaluation) improves the accuracy. I do not know what the effect is for Brahman cattle but in Angus, it is quite large. Table 1. lists the number of progeny equivalents required to have the same level of EPD accuracy for several traits if SNPs were not incorporated in the Angus evaluation. Likely it would be similar for Brahman.
EPDs and now Genomically Enhanced EPDs, can be directly compared for all animals (bulls and females) from all locations and management conditions across all years within an entire breed, even across breeds. It is the most accurate estimator of true breeding value Brahman breeders have available, learn to use them!
