Genetic Testing of Beef Cattle for Parentage, Inherited Traits, and Enhanced EPDs
Doug Mayo, Jackson County Extension Director, Felipe Alves, PhD Student, UF Department of Animal Science, Angela Gonella, UF/IFAS Cattle Reproduction Specialist, and Mark Mauldin, Washington County Extension Ag Agent
Breeding animal selection has been a passion of cattle ranchers for generations. These selection decisions affect the progress of the herd for generations. For centuries, the best information available was the pedigree of an animal and their individual performance. The next big jump in the ability to accurately predict the performance of an animal came about when Expected Progeny Differences (EPDs) were introduced. EPDs were based on large databases within single breeds that pooled pedigree and individual performance into a predictor of performance. There are now newer technologies available that further enhance the accuracy of animal sections by examining the genes in their DNA. When combined with EPDs and pedigrees, DNA testing can further increase the accuracy for predicting future performance of an animal. DNA testing can also be used to test for parent verification, genetic disorders, and other heritable traits. The following video provides a brief overview of this relatively new technology.
The process of DNA testing is quite simple, as it only requires blood or tissue samples from the calf and their potential parents. Sources of tissues for DNA testing include tail hair, semen, and tissue from ear notches, with the majority of samples able to be shipped at room temperature. Most breed associations have adopted DNA tests for parent verification, and a variety of other traits. DNA testing ranges in price from $15-90 per head, with parent verification being the cheapest, to the whole gamut of genetic disorders and evaluation of thousands of genes that affect different types of cattle performance.
The following video, produced by Dr. Matt Spangler, University of Nebraska, demonstrates how to collect samples for DNA testing of cattle.
One of the age old problems facing registered cattle producers was knowing for certain who the parents, in particular the sire, of a given calf were. While it is fairly simple to determine the mother (dam) of a calf, even that can get confused occasionally. However, everyone who has ever raised cattle with multiple bulls, or bulls in neighboring herds knows there can be accidents. One method to have more control for a known father (sire), was to simply break up the breeding herd into single sire groups. However, even that method breaks down when bulls fight through fences, or break in to breed cattle in heat. Then artificial insemination (AI) was introduced, which further confused known parentage, as calves are seldom born on time, based on a 283 day calendar. No matter the system, it can be difficult to know if a calf was sired artificially or by the local herd bull. Tissue such as blood, tail hair, or a small sample of skin from the ear from a calf can be sent to a lab an analyzed for gene or DNA comparison with both parents. The main goal is to increase the accuracy of pedigree information, therefore, providing breeders and their customers with reliable, accurate information. Parent verification is feasible for both purebred and commercial operations to help address situations such as multi-sire breeding pastures, artificial insemination, embryo transfer followed by clean-up bulls, calves switched at birth, and ambiguous data records.
However, if you are going to spend the money on parent verification, you might as well get more useful information from these samples. There are a number of traits that can be predicted from a DNA test, such as hair coat color, horned vs. polled, or the absence of genetic deformities. Breeders can ensure cattle are “homozygous black” (both genes are black, so offspring are black). The same is true for the polled gene. Cattle that only have one dominant black gene will have a black hair-coat, but could have red offspring when bred to cattle with a mixture of red genes. The same holds true for the horned gene. DNA tests also look for rare but serious genetic disorders such as Curly Calf Syndrome (Arthrogryposis Multiplex), Fawn Calf Syndrome (Contractural Arachnodactyly), Dwarfism, Developmental Duplication, Double Muscling, Water Head (Neuropathic Hydrocephalus), Marble Bone (Osteopetrosis), Blue-eyed calves (Oculocutaneous Hypopigmentation), and other disorders that are caused by recessive genes in a breed. Cattle can be carriers of a recessive disorder, but not express the gene until they are mated with another carrier, and then ~25% of their offspring will express the disorder.
Genomically Enhanced EPDs
Every producer has experience with selecting beautiful heifers or dynamic bulls for breeding that have below average quality offspring. The same thing can happen also happen with low accuracy EPDs. The pedigree of a bull and the performance of his whole family may be excellent, but the mixture of the genes he received don’t pass along the family’s best traits. You can use all of the information available and still not get the results you were looking for. The opposite can also be true when you get a real gem of a calf from average parents. This random assortment of genes being passed from generation to generation is what makes cattle breeding so challenging.
The most valuable information that can be gained from DNA testing is that ability to more accurately predict EPD performance. Genomic tests sample around 50,000 gene markers (alleles) for traits known to affect cattle performance. It is not uncommon for the accuracy of EPDs of sale bulls, with no performance data from offspring, to be in the 9-23% range. This is because the expected performance is predicted solely based on the pedigree performance an animal’s family. With Genomic Enhanced EPDs (DNA testing added) the accuracy can double, which is similar to adding the performance data from 10-20 offspring to the prediction accuracy. The actual EPD can increase or decrease once actual offspring performance information is added to the database. Genomic testing improves the accuracy of the pedigree based EPDs, because you have more information. Genomically Enhanced EPDs simply help ranchers make more informed decisions about the best animals to keep for replacement heifers, or the best bulls to use as sires in their herds. The information provided may be similar, but the difference is that it is more consistent.
There is new technology to help breeders and commercial producers make more informed decisions through genetic DNA testing of cattle. DNA testing can confirm that the parents are who you thought they were and prevent embarrassing mistakes of incorrect pedigree-based data. DNA testing can confirm basic traits of importance, such as guaranteeing the hair coat color and polled status of future calves. It can also eliminate carrier animals that can have offspring with rare genetic disorders. DNA testing can also improve the accuracy of EPDs and indexes that are so important for sire and replacement heifer selection. Contact the breed association of the type cattle you raise to find out the types of testing services they recommend. There are even tests designed for commercial cattle with multiple breed backgrounds. There are a variety of options available at varying cost levels, so do your homework before you start collecting samples.