Bull or AI sire selection is one of the riskiest decisions made by beef producers, especially for small herds. Genomic testing can reduce risk and accelerate herd improvement.
In a presentation for the Beef Reproduction Task Force, Dr. Troy Rowan, assistant professor, beef cattle genomics, University of Tennessee, described genomic testing as “assays that capture the complete set of genetic material of an individual.”
“In making a decision on a single animal, whether it’s buying a bull or semen, this a costly investment and one that can generate a lot of income,” said Rowan. “Bulls drive commercial genetics forward; genomics mitigate the risk of getting it wrong.”
The goal in animal breeding is to refine the challenges of bull selection. One problem with young sires, often purchased by owners of cowherds, is that they don’t have genetically evaluated offspring.
Rowan cited the dairy industry as one of the best examples of genomics at work. Prior to genomics, all dairy bulls used for AI were sire-tested. Sire-testing was better than nothing, but a bull’s first daughters were in their first lactation before progeny records were returned.
“Only then were we able to increase expected progeny difference (EPD) accuracies to make decisions on which bulls stay in AI programs and which ones were hamburger,” said Rowan.
The entire cattle genome includes about three billion base pairs. “Genomic tests don’t have all the differences that might exist in a breed, but there are enough markers to account for all the distinct ‘chunks’ of the cow genome,” said Rowan. “Due to the way DNA is inherited, a small subset of intentionally chosen markers can represent the three billion base pairs of the genome.”
EPD accuracy results from adding progeny to calculations within a breed. “Bulls start off with an average of their parents’ EPDs,” said Rowan. “As we integrate more information in genetic evaluations, young sires eventually have progeny, data are recorded and we are more confident that the EPD represents the animal’s genetics they can pass to offspring.”
Cattlemen seeking herd improvement strive to identify animals with the greatest genetic potential as early in life as possible. “We want to identify that a bull is the best, regardless of where he was raised,” said Rowan.
Identifying the best animals as early in their lives as possible accelerates genetic gain within a population, which improves the herd. In commercial herds, this is almost exclusively driven by sire selection, whether it’s via AI or a herd bull. Ninety percent of genetic gain generated in a herd is via bull selection – not necessarily from choosing the right replacement females.
“There’s correlation between the visual appearance of an animal (phenotype) and the genetic potential for weaning weight,” said Rowan. “A bigger bull is likely to have genetics that contribute to early life weight gain, but that isn’t nearly as good a predictor as an EPD that focuses on the genetic component of a trait. Increasing the accuracy of selection is an important aspect of driving genetic progress.”
Also important is intensity of selection – the proportion of animals born this generation that stay in the herd and become parents. “Selection intensity is much more intense at the seedstock level than at the commercial level,” said Rowan. “Genetic variation is important too. If there’s no variation in a trait, we can’t make genetic progress. If we can reduce the generation interval, it helps accelerate genetic gain.”
An animal’s phenotype is influenced by the environment in which it was raised, but an animal can only pass down heritable genetic components of a trait. “Heritabilities are the proportion of a trait that’s controlled by genetics,” said Rowan. “Vaccinations, grazing history, drought and other environmental factors go into the expression of genetic potential.”
While environmental variations can be changed, there’s still the challenge of determining which genetics an animal inherited from its parents.
Random chance contributes to genetic progress, and without that factor, offspring would be exactly as good as the average of its parents. “If you breed two good animals, on average, you expect to have good offspring,” he said. “Mendelian sampling, or dumb luck, is the random shuffle of genes from the parents down to their offspring. Mendelian sampling variance can account for over 50% of the genetic variation in complex traits.”
In practice, genomic testing involves taking DNA samples from individual animals and observing 50,000 genome locations, then turning that information into a numerical representation of how related those animals are to their relatives.
“As we better understand how related animals are to one another, we can pull in different phenotypic information from related animals that share more of the actual DNA with the focal individual,” said Rowan. “That’s the way we’re able to increase the accuracy of EPDs.”
If a group of calves is outperforming parental expectation with higher weaning weights, it’s likely the bull had a favorable random sample of parental genes. “That’s the animal we want to select for the next generation,” said Rowan, “but we don’t want to wait for all his calves to be reported back to the evaluation.”
EPD accuracies change in response to genomic tests being used. “These are progeny equivalents, which say ‘for a given trait, how many records do we need from a bull’s offspring to see the same increase in accuracy we get from a genomic test?’” said Rowan. “For a trait like weaning weight, this says ‘doing a genomic test on a bull is worth 27 progeny records for weaning weight being reported back onto that bull.’ That’s a full calf crop’s worth of confidence we get in increased EPD accuracy through a genomic test.”
Understanding whether the animal received a good Mendelian sample compared to a bad combination of its parents’ genes means more accurate and increased confidence in the bull’s actual genetics that can be passed to offspring.
“The bottom line is that genomic tests reduce risk when purchasing unproven bulls or using unproven AI sires,” said Rowan. “In trying to advance genetic progress, generational interval is important too. If we’re using a bull from 15 years ago because his accuracy is 0.99, we’re losing out on 10 to 15 years of genetic progress that has happened in between. It’s preferable to use younger sires, and genomic testing helps us be more confident that those are the right animals and the EPD we’re looking at represents their actual genetic merit.”
