Filling in the blanks with genetically-enhanced EPDs
July 8, 2015
Many ranchers pray for rain but sometimes it seems like a crystal ball would be handy. "If I just knew when that last heifer would calve" or "I wish I knew what the calf market would be this fall," they say.
They aren't magic, but EPDs have given cattle producers the ability to fairly accurately predict how the offspring of a particular bull will perform. Thanks to genomic testing an unproven bull's EPDs are now more accurate than before.
In recent years, information gathered through genomic testing has been used to enhance traditional expected progeny differences (EPDs), which are referred to as genetically-enhanced EPDs (GE-EPD). The enhanced EPDs are generally more accurate than traditional ones.
And now a new test offers a more affordable option for the seedstock producer to collect genomic information on his cattle.
“GE-EPDs are the best estimate of an animal’s genetic worth as a parent.AGI President Dan Moser
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For commercial and seedstock Angus breeders, Angus Genetics Inc. (AGI), a subsidiary of the American Angus Association, provides services that assist cattlemen in the genetic evaluation of traits of economic importance. "GE-EPDs are the best estimate of an animal's genetic worth as a parent," said Dan Moser, AGI president and director of performance programs. "These values make use of known pedigree, performance and genomic information about an animal, its progeny and other relatives."
AGI has teamed up with two partner labs — GeneSeek and Zoetis — to offer a wide variety of tests including the popular GeneSeek GGP-HD and Zoetis HD50K. Both cost $75; both impact the EPD by the same magnitude; and both include parent verification.
The GGP-HD chip has 145,000 markers, which work across several breeds, while the HD50K has around 70,000 markers, which have been designed specifically for Angus cattle.
However, more markers doesn't mean one test is better than the other. According to AGI, "Chips containing 50,000 markers and above show minimal increase in genetic variation explained when used in a single breed. In fact VanRaden et al. (2012) showed only a 0.4 percent increase in reliability of the proofs of dairy bulls when using an 800,000 marker chip vs a 54,000 marker chip."
Being mindful that the $75 test may be steep for some producers, in mid-June, GeneSeek and Zoetis unveiled a new high-performance genomic profiler for feedstock and commercial cattle. The Zoetis i5OK and GeneSeek GGP-LD cost $45 while maintaining high accuracy in predictive power.
"Widespread adoption of HD50K by Angus seedstock producers created the resource of tested animals required to develop i50K," said Kent Anderson, Zoetis Animal Genetics associate director global technical services. "The motivation to develop the i50K was that enhanced affordability means that even more Angus seedstock animals may be tested and have complete sets of more accurate GE-EPDs – to ultimately drive even more comprehensive and rapid genetic and productivity advancement for the beef industry."
According to AGI, there is no distinguishable difference in the reported accuracy between animals tested using the low- or high-definition genomic tests. Cost is the only major difference, and the more affordable option is made possible through a process called imputation.
"The difference is a strategically developed, lower density genotyping beadchip (fewer markers) and a process called imputation that are used to deliver effectively the same improvements in accuracy of GE-EPD, for all the same traits, but for roughly one-third less cost," said Anderson.
Using the large number of HD50K or GGP-HD genotypes that Angus breeders have submitted, programs have been trained to read or interpret the markers (letters) that are missing on LD tests. AGI offers an example of how imputation works. Consider your ability to read words, sentences or even paragraphs that have letters missing. H_re's an ex_mp_e of a s_nt_nce l_ke th_t. Due to your experience reading over the course of your life, you're able to fill in the blanks that exist even though the letters aren't really there. Imputation works much the same way, according to AGI. Your brain is like the algorithm that is used to fill in the blanks in LD genotypes.
By using Zoetis HD50K or GeneSeek's GGP-LD, Anderson says Angus breeders can make better female selection and mating decisions, while Angus bull buyers can more confidently buy the Angus bulls that fit their needs. Currently, the Zoetis HD50K and i50K are available for Angus and Red Angus. Meanwhile, GeneSeek offers genomic testing options to a larger battery of breeds including: Angus, Hereford, Simmental, Red Angus, Limousin, Gelbvieh, Charolais, Shorthorn, Wagyu, Brangus, Santa Gertrudis, and Akaushi.
"Adding markers increases accuracy in predictive power, but adding the right markers is just as important. How you design the product matters a great deal," said Stewart Bauck, Neon's GeneSeek general manager. "By working in with USDA experts and independent researchers, GeneSeek created the GGP-LD, which provides a highly accurate, affordable profiler for routine use in seedstock selection, production and marketing. With DNA profilers, commercial and seedstock producers can evaluate the future value of breeding stock soon after they are born. They can get reliable information that otherwise would take years to obtain. This helps them focus on raising, managing and marketing cattle of verified genomic merit."
Genomic testing is allowing commercial and seedstock producers to choose for best maternal traits in heifer selection, identify the best calving-ease bulls to use on those heifers, evaluate genetic potential for carcass traits, and even select for female fertility.
"While female fertility is considered moderately heritable, open cows are a large drag on ranch profit, so using genomics to achieve improvements is quite impactful," said Bauck. "Profiling helps you select for heifer fertility. You don't need to wait and find out they won't breed back after their second calf. You can get a good picture of their potential when it is time to select replacements at weaning."
In comparing the low-density vs. high-density genomic testing, Moser predicts that with the majority of animals, low-density testing will be adequate and will become the new standard producers will rely on.
"As we have developed an amazing database of animals tested with HD, it became obvious that we could make almost identical genetic progress using fewer markers now that we have the volume of animals tested on HD," said Moser. "In considering this new option, we looked closely at the dairy industry which has used LD to make a lot of genetic progress in a short period of time. We heard from our customers that price is always a consideration, so the chance to offer something at two-thirds the cost is definitely important."
Moser added that high-density testing will still be used in some cases.
"For some seedstock producers, high-density is part of their brand, and their customers recognize that information," said Moser. "High-definition testing might still be importnat for bulls that are candidates for as AI sires. The most valuable animals might still rely on the high-definition testing, but by using low-definition testing, we can test more animals adding value to our database. The additional accuracy you gain from genomic testing depends on the animal and how much information we already have. If we have a widely-used AI sire with many offspring, he's already established, so his accuracy would be changed minimally. However, for unproven animals, we'll see an added accuracy of EPDs of 5-15 percent."
The ability for commercial and seedstock producers to make rapid genetic change through the use of genomics is great; however, there is still much confusion about genetic testing in the use of animal selection. Moser offers a simple analogy to make it more relatable to those who have questions about the process.
"When I think about genomics, I think about how my own family," said Moser. "I have three children, and they are all different. They are certainly not clones of each other. When people have kids, some are taller than others. They have different hair or eye colors. They are not all the same. If we think about bulls, we know there is variation in their offspring, too. Without genomics, it's hard to know which one of those half or sometimes full siblings have the most complimentary genes that the producer might care about. We can use genomics to see which offspring got the most favorable draw."
Genomics can be used to evaluate a wide variety of traits by enhancing EPDs, including: Calving Ease Direct, Calving Ease Maternal, Birth Weight, Weaning Weight, Yearling Weight, Milk, Carcass Marbling, Carcass Rib, Carcass Fat, Carcass Weight, Dry Matter Intake, RFI, Tenderness, Docility, Yearling height, Scrotal, Mature weight, Mature height, and Heifer Pregnancy, among other traits depending on the test utilized.
"It's an exciting time for me to see value-based marketing come to fruition — from the feedlot to the commercial cow-calf producer," said Moser. "It's rewarding the commercial producers who do have superior genetics, and it motivates them to buy superior bulls.We are moving away from marketing on averages and truly discovering value of the genetics. Genomic results are a way to enhance the current selection tools, predictions for younger animals, and to characterize genetics for traits where it's difficult to measure the phenotype."
Angus breeders wanting to learn more about available genomic tests and place an order may go to http://www.angus.org/AGI/default.aspx.