National Cattle Evaluations Get a Facelift in 2018
A new genetic evaluation recently released includes multiple changes that seedstock and commercial producers can use to improve herds according to Matt Spangler, Associate Professor and Beef Genetics Extension Specialist at University of Nebraska, Lincoln.
Key players in the cattle industry, both in the U.S. and Canada, worked together over a span of four years to create International Genetic Solutions (IGS), to come up with the new Expected Progeny Differences (EPD) evaluation.
The culmination of research, highlighted at the recent Beef Improvement Federation meetings, developed a system of both software and hardware to calculate genetic predictions and create a massive automated cross reference between the 12 participating IGS breed association partners: Simmental, Red Angus, Gelbvieh, Limousin, Maine-Anjou, Chianina, and Shorthorn, and their Canadian counterparts.
The collaboration has yielded the world’s largest genetic evaluation of beef cattle with over 17 million animals and 120,000+ genotypes.
According to Spangler, the majority of the breed associations are making substantial changes to the National Cattle Evaluation (NCE).
“These changes ultimately benefit commercial bull buyers by providing improved Expected Progeny Differences (EPDs) and improved economic selection indices,” Spangler shared.
Spangler said the American Angus Association (AAA) led the way in 2017, with changes to EPDs.
“This change in methodology, known as a ‘single-step’ approach, uses genomic data to augment traditional pedigree using software developed by the University of Georgia. This allows for a more refined estimate of the relationship between animals, and thus more reliable EPD. Although this may have been one of the more widely advertised changes, other changes occurred as well including updates to genetic parameter (e.g., heritability) estimates and changes to the underlying statistical models to estimate EPDs,” Spangler shared.
The American Hereford Association followed with a ‘single-step’ evaluation, using software called BOLT (Biometric Open Language Tools), from Theta Solutions, LLC. The evaluation, according to Spangler, allows for some DNA markers to have larger effects in EPDs.
“This is the primary difference between the approach taken by the AHA and IGS as compared to AAA in terms of incorporating genomic information in their NCE. A notable and simultaneous change to the AHA evaluation was an updating of their economic indices to include more Economically Relevant Traits (ERT) as well as an update in the economic assumptions. These new AHA indices should prove very valuable when selecting Hereford bulls,” according to Spangler.
The concept for BOLT started in 2014 as a research endeavor between the American Simmental Association and Drs. Bruce Golden and Dorian Garrick. Dubbed a revolutionary and powerful genetic evaluation breakthrough, the system allows IGS to leverage genetic evaluation methodology that was once thought to be untenable on large databases — methodology that significantly improves genetic prediction.
The research led to IGS collaborating to come up with a multi-breed genetic evaluation, using BOLT, to produce a ‘single-step’ genomic evaluation, creating a more reliable EPD.
Spangler points out that NCE has never been static, and changes are inevitable, as science continues to advance.
“However, the changes that have occurred in the past few months represent a considerable leap forward. Although change is cursed by some (not all) seedstock producers given the re-ranking of some sires, it should be applauded by commercial bull buyers. These organizations and the scientific community that collaborates with them continue to strive to produce genetic selection tools using the best science available,” Spangler said.
While the technology continues to advance, some producers still find it all a little daunting and are skeptical of the value.
“The accuracy still isn’t there,” says Kenny Rogers, a producer from Yuma, Colo.
Rogers, with Wagon Wheel Ranch, says the tried and true “visual” test is reliable, but he hasn’t given up hope.
“Not saying we can’t get there,” he added.
But the leg work to get there can be confusing in itself. North Dakota State University put together an EPD cheat sheet, to simplify EPD evaluations based on which ones to use and how to use them. https://www.ag.ndsu.edu/publications/livestock/understanding-expected-progeny-differences-for-genetic-improvement-in-commercial-beef-herds
According to the authors, the basic process of utilizing all EPDs is the same, when comparing apples to apples – or two bulls of the same breed. Subtract the EPD values of one bull from the other and look at the difference.
“The calculations are a simple mathematical equation: Bull A has a weaning weight EPD of plus 52 and bull B has a weaning weight EPD of plus 36, so the calves from bull A should average 16 pounds heavier at weaning than those calves sired by bull B (52 – 36 = 16),” according to Carl Dahlen, NDSU Beef Cattle Specialist.
Producers trying to decide which EPDs to use, have choices in growth, reproductive and carcass. In the growth EPDs, there is calving ease, birth weight, weaning weight, yearling weight, and milk production. In the reproductive area there is scrotal, gestation, and stayability. In the carcass EPDs, there is carcass weight, fat, and marbling. And that’s not all! So, which do you prioritize?
According to Dahlen, there are variables to that.
“The answer depends on the goals and current production status of the producer’s herd. For example, producers who sell the entire calf crop at weaning or following a backgrounding phase could use a fairly simple approach to EPDs. The EPDs to emphasize in this scenario represent the direct impact a bull can have on progeny up to the point of weaning or yearling sale,” Dahlen writes.
Birth weight, calving ease, weaning weight, and yearling weight are good places to start in this scenario, according to Dahlen. But keeping replacement heifers, then consider a few more of the EPD options, like mature weight or mature height, and milking ability.
But then, accuracy comes into play. The closer an accuracy rate is to 1, the better the chance on the outcome. While it is all confusing, there is value in it, according to Rogers, but the research needs to continue.
In the meantime…
“The end product is hanging on the rail,” Rogers says. “We’ve been doing this for 50 years. We have [buyers] that come in and want a bull sound on its feet. EPD’s don’t show that.”
Notable changes in the EPD evaluation from BOLT:
Movement of EPDs and reranking. EPDs and indexes will change. These changes will be more dramatic for younger, lower accuracy cattle. The IGS team has tested the changes and proven the new EPDs result in superior predictions of genetic merit.
Shrinking of EPD range. You will notice a reduction in the range of EPDs for most traits. The IGS evaluation team tested the statistical veracity of the reduction and it has proven to be in line with expectations based on the genetic variation in the population.
Improved use of genomics. With the switch to the BOLT software, IGS will use single-step genomic evaluation on all EPDs. Single-step uses DNA markers, pedigree information, and phenotypic data simultaneously in the prediction of EPDs. Previously, molecular breeding values (MBVs) were calculated from the genomic information and those MBVs were blended in a separate procedure into the EPD predictions. The single-step method squeezes more information from the DNA markers than the previous approach allowed. Additionally, with single-step, the genomic information will not only enhance each EPD for the genotyped animals but also will be used in the EPD estimates of relatives.
The table below shows how many progeny records it takes for an animal without genomics to have the same BIF accuracy as the young animal with genomics (but no progeny). In other words, EPD on a genotyped 1-month-old calf will be as accurate as an animal with birth weights on 21 calves, weaning weights on 22 calves, etc. The carcass traits represent actual carcass records, not ultrasound records. You may notice the maternal calving ease gets the least boost from genomics. This is due in part to such few females being genotyped.
TRAIT PROGENY TRAIT PROGENY
CE 15 STAY 25
MCE 3 CW 6
BW 21 MRB 8
WW 22 REA 5
YW 24 FAT 6
MLK 18 DOC 19
It is important to note, continued collection of phenotypic records remains a vital part of genetic predictions. DNA testing will never replace the need to record and submit phenotypes.
It is well established that DNA markers vary greatly in their effect on traits — ranging from large to virtually no impact. To leverage this biological fact in a statistically advantageous manner, the BOLT single-step method only uses markers that have a meaningful impact on the traits of interest, while ignoring those that have little to no effect. Research has shown that by using this approach, BOLT reduces statistical “noise” and thereby increases the accuracy of the EPD prediction compared to other single-step methods.
More accurate accuracy. In the previous IGS evaluation platform and all others in existence other than BOLT, the calculation of the accuracy associated with each EPD is achieved through “approximation” methods. It has long been known these methods are a less than optimal approach to the calculation of accuracy — tending to overestimate accuracy. By employing unique computing strategies that leverage both software and hardware efficiencies, BOLT performs what was previously unthinkable — utilizing a sampling methodology to calculate what is essentially true accuracy. Unlike approximated accuracies, BOLT-derived accuracies will result in predicted movements associated with possible change holding true over time. This is not the case with the previous IGS software or any other system currently in existence.
While the IGS evaluation team and partners are excited to release this new chapter in genetic evaluation, the new genetic evaluation system will only realize its true potential if the selection is made using its EPD and index values. Hands down, there is no better (more accurate) way to select for quantitative traits than an EPD. Economic indexes predict net profit by weighing the EPD for economically relevant traits coupled with economic estimates. To compete with other protein sources, it is imperative that the beef industry adopts the best science and technology to make better breeding selection decisions.
For more information about the IGS Multi-breed Genetic Evaluation powered by BOLT, go to http://www.internationalgeneticsolutions.com. More information can also be found at the respective breed association websites (American Angus Association, American Hereford Association, and American Simmental Association–IGS) as well as http://www.ebeef.org. F
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