IGS Multi-breed Single-step Powered by BOLT (4)
DNA profiles provide additional information about the genetic merit of a DNA tested animal and increase the accuracy of EPDs, which are called Genomic Enhanced EPD or GE-EPDs. In the IGS Single-step process, the DNA marker genotypes are directly incorporated into the genetic evaluation along with the phenotypes (performance data) and the pedigree. As a result, the DNA information has an impact not only on the genotyped individual but also on all the relatives of that genotyped individual. This allows for the DNA information to improve the accuracy of non-genotyped relatives. To measure the impact of DNA information on accuracies of GE-EPDs in the IGS Singlestep genetic evaluations, we compared the average BIF accuracies of GE-EPDs of DNA tested young animals (born in 2016 with no progeny) to the average BIF accuracies of nongenotyped sires born in 2010-2014. Only sires with non-genotyped calves were used for this comparison. We found that the average BIF accuracy of GE-EPD for a DNA tested young animal is equivalent to the average BIF accuracy of a non-genotyped sire with 21, 22 and 24 calves with observed phenotypes for birth, weaning and yearling weights, respectively (Figure 1, where a horizontal line cross a curve for a specific trait (e.g. red line and blue curve cross each other at the data point correspond to y(accuracy)=0.46) and x(progeny)=21 for birth weight)). The progeny equivalent (PE) for direct calving ease was 15 and it was only 3 for total maternal calving ease due to limited genotypes on cows. The PE for milk and stayability were 18 and 25, respectively (Figure 1).
The IGS Multi-breed Single-step powered by BOLT is a breakthrough in GE-EPD accuracy improvement. Enabling technologies such as BOLT software allow for even faster genetic progress with more accurate EPDs earlier in an animal’s life. We (IGS) are dedicated to using the best available technology to deliver more accurate GE-EPDs to our members so they have the best tools available for their selection decisions.
By Mahdi Saatchi, Rohan L. Fernando, Lauren Hyde, Jackie Atkins, Steve McGuire, Wade Shafer, Matt L. Spangler, and Bruce Golden, IGS Genetic Evaluation Team, and Consultants.
The ASA and International Genetic Solution (IGS) partners invested in a new and improved genetic evaluation software called BOLT to replace the Cornell EPD evaluation system. Among other benefits, this enables the use of Single-step methods for incorporating genomic information into the National Cattle Evaluation instead of the blending approach. In the Single-step process, the DNA marker genotypes are directly incorporated into the genetic evaluation along with the phenotypes (performance data) and the pedigree. As a result, the genomic data has an impact not only on the genotyped individual but also on all the relatives of that genotyped individual. This allows for the genomic information to improve the accuracy of non-genotyped relatives.
The IGS Multi-breed Single-step powered by BOLT squeezes more information from the DNA markers by allowing for certain DNA markers to have a larger influence on predicting the genetic merit of an animal than other DNA markers while some DNA markers to have no effects on trait(s) of interest (for progeny equivalents of select traits, see page 46). This model is closer to what we expect based on biology where some parts of an animal’s genome (or genes) play more important roles than other parts of its genome (or genes). This is unique to the IGS Single-step method compared to other organizations where the DNA marker information is used to adjust relationships among the individuals.
Many ASA members and IGS partners wonder if the BOLT EPDs are more accurate than the Cornell derived EPDs in the real world? To answer this question, we performed a validation study where we ran a data set (pedigree, performance, genomics) through both genetic evaluation software (BOLT and Cornell) to compare the accuracies of the EPDs produced. To enable a fair comparison, we removed the performance records of animals born in 2015 and later from the evaluation in both systems to be used as progeny performance records for validation purposes. Table 1 shows the correlations between EPDs and progeny performance of non-genotyped sires evaluated in both systems that have progeny born in 2015 or later with recorded birth, weaning, and yearling weights. As shown, the BOLT EPDs are more accurate than Cornell EPDs as the correlations are higher for BOLT EPDs with sires’ progeny performances.
Table 1- The correlations between BOLT vs. Cornell EPDs with progeny performance of non-genotyped sires for birth, weaning and yearling weights.
|Trait 1||N of Sires||BOLT||Cornell|
To have a better sense of improvement in accuracies, we ranked sires based on either BOLT or Cornell EPDs for birth, weaning and yearling weights. Then, we compared the progeny performance of the top 1% vs bottom 1% ranked sires for each trait in each evaluation system. The results are shown in Table 2.
Table 2 – The average progeny performance of non-genotyped sires ranked based on either BOLT or Cornell EPDs
|Cornell||BOLT vs Cornell|
|Trait||N of sires||Top 1%||
|Difference||Top 1%||Bottom 1%||Difference||Top 1%|
As you can see, the BOLT EPDs ranked sires more accurately than EPDs from the Cornell software, where progenies of top 1% ranked sires based on the BOLT EPDs are +3.1, +16.8 and +40.2 lb heavier at birth, weaning and yearling. These results are exciting and show that our investment in new technology will lead to more accurate EPDs.
Change can be a scary concept to some yet sought after by others. Many ASA members and International Genetic Solution (IGS) partners wonder about the changes on the horizon once the new evaluation, IGS Multi-breed Single-step powered by BOLT, is fully implemented. That change may be nerve-racking but in reality, things should change. Why invest in new and improved methods if you get the same answers? Here are key changes to expect with the new genetic evaluation:
1. Movement of EPDs and reranking. EPDs will change especially in younger, lower accuracy cattle. Members should expect movement in lower accuracy cattle, as seen in the existing evaluations, because they may have new progeny data reported. Some cattle will move in a favorable direction while others will do the opposite. Keep in mind even if the EPDs get worse, the prediction of them is more accurate. With IGS Single-step, we will have more accurate EPDs earlier in an animal’s life.
2. More accurate accuracy. This idea takes a little time to sink in. The accuracy reported for each EPD will be more directly calculated and thus closer to the “real” accuracy. The methods to solve accuracy directly are extremely difficult and take a lot of computer power. With the previous Cornell software, it was not possible to solve for accuracy directly so an approximation method was used to estimate accuracy for each EPD. There were inherent flaws with approximating the accuracy of the previous method. Now with BOLT software, the accuracy reported with the EPD will be more reliable.
3. Reported accuracies will tend to be lower. One of the inherent flaws in the approximation methods used to find accuracy in the previous evaluation, and in all evaluations not produced through BOLT, was they frequently overestimated accuracy, especially for younger animals. This was known for a long time, but there was no way to calculate the accuracies directly. With BOLT, having accuracy more directly solved results in a more reliable accuracy but that accuracy will often be numerically lower than the previous evaluation would predict. However, the newly reported accuracies with BOLT should better represent the possible changes for the EPDs.
4. DNA testing will have a larger impact. With the switch to BOLT software, IGS will use Single-step genomic evaluation on all EPDs (currently using Single Step for Stayability EPDs). Single-step uses the DNA markers, pedigree information, and phenotypic data simultaneously in the prediction of the EPDs. Previously molecular breeding values (MBVs) were calculated from the genomic information and those MBVs were blended separately into the EPD prediction. The Single-step method squeezes more information from the DNA markers than the previous approach allowed. Also, there are biases inherent in the blending process that aren’t a problem with the Single-step approach. Additionally, with Single-step, the genomic information will not only enhance EPDs for the genotyped animal but also will be used in the EPD estimates of relatives.
5. Weekly genetic evaluation runs. With the horsepower behind BOLT, IGS can run genetic evaluations weekly. This has many benefits. It allows members to get more immediate feedback after submitting their records. If members miss a deadline, they can catch the next evaluation run the following week. It allows for more accurate EPDs throughout the year and faster incorporation of the genomics. This also means the EPDs put in print will quickly be outdated.
Genetic evaluation is not stagnant. There will always be improvements as new research in animal breeding, genomics, and statistics advance. BOLT software is revolutionary in the innate flexibility, the computational power, and the statistical methods made possible using this software. IGS Multi-breed Single-step powered by BOLT promises more accurate EPDs, accuracies, and better use of genomics all delivered to you on a weekly basis.
By Drs. Jackie Atkins, Lauren Hyde, and Wade Shafer
It’s here! The Spring 2017 evaluation includes a multi-breed Stay EPD using the much anticipated new genetic evaluation software, dubbed BOLT (Biometric Open Language Tools). The Stay EPD uses a random regression approach to predict stayability developed by Dr. Janusz Jamrozik and colleagues from the University of Guelph and the Canadian Simmental Association. Dr. Scott Speidel at Colorado State University, Dr. Bruce Golden (Theta Solutions), and the genetics team at International Genetic Solutions (IGS) (Lauren Hyde, Wade Shafer, Mahdi Saatchi, and Steve McGuire) worked together to incorporate the new methodology into the IGS evaluation. The new stayability evaluation includes data on animals of varying breed composition, directly incorporates genomic data, produces true accuracy values and provides Stay EPDs to all IGS partners on a common base.
Features of the Multi-breed stayability with BOLT:
1) Multi-breed stayability. As mentioned, the new Stay EPD is calculated for all cattle in the database (not just for purebred and fullblood Simmental, as it was in past evaluations). The calculation of EPDs in this fashion required the new evaluation to account for heterosis, which can be sizable for a trait like stayability. Because stayability has a major impact on profit, having Stay EPDs on all cattle will substantially improve the ability of the All Purpose Index to predict differences in profit on hybrid and cattle of other breeds.
2) Direct incorporation of genomic data. This evaluation represents the first time "Single Step" methodology has been used in the beef industry on a large database. The innovative approach refers to DNA marker results being incorporated directly into the genetic evaluation, rather than being incorporated post evaluation or as a correlated trait. Single Step is widely accepted as the most powerful means of leveraging DNA for genetic prediction. The use of a Single Step approach on a large database (the largest in the beef industry) was made possible through the use of BOLT, ASA's revolutionary new software developed by researchers Dorian Garrick and Bruce Golden through Operation Quantum Leap.
3) More "accurate" prediction of accuracy. Prior to BOLT, the calculation of EPD accuracy was relegated to using indirect methods that were very imprecise, which commonly resulted in calculated accuracies being a poor estimate of the EPD's true accuracy, i.e., an EPD assigned a high accuracy may have truly been a low accuracy EPD and vice versa. Until the development of BOLT, the direct calculation of accuracy was thought to be impossible on a large database due to computational limitations. By leveraging statistical methodology unique to genetic evaluation and cutting-edge computer programming, BOLT calculates accuracy directly, thereby making it a much more "accurate" estimate of true accuracy.
Because the indirect methods used prior to BOLT tended to overestimate accuracy, you will notice that the accuracies associated with our new Stay EPDs will tend to be lower than the accuracies calculated in the prior evaluation of stayability. This does not mean that we are predicting stayability less accurately than we did in our previous evaluation--in fact, due to BOLT's ability to leverage phenotypes and genotypes more effectively we are actually predicting stayability with considerably more accuracy--it does mean that the published accuracy is now a better gauge of how much confidence you should have in an EPD. This fact will help seedstock and commercial producers better manage selection risk.
4) Change in base. Breeders will see significant movement in Stay EPDs from previous evaluations, not only because of improvements in methodology, but also because of a change in base. However, changing the base does not affect the ranking of cattle; it simply shifts all EPDs up or down by the same increment. For a point of reference, in the prior evaluation 21 was the average Stay EPD on purebred animals born over the last 2 years, where the average on the same animals is 11 under our new system.