TOOLS FOR GENETIC PREDICTION HAVE EXPLODED

by: Wes Ishmael

If you long for the good old days when a keen eye and perhaps a basic knowledge of cow families was more than enough to sort bulls, you're not alone. Though genetic selection is more accurate than ever, it can also seem more complex than the Tax Code.

Hard to believe that even a decade or so ago selection was relatively simple. You basically had Expected Progeny Differences (EPDs) for a meager assortment of traits, by today's standards. Growth traits—birth, weaning and yearling—have been part of the mix since multi-trait genetic evaluation came to the fore in the 1980s. There was some measure of milk or maternal contribution to growth, yearling scrotal circumference and the like.

Then came an eruption of new EPDs and ways to derive them.

Depending on how you're pony's hobbled, the most notable of these have been for what are termed Economically Relevant Traits (ERTs). These are measures of traits that directly get at economics, rather than indicator traits that get at the economics indirectly.

For instance, Calving Ease—for which there is now an EPD, both direct and maternal—is an ERT. Birth weight is an indicator trait used previously to predict calving ease, along with gestation length and calving ease scores. Likewise, Heifer Pregnancy is an ERT, as is stayability—the odds a female will still be at work in a herd until at least her sixth birthday. Previously, and again arguably, Gestation Length and Scrotal Circumference were previously used by some as indicator traits that began hinting at the ERTs of reproduction.

Other ERTs include things like docility and feed requirements for cow maintenance.

During the last decade, genetic predictions for carcass traits also blossomed. Now there are EPDs for everything from Carcass Weight, to Yield Grade, to Marbling Score, to Ribeye area. It was the adoption of ultrasound measurements in tandem with or in place of actual carcass performance that enabled breeds to expand carcass-based genetic prediction so far and so rapidly.

Associated with some of these has been the advent of DNA diagnostic tests aimed at further describing the genetic merit of animals.

At last year's Beef Improvement Federation Meeting (BIF) a task force recommended that the appropriate use of genomic information was via incorporation within current breed genetic evaluation. The American Angus Association (AAA) became the first breed to provide that opportunity in January, offering genomic-enhanced EPDs for 14 economically relevant traits.

“The ability to evaluate cattle using EPDs with improved accuracies helps producers minimize some of the risk that comes with using young sires or selecting replacement heifers,” says Bill Bowman, Chief Operating Officer for Angus Genetics, Inc., a division of AAA. “Now producers can more confidently evaluate young cattle for economically important traits such as marbling and feed efficiency, to help ensure they are pointing their herd in the right direction.”

Simplistically, the reason behind that is that through genomics, calves can have EPD accuracies similar to young bulls with progeny, with performance data on them going toward genetic evaluation.

Moreover, in the past few years some commercial producers began discovering the value of using DNA tests to parent-verify calves from multi-sire pastures.

     

Evaluating Across the Fence

Other developments during the past dozen years are aimed at allowing producers to compare the genetic merit of animals in different breed populations. Prior to this, genetic evaluation could be used only to compare within-breed, just as the Estimated Breeding Values (ratios) before them could only be used only for comparing genetic merit within-herd.

Though the idea had been bandied about at least since 1989, it was 1998 when the U.S. Meat Animal Research Center (MARC) released the first across-breed EPD adjustments—still in use today. If you're unfamiliar with them, these adjustments are added or subtracted from the EPD values of a particular breed, in order to make them more directly comparable to those of another. A weakness in them is that they only account for breed differences estimated from a relatively narrow population. Some argue the adjustment factors inflate or deflate reality.

The other development was the notion of multi-breed genetic evaluation. Working with Cornell University, the American Simmental Association (ASA) developed and adopted the first commercially available system for this a decade ago. Since then several other breed associations have conducted genetic evaluation, especially for registered hybrid seedstock, whereby they incorporate EPDs from other organizations into their own evaluations, for the portion of the pedigree unexplained in their own databases.

However, if you truly want to compare seedstock of different breeds and breed combinations head-to-head, you analyze them as a single population.

Growing to Shrink

All told, some breeds now offer EPDs for more than 20 different traits. Turns out this burst of genetic predictions and the tools to derive them was a necessary step to ultimately make possible selection indices, which promise to make selection simpler, while accounting for more information.

The idea of selection indices in genetic evaluation dates back to at least 1940's, according to Dorian Garrick of Colorado State University in an insightful summary of genetic evaluation trends (www.ansci.cornell.edu/nbcec). But, the same challenge still applies: how do you accurately determine the economic values which underlie them?

Keep in mind the science behind such indices also gets at the next step many producers hope will occur, which are decision-support systems that could tell you the best breed, breeds and individuals within them to use in a specific situation to obtain a specific result.

You can currently find selection indices for everything from weaned calf, feedlot and grid values, to one that gets at dollars per cow exposed.

Multiplying Opportunity

The accuracy offered up by all of the tools mentioned in this article is poised to take a giant leap forward with growing interest in multi-breed genetic evaluation and whole genome selection.

As mentioned previously, multi-breed genetic evaluation is nothing new. More than anything, though, increasing use of registered hybrid and composite seedstock is growing interest in multi-breed analysis. That's also one reason some breeds are more interested in it than others.

Predicting genetic differences requires genetic relationships. Typically, breeds that have little relational connectivity to other breeds see less opportunity to utilize it. Plus, any time you switch gears with genetic evaluation and change the look of the numbers you're inviting confusion from commercial producers and marketing nightmares for seedstock producers.

Base years serve as a quick example. EPDs are reported at any given time based on their relationship to a base year; the average EPD value varies by year. Change the base year and the numbers can change dramatically, though the ranking of animals remains the same and the genetic merit of the animal is the same. In multi-breed analysis, a common base year must be chosen for the breeds involved, meaning that all but one of them will see the look of the numbers change for their breeders and commercial users.

Still, in genetic evaluation, volume of data increases prediction accuracy. So, with multi-breed analysis, the opportunity exists to more accurately characterize all of the genetics that exist in an animal and the differences that exist between them. Plus, the increased volume of data increases the accuracy of prediction.

Between that and increasing interest in registered seedstock comprised of more than one breed, several organizations now offer multi-breed analysis.

     

Still the Best Bargain

Snubbed to a different post, though information is never truly free, genetic evaluation information has been the next best thing to it since genetic evaluation began.

EPDs provide a quantum-leap over the eyeball in predicting genetic merit for specific traits. If you ever doubt that, just gander the genetic trends for breeds, tied to a common base year. Seedstock producers have done an extraordinary job of increasing weaning and yearling growth, as well as milking ability, while holding birth weights in check.

You can argue that seedstock producers who pay for the data by registering cattle or enrolling cows in a Total Herd Reporting system have paid a bargain price because genetic evaluation has been so subsidized.

As tax payers, we've all helped pay for it directly with federal funding for genetic evaluation research, and indirectly via state and federal funding for the Land Grant Universities which have been the primary suppliers of genetic evaluation services.

As these more Universities exit that business, it should pay every user of genetic data to keep in mind the asset of genetic evaluation has never been solely about the data. It has included the collective intellectual property of everyone involved. Not just the folks building the statistical models and figuring out how to shove 50 lbs. of data into a 20 lbs. algorithm, but everyone. Take a look at the leading breed organizations and you'll find folks as expert in the machinations of statistical models and genetic evaluation as the folks providing it. Part of their ongoing education comes from their members, the seedstock producers using it to mate cattle more effectively. In turn, a part of their graduate degrees are built upon input from their commercial customers who wonder why: if this is so, why is that also true; why can't you do it this way; what does that have to do with the price of tea in China, etc.

Moving away from subsidized information to private could mean part of this collective intellectual property is lost.







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