Precision Decisions

RightMate technology targets large-effect genes for exacting genetic matching

by Laura Nelson for the Red Angus Genetic Advancement Edition

With a few quick keystrokes, Mahdi Saatchi, Ph.D., shapes the genetic future of a calf crop.

He pushes up the average weaning weight, and the blue target indicating ProS index in the next window drops from $122 to $113. He points to the graphs on the screen.

“When we see that, maybe we consider a different strategy.” The geneticist and RightMate technology developer re-keys a few data points. “Let’s try, instead of increasing weaning weight average, we set a minimum weaning weight; we focus on avoiding the low end and see what that does.”

The blue index target shifts again, recovering some losses. He clicks through the dropdown menu and selects for calving ease.

“You might ask it, reduce variation here; set minimum and maximum … and you see this shape start to change the distribution to get rid of too big and too small.”

Precision Decisions

Saatchi’s Top Genomics developed the RightMate technology as a precision enhancement to modern genetic evaluation tools.

“With this, based on the cows they have and the bulls they select, breeders can interactively see – they can visualize – and adjust their breeding objectives to maximize gain, protect diversity and achieve their objectives with much more precision,” Saatchi explained.

It’s somewhere in this process, while the breeder watches their potential calf crop graphically evolve as Saatchi pushes and prods at different traits, Allied Genetic Resources CEO Marty Ropp adds, that a breeder starts to shift their own thinking from, “’I’m a little bit uncertain of this technology,’ to, ‘This is the neatest thing I’ve ever seen.’”

Precision Decisions

The RightMate technology hinges on the identification and use of large effect genes to reduce genetic uncertainty in specific matings. Unlike single-mutation genes that wholly control traits like coat color, polledness and certain genetic defects, complex traits like growth rates, calving ease, carcass traits and maternal markers like stayability are polygenetic. This means multiple genes – sometimes numbering in the tens of thousands – influence those traits.

Still, even in complex, polygenic traits, there are often specific, large-impact genes that have an outsized effect on the biological manifestation of the trait. Those are the genes the RightMate technology zeros in on to make precise genetic forecasts.

Ropp describes an experience nearly every skilled seedstock breeder has suffered at least once. They study the EPDs to find just the right sire. They know their cow herd well, and they can see how his traits could push the herd in a positive direction.

Many of the matings turn out as planned, but perhaps a handful fall out completely and result in unmarketable outliers. Worse yet, a donor cow mismatches genomically with a sire and an entire flush is wasted.

“On paper, it looked great,” Ropp said. “But what we couldn’t see were the potential problem combinations of large-effect genes that resulted in a wasted mating.”

Like matching homozygous polled to homozygous polled to ensure polled progeny, RightMate looks at dominance or weakness in the large-effect genes that carry an outsized impact on complex performance traits.

“The EPDs give an aggregate of all the genetic potential. That’s important,” Ropp said. “But RightMate goes deeper and predicts those large-effect gene combinations, avoiding the deleterious matches and maximizing the combinations that are as good as they can be.” ease sire with length, bone and rib expression plus an attractive front end.

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Precision Decisions

Artificial Intelligence with a Human Touch

Back at Dr. Saatchi’s computer screen, he hit the “Print Matings” button to the left of the series of blue “Trait Management” bar graphs. As he added new targets or limited variability, the corresponding mating recommendations shifted and re-rank accordingly in the background.

He downloaded and opened the resulting Excel document. Each cow was now listed with her most advantageous matings, and the genetic projections of each mating. Some cows have three matches, others have eight, or 15 out of the possible 20 the breeder submitted. Each potential mating computes the statistical summary of the progeny’s genetic potential and ranks the matings based on the breeder’s objectives.

“This is artificial intelligent technology that helps us maximize all of the data together,” Saatchi said. “We cannot do this by hand.”

While the computer crunched the numbers, the process of using the RightMate technology still starts and ends with a human touch.

“If the technology has a limitation, it’s that it can’t set your breeding objectives for you,” Ropp said. “The breeder still has to make those decisions, set their goals and priorities, and weigh the options the computer gives him.”

Working across breeds and indexes, Saatchi said the technology is ideal for breeders who have or are planning to collect genomic information on their herd.

“Part of what we want to do is help squeeze more information out of the genomic investment a beef breeder has already made,” Saatchi said.

The customer submits a list of their cow registration numbers and a request to transfer genotype information. Some breed associations charge a genotype transfer fee; the Red Angus Association of America’s is $1 per animal.

The breeder can submit up to 20 bulls as potential mates, with registration numbers and a genotype transfer request. Each cow costs $25 to run through the system, with a cap at $5,000 per customer.

Precision Decisions

“You pick the bulls you like based on phenotype, EPDs and pedigree, and our tools match them in the best way to get the most advantageous matings based on your objectives,” Saatchi explained.

He started by removing the bulls that are not genomically suited to specific cow matings. Then, the remaining bulls were ranked based on potential for the outcomes the producer desires. The customer can get on a virtual call with Saatchi to see the graphical results in real-time.

“This is where they can see if they want to put more into their HerdBuilder index, or their GridMaster, ProS or more specific maternal traits. What does that look like? How does it affect other traits? We can sort cows to different objectives and customize those matings, too,” Saatchi said.

Performance & Uniformity, but With Diversity

In 2019, when the first customers beta tested RightMate, they used the precision mating tool on 1,200 cows. The fourth calf crop will be born from those initial herds in spring 2023. In the seven years prior to using the RightMate technology (2013-2019 calf crops), the breeders added an average of +2.09 per year in their Simmental All-Purpose Index. With the three calf crops since making all breeding decisions with the RightMate matchings, they pushed that API forward an average of +3.60 each year.

Ropp said they do not have enough validation data on Red Angus herds to show specific ProS index improvements, but they will see a second calf crop from several Red Angus herds this spring. In 2023, they expect more than 10,000 calves to be born from RightMate pairings.

“It is a quantum leap in traditional thinking to see the amount of genetic improvement and improvement in uniformity we can make at the same time,” Ropp said. “It’s one thing to improve an index by challenging the top two or three traits and forcing them up, but it’s another thing to make improvements for almost every single trait that goes into it, and that’s what we’re seeing here.”

While the heart of the tool helps breeders improve performance and uniformity, that can’t be done by sacrificing genetic diversity, Saatchi said.

“In the long term, genetic diversity is our bank for additional improvement,” Saatchi said, so he also sets customizable parameters to limit the percentage of a mating’s shared genome or inbreeding. “This allows us to make very targeted breeding objectives while protecting genetic diversity.”

In the mating report, Saatchi scrolled over two full screens of columns filled with projected progeny data.

“Some like to see all of the numbers; others just want to know, ‘Will this make more calves in the top percent of this or that?’” he explained. “But they all want to avoid any wasted mating. We want every calf to have the potential for success.”

That shows in the data on his screen, of course, but it’s most marked when the calves hit the ground and the tight bell curve that showed on the computer is now standing in the sorting pen to be pictured for a sale catalog.

“When you use RightMate as a precision mating tool – in combination with EPDs and knowledge on the ground –you can actually see the difference, and more importantly you can measure the improvement,” Ropp said. “It literally changes your expectation of what is possible.” //